ElShamah - Reason & Science: Defending ID and the Christian Worldview
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ElShamah - Reason & Science: Defending ID and the Christian Worldview

Otangelo Grasso: This is my personal virtual library, where i collect information, which leads in my view to the Christian faith, creationism, and Intelligent Design as the best explanation of the origin of the physical Universe, life, biodiversity


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Beyond Evolution: The Origin of Species by Design

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Beyond Evolution: The Origin of Species by Design

This publication stands out not merely as another critique among many questioning the sufficiency of Darwin's Theory of Evolution to account for the vast biodiversity, but it unravels the astonishingly complex and varied processes necessary for the development of complex life forms and the structure of multicellular organisms. It directly confronts and highlights the shortcomings of traditional evolutionary explanations in accounting for the organization of life, offering a holistic perspective on the genuine mechanisms involved. The book undertakes a detailed and critical analysis of the core aspects of Darwinian theory, with a particular focus on molecular-level insights. It refutes Darwinian evolutionary concepts, such as universal common descent and the Tree of Life, and shows the inadequacy of natural selection, genetic drift, and gene flow as sufficient explanations as the origin of complex biological form and architecture, and multitude of life forms. This work illuminates the true mechanisms behind the complexity of life with a level of detail and approach that is unprecedented in the scientific literature, and why these mechanisms cannot be explained by unguided mechanisms, but require an intelligent mind, which instantiated them from their inception fully developed, and apt to thrive, adapt, replicate, and multiply.  

There are 52 key points, ranging from alternative DNA structures to the influence of viruses, highlighting the vast diversity in genetic, biochemical, and physiological mechanisms across life forms. This complexity and variability refute universal common descent and is evidence of polyphyly, which posits that life diversified, adapted, and evolved to a limited degree after the creation of many independent species. The book unravels how the architecture of multicellular organisms arises from a complex interplay of at least 47 key developmental processes, 33 variations of genetic codes, and over 223 epigenetic, manufacturing, and regulatory codes and biological languages. These elements are coordinated through hundreds of signaling networks, embodying functional communication, integration, and systemic complexity. This holistic ensemble hints at a level of organization that indicates the requirement of an intelligent cause for the instantiation of individual species at the inception of life. At close to 1400 pages, this book stands as a transformative work, offering groundbreaking insights into the interwoven complexity of organismal structures. It provides a thorough examination of the subject matter and clarity which will unravel and unmask, how naturalistic unguided causes are inadequate explanations, and can be put to rest. This book provides evidence, that a powerful, conscious, intelligent designer is the best case-adequate explanation, that created life and biodiversity.

https://reasonandscience.catsboard.com/t3264-refuting-darwin-confirming-design

Life's Blueprint: The Essential Machinery for Life to Start
https://reasonandscience.catsboard.com/t3383-life-s-blueprint-the-essential-machinery-for-life-to-start

A list of evidence that points to polyphyly, rather than monophyly, and universal common descent
https://reasonandscience.catsboard.com/t2239-evolution-common-descent-the-tree-of-life-a-failed-hypothesis#10954

Bacteria
https://reasonandscience.catsboard.com/t3379-bacteria-the-first-domain-of-life

Archaea
https://reasonandscience.catsboard.com/t3378-archaea-the-second-domain-of-life

Key Developmental Processes Shaping Organismal Form and Function
https://reasonandscience.catsboard.com/t2316p25-evolution-where-do-complex-organisms-come-from#10629

The Brain of Homo Sapiens and Chimps: Distinctive Characteristics are reasons to be skeptic about shared descent
https://reasonandscience.catsboard.com/t2272-chimps-our-brothers#11024

Processes involved in embryogenesis
https://reasonandscience.catsboard.com/t3381-processes-involved-in-embryogenesis


The Orchestration of Neurogenesis: A Study in Irreducibility and Interdependence
https://reasonandscience.catsboard.com/t3373-the-orchestration-of-neurogenesis-a-study-in-irreducibility-and-interdependence

Unraveling the Molecular Foundations of Instinctual Behavior
https://reasonandscience.catsboard.com/t1732-instinct-evolutions-major-problem-to-explain#11130

What is the Theory of Evolution?
How is the origin of biological form, biodiversity, organismal complexity, and architecture explained by current biology?
Primary, and secondary speciation
Gene duplications
The major ( hypothesized) transitions in evolution
Falsifying Universal Common Ancestry


Beyond Evolution: The Origin of Species by Design Title110

Unraveling the real mechanisms giving rise to biological adaptation, development, complex organismal forms, anatomical novelty,  and biodiversity

Acknowledgements

In traditional book writing, an author is often likened to a craftsman, meticulously choosing each word and weaving them together to create a narrative. However, in the age of artificial intelligence and advanced algorithms, the nature of this craft has evolved, leading to a shift in the role and definition of an "author". As the individual behind this book, I find the term "author" insufficient to describe my role in its creation. While every word you read has been generated by ChatGPT, an AI language model, my involvement has been more akin to a conductor of a symphony. Just as a conductor doesn't play each instrument but orchestrates an entire ensemble to create harmonious music, I've not manually penned each line but have strategically directed and channeled the AI's vast knowledge and capabilities to construct this narrative. This approach to writing involves curating and arranging prompts, refining AI-generated content, and ensuring the final product aligns with a coherent vision. It's a dance between human intention and machine efficiency, where I decide the theme, tone, and direction, and the AI fills in with its vast database of information. The result is a unique blend of human creativity and machine precision. So, as you delve into the pages of this book, I invite you to view it not just as a work authored in the traditional sense, but as a collaborative symphony between human intuition and artificial intelligence. Together, in this new era of content creation, we explore the frontiers of knowledge and storytelling, redefining what it means to be an author in the digital age.


Prologue

Over 160 years have passed since Darwin's "On the Origins of Species". His theory of evolution by natural selection is a cornerstone of modern biology. It claimed to provide a unifying explanation for the diversity of life on Earth. The theory is based on the idea that organisms vary, and these variations can be inherited by the next generation. Natural selection acts on these variations, favoring those that are advantageous for survival and reproduction in a given environment. Over time, this process can supposedly lead to the evolution of new species.

Since its introduction, the theory of evolution has been claimed to be supported by a vast amount of evidence from a wide range of scientific disciplines, including genetics, paleontology, comparative anatomy, and biochemistry. The modern synthesis of the 20th century integrated Darwin's theory with the science of genetics. Darwin's theory also has had practical implications for science and society.

In the annals of scientific inquiry, few theories have sparked as much continuous debate. Darwins suggestion that the diverse forms of life emerged through a process of natural selection has been met with significant scrutiny, particularly from those who observe the natural world and see evidence of deliberate, designed complexity. Critics point to the intricate structures and unfathomable complexity of living organisms, arguing that these features could not have arisen from random mutations and natural selection alone. The eye, with its precise arrangement of lenses, muscles, and photoreceptor cells, stands as a testament to a level of complexity that seems to defy the gradualistic explanations offered by natural selection. This perspective suggests that such marvels of nature are not the product of an undirected process but rather the work of an intelligent designer.

Moreover, the fossil record, often cited in support of Darwinian evolution, presents its own set of challenges to the theory. The expected gradual transitions between species are conspicuously absent in many cases, leading to question the validity of the theory as an explanation for the origin of the vast diversity of life. Instead, the sudden appearance of fully formed species in the fossil record aligns more closely with the notion of special creation, where each species was created as it is, in a form complete and functional from the beginning. The debates extend beyond the realm of biology and into the philosophical and societal implications of Darwin's theory. Critics argue that the reduction of human life to mere products of chance and competition devalues human dignity and morality. The idea that life, in all its complexity and purpose, could be the result of random processes is at odds with the sense of intention and design that we observe in the natural world. The controversy surrounding the teaching of Darwin's theory in educational institutions highlights the deep divide between the materialistic view of life's origins and the perspective that sees evidence of design and purpose in the natural world. This ongoing debate underscores the fundamental differences in how we interpret the natural world and our place within it.

In the realm of scientific inquiry, one of the most compelling and debated subjects remains the question of life's origin and the staggering complexity of biodiversity. The dominant narrative has frequently presented the theory of evolution as the primary, unguided mechanism propelling the emergence and diversity of life. Yet, within the vast expanse of scientific discourse, alternative perspectives and interpretations of the data warrant thoughtful consideration. This book aims to provide readers with a comprehensive overview of the evidence that suggests the possibility of design as a more case-adequate explanation for the origin and biodiversity of life, in contrast to solely unguided evolutionary mechanisms. Readers are invited on a journey of exploration, fostering a deeper understanding and encouraging critical thinking on one of science's most profound questions.

The debate over whether biodiversification and the complexity of life can be fully explained by unguided evolutionary mechanisms or whether the involvement of an intelligent agent is necessary is a fundamental and longstanding philosophical and scientific discussion. This dichotomy reflects a broader conflict between naturalism and theism, two contrasting worldviews that shape our understanding of the origin and development of life. Naturalism is the philosophical perspective that asserts that all phenomena, including the diversity of life, can be explained by natural processes operating according to physical laws. In the context of biology, naturalism holds that evolution through mechanisms such as natural selection, genetic variation, and environmental pressures can account for the complexity and diversity of living organisms. Proponents of naturalism argue that no supernatural or divine intervention is required to explain the natural world. Theism, on the other hand, posits that the existence and characteristics of the natural world are best explained by the presence of an intelligent and purposeful creator or divine being. In this view, the complexity of life, the intricate design of organisms, and the emergence of biodiversity are seen as indicative of intentional design rather than solely the outcome of unguided natural processes. The dispute between naturalism and theism centers on the interpretation of evidence and the underlying assumptions about the nature of reality.

Making sense of the vast diversity of life is still today one of the greatest, if not the greatest intellectual challenge, together with the Origin of Life. The quest about if evolution is true is more than a scientific question. It is a battle that goes beyond science. It is a culture war between naturalism/strong atheism, and creationism/Intelligent Design. If the literal interpretation of the Genesis account in the Bible is true, then Darwin's Theory of Evolution is false, and vice-versa.

Frank Zindler, President of American Atheists,  in 1996:
The most devastating thing though that biology did to Christianity was the discovery of biological evolution. Now that we know that Adam and Eve never were real people the central myth of Christianity is destroyed. If there never was an Adam and Eve there never was an original sin. If there never was an original sin there is no need of salvation. If there is no need of salvation there is no need of a Savior. And I submit that puts Jesus, historical or otherwise, into the ranks of the unemployed. I think that evolution is absolutely the death knell of Christianity.

Beyond Evolution: The Origin of Species by Design 31280610
Conservative Protestants in the 1920s also saw themselves in the midst of a great culture war, with the Bible (depicted here as the Rock of Gibraltar) coming under fierce attack by “battle-ships of unbelief.”

Leaving the Bible aside, the dispute is not about religion versus science, but between case-adequate inferences based on scientific evidence and unwarranted conclusions. The big question is: Is the origin of biodiversity, Darwin's hypothesis of universal common ancestry, and the tree of life,  supported by the evidence unraveled by scientific facts, as the scientific establishment and consensus among professionals in the field advocate for, calling Darwin's Theory, and the recently modified versions of it, an undisputable scientific fact, or does the data lead to another direction?  We can also ask a deeper question, and dissect the issue to the core question: Which of the two has more creative power: Design, or non-design? Intelligence, or non-intelligence? Agency, or non-agency? Conscious creation, or undirected natural, non-intelligent processes? 

Beyond Evolution: The Origin of Species by Design 521

Claim: Herbert Spencer: Those who cavalierly reject the Theory of Evolution as not being adequately supported by facts, seem to forget that their own theory is supported by no facts at all. Like the majority of men who are born to a given belief, they demand the most rigorous proof of any adverse belief, but assume that their own needs none.

Richard Dawkins: "It is absolutely safe to say that, if you meet somebody who claims not to believe in evolution, that person is ignorant, stupid or insane (or wicked, but I'd rather not consider that)."1

John Joe McFadden (2008):  Quite simply, Darwin and Wallace destroyed the strongest evidence left in the 19th century for the existence of a deity. Biologists have since used Darwin's theory to make sense of the natural world. Contrary to the arguments of creationists, evolution is no longer just a theory. It is as much a fact as gravity or erosion. 2

Reply: Opinions like Richard Dawkins have contributed to stigmatizing the proposition of intelligent design as pseudo-science, or as unscientific altogether. But is it justified? Many books have been published on the subject, and articles are frequently being written, defending both views and positions. Those that advocate in favor, often resort to the fact that a majority of biologists are on their side, and argue, because there is a widespread consensus, it must be true. 

A 2019 survey of American biologists found that 98% of them agreed that "evolution by natural selection is the best explanation for the diversity of life on Earth." This survey was conducted by the Pew Research Center, a nonpartisan fact tank that conducts public opinion research. Similar surveys have been conducted in other countries, and the results have been consistent. For example, a 2018 survey of British biologists found that 97% of them agreed that "evolution by natural selection is the best explanation for the diversity of life on Earth." These surveys suggest that the vast majority of biologists worldwide accept Darwin's theory of evolution as the best explanation for biodiversity. While there may be a small minority of biologists who do not accept this theory, they are a very small minority.

Sailing against an unfavorable wind is undoubtedly a challenging and energy-consuming endeavor. However, the pursuit of truth remains the guiding force, pushing us to brave these turbulent waters. In today's world, many individuals may lose faith in a creator due to a lack of proper education to critically assess scientific evidence. Instead, they are swayed by those who advocate for evolution, claiming to possess evidence on their side. In stark contrast, I have dedicated years to probing this subject deeply, allowing the evidence to be my compass without yielding to the temptation of becoming just another anti-evolution book collecting dust on shelves. My purpose is to present a well-researched perspective that questions the prevailing narrative of evolution. Although some may view me as a solitary zealot, blindly adhering to religious beliefs and disregarding contemporary scientific advancements and the consensus among professional biologists, I am not alone. My findings align with those of esteemed investigators in the field. These scientists, committed to philosophical naturalism, may not draw a simplistic conclusion like ".... and therefore, God!!" as that proposition lies beyond the realm of scientific inquiry. However, they candidly acknowledge the limitations and issues within the traditional evolutionary view. Honesty and integrity underscore my approach throughout this journey. My discoveries, mirroring those of respected researchers, rest on solid factual grounds. While some authors might resort to colorful arguments, 

In November 2016, there was a three-day conference in London, a scientific discussion meeting organized by the Royal Society: New trends in evolutionary biology: biological, philosophical, and social science perspectives. On the website, they wrote: Developments in evolutionary biology and adjacent fields have produced calls for revision of the standard theory of evolution 3

Intelligent Design proponents point to a chasm that divides how evolution and its evidence are presented to the public, and how scientists themselves discuss it behind closed doors and in technical publications. This chasm has been well hidden from laypeople, yet it was clear to anyone who attended the Royal Society conference in London,as did a number of ID-friendly scientists. The opening presentation by one of those world-class biologists, Austrian evolutionary theorist Gerd Müller. He opened the meeting by discussing several of the fundamental "explanatory deficits" of “the modern synthesis,” that is, textbook neo-Darwinian theory. According to Müller, the as-yet unsolved problems include those of explaining the following:

Phenotypic complexity (the origin of eyes, ears, and body plans, i.e., the anatomical and structural features of living creatures); Phenotypic novelty, i.e., the origin of new forms throughout the history of life (for example, the mammalian radiation some 66 million years ago, in which the major orders of mammals, such as cetaceans, bats, carnivores, enter the fossil record, or even more dramatically, the Cambrian explosion, with most animal body plans appearing more or less without antecedents); and finally: Non-gradual forms or modes of transition, where you see abrupt discontinuities in the fossil record between different types. As Müller has explained in a 2003 work (“On the Origin of Organismal Form,” with Stuart Newman), although “the neo-Darwinian paradigm still represents the central explanatory framework of evolution, as represented by recent textbooks” it “has no theory of the generative.” In other words, the neo-Darwinian mechanism of mutation and natural selection lacks the creative power to generate the novel anatomical traits and forms of life that have arisen during the history of life. Yet, as Müller noted, the neo-Darwinian theory continues to be presented to the public via textbooks as the canonical understanding of how new living forms arose. The conference did an excellent job of defining the problems that evolutionary theory has failed to solve, but it offered little, if anything, by way of new solutions to those longstanding fundamental problems. 4

In the early chapters of this book, I will delve into the limitations of natural selection and genetic drift in explaining the intricate forms of complex organisms. These traditional theories fall short in their predictive power, leaving unanswered questions about the true mechanisms underlying phenotypic complexity and architecture. However, the heart of this book lies in shedding light on the groundbreaking discoveries made by science in recent years. In these recent findings, we unearth layers of biological sophistication that go far beyond genetics. Our perspective shifts from the reductionist approach to a systems view, considering every actor, from the molecular level to ecology. It is an approach that acknowledges the contributions of every level of organization, from the tiny cells to entire organisms and ecosystems, finally culminating in a conclusion that aligns with the evidence and facts presented.
My background as a machine designer informs my approach to investigating and interpreting the marvels of biological systems. Like the intricate workings of human-made artifacts and devices, biological systems exhibit remarkable parallels. From computers and robotics to energy turbines and factories, we discover that cells are veritable chemical factories teeming with machines. This realization moves beyond analogy and delves into a literal understanding.

Does Darwin's Theory of Evolution replace God? 

Often atheists claim that Darwin's Theory of Evolution replaces God.  Richard Dawkins famously noted that:  “Darwin made it possible to be an intellectually fulfilled atheist.” While Darwin supposedly encountered an alternative explanation for the origin of biodiversity, that does not include an explanation for: 

It's striking how the universe and living organisms display a remarkable level of complexity and intricacy, resembling the work of a designer. When I examine the intricate structures of cells, the interdependent relationships between organisms and their environments, and the elegant laws governing the universe, it's challenging to dismiss the possibility of a deliberate creator. While evolutionary theory offers insights into how species change over time, it doesn't fully address the question of the origin of life or the underlying design that seems to permeate the natural world. The concept of the universe as a winding clock suggests a beginning point, a moment of creation. The Big Bang theory provides an explanation for the origin of the universe, but it doesn't explain the ultimate cause behind this cosmic event. The fact that the universe had a definite starting point raises profound questions about what might have initiated this process. Evolution may account for the diversity of life within the universe, but it doesn't delve into the origins of the universe itself. The finely-tuned constants and laws of physics that enable the existence of life are remarkable. The precision required for a universe that can support life is truly astounding. Evolutionary theory, while illuminating how species change and adapt over time, doesn't explain why the universe seems meticulously fine-tuned to allow for the emergence of life. The existence of these finely tuned parameters and physical laws raises the question of whether they are the result of chance or intention. When I contemplate the inner workings of a cell, I'm struck by its astonishing complexity. Cells are akin to miniature cities, complete with factories, machinery, and information processing systems. The intricate molecular processes and structures within cells appear to point toward a purposeful design. While evolution provides insights into how species diversify, it doesn't account for the origin and complexity of cellular systems. The presence of complex genetic codes and information within living organisms is a profound mystery. DNA's role as a blueprint for life, along with the intricate processes of gene expression, challenges our understanding of how such sophisticated interdependent information systems could arise solely through unguided processes. Evolutionary mechanisms can account for changes within populations, but the origin of the genetic information, the genetic code and language,  and the coding systems themselves remain an unsolved question. Not because science has not investigated it, but because unguided mechanisms are inadequate explanations.  Considering all these aspects, it's not a matter of simply arguing from ignorance or inserting a "God of the Gaps." Instead, it's a rational inference based on the observations and evidence at hand. From what I can discern, the presence of intricate designs, fine-tuned parameters, complex information systems, and the orchestrated interplay of diverse components points toward the involvement of an intelligent agent. Just as my own experience tells me that intelligence can produce sophisticated structures, systems, and information, I find it a logical and reasonable inference to conclude that an intelligent creator is the best explanation for the origins and complexities we observe in the universe and life.

Comparing the Evolution from a calculator to a computer, to the evolution from simple, to complex organisms

Let's embark on an imaginative journey into the world of manufacturing and explore the plausibility of a factory evolving from producing calculators to manufacturing computers. In this scenario, we encounter a factory where occasional manufacturing errors introduce variations in the calculators being produced. By a stroke of serendipity, one of these variations unexpectedly enhances the calculator's functionality, capturing the hearts of users and prompting the factory to permanently incorporate the change. However, the transformation from a calculator factory into a computer factory presents a formidable set of challenges. A calculator, with its simple design, performs basic arithmetic operations and typically features a limited number of buttons for numerical input. On the other hand, a computer encompasses complex processing capabilities, storage, input/output devices, an operating system, and a plethora of software applications. Suppose a manufacturing error results in a calculator with slightly more memory or a larger display. While these changes might enhance the calculator's functionality, they fall short of enabling it to become a computer. Additional components such as a keyboard, storage units, a monitor, and interfaces for peripherals would be required. Alas, these components cannot be easily modified or derived from the existing calculator parts. Even if, by a twist of fate, a neighboring factory inadvertently supplies a computer's motherboard to the calculator factory, numerous modifications would still be necessary to integrate it with the existing calculator components. The buttons on the calculator would need to be reconfigured as keys, the display would have to undergo an upgrade to become a full-fledged monitor, and an array of new interfaces and connections would need to be developed from scratch. 

The transition from a calculator to a computer entails not only significant changes in manufacturing processes but also a fundamental shift in production flow. Computer manufacturing requires advanced techniques such as printed circuit board assembly, soldering, and chip integration, which differ substantially from the processes employed in calculator production. The factory would find itself on an adventurous path, requiring the acquisition of new machinery, retraining of its workforce, and the establishment of new quality control measures tailored to computer production. Furthermore, the transition would necessitate the introduction of entirely different raw materials and supply chains. Computer components, including integrated circuits, processors, memory modules, and hard drives, would need to be sourced and seamlessly integrated into the production process. This would entail forging relationships with new suppliers, implementing specialized import mechanisms, and incorporating additional testing and validation procedures to ensure the quality and functionality of the computer's components. Additionally, the factory would need to adapt its production lines and infrastructure to accommodate the assembly of computers. The manufacturing process would grow in complexity, involving the installation of various components, the integration of software systems, and the meticulous testing and quality assurance of the final product. The transition from a calculator factory to a computer factory transcends simple modifications and adaptations within the existing production process. It requires the integration of specialized components, the development of intricate interactions and systems, the acquisition of new machinery, the implementation of advanced manufacturing techniques, the sourcing of different raw materials, and the establishment of new supply chains and quality control measures. Applying biological evolution through the gradual accumulation of unguided errors is inasmuch an invalid concept within the natural realm, as applying it to the extraordinary transition from a calculator to a computer. It presents an array of challenges that extend beyond the scope of simple modifications and adaptations within an existing production process.

In the scenario of a factory evolving from producing calculators to manufacturing computers, we can draw an analogy to real-life biological systems and explore why the challenges of such a transition apply similarly. This analogy highlights the complexities and limitations of relying solely on random errors and gradual changes to explain the emergence of complex biological structures and functions. In biological evolution, the concept of random mutations acting over long periods of time to generate complex features is often compared to the manufacturing scenario described above. Just as a calculator factory cannot easily evolve into a computer factory solely through small, accidental changes, biological systems face similar challenges when transitioning from simpler forms to more complex ones. In the biological realm, an initial mutation might introduce a minor improvement in an organism's functionality, similar to the way a manufacturing error could enhance a calculator's features. However, transitioning from simple structures to complex ones, like evolving from basic organs to sophisticated systems in organisms, requires the emergence of entirely new features. Just as a calculator's design is insufficient to accommodate the complexity of a computer, gradual modifications are unlikely to account for the emergence of intricate biological features like eyes, wings, or complex physiological processes. As the calculator factory needs to incorporate the making of new components like keyboards, storage units and monitors to become a computer factory, biological evolution would need to seamlessly integrate new anatomical structures, biochemical pathways, and regulatory mechanisms to facilitate the evolution of complex traits. Simply accumulating small, random changes is insufficient to explain the development of these integrated and coordinated systems. The transition from calculators to computers involves a fundamental shift in complexity and functionality. Similarly, the evolution of simple life forms to more advanced ones entails a profound increase in complexity, with the appearance of new genetic information, integrated with regulatory networks, signaling pathways and processing, feedback loops, codes and languages, and intricate cellular processes that work intrinsically, and extrinsically, in an interdependent fashion.

 Intrinsically, because the individual parts are irreducibly complex, and extrinsically, because these parts have only function, integrated in the greater system. The random accumulation of mutations, like manufacturing errors, is not enough to bridge this significant gap. Just as the calculator factory would require new machinery, specialized manufacturing processes, and components to become a computer factory, biological evolution would require the emergence of new genes, proteins, signaling, manufacturing, and regulatory codes, languages, proteins, enzymes, metabolic pathways,  elements to drive the formation of new complex traits. These components are often highly specialized and finely tuned, which poses a challenge for gradual and unguided evolutionary processes. A calculator factory's transition to a computer factory would necessitate the establishment of new supply chains, interactions, and quality control measures. Similarly, in biological systems, evolving complex traits requires the simultaneous development of multiple components that interact precisely within cellular networks. These networks are often irreducibly complex, meaning that removing any one component can render the entire system non-functional. The challenges posed by the transition from calculator production to computer manufacturing in your analogy provide insights into why the concept of gradual, unguided evolution faces significant difficulties when applied to explaining the origin of complex biological structures and functions. The need for specialized components, integrated systems, information-rich genetic, epigenetic, manufacturing, signaling, and regulatory codes, and precisely adjusted and finely orchestrated and tuned interactions aligns with the idea that intelligent design or purposeful guidance might be necessary to explain the complexity and diversity observed in the biological world.

Beyond Evolution: The Origin of Species by Design Adsasd12

Objection: Your argument is basically the old 'irreducible complexity' argument. That's a very weak argument, and is really just an argument from ignorance- not knowing how something evolved does not mean it didn't evolve. All we need to show that evolution is possible for such a system is to show that there are functional, related, less complicated systems possible.
Answer:  Charles Darwin spoke about the "complexity of the eye" in his book "On the Origin of Species." He wrote:

"To suppose that the eye, with all its inimitable contrivances for adjusting the focus to different distances, for admitting different amounts of light, and for the correction of spherical and chromatic aberration, could have been formed by natural selection, seems, I freely confess, absurd in the highest possible degree."

Darwin goes on to explain how the eye could have evolved through incremental steps:

"Yet reason tells me, that if numerous gradations from a perfect and complex eye to one very imperfect and simple, each grade being useful to its possessor, can be shown to exist; if further, the eye does vary ever so slightly, and the variations be inherited, which is certainly the case; and if any variation or modification in the organ be ever useful to an animal under changing conditions of life, then the difficulty of believing that a perfect and complex eye could be formed by natural selection, though insuperable by our imagination, can hardly be considered real."

In essence, Darwin was presenting a potential objection to his theory. One of the core tenets of Darwinian evolution is that beneficial traits — those that confer a survival advantage in a particular environment — will be more likely to be passed on to subsequent generations. This process, known as natural selection, is a driving force behind evolutionary change. If it were conclusively shown that there existed a complex trait that could not have arisen through a series of smaller, beneficial steps, then that would pose a significant challenge to the theory of evolution as proposed by Darwin. In other words, if there was a trait for which there were no possible intermediate stages that offered any survival advantage, then natural selection could not account for the emergence of that trait.

Some try to counter-argue by claiming that just because we might not currently understand or have evidence for the intermediate stages of a trait's development doesn't mean they didn't exist. Demonstrating that no possible beneficial stages could have existed is a tall order. In practice, as we continue to gather more knowledge and refine our understanding of biology and genetics, many previously puzzling evolutionary developments have been illuminated.

The appeal to ignorance is the claim that if something has not been proven to be false must be true, and vice versa. (e.g., There is no compelling evidence that UFOs are not visiting the Earth; therefore, UFOs exist, and there is intelligent life elsewhere in the Universe.) Or: There is a teapot revolving in an elliptical orbit between Earth and Mars. Because nobody can prove otherwise, it's true.  It also does not consider and ignore that there may have been an insufficient investigation to prove that the proposition is either true or false.

This objection becomes pointless when an exhaustive class of mutually exclusive propositions has been established, a framework of examination, and all possibilities have been carefully examined. Applying Bayesian probability, or abductive reasoning to the best explanation, combined with eliminative induction, we can come to well-informed, plausible, and rational conclusions.  

In the Intelligent Design vs. Evolution debate, we have two competing hypotheses, where one can be shown with high certainty false, and the other true. Either an intelligent powerful eternal designer exists and creates the universe, and life, or not.  Eliminative inductions argue for the truth of a proposition by arguing that competitors to that proposition are false. Provided the proposition, together with its competitors, forms a mutually exclusive and exhaustive class, eliminating all the competitors entails that the proposition is true. Since either there is a God, or not, either one or the other is true. Eliminative inductions, in fact, become deductions.

Life cannot come from non-life. Science has not been able to come up with even a plausible, coherent model that would show the possible pathway from random molecules to a self-replicating cell. All tests have failed. On every level. Cells have a codified description of themselves in digital form stored in genes and have the machinery to transform that blueprint through information transfer from genotype to phenotype, into an identical representation in analog 3D form, the physical 'reality' of that description. Specified complexity observed in genes dictates and directs the making of irreducible complex molecular machines, robotic molecular production lines, and chemical cell factories. All historical, observational, testable, and repeatable examples have demonstrated that information and operational functionality come from intelligent sources.

Premise 1: Life is directed and choreographed by instructional, complex, specified information. We find this in the universal genetic code, its 33 distinct variations, and over 230 interconnected manufacturing, signaling, and operational codes 4) . Furthermore, hundreds, if not thousands (in the case of prokaryotes), of complex signaling networks, are interwoven. These networks and codes communicate with and rely upon one another to shape the majestic architecture and immense biodiversity we see in multicellular organisms.
Premise 2: This prodigious reservoir of layered information is far from arbitrary. It's akin to digital semiotic languages, characterized by syntax, semantics, and pragmatics. Whether it's proteins, metabolic pathways, or biomechanical constructs, every component functions with unparalleled precision, adhering to rules optimized for distinct roles. Like an alphabet, these codes are indispensable; having only half a code is akin to possessing half an alphabet—insufficient to convey the crucial information life demands.
Premise 3: Although the molecular structures that convey life are tangible, the very essence of information is ethereal. It's a conceptual entity, operating beyond the capabilities of spontaneous and aimless physical occurrences. To suggest that random processes can spawn semiotic codes is like expecting a rainbow to craft poetry or the wind to draft an architectural blueprint. The directive and purposeful nature evident in biological coding points to intention, foresight, and objective-driven designs.
Conclusion: The breathtaking complexity and evident purpose in the design and diversity of organisms demand an explanation beyond sheer coincident mutations and natural selection. Such intricacies hint not merely at the outcomes of undirected evolution but suggest the craftsmanship of an intentional, intelligent designed setup.

You might be tempted to think, "This is the conclusion; I can stop here." However, I share this insight with you at the outset, not as a full stop, but as an invitation. My hope is to pique your interest and guide you through the journey that led me to this revelation. Instead of placing this at the end, I've chosen to begin with it, to set the stage for the narrative that unfolds.

Biological Complexity and Information: A Case for Intelligent Design

In 1973,  the evolutionary biologist Theodosius Dobzhansky, famously stated that "Nothing in Biology Makes Sense Except in the Light of Evolution". This quote was written a half-century ago. Much has changed since then. Scientific inquiry has made huge leaps of progress and unraveled more than ever before, how complex life is. This has led to the conclusion by many that the intricate complexity and diversity found in biological organisms and their architecture are best explained through the lens of intelligent design rather than unguided evolutionary processes. The remarkable organismal complexity and diversity, as well as the emergence of anatomical novelties and biodiversity, are driven by complex informational codes encoded within genetic and epigenetic systems that operate in an interdependent manner together. These codes involve at least 33 variations of genetic codes and over 230 epigenetic manufacturing, signaling, and regulatory codes as the primary contributors to the formation of organismal form, architecture, and biodiversity. This informational complexity is not simply a result of physical processes but emerges from a digital semiotic language. This language encompasses syntax, semantics, and pragmatics, and it is the means through which functional outcomes are achieved. Every protein, metabolic pathway, organelle, or biomechanical structure is framed as functioning based on these variegated semiotic codes, implying an intentional and purposeful arrangement. Information is not a physical entity but a conceptual one. The generation of semiotic codes requires intentionality and foresight, which physical processes lack. Physical processes can create semiotic code is akin to suggesting that a rainbow can write poetry or a blueprint. Information has only been observed to originate from a mind with goals, intentions, and creative foresight.



Creating a cake or a complex machine both require a clear set of instructions that guide the assembly of raw materials into a functional and organized structure. These examples can help us understand the concept of informational complexity and how it relates to the origin of life and biological organisms. To make a cake, a recipe must contain precise details: the types and quantities of ingredients, the order of mixing, the temperature and baking time, and even the method of decoration. All these instructions combine to create a final product with specific characteristics such as taste, texture, and appearance. The recipe serves as a blueprint that transforms basic ingredients into a coherent and well-defined dessert. Similarly, building a machine involves a detailed blueprint that outlines the arrangement of components, their connections, and how they interact. The blueprint provides a step-by-step guide for assembling the machine in a way that ensures it functions as intended. Without this instructional information, the machine's parts would remain disparate and lack the coherence necessary for proper operation. Drawing a parallel, the machinery of life within a cell and the cell itself can be seen as akin to a complex machine and its components. The genome – the genetic blueprint of an organism – contains the instructions necessary to assemble and operate the intricate cellular machinery. Just as a recipe guides the creation of a cake and a blueprint directs the assembly of a machine, the genetic code encodes the information needed to construct proteins, regulate processes, and coordinate the activities of a living cell. The analogy holds that the origin of life and biological complexity requires an initial blueprint or recipe. The intricate interplay of molecular processes, metabolic pathways, and cellular functions depends on precise and specific information stored through the genetic code. This information directs the synthesis of proteins, the control of gene expression, and the orchestration of cell activities. Just as a recipe or blueprint originates from a mind with intelligence and foresight, the intricate molecular choreography within cells and the design of the cell itself point to an intelligent origin that conceived and guided the development of life's informational complexity. Some have objected that cells are Self-replicating, while human-made factories are not. John von Neumann's Universal Constructor is an example of a man-made self-replicating machine. The fact that life is based on self-replication is a significant hallmark of complexity that is not easily achieved through unintelligent processes. Self-replication is not only an advanced feat, but it also requires precise coordination of various processes and components. 593 proteins are involved in human DNA replication and each has essential roles in maintaining the fidelity of genetic information during replication. Comparing cellular processes to factories and manufacturing lines highlights the intricacies of biochemical pathways. The highly organized and efficient nature of these processes implies the requirement of input of a high level of intelligence and intentionality, much like the organization in a man-made factory.  This book will demonstrate that everything in biology can be comprehended independently of evolution. Understanding biology is achievable through the lens of intelligent design.



1. Richard Dawkins: In short: Nonfiction
2. John Joe McFadden: Evolution of the best idea that anyone has ever had July 1, 2008
3. New trends in evolutionary biology: biological, philosophical and social science perspectives
4. P. NELSON AND D. KLINGHOFFER: Scientists Confirm: Darwinism Is Broken DECEMBER 13, 2016



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What is the Theory of Evolution?

The theory of evolution is an explanation, popularized by Charles Darwin for how life on Earth supposedly changed and diversified over time. It proposes that species of organisms undergo gradual changes in their characteristics and traits over successive generations, leading to the emergence of new species and the diversity of life forms we see today.  Darwin popularized the concept of natural selection as a mechanism driving the process of evolution. Supposedly, all living organisms share a common ancestor. Over time, small changes accumulate in populations through genetic variations and mutations. The environment exerts selective pressures on organisms. Individuals with traits that provide an advantage in surviving and reproducing are more likely to pass on those traits to their offspring. This process leads to the gradual accumulation of beneficial traits in a population over generations.  Individuals within a population vary in their traits due to genetic diversity. Some of these traits are better suited to the environment, allowing those individuals to survive and reproduce more successfully. Over time, accumulated changes would lead to significant differences between populations of the same species. If these differences become substantial enough, new species may eventually emerge through a process known as speciation. Evolution occurs gradually over long periods of time. Small changes accumulate over generations, resulting in significant differences between ancestral and descendant species.  All living organisms, from simple to complex, share a common ancestry. This means that all life forms are connected through a branching tree of evolutionary relationships. The theory of evolution is claimed to be supported by an array of evidence from various scientific disciplines, including paleontology (fossil record), comparative anatomy, embryology, molecular biology, and genetics. The supposed discovery of transitional fossils, the similarities in anatomical structures among different species, and the presence of vestigial structures (organs with reduced or no apparent function) have been claimed to provide strong evidence for evolutionary relationships.  It has undergone refinements and expansions over time as new evidence has emerged, contributing to our understanding of the processes that have shaped the diversity of life on Earth.

Undisputed Facts of Evolution

Change Over Time refers to the observation that species and ecosystems have changed and continue to change over time. The fossil record, comparative anatomy, and genetic evidence all support the idea that organisms have evolved and adapted to their changing environments. Changes in Allele Frequencies refer to the changes in the frequency of different alleles (versions of genes) in a population over generations. This process, driven by mechanisms like natural selection, genetic drift, and gene flow, can lead to the evolution of populations. Limited Common Descent is a concept that acknowledges that certain groups of organisms share a common ancestry but doesn't necessarily imply a single universal common ancestor for all life. The mechanisms responsible for these changes are primarily natural selection acting on random genetic variations or mutations. This is a well-supported aspect of evolutionary theory. Natural selection, coupled with genetic mutations, is a driving force of evolution. Malaria is an example, where natural selection operates on a few specific mutations, and demonstrates the interaction of these mechanisms in real-world contexts.

Not Established as Facts

While the concept of common descent finds wide support in evolutionary biology, the idea of all organisms sharing a single common ancestor (universal common descent) is not universally accepted. Some proponents of Intelligent Design and creationism, for instance, challenge this idea based on opposing evidence, that challenges this view.  The Blind Watchmaker Thesis, a term that was coined by Richard Dawkins, represents the idea that the diversity of life can be explained solely by unguided natural processes, without the need for a guiding intelligence. The question of whether evolutionary mechanisms are entirely sufficient to explain the origin of complex features and designs or not in organisms is a topic of ongoing debate. This book aims to give clear answers to some of the challenging questions, and where the evidence leads to.

The Theory of Intelligent Design contrasts the ToE

Intelligent Design (ID) is a theory that proposes an alternative explanation for the complexity and diversity of life on Earth. It suggests that certain features of the natural world are best explained by the action of an intelligent designer or creator, rather than purely natural processes like evolution. While proponents of ID do not necessarily reject all aspects of evolutionary theory, they do challenge some of its fundamental assumptions.  Evolution posits that all living organisms share a common ancestor and that the diversity of life arose through gradual modifications over time. ID proponents argue that the complexity and diversity of life are better explained by the deliberate intervention of an intelligent designer who provided organisms with the capacity to adapt and change.  Evolution relies heavily on the process of natural selection to explain how traits that enhance survival and reproduction become prevalent in populations. ID proponents contend that certain features of organisms exhibit a level of complexity and specificity that cannot be adequately explained by evolutionary mechanisms, like random mutation and natural selection alone. It is suggested that these features are more plausibly explained by the action of an intelligent designer.  Evolutionary theory cites transitional fossils as evidence for the gradual transition between different species. ID proponents point out that some complex biological structures and systems appear to have emerged suddenly in the fossil record without a clear evolutionary precursor. Such structures could be the result of intelligent design rather than step-by-step evolutionary processes. ID proposes that the information-rich nature of DNA and the complexity of cellular machinery is best explained by design. The origin of biological information and the intricate interplay of cellular processes suggest purposeful design rather than a purely natural origin. The concept of irreducible complexity suggests that certain biological structures are composed of multiple interacting parts, all of which are necessary for the structure to function. Such structures could not have evolved gradually, as the removal of any part would render the structure non-functional. The fine-tuning of physical constants and conditions in the universe, and fine-tuning on a biochemical level that allows life to exist, seems to point to a designed setup. The precise values of these constants and conditions suggest a purposeful arrangement, as even slight changes would make life impossible. Some biological systems exhibit a level of foresight and complexity that implies intentional design. Examples include intricate symbiotic relationships and biological systems that appear to anticipate future needs.

What were the major steps in the evolution of the theory of evolution?

The theory of evolution has undergone significant development and refinement over time. Early naturalists, such as Aristotle and Lamarck, proposed ideas about the changing nature of species and the adaptation of organisms to their environments. However, their explanations lacked a comprehensive mechanism for how species change over time. Charles Darwin's work, especially his book "On the Origin of Species" (1859), introduced the concept of natural selection as the driving force behind the evolution of species. Darwin proposed that organisms with advantageous traits are more likely to survive and reproduce, leading to the gradual accumulation of changes in populations over generations. The emergence of the field of genetics, particularly Gregor Mendel's work on inheritance, provided a mechanism to explain how traits are passed from one generation to the next. The integration of genetics and evolution led to the development of the modern synthesis or neo-Darwinian theory, which combined natural selection with Mendelian genetics. The discovery of the structure of DNA by James Watson and Francis Crick in 1953 revolutionized our understanding of heredity and paved the way for molecular biology. The study of DNA sequences and the genetic code allowed researchers to explore the molecular basis of evolutionary processes. Advances in fields such as paleontology, genetics, genomics, and developmental biology have deepened our understanding of evolutionary mechanisms and patterns. The study of fossils, comparative genomics, molecular phylogenetics, and experimental evolution has provided insights into the relationships between species, the origin of new traits, and the mechanisms driving evolutionary change. In recent decades, the Extended Evolutionary Synthesis (EES) has emerged as a framework that expands on the original neo-Darwinian theory. It incorporates ideas from fields like epigenetics, niche construction, and evolvability to provide a more comprehensive understanding of how organisms evolve. Evolutionary biology continues to be a vibrant and dynamic field with ongoing research and exploration. Advances in technology and interdisciplinary collaborations are contributing to a deeper understanding of complex evolutionary processes, such as the role of horizontal gene transfer, the origin of novel traits, and the influence of environmental factors on evolution. Throughout its history, the theory of evolution has evolved from early concepts of change and adaptation to a comprehensive and multidisciplinary framework that tries to explain the diversity of life and the mechanisms by which species supposedly evolved over billions of years.

4th Century BCE - 18th Century CE: Early Observations and Ideas: Aristotle proposes the concept of the Scala Naturae, a hierarchical view of life. Lamarck suggests the idea of inheritance of acquired characteristics as a mechanism for species change.
19th Century: 1859: Charles Darwin publishes "On the Origin of Species," introducing the concept of natural selection. Late 19th Century: Gregor Mendel's work on inheritance provides insights into the mechanisms of genetic inheritance.
Early 20th Century: 1910s-1930s: The modern synthesis integrates natural selection with Mendelian genetics. 1920s: Ronald Fisher, Sewall Wright, and J.B.S. Haldane develop mathematical models of population genetics.
1930s-1940s: Theodosius Dobzhansky and others apply genetics to natural populations, solidifying the modern synthesis.
Mid-20th Century: 1953: James Watson and Francis Crick discover the structure of DNA. 1960s: Molecular biology and genetic sequencing techniques begin to uncover the molecular basis of heredity.
Late 20th Century - Present: 1970s: The field of molecular evolution explores the genetic changes underlying evolutionary processes. 1980s-1990s: Comparative genomics and molecular phylogenetics provide insights into evolutionary relationships. 1990s-2000s: Advances in developmental biology and paleontology contribute to the understanding of evolutionary mechanisms. 
21st Century: The Extended Evolutionary Synthesis (EES) emerges, incorporating ideas from epigenetics, evolvability, and niche construction.
Ongoing: Interdisciplinary research, technological advancements, and experimental studies continue to expand our understanding of evolution.

Evolution prior to Darwin

The roots of evolutionary biology trace back to the publication of Charles Darwin's groundbreaking work, "On the Origin of Species," in 1859. However, it's essential to recognize that many of Darwin's ideas have older origins. While the belief in species fixity was predominant in Darwin's time, some naturalists and philosophers before him had already speculated about species transformation. Notably, the French naturalist Jean-Baptiste Lamarck (1744–1829) played a crucial role in bringing the question of species change to the forefront. Lamarck's significant work, "Philosophie Zoologique" (1809), presented his idea of transformism, an early concept of evolution. Unlike the modern understanding of evolution, Lamarck's view proposed that lineages of species persist indefinitely without branching or extinction. He attributed species change to an "internal force," some unknown mechanism within organisms, leading to slight differences in offspring over generations, eventually resulting in visible transformations and new species. Lamarck's most remembered and criticized concept is the inheritance of acquired characters. He suggested that an organism could pass on modifications acquired during its lifetime to its offspring. For instance, he used the example of giraffes stretching their necks to reach higher leaves, causing their necks to grow longer. According to Lamarck, this acquired longer neck would be inherited by the giraffe's offspring, ultimately leading to the elongated necks we see today. While Lamarck's theory has been caricatured as suggesting organisms "will" themselves to change, it merely requires flexibility in individual development and the inheritance of acquired traits, without conscious effort from the organisms. While Lamarck did not originate the concept of the inheritance of acquired characters, he significantly influenced modern thinking about it. The idea has been conventionally labeled as Lamarckian inheritance, despite its ancient roots. Unfortunately, Lamarck faced opposition and skepticism from his contemporaries, particularly Georges Cuvier (1769–1832), a skilled anatomist and rival. Cuvier's influence led to the establishment of the belief in the fixity of species among professional biologists. Cuvier's school categorized the animal kingdom into four main branches, and he demonstrated that species could go extinct, contrary to Lamarck's beliefs. Lamarck's ideas eventually reached Britain through the critical discussions of British geologist Charles Lyell (1797–1875) and anatomist Richard Owen (1804–1892). By the first half of the nineteenth century, most biologists and geologists adopted Cuvier's view of species having separate origins and remaining constant until extinction.
As the debate surrounding evolution continued, Darwin's groundbreaking work eventually revolutionized the field, providing a more comprehensive theory of evolution that shaped the future of evolutionary biology.

Charles Darwin

Charles Darwin embarked on a remarkable journey that shaped his ideas in evolutionary biology. Following his voyage aboard the Beagle (1832–37) as a naturalist, Darwin settled in the countryside, blessed with financial independence due to his family's background. The pivotal moment of Darwin's life occurred when he examined his collection of birds from the Galápagos Islands. Initially assuming they were all one species, he soon realized that each island hosted its distinct finch species. This observation led him to contemplate the idea of species changing over time from a common ancestral form, triggered by geographic variation. The real challenge for Darwin was formulating a theory that not only explained species change but also accounted for their remarkable adaptations to their environments. He rejected earlier ideas, including Lamarckism, because they failed to address adaptation adequately. Darwin was particularly fascinated by how woodpeckers, tree frogs, and seeds demonstrated exquisite adaptations for their specific habitats. It was during his reading of Malthus's "Essay on Population" in October 1838 that the key to his theory, natural selection, crystallized. Observing the constant struggle for existence in nature, he realized that favorable variations in organisms would be preserved, while unfavorable ones would perish. This process would lead to the formation of new species over time. Darwin's theory of natural selection posited that organisms better adapted to their environments would leave more offspring, increasing their frequency in subsequent generations. As environmental conditions changed, different forms of a species would become better suited, leading to the formation of new species. Darwin was enthralled by the prospects of this theory and devoted himself to its development. During his work on his theoretical framework, Darwin received a letter from Alfred Russel Wallace, another British naturalist who had independently arrived at a very similar idea of natural selection. With the support of his friends Charles Lyell and Joseph Hooker, Darwin and Wallace's ideas were jointly announced at the Linnean Society in London in 1858. Darwin was already working on an abstract of his comprehensive findings, which culminated in his book,  "On the Origin of Species."

Beyond Evolution: The Origin of Species by Design Image116

"Often a cold shudder has run through me, and I have asked myself whether I may have not devoted myself to a phantasy."

Context This quote comes from a letter from Darwin to his mentor, the geologist Charles Lyell, from 23 November 1859, whilst On the Origin of Species was being published. Darwin expressed how much it means to him that he has Lyell’s support, and here is the quote in context: “I rejoice profoundly that you intend admitting doctrine of modification in your new Edition. Nothing, I am convinced, could be more important for its success. I honour you most sincerely:—to have maintained, in the position of a master, one side of a question for 30 years & then deliberately give it up, is a fact, to which I much doubt whether the records of science offer a parallel. For myself, also, I rejoice profoundly; for think-ing of the many cases of men pursuing an illusion for years, often & often a cold shudder has run through me & I have asked myself whether I may not have devoted my life to a phantasy. Now I look at it as morally impossible that investigators of truth like you & Hooker can be wholly wrong; & therefore I feel that I may rest in peace.”

Reception of Darwin's Theory

Darwin's ideas on evolution and natural selection stirred diverse reactions among different communities. While the concept of evolution became controversial, especially in popular circles due to its apparent contradiction with religious beliefs, professional biologists were more open to accepting the idea. Notably, Thomas Henry Huxley ardently defended evolution against religious objections in Britain. Among biologists, the acceptance of some form of evolution was relatively widespread, although not all of them fully shared Darwin's perspective. Darwinian evolution posited that species evolve based on local conditions, not inherently progressing to higher forms. However, many late nineteenth and early twentieth-century proponents of evolution held a different view of evolution, imagining it as one-dimensional and progressive. Natural selection, on the other hand, faced significant opposition and criticism. Some sophisticated objections claimed that Darwin's theory lacked a satisfactory explanation of heredity. Darwin's "blending" theory of inheritance, where parental attributes blend in offspring, was found to be inadequate to support natural selection. At a popular level, misconceptions about natural selection persisted, with some believing it to be a random process, when, in fact, it is non-random. Another objection raised was the perceived existence of gaps between forms in nature, seemingly insurmountable through natural selection alone. To address these objections, some biologists sought to propose alternative mechanisms to natural selection, including theories of "directed variation." These theories suggested that offspring consistently tended to differ from their parents in a specific direction due to hereditary mechanisms. Lamarckian inheritance, where acquired characteristics were inherited, was one popular theory of directed variation. However, with the rediscovery of Mendel's theory of heredity (Mendelism), natural selection faced further skepticism. Early Mendelians opposed Darwin's natural selection theory, and the Mendelian view prevailed among some biologists who studied large differences between organisms (macromutations). Conversely, biometricians rejected Mendelism and studied smaller differences between individuals, describing the frequency distributions of measurable characters. Despite these debates and critiques, Mendelism eventually allowed for a revival of Darwin's theory, leading to the synthesis of Darwinian evolution and Mendelian genetics, which forms the basis of modern evolutionary biology. The early twentieth century witnessed a rich landscape of ideas and perspectives on evolution.

Introduction of philosophical naturalism

Thomas Huxley and the members of the "X Club" became influential figures in shaping the direction of science in the United Kingdom. The X Club was a group of like-minded scientists and philosophers who shared a strong commitment to materialism, which is the philosophy that everything in the natural world can be explained by natural processes without the need for any supernatural intervention. Huxley, a close friend of Charles Darwin, actively promoted materialism and sought to establish it as the dominant worldview within the scientific community. He believed that engaging in dialogue with creationists, who held religious beliefs, was a futile endeavor. Instead of engaging in scientific discussions, Huxley often resorted to attacking the person rather than addressing their arguments. He saw his major goal as establishing that science and God was incompatible, and he wanted to prevent any challenges to the materialistic worldview from gaining credibility. The X Club's influence extended to the British Royal Society, where they held exclusive control over the presidency for thirteen consecutive years. They succeeded in shaping the society to promote materialism, a legacy that continues even today. Modern evolutionary science has been influenced by this historical approach, leading to a tendency to reject anything that challenges materialism, regardless of its scientific merit. This approach has been effective in maintaining the dominance of materialistic ideas within the scientific community. To challenge evolutionary dogma or to suggest that materialism might be inadequate is met with resistance and rejection. One area where open discussion is discouraged is the investigation of the scope of natural processes in explaining the origin of life. Materialistic bias inhibits simultaneous discussions of the biochemical and genomic information requirements for a natural origin of life and the capabilities of natural processes to meet these needs. This bias prevents an open examination of the gaps and difficulties in evolutionary theory. 

Beyond Evolution: The Origin of Species by Design 1020_110
Michael Faraday, Thomas Henry Huxley, Charles Wheatstone, David Brewster, John Tyndall ( 1876, Wikimedia)

Todd, S.C. correspondence to Nature 401(6752):423, 30 Sept. 1999 : ‘Even if all the data point to an intelligent designer, such a hypothesis is excluded from science because it is not naturalistic’

Mendel's Teachings and Discoveries

Gregor Mendel, an Austrian scientist, lived from July 20, 1822, to January 6, 1884. He is primarily known for his groundbreaking work in the field of genetics and heredity, which laid the foundation for modern understanding of how traits are inherited from one generation to the next. Mendel's experiments and insights paved the way for the development of the science of genetics and had a profound impact on our understanding of evolution. Mendel is best known for his pea plant experiments, which he conducted in the mid-19th century while working as a monk in the Augustinian Abbey of St. Thomas in Brno, Czech Republic. Through careful observations and controlled breeding experiments, Mendel formulated his laws of inheritance, which later became known as Mendelian genetics. These laws include the principles of segregation, independent assortment, and dominance and recessiveness. Mendel's work was initially met with little recognition during his lifetime, but it gained prominence in the early 20th century when other scientists rediscovered his research and realized its significance. Mendelian genetics provided a crucial framework for understanding how traits are passed from parents to offspring, and it contributed to the broader field of evolutionary biology by explaining how genetic variation and inheritance play a role in the process of evolution. Mendel discovered that each individual has two alleles (gene variants) for each trait, one inherited from each parent. These alleles segregate during gamete formation, with only one allele passing to each offspring. Gametes are specialized reproductive cells that are essential for sexual reproduction in organisms. These cells are produced through a process called gametogenesis and have a crucial role in transmitting genetic information from one generation to the next. In most sexually reproducing organisms, there are two types of gametes:  Sperm cells are the male gametes. They are typically small, motile cells that are adapted for swimming to reach and fertilize the egg. Sperm carry genetic information from the father to the offspring.  Eggs, or ova, are the female gametes. They are larger than sperm and are non-motile. Eggs provide the environment and nutrients necessary for the development of the embryo. Eggs carry genetic information from the mother to the offspring. During fertilization, a sperm cell fuses with an egg cell, combining their genetic material to create a unique individual with a diverse set of traits inherited from both parents. This genetic diversity is essential for evolution, as it allows for the accumulation of new combinations of genetic traits over generations.

Beyond Evolution: The Origin of Species by Design 424

Mendel observed that different traits are inherited independently of one another. This means that alleles for different traits are distributed randomly to offspring, leading to new combinations of traits. Mendel also found that some alleles are dominant, masking the expression of recessive alleles in heterozygous individuals. Mendel's work forms a critical foundation for understanding the mechanisms of genetic variation, which is essential for the process of evolution.  Evolution depends on genetic variation within populations. Mendel's laws explain how different combinations of alleles arise and are passed from one generation to the next. This variation provides the raw material for natural selection to act upon. Natural selection acts on the variations present in a population, favoring traits that enhance survival and reproduction. Mendel's principles explain how these traits are inherited and how they can become more or less common over generations. Mendelian genetics plays a role in the formation of new species. As populations accumulate genetic differences over time, reproductive isolation can occur, preventing gene flow between groups. This can lead to the divergence of traits and the formation of distinct species. Mendelian inheritance contributes to the development of adaptations, which are traits that increase an organism's fitness in a specific environment. Over time, beneficial alleles can become more prevalent in a population, leading to better-adapted individuals.  Mendel's principles help explain the effects of genetic drift, which are random changes in allele frequencies in small populations. As alleles are passed from generation to generation, genetic drift can lead to the fixation or loss of alleles, influencing the evolutionary trajectory of a population.

Integrating Genetics and Natural Selection in the Early 20th Century

The early 20th century marked a significant period in the field of evolutionary biology with the development of the modern synthesis, a conceptual framework that united Charles Darwin's theory of natural selection with the principles of Mendelian genetics. During this era, key figures such as Ronald Fisher, Sewall Wright, and J.B.S. Haldane made remarkable contributions to the field, laying the groundwork for our current understanding of population genetics. The early 20th century witnessed the merging of two important streams of thought: Darwinian natural selection and Mendelian inheritance. Prior to this synthesis, there was a disconnect between the gradual process of natural selection proposed by Darwin and the discrete inheritance patterns observed by Mendel. This period saw a renewed focus on heredity and variation, with researchers seeking to reconcile these seemingly disparate concepts.
Ronald Fisher (1890-1962), a British statistician and geneticist, played a pivotal role in developing mathematical models that explained how genetic traits are inherited and how they change in populations over time. He introduced statistical methods to the study of genetics and evolution, providing a quantitative framework for understanding natural selection and genetic drift. Fisher's work laid the foundation for modern statistical genetics and had a profound impact on population genetics theory. Sewall Wright (1889-1988), an American geneticist, introduced the concept of genetic drift and developed the idea of genetic load, which refers to the cumulative detrimental effects of deleterious mutations in a population. He also formulated the concept of "adaptive landscapes," illustrating how genetic variation and natural selection interact to shape the trajectory of evolution. Wright's contributions emphasized the importance of random genetic changes in evolution and enriched the understanding of population genetics. J.B.S. Haldane (1892-1964), a British geneticist and evolutionary biologist, made significant contributions to both theoretical and empirical aspects of population genetics. He developed mathematical models to explore the effects of selection, mutation, and migration on genetic variation within populations. Haldane's work helped elucidate the genetic basis of various traits and provided insights into the rates and processes of evolutionary change.

The collective efforts of Fisher, Wright, and Haldane led to the establishment of mathematical models that quantified how genetic variation is maintained and modified within populations. These models explored concepts such as allele frequencies, genetic equilibrium, and the effects of different evolutionary forces. Their work allowed scientists to make predictions about how populations would change over generations and provided a rigorous framework for studying evolution at the genetic level. The mathematical models and concepts developed during this period formed the basis for understanding how genetic variation is created, maintained, and acted upon by natural selection. The integration of population genetics with Darwinian natural selection marked a turning point in evolutionary biology, providing a comprehensive framework that bridged the gap between the mechanisms of inheritance and the processes of adaptation and speciation. The contributions of Fisher, Wright, Haldane, and other researchers of their time laid the groundwork for modern evolutionary biology. Their mathematical models and theoretical insights revolutionized the field, enabling scientists to explore the intricate interplay between genetics and natural selection and to make quantitative predictions about the patterns and processes of evolution. The early 20th century thus stands as a pivotal era in the development of our understanding of population genetics and its role in shaping the diversity of life on Earth.

"Our Face from Fish to Man: A Portrait Gallery of Our Ancient Ancestors and Kinsfolk Together with a Concise History of Our Best Features" is a book written by William K. Gregory and published in 1929. This book provides an exploration of human evolution by tracing the gradual transformation of facial features and anatomical characteristics from fish-like ancestors to modern humans. It offers readers a visual journey through evolutionary history, showcasing how the faces of our distant relatives and early ancestors supposedly evolved over millions of years. William K. Gregory, a prominent American paleontologist and anatomist, was known for his work in comparative anatomy and the study of vertebrate evolution. In "Our Face from Fish to Man," Gregory used his expertise to present a comprehensive account of the supposed evolutionary changes that led to the distinct facial features of humans.
The book is structured as a portrait gallery, featuring illustrations and reconstructions of various species that are believed to be part of our evolutionary lineage. Gregory's approach combines scientific knowledge with artistic renderings to vividly depict the transformations that he and others imagined took place as our supposed ancestors adapted to changing environments and lifestyles.

The modern synthesis

By the early twentieth century, research in Mendelian genetics had gained significant momentum and had become a major field of study. However, one of the challenges was to reconcile Mendelian genetics, which focused on discrete traits inherited from parents, with the continuous variation observed in real populations, as described by biometricians. This reconciliation was achieved through the work of several scientists, with R.A. Fisher's 1918 paper being particularly influential. Fisher showed that the principles of Mendelian genetics could account for the results known to biometricians, bridging the gap between the two approaches. The next crucial step in the development of evolutionary theory was to demonstrate that natural selection could operate in conjunction with Mendelian genetics. Independently, R.A. Fisher, J.B.S. Haldane, and Sewall Wright made significant contributions to this synthesis, leading to what became known as neo-Darwinism or the modern synthesis of evolution. Julian Huxley's book "Evolution: the Modern Synthesis" (1942) popularized this unified perspective. The works of Fisher, Haldane, and Wright, mainly published around 1930, demonstrated that natural selection could account for the observable variation in natural populations, as well as the laws of Mendelian inheritance. This meant that no additional processes such as the inheritance of acquired characters, directed variation, or macromutations were necessary to explain evolution. Their insights formed the foundation of later evolutionary thinking and became fundamental to the understanding of how natural selection acts on genetic variation to drive evolutionary changes. These advances in theoretical population genetics provided a firm scientific basis for Darwin's theory of natural selection, filling a crucial gap that had persisted for decades. The integration of Mendelian genetics and natural selection marked a transformative moment in the history of evolutionary biology, solidifying the modern synthesis of evolution and laying the groundwork for further advancements in the field.

The reconciliation between Mendelism and Darwinism in the early 20th century sparked a surge of new genetic research, both in the field and laboratory. One prominent figure in this era was Theodosius Dobzhansky, who moved from Russia to the USA in 1927. He conducted influential investigations of evolution in populations of fruit flies (Drosophila), drawing inspiration from the Russian population geneticist Sergei Chetverikov. Dobzhansky's seminal book, "Genetics and the Origin of Species," first published in 1937, became a cornerstone of the modern synthesis, with subsequent editions leaving a lasting impact on the field of evolutionary biology. E.B. Ford, working in the UK, embarked on a comparable research program in the 1920s, focusing on the study of selection in natural populations, primarily moths. He termed his subject "ecological genetics" and summarized his work in the influential book "Ecological Genetics," first published in 1964. Another notable figure, H.B.D. Kettlewell conducted renowned research on melanism in the peppered moth (Biston betularia), which became a famous example of ecological genetic research. Julian Huxley, through his adept synthesis of research from various fields, significantly influenced the modern synthesis. His book "Evolution: the Modern Synthesis," published in 1942, introduced the theoretical concepts of Fisher, Haldane, and Wright to a broad audience, applying them to significant evolutionary questions. As the modern synthesis spread, it also tackled the subject of speciation – the process by which one species splits into two. Before the modern synthesis, speciation was often explained by macromutations or the inheritance of acquired characteristics. For instance, the book "The Variation of Animals in Nature" by G.C. Robson and O.W. Richards (1936) rejected both Mendelism and Darwinism, suggesting that species differences were non-adaptive and unrelated to natural selection. Richard Goldschmidt, in his book "The Material Basis of Evolution" (1940), argued that speciation resulted from macromutations rather than the selection of small variations. The modern synthesis and the incorporation of population genetics into evolutionary biology have revolutionized the understanding of the mechanisms behind evolutionary change and speciation. These advances set the stage for further discoveries and laid the foundation for modern evolutionary thinking.

The question of how new species originate was a central focus for population geneticists such as Fisher, Haldane, Wright, Dobzhansky, and Huxley. They reasoned that the genetic changes studied in populations could lead to divergence and eventual speciation if populations became geographically separated. Ernst Mayr's book "Systematics and the Origin of Species" (1942) became a pivotal work in this context, presenting a comprehensive theory of speciation as part of the modern synthesis. The modern synthesis also brought about a paradigm shift in systematics, challenging the traditional "typological" species concept, which defined species based on similar-looking organisms relative to a standard or "type" form. The new systematics, championed by Julian Huxley in his book "The New Systematics" (1940), rejected this notion and instead embraced a species concept based on the ability to interbreed within gene pools. Morphological similarity to a type form was no longer the defining factor for species; instead, the ability to interbreed became the key criterion. Paleontology, too, underwent a transformation under the influence of the modern synthesis. George Gaylord Simpson's work in "Tempo and Mode in Evolution" (1944) discredited the idea of orthogenesis, which posited an inherent tendency of species to evolve in a particular direction. Simpson demonstrated that fossil evidence aligned with the population genetic mechanisms described by the modern synthesis. By the mid-1940s, the modern synthesis had permeated all areas of biology, as evidenced by the Princeton Symposium on Genetics, systematics, and Paleontology in 1947. The symposium brought together experts from diverse biological fields who shared a common viewpoint rooted in Mendelism and neo-Darwinism. The synthesis became the dominant perspective, though controversies persisted within it, as well as in the counterculture outside.

DNA serves as the fundamental mechanism of heredity in almost all living organisms. It carries the crucial information required to construct a new body and differentiate its various parts. DNA molecules are present in nearly all cells of an organism, including the reproductive cells or gametes. The exact location of DNA within a cell depends on the cell type. There are two primary types of cells: eukaryotic and prokaryotic. Eukaryotic cells are more complex, containing internal organelles and a distinct region called the nucleus, which is surrounded by a membrane. In eukaryotic cells, DNA is housed within the nucleus. On the other hand, prokaryotic cells are simpler and lack a distinct nucleus. In prokaryotic cells, DNA is dispersed throughout the cell with no specific region. Complex multicellular organisms, such as plants and animals, consist of eukaryotic cells. Fungi, including both multicellular organisms like mushrooms and unicellular ones like baker's and brewer's yeast (Saccharomyces cerevisiae), are also eukaryotic. Protozoans, the majority of which are unicellular (e.g., amebas), constitute another group of eukaryotes. Bacteria and Archaea are the two categories of life where cells are prokaryotic. Within the nucleus of a eukaryotic cell, DNA is carried in structures called chromosomes. These chromosomes can be observed through a light microscope during specific stages of the cell cycle. Different species have characteristic numbers of chromosomes; for instance, humans typically have 46 chromosomes, fruit flies (Drosophila melanogaster) have eight, and other species possess varying numbers. While the finer structure of DNA is too minuscule to be directly observed, it can be inferred through X-ray diffraction. The molecular structure of DNA was famously unraveled by Watson and Crick in 1953.

Mid-20th Century: A Molecular Revolution Unravels the Secrets of Life

The mid-20th century marked a pivotal era in the field of biology, as groundbreaking discoveries in molecular biology and genetics transformed our understanding of life's fundamental mechanisms. Two significant milestones stand out during this period: In 1953, James Watson and Francis Crick, working at the University of Cambridge, unveiled one of the most iconic scientific breakthroughs of all time – the elucidation of the structure of DNA. This discovery provided a structural blueprint for understanding how genetic information is stored, transmitted, and replicated within living organisms. The DNA double helix, with its complementary base pairing and specific sequence, became the cornerstone of modern genetics. Watson and Crick's revelation laid the foundation for comprehending the molecular basis of heredity, heralding a new era in biological research. The 1960s witnessed an explosion of discoveries in molecular biology and genetic sequencing techniques that deepened our insights into the mechanisms of heredity. Scientists harnessed the newfound understanding of DNA's structure to unravel the intricate processes of gene expression, regulation, and protein synthesis.

Beyond Evolution: The Origin of Species by Design Sem_t111

Advancements in genetic sequencing techniques enabled scientists to decipher the precise sequence of nucleotides in DNA and RNA molecules. This breakthrough provided a means to decode the genetic information encoded within genomes, unraveling the genetic instructions that dictate an organism's traits and functions. Researchers also explored the role of RNA – a close cousin of DNA – in the cell's machinery. The discovery of transfer RNA (tRNA) and messenger RNA (mRNA) shed light on how genetic information is transcribed from DNA and translated into proteins, which are the workhorses of cellular processes. Furthermore, the deciphering of the genetic code – the correspondence between specific nucleotide triplets (codons) and amino acids – paved the way for understanding how the sequence of DNA nucleotides directs the synthesis of proteins. This code-breaking revelation was a crucial step toward connecting the molecular information stored in DNA with the intricate cellular machinery that governs life. Collectively, these advancements in molecular biology and genetic sequencing techniques revolutionized our understanding of heredity, gene function, and cellular processes. They laid the groundwork for subsequent breakthroughs in fields such as biotechnology, genetic engineering, and personalized medicine, transforming biology from a descriptive science into a molecular discipline with far-reaching practical applications. The mid-20th century thus stands as a period of scientific enlightenment that unveiled the inner workings of life at the molecular level, allowing us to explore the intricate tapestry of genetic information that shapes the diversity and complexity of living organisms.

Late 20th Century - Present: Unveiling Evolution's Molecular and Developmental Secrets

The latter half of the 20th century witnessed a remarkable confluence of scientific disciplines, leading to profound insights into the mechanisms that underlie biological processes. This period has been marked by groundbreaking discoveries in molecular biology, comparative genomics, molecular phylogenetics, developmental biology, and paleontology, each contributing to our ever-deepening understanding of the intricate mechanisms governing life. The 1970s saw the emergence of molecular biology as a distinct field of study. Researchers began to explore how genetic changes, occurring at the molecular level, drive the diversification and adaptation of organisms over time. Techniques like DNA sequencing allowed scientists to compare genetic sequences across species. This provided valuable insights into the relationships between different species. Comparative genomics and molecular phylogenetics in the 1980s-1990s permitted advancements in DNA sequencing technology. Scientists could now analyze entire genomes, comparing the DNA sequences of different species to uncover shared genes, regulatory elements, and structural features. Comparative genomics not only revealed the genetic basis of traits and functions but also provided a powerful tool for deciphering evolutionary relationships among species. Molecular phylogenetics, a field that employs genetic data to construct evolutionary trees, further elucidated the branching patterns of life's tree of descent. The late 20th century and early 21st century witnessed significant strides in developmental biology and paleontology, both of which have contributed crucial insights into the operation of biological systems. Developmental biology unraveled how changes in gene expression and regulation influence the development of complex structures and features, shedding light on how new traits arise. These insights highlighted the role of developmental processes in shaping the diversity of life. Paleontology, aided by advancements in fossil discovery and analysis techniques, provided a glimpse into the distant past. 

Mutations during DNA replication

In the process of cellular reproduction,  an exact duplicate of parental DNA is usually crafted, a meticulous endeavor conducted by an ensemble of enzymes that navigate the fine line between precision and occasional oversight. These enzymes are equipped with a dual purpose: not only to replicate DNA but also to be the vigilant sentinels of genetic integrity. With an unyielding dedication to accuracy, these proofreading and repair enzymes meticulously scan the newly formed DNA strands, correcting the majority of errors that might have crept in during the replication process. Their watchful eyes catch most of the glitches before they solidify, ensuring a faithful replication. Yet, akin to the quiet persistence of stars against a midnight sky, some errors manage to persist even in the face of these vigilant guardians. These stubborn anomalies are aptly named mutations, the subtle hiccups in the script of life.
The story these mutations tell isn't one of chaos. The deviations they introduce in the DNA sequence can paint a fresh portrait on the canvas of protein-coding. As if a master artist has decided to experiment with a new palette, mutations would give birth to proteins with properties distinct from the original design. A dance of possibility would unfold, with some mutants boasting novel attributes that could reshape the function of the cell. While mutations can occur within any cell, it is the ones that emerge during the production of gametes that take center stage in the narrative of evolution. Gametes, the precious carriers of genetic information, house the potential to pass on these genetic surprises to the next generation. It's a symphony of chance, a roll of the dice that would yield offspring who stand apart from their progenitors due to the subtle genetic twists inherited from the past. 

In the intricate realm of genetic information, mutations of various kinds can weave their unpredictable threads. One such mutation is the point mutation, where a single base within the DNA sequence transforms into another. The impact of this transformation hinges upon the nature of this base swap. Imagine a scenario where the DNA sequence shifts just slightly, like a subtle change in a familiar melody. In this  genetic change, some mutations, synonymous or silent mutations, go unnoticed by the protein sequence. These mutations occur between pairs of genetic triplets that actually code for the same amino acid. It's as if the genetic symphony remains harmonious, undisturbed by these silent notes. However, not all mutations remain silent. Some, known as non-synonymous or meaningful point mutations, create a new tune altogether. They change the amino acid that the code represents, introducing a new musical note into the melody. These meaningful mutations often arise due to the specific structure of the genetic code, where certain positions within the genetic triplets hold greater sway over the resulting protein. There's a fascinating distinction in the world of mutations—between transitions and transversions. Transitions are like shifting from one key to another, while transversions are more dramatic, almost like jumping across octaves. These mutations bring about a change in the purine and pyrimidine bases, akin to altering the fundamental building blocks of a composition. In the evolutionary composition, certain changes occur more frequently than others. Transitions, akin to a recurring refrain, find themselves woven more frequently into the melody of change. This pattern lends a distinctive rhythm to the ever-evolving genetic landscape. Yet, mutations can sometimes introduce chaos into this harmonious arrangement. Imagine a single base pair slipping into the DNA sequence, creating a ripple effect. This seemingly minor intrusion can alter the meaning of every genetic note that follows—a cascading symphony of change. These mutations, aptly called frameshift mutations, often lead to a dissonant discord, yielding proteins that are functionally off-key. And then, there's the unexpected halt—an interruption in the genetic conversation. A previously coding triplet might transition to a "stop" codon, abruptly ending the musical narrative. This cessation results in fragmented proteins, echoes of notes that never quite find resolution. In this intricate dance of genetics, mutations play the role of both maestro and improviser. They shift the melody, introduce new themes, and sometimes bring the music to a halt. Each mutation, a tiny spark of creative chaos, adds a unique twist to the evolving genetic composition. In the world of DNA, some sections are like lyrical refrains—repeats of short sequences that create a rhythm unique to each organism. But these sequences, delicate in their repetition, are susceptible to an intricate dance of errors called slippage. Imagine this molecular tango: as the DNA strand is copied, it occasionally slips, like a misplaced step on the dance floor. This slip leads to a sequence missing a beat or echoing the previous note. It's like a hiccup in the musical arrangement, altering the harmony of the genetic composition. This slippage is the craftsman behind the creation of non-coding DNA repeats—like verses that repeat a poetic pattern. Yet, this dance isn't limited to non-coding stretches; it can sway into coding regions, causing disruptive frameshift mutations.

Now, let's delve into a grander symphony—a mutation that can influence larger stretches of DNA. Enter transposition, the "jumping genes." These molecular travelers can duplicate themselves, journeying from one part of the DNA to another, like notes that leap across the musical score. When these elements insert themselves into genes, it's like a rogue note infiltrating a melody, sometimes corrupting it entirely. Yet, if they choose to dance into non-coding regions, the impact might be less profound. Remarkably, transposable elements can waltz with not just their own tune but a partner's too. They can lift a DNA sequence, embracing it in their copycat dance before landing in a new location. This molecular choreography often rewrites the genome's length, adding new layers to the arrangement. It's akin to weaving a pattern of melodies and harmonies, each note a reflection of its origins. But this symphony of change isn't limited to transposition alone. Imagine a moment of unequaled crossing—like two dancers caught in an unexpected embrace. Unequal crossing-over is another genetic dance, one that can duplicate or delete a stretch of DNA, like a musical interlude that stretches or shortens the rhythm. In this genetic ballet, mutations take center stage, each performance a unique alteration in the symphony of life. As sequences slip and elements leap, the genetic composition evolves—a dance where intelligent design weaves its narrative. 

Mutations wield the power to reshape not only the threads but the entire fabric of chromosomes, casting ripples across the genetic landscape. Chromosomal segments may engage in a delicate dance, translocating to distant partners or altering their own positions within the same chromosome. Occasionally, an inversion in the sequence of these genetic chapters occurs, presenting a unique narrative. A grander tale unfolds when whole chromosomes unite in a fusion, a phenomenon etched in the pages of human evolution. In a juxtaposition with our closest kin, chimps, and gorillas, who bear 24 pairs of chromosomes, we emerged with a distinct count of 23. Intriguingly, duplications cast their spell, leaving genetic echoes that reverberate through generations. The implications of these chromosomal mutations transcend easy categorization, as they navigate the intricate network of gene expression.
When the seams of a mutation intersect a protein's path, that protein may fade into obscurity within the mutant organism. Yet, when a molecular junction shatters between proteins, the consequences hang on the delicate balance of gene placement within the genome. The theoretical dichotomy between chromosomes is questioned, but the reality of gene expression, subtly choreographed by neighboring genes, unveils the cascade of phenotypic outcomes from a chromosomal shift. Mutations further enact their transformative script, wielding scissors that snip away or pencils that painstakingly duplicate entire chromosomes. In their most expansive manifestation, mutations orchestrate the duplication of the entire genetic script, a phenomenon dubbed polyploidy. Picture this: a tapestry of normalcy, woven with 20 chromosomes from parental looms. In a mutation of cosmic proportions, all 20 are replicated, yielding a prodigious offspring adorned with 40 chromosomes. This epic spectacle of polyploidy unfolds as a pivotal protagonist in the story of evolution, particularly in the verdant realms of plant evolution.

Gregor Mendel, often referred to as the father of modern genetics, conducted groundbreaking experiments with pea plants in the mid-19th century. His work laid the foundation for understanding the inheritance of traits and the mechanisms of heredity. Mendel's discoveries have significant implications for our understanding of evolution.

The gene-centered view of evolution

The major propagator of the gene-centric view of evolution was British evolutionary biologist Richard Dawkins. He presented and popularized this perspective in his influential book titled "The Selfish Gene," which was first published in 1976. In "The Selfish Gene," Dawkins introduced the idea that genes are the primary units of selection in evolution, and they act in their own self-interest to ensure their survival and replication. According to this view, genes are the drivers of evolutionary change, and organisms are merely vehicles or "survival machines" that exist to serve the interests of their genes. Dawkins' gene-centric view of evolution has had a profound impact on the field of evolutionary biology and did spark significant debates and discussions about the role of genes in shaping the diversity of life on Earth. While it is not the only perspective on evolution, it remains a prominent and influential viewpoint in the scientific community.

Is a gene-centered view of evolution still warranted?

M. Lewis: In the 1960s and 1970s, a scientific shift occurred and evolutionary biologists began viewing genes as the fundamental unit of selection. Noted evolutionary theorist Richard Dawkins wrote the revolutionary, and now classic, book The Selfish Gene in 1976, explaining the new genetic view and making it more accessible to lay people. The controversy between purist gene selectionism and the Multilevel Selection Theory (MST) may seem theoretical, but the reasoning behind the two perspectives profoundly changes the way scientists understand evolutionary changes. The claim now becomes a question: Survival of the fittest what? Gene? Organism? Or group? The gene selectionist perspective proposed by Dawkins and others is the predominant view among modern evolutionary biologists. The main premise relies on the concept of the gene as being the ultimate, fundamental unit of natural selection. By the basic principles of natural selection, genes that are more successful at replicating themselves will, by default, become more numerous in the population. Therefore, a gene that happens to increase the general fitness of the individual in which it is located will be more likely to be passed down to the next generation.5

David Haig (2012):  Are genes alone, or various integrated players on intra and extra-cellular systems levels responsible for defining phenotype, and organismal architecture? David Haig (2012): Gene selectionism is the conceptual framework that views genes as the ultimate beneficiaries of adaptations and organisms or groups as the means for genes’ ends. Rival conceptual frameworks exist. Multi-level selection theory views genes as the lowest level of a nested hierarchy in which each level is subject to selection and each level can be the beneficiary of adaptations. Developmental systems theory similarly denies a privileged role for genes in development and evolution. In this framework, many things other than genes are inherited and many things other than genes have a causal role in development. It is the entire developmental system, including developmental resources of the environment, that reconstructs itself from generation to generation. 6

Matt Ridley (2016): The gene-centered view of evolution that Dawkins championed and crystallized is now central both to evolutionary theorizing and to lay commentaries on natural history such as wildlife documentaries. Genes that cause birds and bees to breed survive at the expense of other genes. No other explanation makes sense, although some insist that there are other ways to tell the story. What stood out was Dawkins’s radical insistence that the digital information in a gene is effectively immortal and must be the primary unit of selection. No other unit shows such persistence — not chromosomes, not individuals, not groups, and not species. 7



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The extended evolutionary synthesis

The Extended Evolutionary Synthesis (EES) is a contemporary and ongoing theoretical framework that seeks to expand and complement the traditional Modern Synthesis, also known as the Neo-Darwinian Synthesis. The Modern Synthesis integrated Darwin's theory of natural selection with Mendelian genetics, providing a foundation for understanding evolution. However, as scientific knowledge has advanced, some researchers have proposed that the Modern Synthesis might not fully capture the complexity and richness of evolutionary processes. The EES was not formulated at a specific moment but rather emerged gradually through the work and contributions of several scientists over the last few decades. Its development can be attributed to various research fields, including evolutionary biology, developmental biology, epigenetics, genomics, and other areas of science that have shed new light on the mechanisms influencing evolution. Niche Construction proposes that organisms actively modify and create their environments, which, in turn, influences their own adaptation. Organisms are not merely passive subjects but can be active agents shaping their adaptive trajectories through their interactions with the environment.  Epigenetics refers to heritable changes in gene expression that occur without alterations in the DNA sequence. Epigenetic modifications can influence gene activity and are subject to natural selection, potentially leading to non-genetic inheritance of certain traits. Developmental plasticity refers to an organism's ability to produce different phenotypes in response to environmental cues. These phenotypic changes might be adaptive. Similar to developmental plasticity, phenotypic plasticity allows an organism to alter its phenotype in response to environmental conditions without changing its genotype. This flexibility can influence an organism's response to changing environments. Evolvability refers to the capacity of a population or species to generate heritable variation that can fuel the process of evolution. Understanding the mechanisms that promote evolvability is a key aspect of the EES.  Heterochrony refers to changes in the timing of developmental events, while heterotopy refers to changes in the spatial organization of structures during development. Both processes can have significant impacts on evolutionary outcomes. The EES recognizes that not all heritable traits are solely transmitted through DNA. Factors like epigenetic marks, symbiotic relationships, and cultural transmission can also play a role in inheritance. The Extended Evolutionary Synthesis represents an effort to incorporate these and other emerging concepts into our understanding of evolution. Proponents argue that by embracing these broader perspectives, we can gain deeper insights into the mechanisms driving evolutionary change and appreciate the complexity of life's history in a more comprehensive manner. The EES remains a topic of ongoing debate and research within the scientific community as scholars work to refine and develop its core principles.

What is the best scientific method and approach to investigate the origin of species? 

Many books are dedicated to providing positive evidence for evolution and resort to a variegated toolbox intending to do so. Libretext, for example, elucidates: "Fossils are a window into the past. They provide clear evidence that evolution has occurred."4 Furthermore, they mention Comparative AnatomyHomologous structuresComparative EmbryologyVestigial Structurescomparative genomicsevidence from biogeography. A very common method is to infer evolution based on phylogenetic comparisonsmeasuring physical features and similarities between organismsphylogenetic trees, and the reconstruction of organismal relationships based on gene and protein treesnested hierarchiescladograms, and evolutionary physiology. By seeing all these different faculties, one can easily be persuaded that these are adequate tools permitting one to come to secure, case-adequate conclusions and inferences, that portray the real picture of the historical facts. But is it so? How can we be certain about this? Observe how the word "compared' goes through most, almost all disciplines like a red line. Is doing phylogenetic and physiological comparisons, and drawing phylogenetic trees the right approach? 

The emergence of new body forms, cell shapes, organs, and functions indeed deserves a comprehensive analysis, not solely restricted to phylogeny. Multicellular organisms exemplify the epitome of interdependence among their cells, where each component plays a crucial role in maintaining overall function. Consider a Merkel sensory cell or a Bud taste cell – their individual functions are only realized when intricately connected with the brain or specific nerve pathways. This highlights the vital interplay between different components in an organism, necessitating a deeper understanding of the processes that gave rise to such complex systems. As we trace the branches of the tree of life, we are inevitably led to a critical juncture where the transition from unicellular to multicellular life forms occurred. At this pivotal point, the emergence of new genes and systems would have been imperative to orchestrate the development of novel body limbs, forms, and organs, all of which are inherently interdependent. This realization leads us to consider the possibility of multiple genes and new instructions arising simultaneously – a concept that challenges conventional wisdom but cannot be ignored. While the hypothesis of new genes and simultaneous instructions might be a hard sell in the face of established scientific beliefs, it is essential to pursue a holistic and unbiased approach to unraveling the complexities in play in biology. The dominant genetic phylogeny comparisons, while valuable, should not overshadow other avenues of investigation that explore the intricacies of function and interdependence in the evolution of life forms.

Beyond Evolution: The Origin of Species by Design 621

Almost a hundred years ago the outstanding American biologist E. B. Wilson wrote: “The key to every biological problem must finally be sought in the cell; for every living organism is, or at some time has been a cell.” This position remains unshakeable, despite impressing successes of molecular biology, and genetics.  In my understanding, the key questions will be answered on the molecular level. Whatever the method is to investigate the origin of biodiversity, the relevant answers have to be found by investigating the cell. 

M.J. BEHE: (1987):  In order to say that some function is understood, every relevant step in the process must be elucidated. The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon such as sight, digestion, or immunity, must include a molecular explanation. It is no longer sufficient, now that the black box of vision has been opened, for an ‘evolutionary explanation’ of that power to invoke only the anatomical structures of whole eyes, as Darwin did in the 19th century and as most popularizers of evolution continue to do today. Anatomy is, quite simply, irrelevant. So is the fossil record. It does not matter whether or not the fossil record is consistent with evolutionary theory, any more than it mattered in physics that Newton’s theory was consistent with everyday experience. The fossil record has nothing to tell us about, say, whether or how the interactions of 11-cis-retinal with rhodopsin, transducin, and phosphodiesterase could have developed step-by-step. Neither do the patterns of biogeography matter, or of population genetics, or the explanations that evolutionary theory has given for rudimentary organs or species abundance.8

M. W. Kirschner (2005)To understand novelty in evolution, we need to understand organisms down to their individual building blocks, down to the workings of their deepest components, for these are what undergo change.9

1. Richard Dawkins:  IN SHORT: NONFICTION April 9, 1989
2. John Joe McFadden: Evolution of the best idea that anyone has ever had July 1, 2008
3. New trends in evolutionary biology: biological, philosophical and social science perspectives
4. Paul Nelson and David Klinghoffer: Scientists Confirm: Darwinism Is Broken December 13, 2016
5. Michaela Lewis: Understanding Evolution: Gene Selection
6. David Haig: The strategic gene 30 March 2012
7. Matt Ridley: In retrospect: The Selfish Gene 27 January 2016
8. MICHAEL J. BEHE: Experimental Support for the Design Inference DECEMBER 27, 1987
9. Dr. Marc W. Kirschner: [url=https://www.amazon.com/Plausibility-Life-Resolving-Darwins-Dilemma/dp/030



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How is the origin of biological form, biodiversity, organismal complexity, and architecture explained by current biology? 

Current biology answers this question through a combination of mechanisms and processes that operate over long periods of time. These explanations are grounded in the principles of evolution, genetics, developmental biology, and ecological interactions.  Biological form, biodiversity, and organismal complexity are claimed to be primarily shaped by the process of evolution through natural selection. Variation in traits within populations provides the raw material for evolution, and advantageous traits are more likely to be passed on to future generations. Over time, accumulated changes in the genetic makeup of populations lead to the emergence of new species, traits, and forms. Evolutionary mechanisms include mutation, natural selection, genetic drift,  and gene flow. Genetic variation arises from mutations, which introduce changes in the DNA sequence. These variations can lead to differences in traits and characteristics among individuals within a population. Mutations can result from errors in DNA replication, exposure to mutagenic agents, or other environmental factors. Natural selection favors traits that enhance an organism's fitness in its environment. Organisms with advantageous traits are more likely to survive, reproduce, and pass those traits on to their offspring. Over time, natural selection can lead to the accumulation of adaptations that contribute to biological form, diversity, complexity, and architecture. The development of biological form and architecture is guided by complex processes of cell division, differentiation, and morphogenesis. Genetic regulation controls the expression of genes during development, influencing the growth and organization of tissues, organs, and body structures. Gene duplication events could lead to the creation of additional copies of genes. Subsequent mutations and changes in regulation result in the divergence of duplicated genes, leading to the evolution of new functions and traits. Environmental factors play a role in shaping the expression of genes and the development of traits. Organisms interact with their environment, and those that are well-suited to their surroundings have a higher likelihood of survival and reproduction. Biodiversity and complexity are influenced by interactions between species in ecosystems. These interactions include competition, predation, symbiosis, and other ecological relationships. New traits can arise through various mechanisms, including gene duplication, mutation, recombination, and regulatory changes. Some traits may provide advantages in specific ecological niches, leading to their persistence and diversification. Over geological timescales, long-term evolutionary trends can lead to the emergence of new body plans, structures, and functions. These trends are influenced by changing environmental conditions and ecological interactions. The explanation provided reflects the naturalistic, evolutionary narrative that is widely accepted and taught in biology textbooks and scientific literature. It outlines the mechanisms and processes that are considered by the scientific community to be sufficient to explain the origin of biological form, biodiversity, organismal complexity, and architecture. This naturalistic explanation is grounded in the principles of evolutionary biology, genetics, developmental biology, and ecology. It is a cornerstone of modern biology.

The development of complex organisms and body architecture involves a combination of intricate mechanisms that work together to shape the structure, function, and organization of living organisms. These mechanisms span multiple levels of biological organization, from molecular interactions to cellular processes to tissue and organ formation. Over long periods of time, evolutionary processes, including natural selection and genetic variation, are claimed to shape the development and body architecture of organisms. Evolutionary changes would lead to the acquisition of new structures, functions, and adaptations.

What are the main critique points made by supporters of Intelligent Design? 

Intelligent design proponents raise several critiques of the prevailing scientific understanding of evolution, particularly the naturalistic explanation for the origin and complexity of life. Specific biological structures and systems are irreducibly complex. This implies that these systems consist of multiple intricate components, all of which are essential for the system to function. Gradual evolutionary steps would not suffice to produce such systems since the removal of any part would render the system non-functional. In response, proponents of evolution argue that apparent irreducible complexity can be explained by step-by-step evolutionary processes. Each intermediate stage may serve a different function or confer an advantage, allowing for the gradual development of complex systems. Certain biological systems contain complex specified information that cannot be explained by random chance or natural mechanisms. These systems display patterns reminiscent of the type of information generated by intelligent agents. The Cambrian Explosion is a period marked by the rapid appearance of diverse animal body plans, which is evidence challenging the explanatory power of naturalistic mechanisms alone. The abrupt emergence of complex life forms poses a challenge to gradual evolution. There are limits to the extent of evolutionary change, particularly regarding the emergence of new body plans or complex structures. Proponents of evolution counter by highlighting the gradual transitions supposedly observed in the fossil record and genetic evidence. 

What is natural selection? 

Merriam-Webster defines selection as the act or process of selecting: the state of being selected one that is selected: CHOICE. Making choices is always assigned/attributed to intelligent action. Darwin however coined the word "natural selection" to mean something different. Many think that natural selection actively selects favorable traits in a population. But in fact, as EvolutionShorts explains:  It is a passive process that does not involve organisms “trying” to adapt. This concept of the organism becoming more suited to its current environment is roughly the basis of adaptive evolution. This is a fundamental principle for natural selection instead of specific desires of species. 

R.Carter:‘Natural selection’ properly defined simply means ‘differential reproduction’, meaning some organisms leave more progeny than others based on the mutations they carry and the environment in which they live. 1

Paul R. Ehrlich (1988): In modem evolutionary genetics, natural selection is defined as the differential reproduction of genotypes (individuals of some genotypes have more offspring than those of others). Natural selection would be occurring if, in a population of jungle fowl (the wild progenitors of chickens), single-comb genotypes were more reproductively successful than pea-comb genotypes. Note that the emphasis is not on survival  (as it was in Herbert Spencer's famous phrase "survival of the fittest") but on reproduction.2

Natural selection is not an acting force but is passive. It does not invent something new. E. Osterloff:  Natural selection is a mechanism of evolution. Organisms that are more adapted to their environment are more likely to survive and pass on the genes that aided their success. This process causes species to change and diverge over time. 3

David Stack (2021): Natural selection was the term Darwin used to describe both the mechanism and the effect of the evolutionary process by which favorable or advantageous traits and characteristics are preserved and unfavorable or disadvantageous ones discarded. The “selection” process is “natural” in the sense that it occurs without any conscious intervention (there is no “selector”) in response to an ongoing “struggle for life.” Traits and characteristics favorable to survival in that struggle are preserved and developed. This, for Darwin, is the basis of evolution. Key to the process is inheritance, but, as he was writing without knowledge of modern genetics, Darwin’s presentation of natural selection did not include any detailed understanding of how inheritance worked. 4

FRANCISCO J. AYALA (2007): With Darwin’s discovery of natural selection, the origin and adaptations of organisms were brought into the realm of science. The adaptive features of organisms could now be explained, like the phenomena of the inanimate world, as the result of natural processes, without recourse to an Intelligent Designer.

In an interview in 1999, Mayr stated: “Darwin showed very clearly that you don't need Aristotle's teleology because natural selection applied to bio-populations of unique phenomena can explain all the puzzling phenomena for which previously the mysterious process of teleology had been invoked”. 5

Variability and Environmental Pressures

Evolutionary processes are influenced by a wide range of factors, including environmental pressures, population size, genetic variation, and more. The theory of evolution doesn't claim that all traits evolve solely due to random mutations. Natural selection operates on existing genetic variation and can amplify or reduce traits based on how they affect an organism's survival and reproduction within a given environment. Evolutionary processes are profoundly affected by the environment in which organisms live. If a certain food source becomes scarce, organisms with traits that allow them to exploit an alternative food source may have a survival advantage. The size of a population can impact the rate and direction of evolution. In smaller populations, random events, known as genetic drift, can have a significant effect on the frequency of specific alleles. While genetic drift is a random process, it can lead to the fixation or loss of alleles over time, impacting the genetic makeup of a population.  Genetic variation is the raw material upon which natural selection acts. Mutations introduce new genetic variation into a population, and recombination during reproduction shuffles existing genetic material. This variation provides the basis for natural selection to favor traits that can eventually confer advantages in a given environment. It's important to note that not all genetic variation results from mutations; other processes, such as recombination, contribute to genetic diversity.  Gene flow, the movement of genes between different populations of the same species, can introduce new alleles and genetic variation. This can counteract the effects of genetic drift and help maintain diversity within populations. Gene flow can also spread advantageous traits from one population to another. Natural selection is the process by which certain traits become more or less common in a population based on their effects on an organism's survival and reproduction. Traits that increase an individual's fitness (ability to survive and reproduce) within a specific environment are more likely to be passed on to the next generation. Over time, this can lead to the accumulation of traits that are well-suited to the environment, a process known as adaptation. While mutations are indeed random, natural selection is not. It is a non-random process that acts on the existing genetic variation in a population. Mutations introduce new possibilities, and natural selection then sifts through these possibilities, favoring traits that provide advantages under specific conditions. The outcome of natural selection is a result of the interaction between genetic variation and environmental pressures. Traits in organisms often interact with each other, and the selective advantage of a trait can depend on the presence of other traits. This phenomenon, known as epistasis, can lead to complex patterns of selection and influence the direction of evolution.

Definitions of fitness

In the realm of evolutionary biology, "fitness" refers to an individual's ability to survive, reproduce, and pass on its genes to the next generation. It encompasses the overall reproductive success of an organism in its specific environment, taking into account factors such as survival rates, the number of offspring produced, and the success of those offspring in reproducing themselves. Fitness is a measure of how well an organism's traits, behaviors, and adaptations enable it to thrive in its ecological niche. Individuals with higher fitness are better equipped to cope with environmental challenges, secure resources, avoid predators, and successfully reproduce. Over successive generations, the traits that contribute to higher fitness tend to become more prevalent in a population, while less advantageous traits may diminish. It's important to note that fitness is a relative concept. The term "fitness" doesn't necessarily imply physical health or athleticism. Instead, it specifically relates to an organism's ability to contribute its genetic material to the next generation, thus influencing the genetic makeup of future populations.

J. Dekker (2007): 1. The average number of offspring produced by individuals with a certain genotype, relative to the numbers produced by individuals with other genotypes. 2: The relative competitive ability of a given genotype conferred by adaptive morphological, physiological, or behavioral characters, expressed and usually quantified as the average number of surviving progeny of one genotype compared with the average number of surviving progeny of competing genotypes; a measure of the contribution of a given genotype to the subsequent generation relative to that of other genotypes. A condition necessary for evolution to occur is variation in the fitness of organisms according to the state they have for a heritable character. Individuals in the population with some characters must be more likely to reproduce, more fit. Organisms in a population vary in reproductive success. We will discuss fitness in Life History when we discuss competition, interference and the effects of neighbor plants.

Three Components of Fitness.  These different components are in conflict with each other, and any estimate of fitness must consider all of them:
1.  Reproduction
2.  Struggle for existence with competitors
3.  Avoidance of predators 6  

S.El-Showk (2012): The common usage of the term “fitness” is connected with the idea of being in shape and associated physical attributes like strength, endurance or speed; this is quite different from its use in biology.  To an evolutionary biologist, fitness simply means reproductive success and reflects how well an organism is adapted to its environment. The main point is that fitness is simply a measure of reproductive success and so won’t always depend on traits such as strength and speed; reproductive success can also be achieved by mimicry, colorful displays, sneak fertilization and a host of other strategies that don’t correspond to the common notion of “physical fitness”.

What then are we to make of the phrase “survival of the fittest”? Fitness is just book-keeping; survival and differential reproduction result from natural selection, which actually is a driving mechanism in evolution. Organisms which are better suited to their environment will reproduce more and so increase the proportion of the population with their traits. Fitness is simply a measurement of survival (which is defined as reproductive success); it’s not the mechanism driving survival.  Organisms (or genes or replicators) don’t survive because they are fit; rather, they are considered fit because they survived. 7

The environment is not stable, but changes. Science would need to have the knowledge of what traits of each species are favored in a specific environment. Adaptation rates and mutational diversity and other spatiotemporal parameters, including population density, mutation rate, and the relative expansion speed and spatial dimensions. When the attempt is made to define with more precision what is meant by the degree of adaptation and fitness, we come across very thorny and seemingly intractable problems. 

As Evolution. Berkley explains: Of course, fitness is a relative thing. A genotype's fitness depends on the environment in which the organism lives. The fittest genotype during an ice age, for example, is probably not the fittest genotype once the ice age is over. Fitness is a handy concept because it lumps everything that matters to natural selection (survival, mate-finding, reproduction) into one idea. The fittest individual is not necessarily the strongest, fastest, or biggest. A genotype's fitness includes its ability to survive, find a mate, produce offspring — and ultimately leave its genes in the next generation. 8

Can fitness be measured? 

Claim: Adam Eyre-Walker (2007): All organisms undergo mutation, the effects of which can be broadly divided into three categories. First, there are mutations that are harmful to the fitness of their host; these mutations generally either reduce survival or fertility. Second, there are ‘neutral’ mutations, which have little or no effect on fitness. Finally, there are advantageous mutations, which increase fitness by allowing organisms to adapt to their environment. Although we can divide mutations into these three categories, there is, in reality, a continuum of selective effects, stretching from those that are strongly deleterious, through weakly deleterious mutations, to neutral mutations and then on to mutations that are mildly or highly adaptive. The relative frequencies of these types of mutation are called the distribution of fitness effects (DFE) 9

R. G. Brajesh et.al., (2019): Mutations occur spontaneously during the course of reproduction of an organism. Mutations that impart a beneficial characteristic to the organism are selected and consequently, the frequency of the mutant allele increases in the population. Mutations can be single base changes called point mutations like substitutions, insertions, deletions, as well as gross changes like chromosome recombination, duplication, and translocation 10

Reply:  A theory must be able to make predictions, and it must be testable.  How can it be tested that random mutations give rise to higher fitness and higher reproduction of the individuals with the new allele variation favored by natural selection, and so spread in the population, and how can the results be quantified? This seems in fact to be a core issue that raises questions. The environmental conditions of a population, the weather, food resources, temperatures, etc. are random How do random events, like weather conditions, together with random mutations in the genome, provoke a fitness increase in an organism and a survival advantage over the other individuals without the mutation? 

T.Bataillon (2014): The rates and properties of new mutations affecting fitness have implications for a number of outstanding questions in evolutionary biology. Obtaining estimates of mutation rates and effects has historically been challenging, and little theory has been available for predicting the distribution of fitness effects (DFE); Future work should be aimed at identifying factors driving the observed variation in the distribution of fitness effects. What can we say about the distribution of fitness effects of new mutations? For the distribution of fitness effects DFE of beneficial mutations, experimentally inferred distributions seem to support theory for the most part. Distribution of fitness effects DFE has largely been unexplored and there is a need to extend both theory and experiment in this area. 11

Christopher J Graves (2019): When fitness effects are invariant across a lineage, the long-term fate of an allele can be deduced in a relatively straightforward manner from its recursive effects on survival and reproduction across descendent carriers. In other cases, the evolutionary success of an allele is not an obvious consequence of its effects on individuals. For example, variable environments can cause the same allele to have differing effects on fitness depending on an individuals’ environmental context. 12

V. Ž. Alif et.al., (2021): The concept of fitness is central to evolutionary theory. Natural selection maximizes fitness, which is therefore a driving force of evolution as well as a measure of evolutionary success. One definition  of fitness is how good an individual is at spreading its genes into future generations, relative to all other individuals in the population. A universal definition of fitness in mathematical terms that applies to all population structures and dynamics is however not agreed on. Fitness it is difficult to measure accurately. One way to measure long-term fitness is by calculating the individual’s reproductive value, which represents the expected number of allele copies an individual passes on to distant future generations. However, this metric of fitness is scarcely used because the estimation of individual’s reproductive value requires long-term pedigree data, which is rarely available in wild populations where following individuals from birth to death is often impossible. Wild study systems therefore use short-term fitness metrics as proxies, such as the number of offspring produced. 13

The above confession demonstrates that a key question, namely how mutations in fact affect fitness has not been answered. I go further and say: Darwin's Theory can in reality not be tested, nor quantified. The unknown factors in each case are too many, and the variations in the environment, and population sizes undergo large seasonal fluctuations, providing more opportunities for mutations when the population size is large and a greater probability of fixation of mutation x during the recurring bottlenecks, and population and species behavior vary too. It cannot be defined what influence the given environment exercises in regard to specific animals and traits in that environment, nor how the environmental influence would change the fitness and reproduction success of each distinct animal species. Nor how reproduction success given new traits would change upon environmental changes.  What determines whether a gene variant spreads or not would depend theoretically on an incredibly complex web of factors - the species' ecology, its physical and social environment, altered nutrient conditions,  and sexual behavior. A further factor adding complexity is the fact that high social rank is associated with high levels of both copulatory behavior and the production of offspring which is widespread in the study of animal social behavior. 

Beyond Evolution: The Origin of Species by Design 1121

As alpha males have on average higher reproductive success than other males since they outcompete weaker individuals, and get preference to copulate if other (weaker)  males gain beneficial mutations (or the alphas' negative mutations) as the alphas can outperform and win the battle for reproduction,  thus selection has an additional hurdle to overcome and spread the new variant in the population. This does not say anything about the fact that it would have to be determined what gene loci are responsible for sexual selection and behavior, and only mutations that influence sexual behavior would have an influence on fitness and the struggle to contribute more offspring to the next generation.   It is in praxis impossible to isolate these factors and see which is of selective importance,  quantify them, plug them in (usually in this context) to a mixed multivariate computational model, see what's statistically significant, and get meaningful, real-life results. The varying factors are too many and nonpredictive. Darwin's idea, therefore, depends on a variable, unquantifiable multitude of factors that cannot be known, and cannot be tested, which turns the theory at best into a non-testable hypothesis, which then remains just that: a hypothesis. Since Darwin's idea cannot be tested, it's by definition, unscientific. 

If fitness is a relative thing, it cannot be detected and proven that natural selection is the mechanism that generates variations that produce more offspring, and therefore the new trait spreads in the population. Therefore, mutations and natural selection cannot be demonstrated to have the claimed effects. What is the relation between mutations in the genome, and the number of offspring? What mutations are responsible for the number of offspring produced? If the theory of evolution is true, there must be a detectable mechanism, that determines or induces, or regulates the number of offspring based due to specific genetic mutations. Only a specific section in the genome is responsible for this regulation.

Challenges in Understanding the relationship between reproductive mechanisms, environmental pressures, and evolutionary outcomes

There are specific regions in the genome responsible for each  mechanism of reproduction, being it sexual, or asexual reproduction, that is:  

1. Regulation and programming of sexual attraction ( hormones, pheromones, instinct, etc.)
2. Frequency of sexual intercourse and reproduction
3. The regulation of the number of offspring produced

What influence do environmental pressures have on these 3 points? What pressures induced organisms to evolve sexual, and asexual reproduction?  Are the tree mechanisms mentioned not amazingly various and differentiated, and does each species have individual, species-specific mechanisms? Some have an enormous number of offspring that helps the survival of the species, while others have a very low reproduction rate (like whales). How could environmental pressures have induced this amazing variation, and why?  That means also on a molecular level, enormous differences from one species to the other exist.  how could accidental mutations have been the basis for all this variation? Would there not have to be SPECIFIC environmental pressures resulting in the selection of  SPECIFIC traits based on mutations of the organism to be selected that provide survival advantage and fitness? ( genome or epigenome, whatever )  AND higher reproduction rates of the organism at the same time? What is the chance, that random mutations provoke positive phenotypic differences, that help the survival of the individual? What kind of environmental factors influence the survival of a species? What kind of mutations must be selected to guarantee a higher survival rate? The lack of predictive power of natural selection is due to different environmental conditions that turn it impossible to quantify the effects and measure their outcome. 

Environmental pressures play a significant role in shaping reproductive mechanisms. For example, changes in resource availability, competition, and predation can influence an organism's reproductive behaviors and strategies. In response to environmental cues, such as temperature, daylight duration, or food availability, organisms may adjust their hormonal profiles and reproductive behaviors. Both sexual and asexual reproduction change in response to different environmental pressures. Sexual reproduction promotes genetic diversity, which can enhance a population's ability to adapt to changing environments and reduce susceptibility to diseases. Asexual reproduction, on the other hand, allows for rapid population growth in stable environments. The change of these mechanisms is influenced by factors like predation, resource availability, and competition. Environmental conditions shape the trade-offs between producing a large number of offspring versus investing more resources in fewer offspring with higher chances of survival. These strategies are influenced by factors such as predation risk, resource availability, and habitat stability.  The complexity of these interactions poses challenges to quantifying and measuring the outcomes of evolutionary processes. The interplay between genetic variation, environmental pressures, and reproductive strategies is intricate and context-dependent. This complexity does make predicting specific outcomes challenging. Predictive power is limited due to the multifaceted nature of interactions, where outcomes can be influenced by a combination of genetic, environmental, and historical factors. That's why evolution cannot be supported by empirical data and evidence, and cannot provide a comprehensive framework for understanding the diversity of life.

The intricacies and limitations of studying evolution are due to the vastness of genetic and environmental factors involved. 

Ivana Cvijović (2015): Temporal fluctuations in environmental conditions can have dramatic effects on the fate of each new mutation, reducing the efficiency of natural selection and increasing the fixation probability of all mutations, including those that are strongly deleterious on average. This makes it difficult for a population to maintain specialist adaptations, even if their benefits outweigh their costs. Temporally varying selection pressures are neglected throughout much of population genetics, despite the fact that truly constant environments are rare. The fate of each mutation depends critically on its fitness in each environment, the dynamics of environmental changes, and the population size. We still lack both a quantitative and conceptual understanding of more significant fluctuations, where selection in each environment can lead to measurable changes in allele frequency. 14

Comment: Ivana Cvijović's work emphasizes the impact of temporal fluctuations in environmental conditions on the fate of mutations and natural selection. These fluctuations complicate our understanding of how mutations are fixed or eliminated, they negate the ability to study and test evolutionary principles. Evolution, therefore, cannot be precisely tested through observations of adaptation and natural selection in the respective environments. Temporal fluctuations in environmental conditions can lead to variable selection pressures acting on a population over time. This can result in situations where mutations that might be advantageous in one environment become disadvantageous or neutral in another. Such fluctuations can blur the relationship between genotype and fitness, making it difficult to predict the fate of mutations in changing environments. The fitness landscape, which maps the relationship between genotypes and reproductive success, can shift over time due to environmental changes. Fluctuating selection pressures can create dynamic fitness landscapes, where the fitness of a particular genotype varies across different environmental states. This complexity makes it challenging to determine how mutations will be favored or eliminated in the long term. Temporal fluctuations can affect the fixation probability of mutations. In some environments, mutations that are strongly deleterious on average might become fixed due to the transient benefits they provide under specific conditions. This variability in fixation probability complicates the straightforward relationship between mutation and selection. The presence of temporal fluctuations introduces uncertainty into the long-term evolutionary trajectories of populations. It becomes challenging if not impossible to make precise predictions about which mutations will become fixed, as their fate depends on the specific sequence of environmental changes and their timing. Cvijović's work highlights the lack of a complete understanding of how significant fluctuations in selection pressures lead to measurable changes in allele frequency. The complexity of these interactions makes it difficult to quantitatively model and predict the outcomes of evolution in fluctuating environments. These challenges posed by temporal fluctuations are insurmountable. Evolutionary biologists try to overcome these limiting factors often by focusing on simplifications and controlled experiments to study specific aspects of evolution. This does not, however, allow researchers to gain consistent and truthful insights into fundamental processes that shape organismal complexity by evolutionary pressures.

L.Bromham (2017): The search for simple unifying theories in macroevolution and macroecology seems unlikely to succeed given the vast number of factors that can influence a particular lineage’s evolutionary trajectory, including rare events and the weight of history. Patterns in biodiversity are shaped by a great many factors, both intrinsic and extrinsic to organisms. Both evidence and theory suggests that one such factor is variation in the mutation rate between species. But the explanatory power of the observed relationship between molecular rates and biodiversity is relatively modest, so it does not provide anything like the predictive power that might be hoped for in a unifying theory. However, we feel that the evidence is growing that, in addition to the many and varied influences on the generation of diversity, the differential rate supply of variation through species-specific differences in mutation rate has some role to play in generating different rates of diversification. 15

Comment:  L. Bromham's perspective highlights the multitude of factors influencing evolutionary trajectories. The complex interplay of these factors does render evolution untestable.  Bromham is emphasizing the challenges and complexities involved in understanding the full scope of factors that influence trajectories and patterns in biodiversity. The evolutionary trajectory of a lineage is influenced by a vast array of factors, including intrinsic genetic and physiological characteristics as well as extrinsic environmental factors. The sheer number and complexity of these factors make it challenging to isolate and quantify each individual influence. Rare events, historical contingencies, and chance occurrences can play a significant role in shaping evolutionary outcomes. These unpredictable events can lead to divergent paths and outcomes that are difficult to anticipate or replicate in controlled experiments. Bromham mentions the variation in mutation rates between species as a contributing factor to patterns of biodiversity.  The precise impact on diversification rates varies across different lineages. Bromham notes that the observed relationship between molecular rates (such as mutation rates) and biodiversity does not provide the level of predictive power that might be desired in a unifying theory. While certain factors may contribute to the overall pattern, they may not be sufficient on their own to fully explain or predict complex evolutionary processes. The interaction and context-dependency of different factors lead to non-linear and unpredictable outcomes. For instance, the combined effect of mutation rate variation, environmental changes, and other factors lead to unexpected patterns of diversification. Bromham's perspective underscores the complexity and challenges inherent in understanding the full range of factors that influence evolution. These factors make evolution difficult to predict and isolate, therefore, they do render the entire theory of evolution untestable. Employing controlled experiments and comparative analyses, to explore and test different components of evolutionary processes, are inadequate methods, that have little, if nothing to do, with real-life environments, and pressures acting on populations. That turns the theory of evolution unsupported by trustworthy empirical evidence and cannot be a scientifically valid framework for understanding the diversity of life on Earth.

Z. Patwa (2008): To date, the fixation probability of a specific beneficial mutation has never been experimentally measured. 16

Comment: Z. Patwa's observation invalidates the broader theory of evolution since it impacts the completeness of the understanding of evolutionary processes.  Fixation probabilities play a crucial role in understanding the dynamics of how specific genetic variants spread within a population. Without experimental measurement, our ability to precisely quantify the likelihood of fixation for a particular beneficial mutation hinders the ability to predict and model the speed and efficiency of adaptation in response to changing environments. The inability to experimentally measure fixation frequency and probabilities impact the quantification and precision of evolutionary theory. Models and predictions that rely on precise values for fixation probabilities are subject to great uncertainty. The study of fixation probabilities provides insights into population genetics, which is essential for understanding genetic diversity, genetic drift, and the impact of selection. The inability to directly measure these probabilities hinders the ability to uncover genetic dynamics within populations.  In natural populations, evolutionary processes occur within complex ecological and environmental contexts. The absence of experimental fixation probability measurements limits understanding of how these processes unfold in intricate, real-world scenarios.

R. G. Brajesh (2019): The genotypic mutational space of an organism is so vast, even for the tiniest of organisms like viruses or even one gene, that it becomes experimentally intractable. Hence, studies have limited to studying only small parts of the genome. For example, experiments have attempted to map the functional effect of mutations at important active site residues in proteins, like Lunzer et al. engineered the IDMH enzyme to use NADP as cofactor instead of NAD, and obtain the fitness landscape in terms of the mutational steps. Other experiments have attempted to ascertain how virulence is affected by mutations at certain important loci in viruses. However, due to the scale of the genotypic mutational space, it has been extremely difficult to experimentally obtain fitness landscapes of larger multicomponent systems, and study the statistical properties of these landscapes like the Distribution of Fitness Effects (DFE). Attempts have also been made to back-calculate the underlying DFE by experimentally observing how frequently new beneficial mutations emerge and of what strength, but the final results were inconclusive. As a result, how the beneficial, neutral, and deleterious mutations and their effects are distributed, when the organism genotype is at different locations on the fitness landscape, has remained largely intractable. 17

Comment: R. G. Brajesh's 2019 statement highlights the daunting challenge posed by the vast genotypic mutational space when attempting to experimentally study and quantify the effects of mutations on fitness. This limitation does introduce complexities to the empirical investigation of evolutionary biology. The genotypic mutational space refers to the myriad possible combinations of genetic variations that can occur within an organism's genome. This space is incredibly vast, even for small organisms or individual genes, and exploring all possible mutations is experimentally infeasible due to time, resources, and technical constraints.  Researchers have focused on studying smaller portions of the genome, such as specific genes or active site residues in proteins, to understand the functional effects of mutations. These studies provide valuable insights into how mutations can influence specific traits or functions. Fitness landscapes illustrate how different genotypes correspond to varying levels of fitness in a given environment.  The scale of the genotypic mutational space makes it exceptionally difficult to experimentally map fitness landscapes and determine statistical properties, such as the DFE, for larger multicomponent systems. This limitation poses challenges in obtaining comprehensive insights into how genetic changes affect an organism's overall fitness.  Attempts to deduce the DFE by observing the emergence of new beneficial mutations have limitations, and the results are inconclusive. The experimental limitations discussed by Brajesh highlight the inherent complexity of biological systems and the practical constraints of conducting empirical research on the scale required to explore the entirety of genotypic mutational space. Indirect methods, computational simulations, and mathematical models can not provide solid real-world empirical data on the distribution of fitness effects and the dynamics of evolution.  

Adam Eyre-Walker (2007): The distribution of fitness effects DFE of deleterious mutations, in particular the proportion of weakly deleterious mutations, determine a population's expected drift load—the reduction in fitness due to multiple small-effect deleterious mutations that individually are close enough to neutral to occasionally escape selection, but can collectively have important impacts on fitness. The DFE of new mutations influences many evolutionary patterns, such as the expected degree of parallel evolution, the evolutionary potential and capacity of populations to respond to novel environments, the evolutionary advantage of sex, and the maintenance of variation on quantitative traits, to name a few. Thus, an understanding of the DFE of mutations is a pivotal part of our understanding of the process of evolution.  Furthermore, the available data suggest that some aspects of the DFE of advantageous mutations are likely to differ between species18

Comment: The distribution of fitness effects (DFE) of new mutations has far-reaching consequences, affecting several evolutionary patterns and phenomena. The DFE of weakly deleterious mutations contributes to a population's drift load, which is the reduction in overall fitness due to the accumulation of these mutations. This is important because even though such mutations might escape immediate strong selection, their gradual build-up can still have significant negative effects on a population's fitness. The DFE influences a population's ability to respond to novel environments and challenges. It shapes the evolutionary potential of a population by affecting how quickly it can adapt to changing conditions. The DFE of mutations plays a role in explaining the evolutionary advantage of sexual reproduction over asexual reproduction. Sexual reproduction can help shuffle genetic variation, potentially reducing the impact of weakly deleterious mutations and aiding in the removal of harmful mutations from the population.  DFE of advantageous mutations might vary between species. This highlights the complexity of evolution and the ways in which different species may have unique genetic and adaptive strategies. Eyre-Walker underscores the intricate and multifaceted nature of evolution, showcasing that the interplay of mutation effects, selection pressures, and other factors can lead to complex, difficult-to-predict outcomes.



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5Beyond Evolution: The Origin of Species by Design Empty Primary, and secondary speciation Wed Aug 09, 2023 11:16 am

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Taxonomic Hierarchy: The Organizational Ranks of Life

1. Domain: The highest, most inclusive rank in the taxonomic hierarchy. Three primary domains are recognized: Bacteria, Archaea, and Eukarya.
2. Kingdom: A rank that further divides domains. For instance, the domain Eukarya contains kingdoms like Animalia, Plantae, Fungi, and Protista.
3. Phylum: Within kingdoms, organisms are classified into phyla. For animals, an example is Chordata, which includes vertebrates.
4. Class: Phyla are divided further into classes. Within Chordata, Mammalia is a class consisting of mammals.
5. Order: Classes break down into orders. For mammals, Primates is an order including humans, apes, and monkeys.
6. Family: Within orders, organisms are grouped into families. In the Primate order, the family Hominidae comprises great apes and humans.
7. Genus: Families break down into genera. For instance, Homo is a genus within the Hominidae family.
8. Species: The most specific taxonomic rank, species represent individual evolutionary lineages. Homo sapiens refers to modern humans.

Beyond Evolution: The Origin of Species by Design 2217

Primary, and secondary speciation

J. Wells (2006):  In 1997, evolutionary biologist Keith Stewart Thomson wrote: “A matter of unfinished business for biologists is the identification of evolution’s smoking gun,” and “the smoking gun of evolution is speciation, not local adaptation and differentiation of populations.” 19

Secondary speciation does not solve Darwin’s problem. Only primary speciation — the splitting of one species into two by natural selection — would be capable of producing the branching-tree pattern of Darwinian evolution. But no one has ever observed primary speciation. Evolution’s smoking gun has never been found.  there are observed instances of secondary speciation — which is not what Darwinism needs — but no observed instances of primary speciation, not even in bacteria. British bacteriologist Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of twenty to thirty minutes, and populations achieved after eighteen hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another.”

Alan H. Linton looked for confirmed reports of primary speciation and concluded in 2001: “None exists in the literature claiming that one species has been shown to evolve into another. Bacteria, the simplest form of independent life, are ideal for this kind of study, with generation times of twenty to thirty minutes, and populations achieved after eighteen hours. But throughout 150 years of the science of bacteriology, there is no evidence that one species of bacteria has changed into another. 20

The notion that primary speciation has not been directly observed refers to the challenge of capturing the intricate process of one species splitting into two distinct species over a short period of time. While we have numerous examples of populations adapting to their environments and accumulating genetic changes, directly observing the complete transition from one species to another can be difficult due to the gradual nature of the process and the limitations of time scales in scientific observation. The example of bacteria highlights a point of contention in the context of primary speciation. Bacteria have short generation times and rapid reproductive rates, making them potential candidates for observing evolutionary changes over shorter time spans. There is no evidence of one species of bacteria evolving into another underscores the complexity of tracing speciation in organisms with high genetic variability and rapid reproduction. The fossil record provides valuable insights into the history of life on Earth, but it also has limitations. Fossilization is a rare process, and transitional forms are not always perfectly preserved. This can lead to gaps in the fossil record and make it challenging to directly observe the gradual transition from one species to another. The traditional Darwinian theory of evolution has been extended and refined over time through the integration of various fields such as genetics, molecular biology, and paleontology. The Modern Synthesis combines natural selection with genetics, providing a more comprehensive framework for understanding how species change over time. Additionally, the study of molecular genetics has provided insights into the mechanisms of speciation at the genetic level. While the Modern Synthesis and its extended versions have significantly advanced our understanding of how species change over time and the mechanisms underlying evolution, there are still gaps and challenges in fully explaining the origin of new species.  The process of speciation is complex and can involve a multitude of factors, including genetic, ecological, geographical, and environmental influences. While the Modern Synthesis and extended evolutionary theories have provided a more comprehensive framework, the exact interplay of various factors in driving the formation of new species is intricate and has not been elucidated.  Speciation is not a one-size-fits-all process. There are different modes of speciation, including allopatric (geographic isolation), sympatric (within the same geographical area), and parapatric (partial geographic isolation) speciation, among others. These different modes can involve various genetic and ecological mechanisms, making it challenging to provide a single, unified explanation for the origin of new species.

The study of molecular genetics has revealed instances of hybridization, where individuals from different species interbreed, leading to the mixing of genetic material. This can result in the formation of hybrid species. However, understanding the genetic and ecological factors that contribute to the establishment and long-term success of these hybrid species is still an active area of research. In certain cases, new species can rapidly diversify to exploit new ecological niches, a process known as adaptive radiation. This rapid diversification challenges our ability to fully capture the mechanisms and patterns of speciation within the framework of traditional and extended evolutionary theories. Genomes are complex entities with intricate interactions among genes, regulatory elements, and non-coding regions. The emergence of new species could involve genetic changes that may have epistatic effects, where the interaction between genes leads to non-linear outcomes. Understanding how these complex interactions contribute to speciation is a complex task. Speciation is an example of macroevolution, involving significant changes in morphology, behavior, genetics, and more. The mechanisms underlying the emergence of macroevolutionary features and the origin of new species require a more nuanced understanding of emergent properties that arise from intricate interactions within complex biological systems.

Primary Speciation

Primary speciation, also referred to as allopatric speciation, involves the divergence of two populations of a single species into distinct species due to geographic isolation. This process occurs when populations of a species become separated by geographical barriers such as mountains, rivers, or oceans. Over time, each isolated population accumulates genetic differences through mutation, genetic drift, and natural selection. Eventually, these differences become substantial enough that if the populations come into contact again, they are unable to interbreed and produce fertile offspring. This results in the formation of two separate species.

Secondary Speciation (Polyploidy)

Secondary speciation, as mentioned in the context of polyploidy, involves the evolution of new species within the same geographical range as an existing species. Polyploidy occurs when an organism has more than two complete sets of chromosomes. This can arise through various mechanisms, such as errors during cell division or hybridization between different species. In plants, for example, polyploidy is relatively common and can lead to the formation of new species.

Polyploidy does not confer major new morphological characteristics. The process of polyploidy itself does not necessarily result in dramatic changes in an organism's appearance or physical traits. This is because polyploidy often involves a duplication of the existing set of genes, rather than the acquisition of entirely new genetic information. As a result, polyploid individuals may exhibit increased size or other subtle variations, but they might not undergo the same level of morphological innovation observed in other forms of evolutionary change.

Darwin's theory of evolution by natural selection relies on the concept of gradual divergence through the accumulation of small changes in populations over time. The branching-tree pattern of speciation, where species split and diverge repeatedly, supports this idea. Primary speciation aligns well with this pattern, as it involves the accumulation of genetic changes due to isolation and adaptation to different environments. Secondary speciation, particularly through polyploidy, challenges the traditional branching-tree pattern to some extent. While it can lead to the rapid formation of new species, its impact on morphology and its divergence from the primary speciation model raise questions about how this process fits within the broader context of Darwinian evolution.

Species Concept and Demarcation

The concept of a species, at its most fundamental level, is an attempt to categorize and understand the vast diversity of life. Yet, determining where one species ends and another begins is not always clear-cut. This "species problem" or demarcation issue has been a long-standing challenge in biology. Traditionally, species were categorized based on morphological characteristics — the physical differences in form and structure. If two animals looked different enough from one another, they were considered separate species. For centuries, this was the standard method for classifying life, but it had its limitations. Morphological variations can occur within a species due to various factors like age, diet, or environment, leading to potential misclassifications. In the 20th century, the biological species concept gained prominence. This defines a species as a group of individuals that can interbreed and produce fertile offspring in natural conditions but cannot do so with members of other groups. This concept works well for many animals, especially sexually reproducing ones, but it has limitations. For instance, it doesn't easily apply to organisms that reproduce asexually or to species that can hybridize. With advances in DNA sequencing technology, a genetic approach to species demarcation has become more popular. Species are defined based on the genetic differences between populations. However, determining the exact degree of genetic difference required to delineate species remains a challenge. Ecological and evolutionary species concepts consider a species as a set of organisms adapted to a particular set of resources or niche in the environment (ecological) or as a lineage evolving separately from others with its own unitary evolutionary role and tendencies (evolutionary). While these concepts provide broader perspectives, they can be challenging to apply uniformly across the vast diversity of life.

Challenges in Demarcation

Some species can interbreed and produce hybrids. For example, lions and tigers can produce ligers. Does this mean they're the same species? The biological species concept would argue they are different species since they don't typically mate in the wild, but it highlights the challenge of strict demarcation. Ring species are situations where neighboring populations can interbreed, but at the end of the "ring," the populations cannot mate with one another. The classic example is the salamander species around California's Central Valley. Cryptic species are organisms that look virtually identical morphologically but are genetically distinct enough to be considered separate species. This poses challenges for the morphological species concept. Rapidly evolving organisms: Some organisms, especially microorganisms, evolve rapidly, blurring the lines between populations and species. Species demarcation in zoology remains a complex issue, with multiple overlapping concepts and methods in play. The "species problem" underscores the dynamic nature of life and the challenges inherent in attempting to fit it into neat, fixed categories. While classifications are essential for scientific communication and study, they are, in many ways, human constructs applied to the intricate web of life.

Large-scale evolution by natural selection is a non-testable hypothesis

Differential reproduction refers to the unequal success of different individuals or groups in producing offspring and passing on their genes to the next generation. In the wild, this concept is often central to the process of natural selection, which drives evolutionary changes over time. While adaptation and differentiation of populations through the process of speciation have been observed both in laboratory and natural settings, significant transitions or innovations, such as the origin of complex body plans, new organs, or novel adaptations, have not been observed. While microevolutionary processes have been observed, macroevolutionary transitions involving major innovations or the origin of complex traits have not been directly observed in real-time. Furthermore, the exact mechanisms and intricacies driving the origin of macroevolutionary novelties are complex and are not understood. Measuring differential reproduction in the wild can be complex and challenging due to various factors, such as environmental conditions, species interactions, and ecosystem dynamics. Additionally, the inherent variability in natural populations introduces noise into data collection and interpretation. Theoretical models and statistical tools cannot imitate, or substitute natural environments. The complexity of natural systems makes it impossible to isolate and quantify specific factors influencing reproductive success. That is why the evolution rate by natural selection is an unpredictable hypothesis, and essentially unscientific.

1. P. R. Ehrlich (1988): In modem evolutionary genetics, natural selection is defined as the differential reproduction of genotypes (individuals of some genotypes have more offspring than those of others) based on the mutations they carry and the environment in which they live. Organisms that are better suited to their environment will reproduce more and so increase the proportion of the population with their traits. ( More reproduction of a genotype = survival of the fittest = measure of  fitness)  
2. T. Bataillon (2014): Obtaining estimates of mutation rates and effects has historically been challengingI. Cvijović (2015): The fate of each mutation depends critically on its fitness in each environment, the dynamics of environmental changes, and the population size. We still lack both a quantitative and conceptual understanding of more significant fluctuations, where selection in each environment can lead to measurable changes in allele frequency.C. J. Graves (2019): Variable environments can cause the same allele to have differing effects on fitness depending on an individual’s environmental context. V. Ž. Alif (2021): Fitness is difficult to measure accurately. The metric of fitness is scarcely used because the estimation of an individual’s reproductive value requires long-term pedigree data, which is rarely available in wild populations where following individuals from birth to death is often impossible. D.Coppedge (2021): The central concept of natural selection cannot be measured. This means it has no scientific value.
3. The key question, namely how mutations in fact affect fitness has not been answered. Darwin's Theory can not be tested, nor quantified. The unknown factors are too many, the variations in the environment, and population and species behavior vary too. It cannot be defined what influence the given environment exercises in regard to specific animals and traits in that environment, nor how the environmental influence would change the fitness and reproduction success of each distinct animal species. Large-scale evolution is at best a non-testable hypothesis, which then remains just that: a hypothesis. Since Darwin's idea cannot be tested, it's by definition, unscientific, and anyone claiming that natural selection explains biodiversity makes that claim based on blind confidence and belief. Not evidence. 

Testing and Quantifying Effects of Mutations on Fitness 

Studying the precise influence of individual mutations on fitness in real-world populations can be challenging due to the multitude of interacting factors. Evolutionary biologists try to overcome the outlined problems and employ a variety of approaches to study mutations and their effects on fitness, including laboratory experiments, field studies, computer simulations, and statistical analyses. These methods allow researchers to examine the distribution of fitness effects, estimate mutation rates, and make predictions about the evolution of populations over time. While it may be difficult to isolate every factor, scientific methods strive to account for as many variables as possible and make probabilistic predictions. Obtaining empirical and quantifiable results presents challenges. Biological systems are incredibly complex and interconnected, and the effects of mutations on fitness can be influenced by a myriad of factors. In real-world populations, it's often difficult to isolate a single mutation's impact on fitness from the background noise of other genetic variations, environmental fluctuations, and interactions with other organisms. This complexity makes it challenging to establish direct cause-and-effect relationships between specific mutations and changes in fitness. Natural environments are dynamic and ever-changing. Different populations of the same species may experience distinct environmental pressures and selective forces. As a result, the fitness effects of a particular mutation can vary across different populations and over time. This variability can make it difficult to generalize findings from one population to another and predict the long-term consequences of specific mutations. Evolution operates over long timescales, making it challenging to directly observe and measure evolutionary changes in real-time. While laboratory experiments and short-term studies can provide insights, they may not capture the full complexity of natural evolutionary processes. Additionally, obtaining long-term observational data for wild populations can be logistically challenging and often requires tracking individuals across generations, which is not feasible. The effects of mutations on fitness are often context-dependent and subject to trade-offs. A mutation that confers a fitness advantage in one scenario may have disadvantages in another. For example, a mutation that enhances an organism's ability to acquire food may also increase its susceptibility to predation. Such trade-offs can complicate the interpretation of experimental results and predictions about the spread of mutations in populations. Some experimental approaches, especially those involving direct manipulation of natural populations, can raise ethical and practical concerns. Researchers must balance the need to gather empirical data with the potential impacts on the organisms and ecosystems under study. These constraints can limit the types of experiments that can be conducted and the extent to which natural selection can be directly observed and quantified.

No evidence of natural selection contributing to the increase in organismal complexity

And if that was not already bad news, it gets worse than that: M.Lynch (2007): Myth: Natural selection promotes the evolution of organismal complexity. Reality: There is no evidence at any level of biological organization that natural selection is a directional force encouraging complexity. What is in question is whether natural selection is a necessary or sufficient force to explain the emergence of the genomic and cellular features central to the building of complex organisms. 22

Molly K Burke et.al. (2010),"Genomic changes caused by epigenetic mechanisms tend to fail to fixate in the population, which reverts back to its initial pattern." That's not all that doesn't fixate. Despite decades of sustained selection in relatively small, sexually reproducing laboratory populations, selection did not lead to the fixation of newly arising unconditionally advantageous alleles. This is notable because in wild populations we expect the strength of natural selection to be less intense and the environment unlikely to remain constant for ~600 generations. Consequently, the probability of fixation in wild populations should be even lower than its likelihood in these experiments.23

Comment: The study conducted by Molly K Burke and colleagues in 2010 sheds light on the dynamics of genomic changes caused by epigenetic mechanisms and the challenges faced by advantageous alleles in achieving fixation within populations, both in the laboratory and natural settings. This observation has important implications for the understanding of evolution and the factors that influence genetic variation within populations.  The study suggests that genomic changes driven by epigenetic mechanisms tend not to fixate within populations. This implies that even though certain epigenetic modifications may occur and contribute to genetic diversity, they may not become permanent fixtures in a population's genome. This could be due to various factors, including the reversibility of epigenetic changes and the potential lack of strong selective pressures to maintain these modifications over long periods. The research highlights a paradox where sustained selection in laboratory populations, even for advantageous alleles, did not necessarily lead to their fixation. This challenges the expectation that beneficial traits would inevitably become fixed within a population under strong and sustained selection. This observation underscores the complexity of genetic dynamics and the interplay between selection, drift, and other factors in shaping allele frequencies. The study also draws attention to the differences between laboratory and wild populations. In natural environments, the strength of natural selection may vary, and the environment is often subject to fluctuations over time. The findings suggest that making predictions about the fixation of advantageous alleles based solely on selection and fitness advantage may overlook important factors that influence evolutionary outcomes. The study reminds  that the process of fixation is influenced by a combination of genetic, environmental, and stochastic factors, and therefore, predicting fixation cannot be straightforward.

Ben Bradley (2022): As soon as contemporary scientists accept that, as per Darwin’s argument in Origin, natural selection does not cause, but results from the ordinary activities of organisms, contemporary evolutionary theorists must address a new foundational challenge: the need to construct a viable, evidence-based picture of the natural world. 24

Comment: In other words, natural selection is not an actor, but a reactor. It is not a protagonist, but passively "selects" or unconsciously, without "intention" gives "preference" to those alleles that are somehow beneficial and therefore are favored to spread into the population and become dominant variants.  It does not "invent" something new. But that is precisely what is required if the tree of life ought to be true. It has to add de novo genes from scratch, with new information, that directs the making of new organismal structures, like limbs, eyes, ears, different cells, organs, and new body plans and forms. 

Adam Levy (2019): The ability of organisms to acquire new genes is testament to evolution’s “plasticity to make something seemingly impossible, possible”, says Yong Zhang, a geneticist at the Chinese Academy of Sciences’ Institute of Zoology in Beijing, who has studied the role of de novo genes in the human brain. But researchers have yet to work out how to definitively identify a gene as being de novo, and questions still remain over exactly how — and how often — they are born.25

Comment:  So Levy confesses, in 2019, there is no answer to this all-relevant question of whether evolution can generate a gene de novo - it has yet to be worked out. 
But then, Levy makes the following claim at the end of the article: Although de novo genes remain enigmatic, their existence makes one thing clear: evolution can readily make something from nothing. “One of the beauties of working with de novo genes,” says Casola, “is that it shows how dynamic genomes are.” Remarkable. On the one hand, in the article, Levy admits that researchers do not know (yet) how evolution can generate genes de novo, but in the end, surprise surprise (not): evolution can readily make something from nothing.....   Levy conveyed that researchers have yet to definitively identify the mechanisms and frequency of de novo gene birth.  The process of generating genes de novo is inherently complex and would involve a combination of mechanisms such as gene duplication, sequence divergence, and functional innovations from non-coding regions. Such complexities can make it challenging to definitively identify de novo genes and elucidate their origins. The process of confirming evolutionary novelties, including the origin of de novo genes, requires a combination of experimental evidence, comparative genomics, and theoretical modeling. Confirming such novelties is an insurmountable challenge.

Beyond Evolution: The Origin of Species by Design 37025610

Horizontal Gene Transfer

Libretext: Horizontal gene transfer (HGT) is the introduction of genetic material from one species to another species by mechanisms other than the vertical transmission from parent(s) to offspring. These transfers allow even distantly-related species (using standard phylogeny) to share genes, influencing their phenotypes. It is thought that HGT is more prevalent in prokaryotes, but that only about 2% of the prokaryotic genome may be transferred by this process. 25

M.Syvanen (2012): The flow of genes between different species represents a form of genetic variation. When I first started writing in 1982 about the implications of horizontal gene transfer (HGT) for macroevolutionary trends, the existence of the phenomenon was not yet accepted, given that evidence came only from isolated examples of bacterial plasmid transfer events and a case involving a retrovirus in mammals. There was great explanatory power in a theory that incorporated the notion of horizontally transferred genes as a source of genetic variation upon which natural selection acts. Reports of HGT in nature trickled in, but investigators debated the significance of HGT and the methodology for identifying it. In fact, only in the past 14 years has the number of examples of naturally occurring HGT become too large to ignore. With the recent availability of genome sequence data, the pace of discovery has picked up and interest in the phenomenon has increased. We now know that the ability of genes to function perfectly well across species boundaries has resulted in a significant horizontal flow of genes. Whether the genes are transferred by transposons, viruses, bacteria, or other vectors, or perhaps through direct contact or initial hybridization-like events, the horizontal flow of genes is a part of the story of life. Although the phenomenon of HGT is now widely accepted, current theoretical constructs remain quite resistant to many of its deeper implications. The first area I touch upon concerns the role of phylogenetic trees as a model for biological history. A second and related area concerns the continued speculation about and search for what is called the last universal common ancestor (LUCA) and the evolutionary significance of the biological unities. A third question involves the rethinking of higher taxonomic nomenclature. The chaotic phylogenetic relationships among plants remain unresolved, and consideration of horizontal gene flow could help solve the puzzle. 26

Shelly Hamilich (2022): Our results suggest that horizontal gene transfer between hosts and their microbiota is a significant and active evolutionary mechanism that contributed new traits to plants and their commensal microbiota. 27

Comment: Rightly, Coppedge points out that: Information shared is not the same as information innovated, nor is borrowing a book as difficult as writing one. 28

Rama P. Bhatia (2022): the fitness effects of horizontally transferred genes are highly dependent on the environment. 29

Comment: The same problem to natural selection applies to HGT: since environmental factors influencing fitness effects would have to be taken into consideration in order to measure/calculate the influence of HGT in fitness, and since that is a variable that is stochastic, and cannot be measured, it becomes de facto impossible to detect up to what degree HGT influences fitness in populations in their natural environment.   Assessing the precise impact of HGT on fitness and evolution can be quite complex due to several factors. Environmental conditions are highly variable and can significantly influence the fitness effects of genes acquired through HGT. What may be beneficial in one environment could be detrimental in another. This introduces a level of uncertainty and complexity when trying to measure the net impact of HGT on fitness, especially across diverse habitats. As with any genetic change, the fitness effects of horizontally transferred genes are subject to randomness and chance. Even if a gene is advantageous in a certain environment, its effects might not always manifest predictably due to interactions with other genes or complex cellular pathways. Measuring fitness effects accurately in natural populations is inherently difficult. Fitness is multifaceted and influenced by a range of factors, including survival, reproduction, competition, and interactions with other species. Isolating the direct impact of HGT from these confounding factors is challenging. Evolution is supposed to be a gradual and ongoing process that occurs over generations. The effects of HGT on fitness may not be immediately obvious and can depend on the long-term dynamics of a population, making it harder to detect and quantify short-term effects. Genes do not operate in isolation but interact with other genes and the environment. The effects of an HGT event might depend on the genetic background of the recipient organism and its interactions with existing genes, further complicating the assessment of fitness effects. Populations are not static; they experience gene flow, migration, and genetic exchange. This can result in HGT events becoming widespread or disappearing due to movement between different environments, further obscuring the direct impact of HGT on fitness.
Given these challenges, accurately quantifying the degree to which HGT influences fitness in natural populations within their native environments is a formidable task. Researchers often resort to a combination of laboratory experiments, computational simulations, and field observations to gain insights into the potential effects of HGT. However, due to the inherent complexity and variability of ecosystems, it is unlikely that we will have a definitive answer about the exact degree of influence HGT has on fitness in all scenarios.



Last edited by Otangelo on Sun Sep 17, 2023 8:29 am; edited 18 times in total

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6Beyond Evolution: The Origin of Species by Design Empty Gene duplications Thu Aug 10, 2023 8:28 am

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Gene duplications

What is Gene duplication?  

Gene duplication is a fundamental genetic process in which an organism's DNA makes an extra copy of a particular gene or a segment of its genome. This duplication event leads to the presence of two or more identical or highly similar copies of the same gene within the genome of an individual.  There are several ways gene duplication can occur:  In this type of duplication, the copies of the gene are located adjacent to each other on the same chromosome. Tandem duplications often result from errors in DNA replication or recombination. This involves duplicating larger segments of a chromosome, which can encompass multiple genes and regulatory elements. These duplicated segments can be found on the same chromosome or on different chromosomes.  This is a more dramatic form of duplication where an entire set of chromosomes is duplicated, resulting in multiple copies of all genes in an organism's genome. Polyploidy is relatively common in plants and has played a significant role in their evolution.

How does Gene duplication occur? 

Gene duplication can occur through various mechanisms, often as a result of errors during DNA replication, recombination, or other genetic processes. During the process of homologous recombination, which helps ensure accurate DNA repair and genetic diversity, misalignment can occur between chromosomes. This misalignment can lead to a crossover event in which one chromosome gains an extra copy of a gene, while the other loses that copy. This can result in a duplicated segment in one chromosome and a deleted segment in the other. Replication Slippage occurs when DNA polymerase, the enzyme responsible for copying DNA during replication, slips or stutters during the replication process. This can lead to the addition or deletion of one or more DNA base pairs. If the slippage occurs within a repetitive region of DNA, it can result in the generation of a duplicated sequence. Transposons are DNA sequences that can move within a genome. They can sometimes carry genes with them as they transpose to new locations. If a transposon carrying a gene inserts itself into a new genomic location, it can lead to gene duplication.  Retrotransposons are a specific type of transposon that can copy themselves via an RNA intermediate. Occasionally, the RNA molecule can be reverse-transcribed back into DNA and inserted into a new genomic location, including near or within an existing gene, leading to duplication.: DNA repair mechanisms can sometimes inadvertently result in gene duplication. For example, if DNA is damaged and needs to be repaired, the repair machinery might copy a section of DNA and insert it into the damaged region, resulting in duplication. During the formation of gametes (sperm and egg cells), mistakes can occur in chromosome segregation. If a mistake results in unequal distribution of chromosomes or chromatids, it can lead to one gamete receiving an extra copy of a gene.

Gene duplication will get you a new allele, but not a novelty - additional new information - which is what evolution needs

J.Dulle: Duplicating existing information cannot produce new information.  Just as saying, “duplicating a gene does not increase the net information content of the cell” three times does not triple the information content of the sentence, duplicating a gene cannot increase the information content of the cell.  Gene duplication cannot help an organism perform some new function.  Trying to get new biological information/function by duplicating an existing gene is like thinking you can obtain an engine for your car by making a second steering wheel! 30

M. Hurles (2004): A duplicated gene newly arisen in a single genome must overcome substantial hurdles before it can be observed in evolutionary comparisons. First, it must become fixed in the population, and second, it must be preserved over time. Population genetics tells us that for new alleles, fixation is a rare event, even for new mutations that confer an immediate selective advantage. Nevertheless, it has been estimated that one in a hundred genes is duplicated and fixed every million years, although it should be clear from the duplication mechanisms described above that it is highly unlikely that duplication rates are constant over time. However, once fixed, three possible fates are typically envisaged for our gene duplication. Despite the slackened selective constraints, mutations can still destroy the incipient functionality of a duplicated gene: for example, by introducing a premature stop codon or a mutation that destroys the structure of a major protein domain. 31

Comment: The emergence of complex traits, such as intricate biochemical pathways or functional organs, requires coordinated interactions among multiple genes and regulatory elements. This challenge aligns with the idea that the simultaneous evolution of multiple components, as required for irreducibly complex systems, is difficult to achieve solely through gene duplication. The challenge of functional integration is consistent with the hurdles duplicated genes face after fixation. Becoming part of existing gene regulatory networks and achieving meaningful functions demand precise orchestration of gene expression and interactions, which may be influenced by epigenetic and developmental complexity. The variations produced by duplication have not been shown to lead to entirely unprecedented functions or structures. The interdependence of components in complex biological features requires coordinated changes beyond the scope of gene duplication alone. Epigenetics and developmental complexity align with the recognition of additional layers of intricacy in shaping biological traits. These mechanisms contribute to the formation of complex structures and functions beyond what gene duplication alone explains.

A. K. Holloway (2007): The fate of gene duplicates subjected to diversifying selection was tested experimentally in a bacterial system. In a striking contradiction to our model, no such conditions were found. The fitness cost of carrying both plasmids increased dramatically as antibiotic levels were raised, and either the wild-type plasmid was lost or the cells did not grow. 32

J. Esfandiar (2010): Although the process of gene duplication and subsequent random mutation has certainly contributed to the size and diversity of the genome, it is alone insufficient in explaining the origination of the highly complex information pertinent to the essential functioning of living organisms. Gene duplication and subsequent evolutionary divergence certainly adds to the size of the genome and in large measure to its diversity and versatility. However, in all of the examples given above, known evolutionary mechanisms were markedly constrained in their ability to innovate and to create any novel information. This natural limit to biological change can be attributed mostly to the power of purifying selection, which, despite being relaxed in duplicates, is nonetheless ever-present.33

Comment: After gene duplication and the arising of a divergent gene, complementary changes involving the regulation of gene expression of that new gene would have to be instantiated in parallel. New gene products require a rewiring of the gene regulatory architecture to function optimally and be integrated into the existing cellular networks. That new information does not have only to be added to the genome, but on top of the gene itself, the gene regulatory program as well has to be reprogrammed with new instructions, on when to express the new gene. Neofunctionalization of the new gene would depend on the right timing of expression. That requires as well the addition of new transcription factor markers, that bind at the right place in the genome. 

This is pointed out in the following quote:

Johan Hallin (2019): One category of molecular changes that appears to play a key role in the evolution of genes that originate from gene duplication (duplicates or paralogs) are regulatory changes, i.e., changes in the gene itself or elsewhere in the genome that determine when, where, and at what level a gene is transcribed and translated. The immediate effect of gene duplication could favor gene retention or loss, or if the expression change is effectively neutral, the duplicate could remain neutral for extended periods of time. 34

Alternative evolutionary forces to natural selection

Michael Lynch (2007): First, evolution is a population-genetic process governed by four fundamental forces. Darwin articulated one of those forces, the process of natural selection. The remaining three evolutionary forces are nonadaptive in the sense that they are not a function of the fitness properties of individuals: mutation is the ultimate source of variation on which natural selection acts, recombination assorts variation within and among chromosomes, and genetic drift ensures that gene frequencies will deviate a bit from generation to generation independent of other forces. Given the century of work devoted to the study of evolution, it is reasonable to conclude that these four broad classes encompass all of the fundamental forces of evolution. 35

Eugene V Koonin (2009):“Evolutionary-genomic studies show that natural selection is only one of the forces that shape genome evolution and is not quantitatively dominant, whereas non-adaptive processes are much more prominent than previously suspected.” There’s quite a lot of this sort of thing around these days, and we confidently predict a lot more in the near future. There is no consistent tendency of evolution towards increased genomic complexity, and when complexity increases, this appears to be a non-adaptive consequence of evolution under weak purifying selection rather than an adaptation. 36

Random genetic drift

H. Allen Orr (2008): Until the 1960s almost all biologists assumed that natural selection drives the evolution of most physical traits in living creatures,  but a group of population geneticists led by Japanese investigator Motoo Kimura sharply challenged that view. Kimura argued that molecular evolution is not usually driven by “positive” natural selection—in which the environment increases the frequency of a beneficial type that is initially rare. Rather, he said, nearly all the genetic mutations that persist or reach high frequencies in populations are selectively neutral—they have no appreciable effect on fitness one way or the other. (Of course, harmful mutations continue to appear at a high rate, but they can never reach high frequencies in a population and thus are evolutionary dead ends.) Since neutral mutations are essentially invisible in the present environment, such changes can slip silently through a population, substantially altering its genetic composition over time. The process is called random genetic drift; it is the heart of the neutral theory of molecular evolution. By the 1980s many evolutionary geneticists had accepted the neutral theory. But the data bearing on it were mostly indirect; more direct, critical tests were lacking. Two developments have helped fix that problem. First, population geneticists have devised simple statistical tests for distinguishing neutral changes in the genome from adaptive ones. Second, new technology has enabled entire genomes from many species to be sequenced, providing voluminous data on which these statistical tests can be applied. The new data suggest that the neutral theory underestimated the importance of natural selection. 37

Comment: H. Allen Orr's statement highlights the shift in perspective that occurred in the field of evolutionary biology during the 1960s and onward. Motoo Kimura's neutral theory of molecular evolution challenged the prevailing assumption that natural selection was the primary driver of most physical traits in living organisms. Kimura argued that many genetic mutations that persist or reach high frequencies in populations are selectively neutral, meaning they have no significant effect on an organism's fitness. Instead, these mutations can accumulate through a process called random genetic drift, altering a population's genetic composition over time. The emergence of complex biological features, such as intricate biochemical pathways, functional organs, and sophisticated behaviors, cannot be adequately explained by a purely random process like genetic drift. The coordinated interaction of multiple genes and regulatory elements required to develop such features is more consistent with intentional design. Random genetic drift, being a stochastic process, lacks the capacity to generate the specific and finely-tuned information necessary for the development of diverse and complex life forms. Furthermore, certain biological systems are too complex to have evolved gradually through random genetic drift. Removing any component of such systems would render them non-functional, making it implausible for these systems to arise through a series of neutral mutations. The theory might be difficult to test and falsify definitively due to its reliance on subtle statistical differences in genetic data. Attributing the origin of biodiversity primarily to random genetic drift without a clear underlying mechanism does not provide a comprehensive and satisfying explanation for the diversity of life.

P. Gibson (2013): In conclusion, numerical simulation shows that realistic levels of biological noise result in a high selection threshold. This results in the ongoing accumulation of low-impact deleterious mutations, with deleterious mutation count per individual increasing linearly over time. Even in very long experiments (more than 100,000 generations), slightly deleterious alleles accumulate steadily, causing eventual extinction. These findings provide independent validation of previous analytical and simulation studies. Previous concerns about the problem of accumulation of nearly neutral mutations are strongly supported by our analysis. Indeed, when numerical simulations incorporate realistic levels of biological noise, our analyses indicate that the problem is much more severe than has been acknowledged, and that the large majority of deleterious mutations become invisible to the selection process. 38

E. V. Koonin (2022): Modern evolutionary theory, steeped in population genetics, gives a detailed and arguably, largely satisfactory account of microevolutionary processes: that is, evolution of allele frequencies in a population of organisms under selection and random genetic drift. However, this theory has little to say about the actual history of life, especially the emergence of new levels of biological complexity, and nothing at all about the origin of life. The preponderance of neutral and slightly deleterious changes provides for evolution by genetic drift whereby a population moves on the same level or even slightly downward on the fitness landscape, potentially reaching another region of the landscape where beneficial mutations are available. 39

Jerry A. Coyne (2009): Both drift and natural selection produce genetic change that we recognize as evolution. But there’s an important difference. Drift is a random process, while selection is the anti-thesis of randomness. … As a purely random process, genetic drift can’t cause the evolution of adaptations. It could never build a wing or an eye. That takes nonrandom natural selection. What drift can do is cause the evolution of features that are neither useful nor harmful to the organism 40

Michael Lynch (2007): Contrary to popular belief, evolution is not driven by natural selection alone. Many aspects of evolutionary change are indeed facilitated by natural selection, but all populations are influenced by non-adaptive forces of mutation, recombination, and random genetic drift. These additional forces are not simple embellishments around a primary axis of selection, but are quite the opposite—they dictate what natural selection can and cannot do … A central point to be explained is that most aspects of evolution at the genome level cannot be fully explained in adaptive terms, and moreover, that many features could not have emerged without a near-complete disengagement of the power of natural selection. This contention is supported by a wide array of comparative data, as well as by well-established principles of population genetics” 41

George Ellis (2018): If most of the variation found in evolutionary lineages is a product of random genetic drift, how does apparent design arise? It surely can’t be an accidental by-product of random events – that was the whole point of Darwin’s momentous discovery (Darwin 1872) of a mechanism to explain apparent design that is so apparent in all of nature. On the face of it, Lynch, Myers, and Moran seem to be saying the ID people are right: evolution cannot dapt life to its environment, because random effects dominate.

Comment:  Genetic drift is increasingly recognized as having limitations in accounting for the emergence of complex biological features and the diversity of life.  The simulations by Gibson suggest that realistic levels of biological noise result in a high selection threshold, leading to the ongoing accumulation of low-impact deleterious mutations over time. This accumulation of slightly deleterious mutations, as noted by Koonin, can lead to a population moving on the fitness landscape in a direction that may not necessarily lead to adaptive changes. This raises concerns about the long-term viability of populations and the potential for extinction.  Coyne emphasizes the crucial distinction between genetic drift and natural selection. While genetic drift is a random process, natural selection is a non-random mechanism that drives adaptations. Drift, as a purely random process, lacks the ability to generate the intricate and functional features observed in living organisms, such as wings or eyes. It can only lead to the evolution of features that are neutral or have no clear impact on fitness.  Lynch points out that many aspects of organismal change cannot be fully explained by adaptive terms alone. Non-adaptive forces like mutation, recombination, and random genetic drift play essential roles in shaping genetic diversity but may not always lead to adaptations. Lynch suggests that a near-complete disengagement of natural selection's power is necessary to explain certain features, indicating that drift alone may not provide a comprehensive explanation. Ellis raises a significant point about the apparent design observed in nature. While genetic drift can lead to random effects, it is inadequate in explaining the apparent design and complexity found in organisms.  These quotes collectively convey the view that while random genetic drift is a valid evolutionary process, it falls short in providing a complete and satisfying explanation for the origin of biodiversity. The emergence of complex biological features, the development of intricate structures, and the diversity of life forms are often attributed to other non-random processes. While random drift may contribute to the evolution of certain traits, it is not considered the primary driving force behind the remarkable diversity and complexity of life on Earth.

What are the boundaries, or limits of beneficial mutations? 

Natural selection does not create or add something. The innovations that permit organisms to evolve have to come from the variations/mutations of pre-existing traits in the genome. It is accidental mutations that would have to convey innovation, that natural selection would select and fix in the genome. There would not only have to be variation but also an increase in genome size. The smallest known free-living bacterium today is called Pelagibacter Ubique. It has a genome of 1,3 million nucleotides. If we suppose that the Last Universal Common Ancestor had the genome size of P.Ubique, it would have to increase to get to 3 billion nucleotides, the size of a human genome 2300 times larger in size.

Behe's second book ( After Darwin's Black Box 1996), The Edge of Evolution (2008) 42, gave a lot to talk about. 
Gert Korthof (2007): The book "Edge of Evolution" is principally about the probability of new protein-protein binding sites arising by chance and necessity. Experimental evidence (mostly chloroquine resistance) shows such protein-protein binding sites to be difficult to evolve by chance mechanisms. He says the empirical (extrapolation) of the "edge" of evolution is no more than two coordinated protein-protein binding sites could have evolved in a lineage in all the time available on earth. The flagellum has perhaps dozens of such sites. It is a quantitative argument. 43

M. Behe: Edge of evolution (2008): Recall the example of sickle cell disease. The sickle cell mutation is both a life saver and a life destroyer. It fends off malaria but can lead to sickle cell disease. However, hemoglobin C-Harlem has all the benefits of sickle, but none of its fatal drawbacks. So in western and central Africa, a population of humans that had normal hemoglobin would be worst off, a population that had half normal and half sickle would be better off, and a population that had half normal and half C-Harlem would be best of all. But if that’s the case, why bother with sickle hemoglobin? Why shouldn’t evolution just go from the worst to the best case directly? Why not just produce the C-Harlem mutation straightaway and avoid all the misery of sickle? The problem with going straight from normal hemoglobin to hemoglobin C-Harlem is that, rather than walking smoothly up the stairs, evolution would have to jump a step. C-Harlem differs from normal hemoglobin by two amino acids. In order to go straight from regular hemoglobin to C-Harlem, the right mutations would have to show up simultaneously in positions 6 and 73 of the beta chain of hemoglobin. Why is that so hard? Switching those two amino acids at the same time would be very difficult for the same reason that developing resistance to a cocktail of drugs is difficult for malaria—the odds against getting two needed steps at once are multiple of the odds for each step happening on its own. What are those odds? Very low. The human genome is composed of over three billion nucleotides. Yet only a hundred million nucleotides seem to be critical, coding for proteins or necessary control features. The mutation rate in humans (and many other species) is around this same number; that is, approximately one in a hundred million nucleotides is changed in a baby compared to its parents (in other words, a total of about thirty changes per generation in the baby’s three-billion-nucleotide genome, one of which might be in coding or control regions).  In order to get the sickle mutation, we can’t change just any nucleotide in human DNA; the change has to occur at exactly the right spot. So the probability that one of those mutations will be in the right place is one out of a hundred million. Put another way, only one out of every hundred million babies is born with a new mutation that gives it sickle hemoglobin. Over a hundred generations in a population of a million people, we would expect the mutation to occur once by chance. That’s within the range of what can be done by mutation/selection. To get hemoglobin C-Harlem, in addition to the sickle mutation we have to get the other mutation in the beta chain, the one at position 73. The odds of getting the second mutation in exactly the right spot are again about one in a hundred million. So the odds of getting both mutations right, to give hemoglobin C-Harlem in one generation in an individual whose parents have normal hemoglobin, are about a hundred million times a hundred million (10^16 ). On average, then, nature needs about that many babies in order to find just one that has the right double mutation. With a generation time of ten years and an average population size of a million people, on average it should take about a hundred billion years for that particular mutation to arise—more than the age of the universe.  Hemoglobin C-Harlem would be advantageous if it were widespread in Africa, but it isn’t. It was discovered in a single family in the United States, where it doesn’t offer any protection against malaria for the simple reason that malaria has been eradicated in North America. Natural selection, therefore, may not select the mutation, and it may easily disappear by happenstance if the members of the family don’t have children, or if the family’s children don’t inherit a copy of the C-Harlem gene. It’s well known to evolutionary biologists that the majority even of helpful mutations are lost by chance before they get an opportunity to spread in the population. 7 If that happens with C-Harlem, we may have to wait for another hundred million carriers of the sickle gene to be born before another new C-Harlem mutation arises. 44

Of course, providing such a powerful argument demonstrating the edge/limit of evolution, would not keep the opponents silent. Sean Carroll, an evolutionary developmental biologist, wrote a critical response in the magazine Science, named "God as Genetic Engineer", to which Behe responded on his Amazon blog. The link can be accessed in the bibliography of this chapter. 45

Gunter Bechly (2018):Michael Behe discovered the waiting time problem as a problem for darwinism in his book the age of evolution and he didn't make a mathematical calculation but he looked at the empirical data from malaria drug resistance and what he found is that a lot of the malaria drugs resistance developed very quickly in a few years because only point mutations were necessary but in the case of chloroquine the drug chloroquine it took several decades and the reason was it was discovered later that there you needed a coordinated mutations to mutations neutral for each other had to come together to produce this kind of resistance against chloroquine and then he  simply transpose the data if you look at the vast population size of malaria microbes compared to the population size of vertebrates and their short generation time and you transpose these data he came up to the hypothesis that invertebrates were a single coordinated change he would have to need longer than the existence of the whole universe 10 to the power of 15 years now this is of course would be a problem and for example in human evolution we have all these nice fossils so if the signal coordinated change would take longer than the universe then then it would be game over so of course evolutionary biologists tried to repute me and indeed in 2008 the earth and Schmidt they published a paper in genetics where they said they have refuted his result was completely unrealistic they did they made a mathematical calculation based on the methodological apparatus of population genetics and simulations and they came with a number of 260 million years. Wonderful this is really much shorter than Big E the problem is we have only 6 million years available since the splitting of the human lineage from the chimp lineage so that is what evolutionary biologists say is the time needed for a single coordinated mutation and you have to keep in mind this is a mathematical model which always involves simplifications and simplifications may involve errors so what is more likely that the empirical data from B from a lot of drug resistance are closer to the truth or the mathematical simulation I would suggest that rather this ten to the power of 15 is closer to the real constraint in nature but anyway we arrive at times that are much too long for evolution to occur. 46

Behe expanded on his arguments about the limitations of evolution and presented his perspective on the boundaries of what evolutionary processes can achieve. Building on his concept of irreducible complexity introduced in his earlier book "Darwin's Black Box," Behe asserted that certain biological systems are so intricately interdependent that they cannot evolve through gradual, step-by-step processes. He suggested that such systems require multiple components to be present simultaneously in order to function, making their evolution through random mutations and natural selection highly improbable. Behe explored the idea that beneficial mutations required for complex adaptations are relatively rare. He argued that the probability of multiple, coordinated mutations occurring simultaneously to produce a new complex trait is extremely low, leading to skepticism about the feasibility of certain evolutionary pathways. Behe examined the evolution of drug resistance in malaria parasites as a case study. He contended that while some mutations can confer resistance to drugs, they typically involve loss of function or minor changes. He suggested that these mutations do not exemplify the generation of complex new traits through evolutionary mechanisms.

The waiting time problem in a model hominin population

Rick Durrett (2008): We now show that two coordinated changes that turn off one regulatory sequence and turn on another without either mutant becoming fixed are unlikely to occur in the human population. Theorem 1 predicts a mean waiting time of 216 million years. 47

John Sanford (2015): Biologically realistic numerical simulations revealed that a population of this type required inordinately long waiting times to establish even the shortest nucleotide strings. To establish a string of two nucleotides required on average 84 million years. To establish a string of five nucleotides required on average 2 billion years. We found that waiting times were reduced by higher mutation rates, stronger fitness benefits, and larger population sizes. However, even using the most generous feasible parameters settings, the waiting time required to establish any specific nucleotide string within this type of population was consistently prohibitive.48

John Sanford (2016): Our paper shows that the waiting time problem cannot honestly be ignored. Even given best-case scenarios, using parameter settings that are grossly overgenerous (for example, rewarding a given string by increasing total fitness 10 percent), waiting times are consistently prohibitive. This is even for the shortest possible words. The establishment of just a two-letter word (two specific mutations within a hominin population of ten thousand) requires at least 84 million years. A three-letter word requires at least 376 million years. A six-letter word requires over 4 billion years. An eight-letter word requires over 18 billion years (again, see Table 2 in the paper). The waiting time problem is so profound that even given the most generous feasible timeframes, evolution fails. The mutation/selection process completely fails to reproducibly and systematically create meaningful strings of genetic letters in a pre-human population. 49

Comment: John Sanford's argument poses a significant challenge to the plausibility of evolution through mutation and natural selection. Even under highly favorable conditions, where mutations are rewarded with significant fitness gains, the waiting times for the evolution of even short genetic sequences are so long that they render the process of evolution unfeasible. These conclusions are primarily rooted in calculations of the waiting times needed for the evolution of specific genetic sequences. He presents examples using the analogy of forming words of increasing length through mutations. For instance: Even achieving a two-letter word (representing two specific genetic mutations) within a hypothetical population of hominins with ten thousand individuals requires at least 84 million years.  Expanding on this, a three-letter word (three specific mutations) would demand a waiting time of at least 376 million years. Sanford's calculations indicate that a six-letter word (six specific mutations) would necessitate over 4 billion years. Going further, an eight-letter word (eight specific mutations) would require over 18 billion years. Even with exceedingly generous assumptions about mutation rates and selection benefits, these waiting times are far longer than the generally accepted age of the Earth and even the universe, making the likelihood of evolution producing these genetic sequences within feasible timeframes extremely low.

Critics argue that Sanford's analogy of forming words through random mutations oversimplifies the complex mechanisms of genetic evolution. Sanford's analysis doesn't take into account other mechanisms such as genetic drift, recombination, and the potential for multiple simultaneous mutations that could speed up the evolutionary process.  Critics also contend that Sanford's calculations rely on relatively small population sizes, whereas actual populations are much larger, which can impact the rate of beneficial mutations.  Sanford's analysis largely ignores the role of neutral mutations that can provide a stepping stone for later beneficial mutations. Critics argue that Sanford's focus on the waiting time for specific genetic sequences overlooks the fact that evolution works in response to changes in the environment, which can drive the emergence of beneficial traits. While the criticisms raised against Sanford's arguments do carry weight, these objections are not sufficiently compelling to undermine his main claims. Sanford's focus on waiting times is to highlight the immense challenges posed by the accumulation of multiple beneficial mutations. While genetic drift, recombination, and multiple simultaneous mutations can play a role in speeding up evolution, Sanford's goal is to emphasize the significant timeframes even when considering conservative factors. While larger population sizes can increase the likelihood of beneficial mutations, Sanford's calculations using smaller population sizes still underscore the immense time required for specific sequences to arise. Even with larger populations, waiting times would still be substantial, making the overall point about the challenges of waiting times valid. Sanford's focus is specifically on the waiting time for meaningful, functional sequences to emerge, and neutral mutations, while relevant, do not necessarily address the issue of the time required for complex adaptations to develop. Evolution responds to changes in the environment, but this aspect doesn't negate Sanford's argument about waiting times. Even with environmental pressures, the waiting time problem still poses a substantial challenge, especially when considering the specific mutations required for complex adaptations.

Gene polyfunctionality and overlapping codes cause constraints

John C. Sanford (2013): “There is growing evidence that much of the DNA in higher genomes is poly-functional, with the same nucleotide contributing to more than one type of code. Such poly-functional DNA should logically be multiply-constrained in terms of the probability of sequence improvement via random mutation. We describe a model of this relationship, which relates the degree of poly-functionality and the degree of constraint on mutational improvement. 50

Comment: John C. Sanford's perspective, as presented in his 2013 work, raised points that challenge certain aspects of traditional evolutionary thinking. Sanford focused on the concept of poly-functionality in DNA sequences and its potential implications for the evolutionary process. Sanford suggested that many segments of DNA in higher genomes have multiple functions, contributing to different genetic codes simultaneously. In this view, a single nucleotide or sequence of nucleotides can serve various purposes, such as coding for proteins, regulatory elements, or other functional elements within the cell. Sanford argued that the poly-functional nature of DNA sequences imposes multiple constraints on the potential for random mutations to lead to improvements. If a DNA sequence serves more than one function, any mutation that changes it could disrupt one or more of these functions. This raises the bar for the likelihood of a beneficial mutation occurring since it would need to simultaneously improve all relevant functions. The argument challenges the conventional view of evolution's reliance on the gradual accumulation of small mutations as the primary mechanism for generating complexity. He contended that the presence of multiple functions for a given DNA sequence increases the likelihood of detrimental effects from mutations, making the development of new functional features more difficult. The poly-functional nature of DNA sequences highlights a potential hurdle for the evolutionary process. He suggested that random mutations, which are assumed to be the driving force behind the emergence of new traits, might have a lower chance of success when multiple functions are at play. This could impact the probability of generating new and beneficial traits, potentially slowing down or impeding the evolutionary process as traditionally understood.

D. Joseph (2021): “Genomes are the genetic specifications that allow life to exist. Specifications are obviously inherently SPECIFIC. This means that random changes in specifications will disrupt information with a very high degree of certainty. This has become especially clear ever since the publication of the ENCODE results, which show that very little of our genome is actually ‘junk DNA’. The ENCODE project also shows that most nucleotides play a role in multiple overlapping codes, making any beneficial mutations which are not deleterious at some level vanishingly rare. In the abstract of the paper titled “Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation”, the authors describe why these overlapping genetic codes present a profoundly serious challenge to evolutionary theory. 51

a) The probability of beneficial mutation is inversely related to the degree that a sequence is already optimized for a given code; 
b) The probability of beneficial mutation drastically diminishes as the number of overlapping codes increases. 

The growing evidence for a high degree of optimization in biological systems, and the growing evidence for multiple levels of poly-functionality within DNA, both suggest that mutations that are unambiguously beneficial must be especially rare. The theoretical scarcity of beneficial mutations is compounded by the fact that most of the beneficial mutations that do arise should confer extremely small increments of improvement in terms of total biological function. This makes such mutations invisible to natural selection. Beneficial mutations that are below a population's selection threshold are effectively neutral in terms of selection, and so should be entirely unproductive from an evolutionary perspective. We conclude that beneficial mutations that are unambiguous (not deleterious at any level), and useful (subject to natural selection), should be extremely rare.” 52

Comment:  The concept of overlapping genetic codes and their potential impact on evolutionary processes raises important questions about the feasibility of evolution driving the emergence of new body plans. D. Joseph's assertion that genomes are inherently specific and that random changes can disrupt information with a high degree of certainty underscores the challenges that overlapping codes pose to the traditional understanding of how genetic changes drive large-scale morphological evolution. At the heart of this argument is the notion that biological systems are intricately optimized and finely tuned to carry out multiple functions simultaneously. Overlapping genetic codes refer to the phenomenon where a single stretch of DNA can encode information for multiple functional elements, such as genes or regulatory regions. This idea challenges the simplistic view that mutations can lead to straightforward improvements in biological function, as mutations affecting one aspect of the code may inadvertently disrupt other functions. Consider a scenario where a specific sequence of DNA is optimized to serve several functions due to overlapping codes. A mutation that might appear beneficial in the context of one code could disrupt the functionality of another code that also relies on the same sequence. This intricate interdependence makes it increasingly difficult for random mutations to lead to advantageous changes without negatively impacting other vital functions. In light of this, the evolution of new body plans – dramatic changes in an organism's overall structure – becomes a more intricate puzzle. The optimization and multi-functionality of genetic codes from the outset may limit the scope for significant beneficial mutations that could drive the formation of entirely new body plans. The concept of overlapping codes aligns with the emerging understanding that much of the genome previously labeled as "junk DNA" actually plays crucial regulatory and functional roles. The ENCODE project's findings underscore the complexity and interconnectedness of genetic information. This complexity suggests that even seemingly small changes can have far-reaching consequences, and the likelihood of mutations leading to advantageous adaptations may be much lower than previously assumed. From this perspective, the notion of evolution as a driving force for the emergence of entirely new body plans faces significant challenges. The highly optimized nature of genetic codes and their multi-functionality suggest that the scope for beneficial mutations capable of leading to large-scale morphological changes may be severely limited.

Up to 10, and maybe even more different functions within the same gene section

The number of different functions within the same gene section can vary widely based on the specific genomic context and the intricacies of molecular biology. Genes and their associated regulatory elements can have multiple functions that contribute to various aspects of cellular processes and organismal development. 

1. Protein Coding: The primary function of protein-coding genes is to provide the instructions for building specific proteins, which are essential for various cellular functions and processes.
2. Alternative Splicing: Many genes can produce multiple protein isoforms through a process called alternative splicing. Different combinations of exons can be included or excluded from the final mRNA, leading to the production of distinct protein variants from a single gene.
3. Gene Regulation: Within a gene section, there are regulatory elements like promoters and enhancers that control when and where the gene is expressed. These elements play a crucial role in determining the levels of gene expression in different cell types and under various conditions.
4. Non-Coding RNA: Some gene sections produce non-coding RNAs, which have diverse regulatory functions. For example, microRNAs can inhibit the translation of target mRNAs, while long non-coding RNAs can influence gene expression and chromatin organization.
5. Epigenetic Regulation: Gene sections may contain elements involved in epigenetic modifications, such as DNA methylation or histone modifications, which can influence gene expression patterns across generations.
6. Structural Roles: Certain gene sections contribute to the three-dimensional organization of the genome within the nucleus, impacting how genes interact with each other and with regulatory elements.
7. Mobile Genetic Elements: Transposons and retrotransposons are mobile genetic elements that can be present within gene sections. These elements can influence genome stability, evolution, and gene regulation.
8. Chromatin Organization: Gene sections may contribute to the organization of chromatin into distinct domains, affecting the accessibility of DNA to transcriptional machinery.
9. Functional RNA Elements: Some gene sections produce functional RNA elements, such as ribosomal RNA (rRNA) and transfer RNA (tRNA), which are critical components of protein synthesis.
10. Post-Transcriptional Regulation: Gene sections may contain elements involved in post-transcriptional regulation, including mRNA stability, localization, and translation efficiency.

As incredible as it seems, all of these different functions can exist within the same gene section. The same gene section can be read differently, leading to the expression of multiple distinct functions depending on the reading frame and how the genetic information is processed. The functions described often overlap or interact with each other within the same genomic region. Overlapping regions of the genome can encompass multiple, distinct functions simultaneously. The functions of overlapping regions are interconnected and can influence each other in intricate ways. For example, a gene section that codes for a protein might also contain regulatory elements that control its expression, alternative splicing sites that generate different protein isoforms, and non-coding RNA sequences that participate in various regulatory processes. The interplay between these functions contributes to the overall behavior and adaptability of the genome. The discovery and understanding of these overlapping functions add to the awe-inspiring nature of biology and genetics. The genetic code is read in sets of three nucleotides (codons), and the sequence of codons determines the amino acids that will be incorporated into a protein. However, the same DNA sequence can be read in different reading frames, resulting in the production of different protein sequences. Additionally, alternative splicing can lead to the inclusion or exclusion of different exons, further diversifying the protein isoforms that can be generated from the same gene section.  Some gene sections contain overlapping regions where different functional elements reside. For instance, a single DNA sequence might contain both protein-coding regions and regulatory elements that control gene expression. This overlapping arrangement allows a single gene section to contribute to multiple functions. In addition to protein-coding mRNAs, the same gene section can produce non-coding RNAs with distinct regulatory functions. These non-coding RNAs can participate in gene regulation, chromatin modification, and other processes, contributing to the functional diversity of the genome.  The same gene section can be subject to different epigenetic modifications, such as DNA methylation and histone modifications, which influence gene expression. These modifications can affect how the gene section is read and processed, leading to different functional outcomes.  The cellular context, environmental conditions, and developmental stage can also influence how a gene section is read and which functions are expressed. Gene regulation is a dynamic process that responds to various cues, allowing cells to adapt and perform different functions as needed. As you traverse these various readings, it becomes clear that the same gene section is a multifaceted masterpiece, capable of contributing to a remarkable array of biological processes. This inherent versatility is a testament to the elegant design of the genome, where a single sequence of DNA can generate a symphony of functions, orchestrating the intricacies of life itself.  

K. Donohue (2019) writes in the science article: Multi-tasking as an ancient skill: When one gene does many things well:
Multi-tasking is in our DNA. Many genes perform more than one function, and the question is how well they can do them all. 53 

Comment: The concept of multitasking in gene function is supported by the findings presented in this scientific paper from 2019. This research underscores how the same gene section can be involved in multiple functions that contribute to different aspects of an organism's life history and adaptation to its environment. The study provides concrete evidence of the multitasking capabilities of gene sections and supports the idea that genes can have diverse effects beyond their primary known functions. The findings of this study align with the notion that genes can perform multiple roles, contributing to the complexity and versatility of biological systems.

Y. Pritykin (2015) writes in: Genome-Wide Detection and Analysis of Multifunctional Genes:
Many genes can play a role in multiple biological processes or molecular functions. Identifying multifunctional genes at the genome-wide level and studying their properties can shed light upon the complexity of molecular events that underpin cellular functioning, thereby leading to a better understanding of the functional landscape of the cell. We find that multifunctional genes are significantly different from other genes with respect to their physicochemical properties, expression profiles, and interaction properties. We also observe that multifunctional genes tend to be more conserved.     54

Comment: This scientific paper further supports the concept of gene multitasking or multifunctionality by presenting a comprehensive computational approach to identify and characterize genes that perform multiple functions. This study goes beyond simple gene annotations and delves into the intricate relationships between various biological processes and molecular functions associated with genes. The findings align with the idea that many genes are endowed with a high degree of functional plasticity, capable of performing diverse roles within the cell. The study identifies multifunctional genes by analyzing existing functional annotations and demonstrates that this phenomenon is prevalent across different organisms. This supports the notion that gene multifunctionality is a common and important aspect of genetic regulation and cellular function.  The study emphasizes the importance of considering semantic distinctness when identifying multifunctional genes. This acknowledges that genes may have multiple functional roles that are not necessarily categorized under the same label within functional ontologies. Genes can carry out different functions in distinct biological contexts, reflecting the complex adaptability of genetic information. Multifunctional genes exhibit distinct properties and characteristics compared to other genes. These properties include their positions within protein interaction networks, evolutionary conservation, essentiality, expression profiles, and structural features. This broad spectrum of attributes highlights the multifaceted nature of gene functions.  Multifunctional genes might carry out different molecular functions while participating in various biological processes. This implies that a gene's multifunctionality is context-dependent, driven by factors such as cell type, developmental stage, or environmental conditions.

Beyond Evolution: The Origin of Species by Design 1222

Imagine a complex and intricately designed Swiss watch, composed of numerous gears, springs, and mechanisms, all working together to keep precise time. Now, consider the idea that this watch could have emerged gradually, piece by piece, through a series of random and accidental events. In the evolutionary narrative, this watch would have started as a simple prototype, perhaps just a single gear. Over time, small changes, like accidental tweaks to the shape of the gear teeth, accumulate. Gradually, new features emerge – more gears are added, springs appear, and various mechanisms form. Eventually, this process is said to have led to the creation of a fully functional, intricate timekeeping device. However, let's take this analogy a step further. Imagine that each gear in the watch not only serves its primary timekeeping function but also has the ability to perform additional tasks simultaneously. Some gears now also regulate the temperature inside the watch, others emit melodic chimes at specific intervals, and some even calculate complex mathematical equations. Each gear's precise design and coordination with others are crucial for these additional functions to work flawlessly. Now, consider the challenges posed by this scenario. The intricate interplay of multiple functions within each gear suggests an incredible level of complexity – far beyond what we typically attribute to random mutations and natural selection. The idea that these gears evolved to handle multiple functions, each with its own distinct requirements, becomes increasingly difficult to accept. It's as if the process of assembling this watch involved randomly changing gears and springs, yet each random tweak resulted in perfectly synchronized additional functions. Furthermore, let's say that some gears in this evolving watch started as simple components and gradually gained more functions over time. The question arises: how did these gears avoid losing any of their already-established functions during the acquisition of new ones? The delicate balance and coordination required for multiple functions to coexist within a single gear challenge the notion of incremental, step-by-step evolution. In this analogy, the watch's intricate design, precise coordination of functions, and the challenge of maintaining multiple functions within a single component mirror the complexities observed in multifunctional genes. Just as the Swiss watch suggests intelligent design, the multifaceted capabilities of genes hint at a level of purposeful engineering that seems at odds with the idea of gradual, unguided evolution. Just as the watch's functions are finely tuned to work together, so too are the functions of multifunctional genes, inviting us to consider an alternative perspective on the origins of life's complexity.

The idea of multifunctional genes arising through gradualistic evolutionary processes presents significant challenges that are difficult to reconcile. While the evolutionary narrative seeks to explain the emergence of complex traits and functions over time, the concept of a single gene section performing numerous distinct functions simultaneously raises serious questions about the plausibility of such a scenario. First and foremost, the intricate interplay of multiple functions within a single gene section suggests a level of complexity and precision that is far beyond what we typically associate with random mutations and natural selection. Evolutionary mechanisms are often portrayed as acting in a stepwise fashion, with small changes accumulating over time to produce novel features. However, the notion that a gene section could evolve to serve multiple functions, each with its own specific requirements and intricate interactions, seems to strain the limits of what can reasonably be attributed to chance events. Consider the example of alternative splicing producing different protein isoforms from the same gene section. The precise coordination required to generate distinct protein variants, each with its own functional role, implies a level of orchestration and design that is difficult to envision as arising solely through random mutations. Furthermore, the idea that a single gene section could be responsible for coding both proteins and regulatory elements, each with distinct functions, challenges our understanding of how genetic information is organized and processed. The evolutionary explanation also relies on the concept of gene duplication as a mechanism for generating new functions. While gene duplication can theoretically provide raw material for evolution, the subsequent process of evolving multiple functions within the duplicated genes requires an intricate dance of mutations that must somehow avoid disrupting existing functions. It becomes increasingly implausible to attribute this level of precision and complexity to blind, unguided processes. Additionally, the robustness and adaptability observed in multifunctional genes pose a challenge. The concept of a fail-safe mechanism, where multiple functions are contained within a single gene to ensure redundancy, aligns more naturally with the idea of purposeful design rather than gradual, trial-and-error processes. The notion that multiple functions could evolve and be preserved over time without compromising each other suggests a level of foresight and engineering that seems incompatible with the concept of random mutation and natural selection. Furthermore, the observed interdependence of functions within multifunctional genes raises questions about the order in which these functions supposedly emerged. Did one function evolve first, followed by the gradual addition of others? If so, how did the gene avoid losing any of its already-established functions during the acquisition of new ones? The complexity and delicate balance required for such a scenario to unfold challenge the notion of incremental, stepwise evolution.



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Multiple mutations are needed to get a positive functional outcome

J. B. Fischer: (2007): What about a case where 10 mutations are needed before there is a benefit? If each mutation by itself is neutral, natural selection has nothing to act on. Then the probability of all ten specific mutations ending up in one organism, even if they are acquired sequentially over many generations, is vanishingly small. Once a structure already exists, natural selection can fine-tune it. However, in some cases, natural selection is not sufficient, because multiple mutations are required, which are not beneficial in themselves. They are only beneficial after the basic structure is completed and functioning. Small mutations happen, which cause changes within a species. However,  natural selection cannot have been responsible for the huge differences between the major groups of living things with their vastly different body structures. If evolution is the only cause of the diversity of life, then pathways must exist where multiple mutations are each beneficial in themselves. Until recent advances in DNA research and biochemistry, it has not been possible to propose a detailed, step-by-step, beneficial pathway to a new biological system. 55

Fischer highlights a scenario where individual mutations provide no immediate benefit, making them essentially neutral in terms of natural selection. In such cases, natural selection would not act upon these mutations since they neither confer an advantage nor a disadvantage to the organism's survival or reproductive success.  Fischer's point about the need for multiple mutations to work together to create a beneficial trait reflects the idea of cumulative evolution. While each mutation by itself might not provide an advantage, their combined effects would lead to a significant adaptive change over time. However, the challenge lies in the probability of these specific mutations occurring sequentially in the same lineage. Fischer suggests that the likelihood of ten specific mutations occurring in a single lineage is extremely low. This is due to the random nature of mutations and the vast number of possible genetic changes that could occur. Evolutionary time spans are incredibly long, and given the sheer number of organisms and generations, the improbable can become probable over vast timescales.  Fischer brings up the concept that natural selection can fine-tune existing structures but might not account for the initial emergence of highly complex structures seen in major groups of organisms. The stepwise development of such structures via gradual, incremental mutations seems not to be a sufficient explanation.

Sophisticated mechanisms prevent cells to accumulate harmful mutations

Imagine changing a blueprint that instructs how to make all the complicated parts of a complex factory, and how they have to be assembled and joined to get the factory's intended end function, inserting different sizes of various sorts, instructing the replacement of one kind of material with another, changing the instructions to assemble the machines in a way that in the end, it cannot convey the intended function. It would result in catastrophic consequences. Sometimes, even switching one tiny thing with another can mean a total inability of a factory to exercise its intended functions. The chance that a random change would instead of driving havoc, improve the functioning of the factory, is negligible.  In the same sense, any random mutation in the genome is likely to result in the synthesis of a protein that does not function properly or not at all. Most mutations are detrimental, causing genetic disorders or even cancer and death. Just as a factory requires a precise blueprint to ensure that its components are assembled correctly and function as intended, living organisms rely on their genetic information stored in DNA to carry out various functions. Genes encode instructions for building proteins, which are the workhorses of biological processes. Mutations, or changes in the DNA sequence, can disrupt these instructions and potentially lead to malfunctioning proteins. Cells have  sophisticated mechanisms to detect and repair DNA damage, including mutations. DNA repair pathways constantly monitor the genome for errors and correct them. This surveillance helps prevent the accumulation of harmful mutations that could otherwise lead to diseases or other detrimental effects.  Many genes and genetic sequences have remained relatively unchanged over long periods of time because alterations to crucial functions can have deleterious consequences. This conservation of functional elements reflects the importance of maintaining proper biological processes.  Biological systems often incorporate redundancy and robustness. Multiple genes can encode similar functions, ensuring that even if one gene is mutated, the overall function can still be maintained. Additionally, the intricate networks of interactions within cells can compensate for minor disruptions, preventing catastrophic failures. 

What drives genome size evolution? 

Aditi Gupta (2016): Genome sizes vary widely, from 250 bases in viroids to 670 billion bases in some amoebas. This remarkable variation in genome size is the outcome of complex interactions between various evolutionary factors such as mutation rate and population size. While comparative genomics has uncovered how some of these evolutionary factors influence genome size, we still do not understand what drives genome size evolution. Specifically, it is not clear how the primordial mutational processes of base substitutions, insertions, and deletions influence genome size evolution in asexual organisms. 56

Comment: The precise mechanisms and drivers behind these changes remain elusive. Several reasons contribute to the uncertainty and lack of a clear understanding in this area: Genomes are incredibly complex entities, consisting of thousands to billions of base pairs of DNA. They contain not only protein-coding genes but also non-coding regions, repetitive sequences, and elements with regulatory functions. This intricate organization makes it challenging to pinpoint specific drivers of genome size changes. Genome size can be influenced by a multitude of factors, including changes in the number of genes, the presence of repetitive sequences, mobile genetic elements, and the expansion or contraction of non-coding regions. These factors can interact in complex ways, making it difficult to isolate individual drivers. Organisms exhibit a wide range of genome sizes, even within closely related species. While some patterns have been observed, the diversity of life forms and their genomes complicates efforts to identify universal drivers that apply across all taxa. The timescales over which genome size changes would supposedly occur would extend over millions of years, making it difficult to directly observe and study these changes in real time. This lack of long-term observational data limits the ability to develop detailed and comprehensive explanations.  While scientists continue to investigate this fascinating topic, it remains an ongoing puzzle in the realm of evolutionary biology.

Mathematical Methods of Population Genetics: A Window into Evolutionary Dynamics? 

Mathematical methods of population genetics provide a quantitative framework for understanding the dynamics of gene distributions within evolving populations. These methods involve both deterministic and stochastic models, each shedding light on different aspects of evolution. Deterministic models approximate infinitely large population sizes, allowing for the study of mean gene frequencies, while stochastic models account for probabilistic processes in finite-sized populations. Together, these methods offer insights into how genetic traits change over time due to selection, mutation, and random drift. In deterministic models, populations of diploid organisms  (Diploid organisms are those that possess two sets of chromosomes in their cells, with one set inherited from each parent) are described based on gene frequencies of different alleles in a given locus. Gene frequencies of different alleles in a given locus refer to the proportions or relative frequencies at which different forms of a gene (alleles) are present within a population. A gene locus is a specific location on a chromosome where a particular gene is found. In a population, individuals can have variations of that gene at the same locus, known as alleles. For example, consider a gene that determines eye color. In this case, the gene locus is the specific location on the chromosome where the eye color gene is located. Within a population, different alleles of this gene may exist, such as alleles for brown eyes, blue eyes, green eyes, etc. Gene frequencies provide insights into the genetic diversity and dynamics of a population. They are often represented as proportions or percentages and can help researchers understand how different alleles are distributed within a population and how they may change over time due to evolutionary forces. The fitness of these alleles influences their prevalence within the population. Mathematical equations track changes in gene frequencies over time, considering factors like selection pressure and mutation rates. The Hardy-Weinberg principle, which assumes random mating, is often applied in such models. These equations provide a description of how natural selection acts on different genetic variants, leading to changes in allele frequencies. Stochastic models recognize the limitations of deterministic approaches when dealing with real-world finite populations. These models involve probabilistic methods, such as Markov chains and the Fokker-Planck equation, to analyze gene frequency dynamics. They take into account random drift due to finite population sizes, which can result in fluctuations in gene frequencies even in the absence of selection. Stochastic models provide a more realistic representation of evolutionary processes in smaller populations. 

While mathematical models of population genetics offer valuable insights into evolutionary dynamics, they face limitations, especially when it comes to explaining the origin of biological complexity and new forms.  Mathematical models often make simplifying assumptions about the genetic interactions and mechanisms at play. These assumptions do not fully capture the intricacies of biological reality.  These models primarily address changes in gene frequencies within a population based on existing genetic variation. They do not provide a complete explanation for the emergence of entirely new traits or features.  Mathematical models, particularly deterministic ones,  lack the mechanistic detail required to explain the molecular and genetic processes underlying the origin of complex structures. Many mathematical models focus on gene frequencies and selection but overlook the role of developmental processes in shaping the expression of traits and the emergence of novel forms. Mathematical models of population genetics are often better suited to describing microevolutionary changes within species rather than the larger-scale transformations associated with macroevolution and the origin of new body plans. To address these limitations and provide a more comprehensive understanding of evolution, researchers increasingly integrate mathematical population genetics with other disciplines, such as developmental biology, paleontology, genomics, and systems biology. This interdisciplinary approach attempts to bridge the gap between genetic changes and the emergence of complex phenotypes, offering a more holistic perspective on the evolutionary process. While mathematical methods of population genetics offer tools for studying evolution, they are just one piece of the broader puzzle. By combining these methods with insights from other fields, scientists strive to unravel the complex mechanisms responsible for the origin of biological form and complexity over evolutionary timescales. Living beings possess distinct properties that set them apart from the inanimate world. Unlike the predictability and simplicity of physical systems, biological systems are characterized by historical processes, context dependence, and emergent properties. The intricate relationships among various subsystems and between the system and its environment contribute to the complexity of living entities. The historical attempts by mathematicians to tackle biological complexity, yet notes that traditional mathematical approaches have limitations when dealing with living systems as a whole. While mathematics has proven effective in solving isolated problems in biology, it struggles to capture the intricate interplay of relationships, historical changes, and emergent properties that define the essence of living organisms. "Mathematics of the living" would require to focus on capturing the historical dimension, context dependence, and emergent properties of biological systems. A pluralistic approach that recognizes the unique characteristics of biology and its historical dimension has to be included. This stance aligns with methodological and epistemological pluralism, emphasizing the necessity of distinct tools for understanding living systems.

Conclusion 

D.Coppedge (2021): The central concept of natural selection cannot be measured. This means it has no scientific value. 57

The positive effects of natural selection on differential reproduction cannot be tested, since too many unknown variables have to be included, and that cannot lead to meaningful, quantifiable results that permit a clear picture. 
Natural selection operates within intricate ecological and genetic systems, making it difficult to isolate and control all variables. This complexity hinders precise experimental testing of specific evolutionary scenarios. Evolutionary processes supposedly occur over vast timescales and involve countless generations. Tracking these changes experimentally across time and space is infeasible and cannot lead to quantifiable results. Natural populations exhibit genetic diversity and respond to environmental changes in unpredictable ways, making it challenging to predict and measure the outcomes of natural selection accurately.  Evolution involves a multitude of interactions between genes, organisms, and environments, as well as trade-offs between different fitness components. These complexities complicate experimental design and interpretation. The fossil record, comparative genomics, biogeography, molecular biology, experimental evolution, and more are not sufficient to corroborate evolution as the driving force for biodiversity, and organismal form.  The limitations in directly testing evolutionary scenarios do render the theory of evolution untestable or unscientific.

1. Robert Carter: Genetic entropy and simple organisms 25 October 2012
2. Paul R. Ehrlich Natural Selection 1988
3. Natural History Museum: What is natural selection?
4. David Stack: Charles Darwin: Theory of Natural Selection 01 January 2021
5. Ernst Mayr: WHAT EVOLUTION IS A Conversation With Ernst Mayr [12.31.99]
6. J.Dekker: Natural Selection and its Four Conditions 2007
7. S.El-Showk: Natural selection: On fitness 2012
8. Evolution.Berkley: Evolutionary fitness
9. Adam Eyre-Walker: The distribution of fitness effects of new mutations August 2007
10. R. G. Brajesh: [size=12]Distribution of fitness effects of mutations obtained from a simple genetic regulatory network model 08 July 2019
11. Thomas Bataillon: Effects of new mutations on fitness: insights from models and data 2014 Jul
12. Christopher J Graves: Variability in fitness effects can preclude selection of the fittest 2019 Sep 30
13. Vita Živa Alif: What is the best fitness measure in wild populations? A case study on the power of short-term fitness proxies to predict reproductive value November 19, 2021
14. Ivana Cvijović: Fate of a mutation in a fluctuating environment August 24, 2015
15. L.Bromham : Darwinism for the Genomic Age: Connecting Mutation to Diversification  07 February 2017
16. Z Patwa: The fixation probability of beneficial mutations 29 July 2008
17. R. G. Brajesh: Distribution of fitness effects of mutations obtained from a simple genetic regulatory network model  08 July 2019
18. Adam Eyre-Walker: The distribution of fitness effects of new mutations August 2007
19. J.Wells:  The Politically Incorrect Guide to Darwinism and Intelligent Design
20. J.Wells: Selection and Speciation: Why Darwinism Is False May 15, 2009
21. R. DeSalle: Molecular Systematics and Evolution: Theory and Practice 2002
22. Michael Lynch: The frailty of adaptive hypotheses for the origins of organismal complexity May 15, 2007
23. Molly K Burke et.al.,: Genome-wide analysis of a long-term evolution experiment with Drosophila 2010 Sep 30
24. Ben Bradley: Natural selection according to Darwin: cause or effect? 11 April 2022
25. Adam Levy: How evolution builds genes from scratch 16 October 2019
26. Michael Syvanen: Evolutionary Implications of Horizontal Gene Transfer 21 August 2012
27. Shelly Hamilich: Widespread horizontal gene transfer between plants and their microbiota August 26, 2022
28. David Coppedge: Gene Sharing Is More Widespread than Thought, with Implications for Darwinism September 20, 2022
29. Rama P. Bhatia: Environment and the Evolutionary Trajectory of Horizontal Gene Transfer April 01, 2022
30. J.Dulle: The (In)adequacy of Darwinian Evolution
31. Matthew Hurles: Gene Duplication: The Genomic Trade in Spare Parts July 13, 2004
32.  Alisha K Holloway: Experimental evolution of gene duplicates in a bacterial plasmid model 2007 Feb
33. Joseph Esfandiar: Is gene duplication a viable explanation for the origination of biological information and complexity? 22 December 2010
34. Johan Hallin: Regulation plays a multifaceted role in the retention of gene duplicates November 22, 2019
35. Michael Lynch: The Origins of Genome Architecture 2007
36. Eugene V Koonin: Darwinian evolution in the light of genomics 2009 Mar
37. H. Allen Orr: Testing Natural Selection  2008
38. Paul Gibson : Can Purifying Natural Selection Preserve Biological Information? – May 2013
39. Eugene V. Koonin :Toward a theory of evolution as multilevel learning February 4, 2022
40. Jerry A. Coyne, Why Evolution is True, p. 123. 2009
41. Michael Lynch: The Origins of Genome Architecture 2007
42. Michael Behe: The Edge of Evolution: The Search for the Limits of Darwinism 2008
43. Gert Korthof: Either Design or Common Descent 22 July 2007
44. Michael Behe: The Edge of Evolution: The Search for the Limits of Darwinism 2008
45. Michael Behe's Amazon Blog: Response to Critics, Part 2: Sean Carroll June 26, 2007
46. G.Bechly: Fossil Discontinuities: A Refutation of Darwinism and Confirmation of Intelligent Design 2018
47. Rick Durrett: Waiting for Two Mutations: With Applications to Regulatory Sequence Evolution and the Limits of Darwinian Evolution 2008 Nov  3
48. John Sanford: The waiting time problem in a model hominin population 17 September 2015
49. John Sanford: The Origin of Man and the “Waiting Time” Problem August 10, 2016
50. John C. Sanford: Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation 2013
51. D. Joseph: GENETIC DEGENERATION—EVIDENCE FOR INDEPENDENT ORIGINS  August 15, 2021
52. John C. Sanford: Multiple Overlapping Genetic Codes Profoundly Reduce the Probability of Beneficial Mutation 2013
53. Kathleen Donohue: Multi-tasking as an ancient skill: When one gene does many things well 01 April 2019
54.  Yuri Pritykin: Genome-Wide Detection and Analysis of Multifunctional Genes October 5, 2015
55. John Michael Fischer: Debunking Evolution 2022
56. Aditi Gupta: Evolution of Genome Size in Asexual Digital Organisms 16 May 2016
57. David F. Coppedge Evolutionary Fitness Is Not Measurable November 20, 2021



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The major ( hypothesized) transitions in evolution

The major transitions in evolution refer to significant events in the history of life on Earth where new levels of complexity, organization, and cooperation emerged. These transitions involve the evolution of novel structures, functions, and interactions that have shaped the diversity of life. While not all of these transitions are universally agreed upon, they provide a framework for understanding the progression of life's complexity according to Darwins evolutionary framework.

1. Origin of Life and Viruses

Life

Life is a complex and multifaceted phenomenon that encompasses a wide range of attributes, behaviors, and processes exhibited by living organisms. While defining life precisely can be challenging due to its diversity, there are several key characteristics that are commonly associated with living systems.

Key Characteristics of Life

Cellular Organization: All living organisms are composed of one or more cells, which are the basic structural and functional units of life. Cells carry out essential life processes and are the building blocks of all living things.
Reproduction: Living organisms have the ability to reproduce and pass on their genetic information to the next generation. Reproduction is a fundamental process that allows life to continue over time.
Metabolism: Life requires energy to maintain its structure and carry out various functions. Metabolism refers to the set of chemical reactions that occur within a living organism to convert nutrients into energy and build and repair cellular structures.
Homeostasis: Living organisms have the ability to maintain a stable internal environment despite external changes. This balance, known as homeostasis, is necessary for the proper functioning of cells and organisms.
Growth and Development: Living organisms exhibit growth, which involves an increase in size or complexity. Development refers to the process of changes and maturation that organisms undergo throughout their lifetimes.
Response to Stimuli: Living organisms can sense and respond to changes in their environment. This responsiveness allows them to adapt and survive in various conditions.
Evolution: Life is subject to change over time through the process of evolution. This involves genetic variation, natural selection, and adaptation to changing environments.

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Diversity of Life

Life on Earth is incredibly diverse, ranging from microorganisms to plants, animals, fungi, and more. Organisms inhabit a wide range of environments, from deep-sea hydrothermal vents to extreme deserts to lush rainforests. This diversity reflects the adaptation of life forms to various ecological niches and environmental conditions. The study of life has profound implications for our understanding of the natural world and our place within it. Research in biology, genetics, ecology, and other fields enhances our knowledge of the complexity and interconnectedness of life. However, the question of how life originated remains a subject of ongoing scientific investigation. Hypotheses about the origins of life include hypotheses about prebiotic chemistry, the role of RNA in early life, and the possibility of life originating in extreme environments.

Viruses

Viruses are small infectious agents that exist in a gray area between living organisms and non-living particles. They consist of genetic material (either DNA or RNA) enclosed within a protein coat called a capsid. Unlike cells, viruses lack the cellular machinery necessary for metabolism and reproduction. Viruses vary in size and shape, with structures that range from simple to complex. The basic viral structure consists of genetic material surrounded by a protective protein coat. Some viruses also have additional layers, such as lipid envelopes derived from host cell membranes. Viruses are incapable of independent reproduction. Instead, they must infect a host cell to reproduce. Once inside a host cell, viruses use the cellular machinery to replicate their genetic material and produce new virus particles. This often leads to the destruction of the host cell during the process of viral replication. Viruses infect all forms of life, including animals, plants, fungi, bacteria (bacteriophages), and archaea. Viral infections can cause a wide range of diseases, from common colds and influenza to more severe illnesses such as HIV/AIDS, Ebola, and COVID-19. However, not all viruses are pathogenic; some viruses have evolved mutualistic or commensal relationships with their hosts. Viruses evolve rapidly due to their high mutation rates and short generation times. This rapid evolution allows viruses to adapt to changing environments and host defenses. Viruses can also exchange genetic material with each other, leading to the creation of new strains and potentially contributing to the emergence of novel diseases. Viruses are classified based on several factors, including their genetic material, structure, and mode of replication. Viruses are typically divided into several groups, including DNA viruses, RNA viruses, retroviruses, and more.

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2. Prokaryote to Eukaryote Transition 

This transition involves the evolution of eukaryotic cells, which have a nucleus and membrane-bound organelles, from prokaryotic ancestors. This event likely included the endosymbiotic acquisition of mitochondria and possibly other organelles.

Distinctions and characteristics of prokaryotic and eukaryotic cells

Prokaryotic Cells

Prokaryotic cells are simpler in structure compared to eukaryotic cells. They lack distinct nuclei and membrane-bound organelles. Instead, their genetic material is found in the form of a single, circular DNA molecule located in the nucleoid region. Prokaryotic cells are typified by their two main domains: Bacteria and Archaea. Prokaryotic cells carry out essential cellular functions, such as metabolism, reproduction, and response to stimuli, but they do so within a more basic framework. These cells possess ribosomes for protein synthesis and a plasma membrane that encloses their cytoplasm. Additionally, they often have a rigid cell wall composed of peptidoglycan (in bacteria) or other unique compounds (in archaea), providing structural support and protection.

Archaea 

Archaea are prokaryotic microorganisms that exhibit molecular characteristics that set them apart from both bacteria and eukaryotes. Despite their prokaryotic nature, they possess traits that differentiate them significantly from bacteria. For example, their cell membranes are composed of unique lipids, such as isoprenoid ethers, rather than the fatty acids found in bacterial and eukaryotic cell membranes. The classification of archaea as a distinct group of microorganisms is attributed to the work of microbiologists Carl R. Woese and Ralph S. Wolfe. They conducted genetic analyses of the ribosomal RNA (rRNA) and discovered that prokaryotes could be categorized into two primary domains: Bacteria (Eubacteria) and Archaea (initially known as Archaebacteria). Archaea are known for their ability to thrive in extreme environments that would be inhospitable to most other life forms. These extremophiles have been found in environments such as hot springs, deep-sea hydrothermal vents, acidic and alkaline waters, and highly saline environments. Some notable examples include:

Thermophiles: These archaea thrive in high-temperature environments, such as hot springs and hydrothermal vents. They are adapted to temperatures above the boiling point of water.
Halophiles: These archaea flourish in highly saline environments, such as salt flats and salt lakes. They have evolved mechanisms to cope with osmotic stress caused by high salt concentrations.
Methanogens: These anaerobic archaea produce methane as a metabolic byproduct. They inhabit environments devoid of oxygen, such as the digestive tracts of animals and anaerobic sediments.

The unique characteristics of archaea, coupled with their ability to survive in extreme conditions, make them valuable subjects of study for understanding the origins and evolution of life on Earth. Some archaea resemble the earliest life forms that likely existed in the harsh environments of early Earth. 

Bacteria

Bacteria are single-celled prokaryotic microorganisms that are widespread and incredibly diverse. They are found in virtually every environment on Earth and play crucial roles in various ecological and biological processes. Bacteria are characterized by their simple cellular structure. They lack a nucleus and membrane-bound organelles, distinguishing them from eukaryotic cells. Instead, their genetic material is located in a single, circular DNA molecule within the nucleoid region. Bacterial cells are surrounded by a cell wall, which provides structural support and helps protect the cell from its environment. The plasma membrane encloses the cytoplasm and controls the passage of nutrients and waste. Bacteria exhibit remarkable diversity, with a vast array of shapes, sizes, and metabolic capabilities. They are classified based on various characteristics, including their shape (such as cocci, bacilli, or spirilla), arrangement (such as clusters or chains), and staining properties (Gram-positive or Gram-negative). Bacteria are divided into several phyla, with the most well-known being Proteobacteria, Firmicutes, Actinobacteria, and Cyanobacteria. Bacteria display a wide range of metabolic strategies. They can be autotrophic, obtaining energy from inorganic sources, or heterotrophic, relying on organic compounds for energy. Some bacteria are photosynthetic and use light energy to synthesize organic molecules, similar to plants. Others are chemosynthetic and derive energy from chemical reactions. Bacteria are essential components of ecosystems due to their critical roles in nutrient cycling and decomposition. Decomposer bacteria break down organic matter, releasing nutrients that can be reused by other organisms. Nitrogen-fixing bacteria convert atmospheric nitrogen into forms that plants can use for growth, contributing to the fertility of ecosystems. While many bacteria are harmless or even beneficial, some are pathogenic and can cause diseases in humans, animals, and plants. Pathogenic bacteria can produce toxins, invade host tissues, and disrupt normal physiological processes. Bacteria have significant biotechnological applications. They are used in industrial processes, such as fermentation for food production and the synthesis of antibiotics and enzymes. Genetic engineering techniques allow scientists to modify bacteria for various purposes, including the production of biofuels and the creation of genetically modified organisms (GMOs) for research or agricultural purposes.

Eukaryotic Cells

Eukaryotes are organisms that have cells with distinct nuclei containing genetic material and various membrane-bound organelles. These organisms include a vast array of life forms, ranging from microscopic algae to large animals and plants. Eukaryotic cells are defined by their compartmentalized structure. They possess a true nucleus, which houses the cell's genetic material in the form of linear chromosomes. The nucleus is separated from the cytoplasm by the nuclear envelope. Eukaryotic cells also contain various organelles, each with specific functions. These organelles include the mitochondria (energy production), endoplasmic reticulum (protein synthesis and lipid metabolism), Golgi apparatus (protein modification and packaging), lysosomes (waste disposal), and more. Eukaryotes are incredibly diverse and are classified into several major groups: animals, plants, fungi, and protists. This diversity is evident in their size, shape, reproduction methods, and modes of nutrition.

Animalia: Animals are multicellular eukaryotic organisms that exhibit a wide range of characteristics and behaviors. They have complex organ systems and sensory structures that allow them to interact with their environment.
Plantae: Plants are multicellular eukaryotic organisms that carry out photosynthesis, converting light energy into chemical energy. They provide oxygen and are essential for ecosystems by serving as primary producers.
Fungi: Fungi are eukaryotic organisms that play vital roles in ecosystems as decomposers. They absorb nutrients from their surroundings and can form symbiotic relationships with plants.
Protista: Protists are a diverse group of eukaryotic microorganisms that do not fit neatly into the categories of plants, animals, or fungi. They can be unicellular or multicellular and exhibit a range of ecological roles.

Eukaryotes are integral to ecosystems. They are involved in various ecological processes such as nutrient cycling, pollination, and food chains. Many eukaryotes also form mutualistic relationships with other organisms, contributing to the stability and health of ecosystems. In human health, eukaryotes have both positive and negative impacts. Some eukaryotes are beneficial, such as the plants and animals that form the basis of our food supply. However, eukaryotic pathogens can also cause diseases, ranging from fungal infections to parasitic diseases caused by protists.

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3. Single-Celled to Multicellular Transition

The transition from single-celled to multicellular organisms would mark a pivotal moment in the history of life on Earth. It would have brought about a profound shift in the complexity and organization of life forms. This evolutionary leap would have allowed cells to collaborate and specialize, leading to the emergence of diverse complex multicellular organisms. In single-celled organisms, every cell performs all the necessary functions for survival—such as feeding, reproduction, and responding to the environment. With the advent of multicellularity, cells would now work collectively and specialize in different tasks. This division of labor would have allowed cells to become more efficient and to focus on specific functions within the organism.  Multicellularity enables cells to differentiate into various specialized types. These specialized cell types could perform specific functions crucial to the survival and functioning of the entire organism. For example, in animals, there are nerve cells for communication, muscle cells for movement, and epithelial cells for protection and lining of organs.  As specialized cells aggregated, they began forming tissues—groups of cells that work together to perform specific functions. The arrangement of tissues led to the development of organs, which are complex structures composed of multiple tissue types that collaborate to carry out essential functions. This higher level of organization allowed for more efficient resource utilization and a greater range of possible tasks.  Multicellularity provided organisms with an increased capacity for adaptation. The presence of different cell types allowed for greater versatility in responding to various environmental conditions. Some cells could specialize in detecting changes in the environment, while others could carry out actions to respond to those changes, contributing to the overall survival of the organism. Multicellularity also would have facilitated the emergence of reproductive specialization. Within a multicellular organism, some cells could be dedicated solely to reproduction, while others carried out other essential functions. This allowed for more efficient reproduction and the generation of new individuals with a higher degree of complexity. The transition to multicellularity would have paved the way for the evolution of complex body plans and diverse forms of life. Over time, organisms would evolve greater structural and functional complexity due to the interactions between different cell types and tissues. This complexity allowed for the emergence of various ecological niches and the subsequent diversification of life forms. Multicellularity enabled the growth of organisms beyond the limitations imposed by single cells. Larger and more intricate body structures became possible, allowing for greater mobility, access to new resources, and the colonization of diverse habitats.

4. Colonization of Land 

Beyond Evolution: The Origin of Species by Design 0ade2f10

William K. Gregory | Our face from fish to man; a portrait gallery of our ancient ancestors and kinsfolk together with a concise history of our best features (1929)

The transition from aquatic environments to terrestrial habitats would have been a monumental step in the evolution of life on Earth. This transition would have brought about a range of challenges that organisms had to overcome through various adaptations to thrive in a new and often more demanding environment. One of the most significant challenges of transitioning to terrestrial habitats was the risk of desiccation, or drying out. Aquatic organisms are constantly surrounded by water, which provides a stable environment for maintaining hydration. Terrestrial environments, however, can be prone to fluctuations in moisture levels. To cope with this challenge, many early terrestrial organisms would have had to develop adaptations such as waxy coatings on their surfaces (cuticles in plants, for instance) to prevent water loss, as well as specialized structures like stomata in plants that regulate gas exchange while minimizing water loss. In water, buoyancy supports the bodies of organisms, allowing them to move with minimal effort. On land, the presence of gravity would have necessitated adaptations to support and move the body against the force of gravity. In plants, the evolution of lignified cell walls and the development of vascular tissues (xylem and phloem) would have allowed for structural support and efficient water transport. In animals, endoskeletons and exoskeletons would have provided support and protection while enabling mobility on land. In water, oxygen is dissolved and readily available for organisms to extract. Terrestrial organisms had to evolve respiratory systems to efficiently exchange gases, particularly oxygen, and carbon dioxide, in the less dense atmosphere. Lungs in vertebrates and tracheal systems in insects are examples of adaptations that facilitate gas exchange while preventing excessive water loss. The transition to land would have brought new challenges to reproductive strategies. In aquatic environments, many organisms release their gametes directly into the water. On land, organisms needed adaptations to ensure the survival of their offspring. For instance, plants would have had to develop various mechanisms for seed dispersal, and animals evolving strategies like internal fertilization, amniotic eggs (in reptiles and birds), and parental care to protect developing embryos from desiccation and predation. Terrestrial habitats presented different nutrient and resource availability compared to aquatic environments. Plants would have to develop root systems to anchor themselves in soil and acquire water and minerals. Fungi formed mutualistic partnerships with plants (mycorrhizal associations) to enhance nutrient uptake. Herbivores had to adapt to feeding on terrestrial vegetation, while carnivores found new prey sources and hunting techniques. Terrestrial habitats often experience wider temperature variations compared to aquatic environments. Organisms had to develop strategies to regulate body temperature and cope with extreme conditions. Ectothermic animals (cold-blooded) relied on behavior and external factors to control body temperature, while endothermic animals (warm-blooded) evolved mechanisms like insulation, panting, and sweating to maintain a stable internal environment. Land-dwelling organisms needed adaptations to perceive and respond to new stimuli in their environment. Enhanced visual, auditory, olfactory, and tactile senses allowed them to detect potential predators, locate resources, and communicate with conspecifics more effectively. The transition from aquatic to terrestrial environments required organisms to undergo diverse adaptations that would have allowed them to deal with challenges related to desiccation, gravity, resource availability, gas exchange, reproduction, temperature regulation, and sensory perception. These adaptations would have paved the way for the colonization of new habitats and the subsequent diversification of life forms on land.

Major transitions in the evolution of early land plants

Plant tissue classification
Dermal tissue, Vascular tissue, Ground tissue, Meristematic tissue

Deployment of gametophytic structures and mechanisms, as well as a number of major innovations.

1. The last common ancestor of land plants probably was a leafless axial gametophyte bearing morphologically simple unisporangiate sporophytes.
2. Stomata in mosses, hornworts and polysporangiophytes probably are homologous; the monophyletic lineage encompassing these three groups is therefore referred to as the ‘stomatophytes’.
3. Stomata are a sporophyte innovation, possibly with the ancestral functions of producing a controlled transpiration-driven flow of water and solutes from the parental gametophyte and facilitating the separation of maturing spores before release.
4. Stomata/air spaces and sporophyte vascularization, the latter probably by deployment of vascular tissue from the gametophyte, were pivotal to the divergence of the stomatophyte lineage.
5. Determinate sporophyte development based on embryonic meristematic activity is the ancestral condition in land plants, still present in modern liverworts and mosses.
6. An indeterminate sporophyte body (the sporophyte shoot) developing from an apical meristem (SAM) is the fundamental innovation of polysporangiophytes.
7. Poikilohydry is the ancestral condition in land plants; homeohydry evolved in the sporophyte of polysporangiophytes.
8. Symbiotic associations with fungi
9. Hydroids are an imperforate type of WCC evolved in advanced (peristomate) mosses; hydroids are not homologous to xylem vascular cells.
10. Xylem vascular cells evolved in the sporophyte of polysporangiophytes, either from pre-existing perforate vascular cells or de novo, in parallel with the establishment of homoiohydry.
11. Food-conducting cells first evolved in the gametophyte generation at the dawn of land plant evolution.

It is estimated ( claimed ) that the transition to multicellularity would have required to take place at least 25 times – in other words, 25 different cellular lineages would have had to evolve independently making the jump to communally organized life

Explaining organismal form depends on explaining how organs, tissues, and cells form and gain shape. 

5. Origin of Complex Animals 

The emergence of complex animals with distinct tissues, organs, and bilateral symmetry would have marked a significant shift in animal evolution. The Cambrian explosion, supposedly around 540 million years ago, would have been a notable period during which many major animal groups appeared. Certainly, the emergence of complex animals with distinct tissues, organs, and bilateral symmetry represents a key milestone in the evolutionary history of life on Earth. This transition would have marked a shift from simple, primarily sessile organisms to the development of more complex and diverse forms capable of greater mobility, predation, and interaction with their environment. The Cambrian explosion stands out as a remarkable period in which there would have been a rapid diversification of major animal groups. This explosion of diversity and complexity in life forms is evident from the rich fossil record found in Cambrian-age rocks. Many of the organisms in the Cambrian strata exhibit bilateral symmetry—a body plan where an organism can be divided into two similar halves along a central axis. This symmetry allowed for more efficient movement and the development of specialized sensory structures, such as eyes and appendages, which enabled organisms to navigate their environment with greater precision. The Cambrian explosion brought about the development of animals with distinct tissue layers, leading to the formation of organs and more complex body structures. This would have allowed for the specialization of different body parts and the evolution of more efficient feeding, digestion, locomotion, and other vital functions. The emergence of complex animals with mobility and sensory structures would have coincided with an increase in predation and defensive strategies. Organisms developed adaptations for hunting and evading predators, including more sophisticated mouths, jaws, and protective coverings. This interplay between predators and prey supposedly drove the arms race of evolutionary innovation during this period. The Cambrian explosion saw the rise of various body plans, representing the emergence of major animal phyla. These include arthropods (e.g., trilobites), mollusks (e.g., snails and clams), echinoderms (e.g., starfish), and chordates (ancestors of vertebrates). The diversity of body plans paved the way for a wide range of ecological roles and interactions within ecosystems. The Cambrian explosion coincided with an increase in the prevalence of mineralization in the skeletons of some organisms, leading to improved fossilization potential. This has contributed to the exceptional preservation of Cambrian fossils, providing valuable insights into the architecture of these animals. The exact triggers and drivers of the Cambrian explosion are still a subject of scientific debate. Factors such as changes in environmental conditions, increased oxygen levels, the evolution of predator-prey interactions, and genetic innovations are claimed to have played roles in this burst of evolutionary creativity.

Beyond Evolution: The Origin of Species by Design 3511

Tamisiocaris is a fascinating extinct arthropod that lived during the Cambrian period, approximately 500 million years ago. It is known from exceptionally well-preserved fossils found in the Burgess Shale, a famous fossil site located in British Columbia, Canada. Tamisiocaris is a remarkable example of the diverse and complex organisms that emerged during the Cambrian explosion.

Six major transitions in animal evolution  

Animal tissue classification
There are four basic types of animal tissues: muscle tissue, nervous tissue, connective tissue, and epithelial tissue

1.  origin of multicellularity;
2.  symmetry, two germ layers, neurons;
3.  bilateral symmetry, three germ layers, axial nerve cord, through gut;
4.  dorsoventral axis inversion;
5.  neural crest, new cell types;
6.  migratory mesoderm paired appendages, jaws. 

- Multicellular organisms with some cellular differentiation (sponges, algae, fungi).
- Differentiated systems of organs and tissues (coelenterates, flatworms, higher plants).
- Organized central nervous system, well-developed sense organs, limbs (arthropods, vertebrates).
- Homeothermic metabolism (warmblood) (mammals, birds).

6. Vertebrate Terrestrialization 

The supposed evolution of vertebrates from aquatic to terrestrial environments would have been a momentous transition that would have required a series of remarkable adaptations. This shift from water to land necessitated changes in anatomical structures, physiological processes, and behavioral strategies to thrive in the challenges of terrestrial life. Tetrapods, a group that includes amphibians, reptiles, birds, and mammals, would have been the result of this evolutionary journey. One of the most defining adaptations for life on land would have been the evolution of limbs. Limbs allowed vertebrates to move effectively on solid ground and provided the means to explore and exploit new habitats. The evolution of jointed limbs and digits would have allowed for diverse modes of locomotion—walking, running, climbing, and even flying in the case of birds. Vertebrates that transitioned to terrestrial environments would have needed adaptations to extract oxygen from the air. While aquatic vertebrates primarily rely on gills for gas exchange, terrestrial vertebrates would have developed lungs. These specialized respiratory structures would have allowed for the efficient exchange of gases in the relatively drier terrestrial atmosphere. The expansion of rib cages and the development of a diaphragm facilitated lung ventilation. Unlike aquatic environments, terrestrial habitats can be prone to desiccation. To avoid dehydration, terrestrial vertebrates would have evolved adaptations to conserve water. Reptiles, for example, would have developed impermeable skin and efficient excretory systems to minimize water loss. Mammals would have evolved more efficient kidneys and urinary systems for water conservation. Terrestrial environments presented new sensory challenges, such as increased visual and olfactory cues. Vertebrates would have evolved adaptations to perceive and respond to these stimuli. For example, the evolution of better-developed eyesight and olfaction would have allowed for the detection of potential predators, prey, and mates in terrestrial habitats. Terrestrial life required adaptations in reproductive strategies. Vertebrates would have developed mechanisms for internal fertilization to prevent the desiccation of gametes and embryos. Amniotic eggs, which are characteristic of reptiles and birds, would have provided a protective environment for the developing embryo, enabling reproduction away from water. The temperature variation in terrestrial environments necessitated the evolution of mechanisms for thermoregulation. Endothermic vertebrates (mammals and birds) would have evolved the ability to maintain a stable internal body temperature, enabling them to be active in a wide range of temperatures. Ectothermic vertebrates (most reptiles) rely on external heat sources to regulate their body temperature. The shift to land would have required adaptations in the vertebrate skeleton. Limbs became load-bearing structures, and the transition from fins to limbs brought about changes in the arrangement of bones and joints. The development of stronger limbs and articulated joints would have allowed vertebrates to support their body weight and move effectively on land. The emergence of tetrapods would have marked a significant step in the evolution of life on Earth, contributing to the colonization of diverse terrestrial ecosystems. From amphibians that retained connections to aquatic habitats to the subsequent diversification of reptiles, birds, and mammals, the transition to land required a multitude of adaptations that shaped the morphology, physiology, and behavior of terrestrial vertebrates. 

Beyond Evolution: The Origin of Species by Design Tiktaalik

7. Origin of Flight

Flight has enabled organisms to access new habitats, exploit novel resources, and develop a wide range of ecological roles. This significant transition has had profound impacts on the diversity and complexity of life on Earth.
Insects were supposedly among the first animals to evolve flight, and this adaptation would have led to their remarkable diversity. Insects were able to exploit diverse niches, from pollination to predation, by taking advantage of their aerial mobility. The hypothesized evolution of flight allowed insects to rapidly colonize various ecosystems and diversify into countless species that play essential roles in ecosystems as pollinators, decomposers, herbivores, and predators. Insects have wings, which are specialized extensions of the exoskeleton. Over time, different groups of insects would have evolved various wing shapes and sizes to suit their ecological needs. Some insects have adaptations like transparent wings for efficient flight and camouflage. Many flying insects undergo metamorphosis, transitioning through different life stages such as egg, larva, pupa, and adult. This allows them to exploit different ecological niches at various stages of their life cycle and contributes to their ecological success.

Evolution of Flight in Vertebrates

The claimed evolution of flight in vertebrates involved a transition from an aquatic or terrestrial lifestyle to an aerial one. The development of wings and other adaptations would have enabled vertebrates to overcome the challenges of air resistance, gravity, and thermoregulation. Birds are the most prominent group of vertebrates with the ability to fly. Their lightweight bones, strong muscles, and unique respiratory system (air sacs) enable them to achieve powered flight. Flight has allowed birds to occupy a wide range of habitats, from forests to open oceans, and engage in activities like migration and aerial foraging.  Bats are the only mammals capable of sustained flight. Their wing structure is formed by a membrane of skin stretched over elongated finger bones. Bats have diversified into numerous species, each adapted to a specific ecological niche. They play crucial roles in pollination, insect control, and seed dispersal. Pterosaurs were reptiles that are claimed to have lived during the Mesozoic era and are the only vertebrates apart from birds to achieve powered flight. Pterosaurs had a variety of wing shapes, including elongated wings for gliding and broad wings for powered flight.

Ecological Impacts

Flight allowed insects to access food resources (nectar, pollen, prey) that were otherwise inaccessible to non-flying organisms. In vertebrates, flight facilitated the exploration of new territories and access to food resources such as flying insects, fish, and plant material. Both flying insects and vertebrates engage in migration, allowing them to exploit seasonal resources across vast distances. This behavior influences ecosystem dynamics and contributes to the distribution of species. Flight provided an advantage in predator-prey interactions. Predatory flying insects could capture prey from different angles, while potential prey could escape danger by taking to the air. In vertebrates, aerial predators like birds of prey and bats evolved to exploit this advantage.  Flying insects such as bees and butterflies play a crucial role in pollination, enabling the reproduction of many plant species. Flying vertebrates, such as bats and birds, also contribute to pollination and seed dispersal.

8. Origin of Flowers and Angiosperms

The emergence and subsequent dominance of flowering plants, also known as angiosperms, is said to have marked a significant turning point in the evolution of terrestrial ecosystems. Their rapid diversification and widespread success would have had far-reaching effects on the interactions between plants, animals, and the environment. Angiosperms would have introduced novel strategies for pollination that facilitated the coevolution between plants and pollinators. Flowers, with their attractive colors, shapes, and scents, would have evolved to attract specific pollinators, such as insects, birds, and bats. This led to intricate relationships between plants and pollinators, where both parties benefited. As plants evolved to rely on animals for pollination, they developed features that catered to the preferences and capabilities of their pollinators. In return, animals received a reliable food source in the form of nectar or pollen. This coevolutionary process would have given rise to the remarkable diversity of flower forms and specialized pollination mechanisms seen today. Angiosperms also diversified seed dispersal mechanisms, which aided their colonization of new habitats. Fruits, a unique characteristic of flowering plants, serve as containers for seeds and are often designed to be attractive to animals. Animals consume these fruits, and the seeds within are either ingested and later excreted intact, or they adhere to the animal's fur or feathers, allowing them to be carried to new locations. This strategy enabled angiosperms to disperse their offspring over larger distances, increasing their chances of survival and colonization in diverse environments.  The success of angiosperms led to an explosion of plant diversity, with an estimated 300,000 to 400,000 species currently recognized. This vast array of species led to the creation of varied habitats, as different plants adapted to different niches within ecosystems. This diversification, in turn, provided a greater range of resources and microhabitats for animals, leading to increased biodiversity overall. The rapid growth and turnover of angiosperms have had profound effects on nutrient cycling and ecosystem dynamics. Their efficient nutrient uptake and decomposition contribute to the cycling of carbon, nitrogen, and other essential elements, shaping soil fertility and productivity. This impact can extend to the larger ecosystem, influencing nutrient availability for other plants, animals, and decomposers. The rise of angiosperms would have significantly influenced human history. Many of the plants we rely on for food, medicine, and other resources are angiosperms. The domestication of various flowering plant species, such as wheat, rice, and fruits, has been crucial for the development of agriculture and the sustenance of human civilizations.

9. Evolution of Social Behavior

The supposed evolution of sociality would have brought about remarkable levels of organization and cooperation within various species. From cooperative breeding to eusociality, different forms of social behavior would have shaped the lives of numerous animals and significantly impacted their survival, reproduction, and ecological interactions.  Cooperative breeding occurs when individuals in a social group assist in raising the offspring of others, usually the dominant breeding pair. This behavior is observed in various birds, mammals, and even some insects. In cooperative breeding systems, non-breeding individuals, often siblings or offspring from previous breeding seasons, help with tasks like foraging, nest-building, and guarding. This behavior enhances the survival of the breeding pair's offspring and can be advantageous in environments where resources are limited or unpredictable. By sharing the workload, individuals increase the chances of overall group success. Eusociality is the highest level of social organization, characterized by overlapping generations, cooperative care of offspring, and reproductive division of labor. This phenomenon is most commonly seen in insects like ants, bees, wasps, and termites. Eusocial colonies are organized into castes, where individuals perform specific roles according to their physiology and behavior. The division of labor can be extreme, with individuals specialized for tasks like reproduction, foraging, defense, and caring for the young. Eusocial insects often live in complex societies with elaborate communication systems that allow them to coordinate their activities. Beyond eusocial insects, many other animal species exhibit complex social behaviors that involve intricate interactions between individuals. These behaviors can include cooperation in hunting, territory defense, raising young, and information sharing. Some examples include dolphins, elephants, primates (such as chimpanzees and bonobos), and certain bird species. In these societies, individuals form alliances, engage in reciprocal relationships, and communicate through various vocalizations, gestures, or other forms of signals.  The evolution of sociality offers several advantages for individuals and their groups. Cooperative behaviors can enhance the survival and reproduction of both helpers and breeders. For example, in cooperative breeding, non-breeding individuals gain experience that improves their future reproductive success. In eusocial colonies, division of labor and cooperation allow for efficient resource utilization and protection from predators.  While sociality has many benefits, it also poses challenges. Conflict can arise over resources, breeding opportunities, and dominance hierarchies. Strategies to minimize conflicts, such as kin selection (favoring relatives) and reciprocal altruism (helping others with the expectation of future help), have evolved to maintain cooperation within groups. The study of animal social behavior has provided insights into the evolution of human societies. Concepts like kin selection, cooperation, and conflict resolution seen in animal societies have parallels in human social dynamics. However, human societies are also uniquely complex due to cultural, cognitive, and technological factors. The claimed evolution of sociality, including cooperative breeding, eusociality, and complex animal societies, has introduced new levels of organization and cooperation within species. These social behaviors have shaped the lives of diverse animals, influencing their reproductive success, survival, and interactions with their environments. The study of sociality provides valuable insights into the mechanisms that drive cooperation, conflict resolution, and the establishment of complex societies in both animals and humans.

10. Cultural Evolution in Humans

The development of human culture has been a transformative process that sets our species apart and has enabled us to adapt to a wide range of environments. Human culture encompasses a complex interplay of language, tool use, agriculture, technology, and more. This cultural evolution has significantly impacted our ability to thrive as a species.  Language is one of the most defining features of human culture. The evolution of complex language systems allowed us to communicate abstract concepts, share knowledge, and coordinate group activities. Language enabled the transmission of information across generations, paving the way for the accumulation of knowledge and cultural practices. It also facilitated cooperation, as individuals could convey intentions, emotions, and plans to others, enhancing group dynamics and collaborative endeavors. The ability to create and use tools was a pivotal step in human cultural evolution. Early humans began using simple tools for tasks like hunting, foraging, and crafting. Over time, tool use became more sophisticated, leading to the development of complex technologies. Tools extended our physical capabilities and allowed us to exploit a wider range of environments. The innovation of tools and technologies has been a driving force in adapting to different landscapes, from crafting shelter and clothing to harnessing fire for cooking and protection.  The shift from hunting and gathering to agriculture marked a revolutionary transformation in human history. The domestication of plants and animals allowed for the establishment of settled communities and the cultivation of food resources. Agriculture provided a stable and dependable source of sustenance, leading to population growth, division of labor, and the emergence of complex societies. It also laid the foundation for the development of trade, specialization, and the accumulation of wealth.  Human culture has allowed us to adapt to diverse environments around the world. Different cultures developed unique solutions to the challenges posed by their surroundings. For instance, indigenous cultures in various regions developed specialized knowledge of local flora and fauna, enabling sustainable resource management and survival in often harsh conditions. These adaptations showcase the remarkable flexibility of human culture in responding to environmental constraints. The ongoing development of technology has led to rapid changes in human society. From the Industrial Revolution to the Information Age, technological advancements have transformed the way we live, work, and interact. Technologies such as transportation, communication, medicine, and information systems have shaped modern societies and facilitated globalization, allowing cultures to interact and exchange ideas on a global scale. Human culture is incredibly diverse, encompassing a vast array of languages, belief systems, traditions, and practices. This diversity reflects our ability to adapt to a wide range of environments and circumstances. Cultural identity plays a crucial role in shaping individual and group identities, influencing social interactions, values, and worldviews. The development of human culture, including language, tool use, agriculture, and technology, represents a profound transition that has empowered our species to adapt to various environments. This cultural evolution has not only shaped our survival and success but has also defined the essence of what it means to be human. It continues to drive innovation, collaboration, and the exploration of new frontiers in our ever-changing world.

Beyond Evolution: The Origin of Species by Design _colli10

Ádám Kun: The major evolutionary transitions and codes of life December 2021



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The origin of viruses is another mystery besides  the origin of life 

Nejc Kejzar (2022): Viruses play a central role in all ecological niches; the origin of viruses, however, remains an open question. Phylogenetic analysis of distantly related viruses is hampered by a lack of detectable sequence similarity 1

Viruses are essential agents for life
C. A. Suttle (2005): Viruses exist wherever life is found. They are a driver of global geochemical cycles and a reservoir of the greatest genetic diversity on Earth. In the oceans, viruses probably infect all living things, from bacteria to whales. They affect the form of available nutrients and the termination of algal blooms. Viruses can move between marine and terrestrial reservoirs, raising the spectre of emerging pathogens. Because viruses are significant agents of microbial mortality, they have an effect on nutrient cycling. Moreover, the narrow host range of most viruses suggests that infection is important in controlling the composition of planktonic communities. Viruses are catalysts that accelerate the transformation of nutrients from particulate (living organisms) to dissolved states, where it can be incorporated by microbial communities. 2

H.Ross (2020) : Viruses are rarely in the spotlight when it comes to elucidating biological origins. Unjustifiably so, since they are essential for life. Hugh Ross (2020): Without viruses, bacteria would multiply and, within a relatively short time period, occupy every niche and cranny on Earth’s surface. The planet would become a giant bacterial slime ball. Those sextillions of bacteria would consume all the resources essential for life and die. Viruses keep Earth’s bacterial population in check. They break up and kill bacteria at the just-right rates and in the just-right locations so as to maintain a population and diversity of bacteria that is optimal for both the bacteria and for all the other life-forms. It is important to note that all multicellular life depends on bacteria being present at the optimal population level and optimal diversity. We wouldn’t be here without viruses! Viruses also play a crucial role in Earth’s carbon cycle. They and the bacterial fragments they create are carbonaceous substances. Through their role in precipitation, they collect as vast carbonaceous sheets on the surfaces of the world’s oceans. These sheets or mats of viruses and bacterial fragments sink slowly and eventually land on the ocean floors. As they are sinking they provide important nutrients for deep-sea and benthic (bottom-dwelling) life. Plate tectonics drive much of the viral and bacterial fragments into Earth’s crust and mantle where some of that carbonaceous material is returned to the atmosphere through volcanic eruptions.3 

Virus-archaea interactions play a central role in global biogeochemical cycles. Ramesh K Goel (2021): Viruses play vital biogeochemical and ecological roles by (a) expressing auxiliary metabolic genes during infection, (b) enhancing the lateral transfer of host genes, and (c) inducing host mortality. Even in harsh and extreme environments, viruses are major players in carbon and nutrient recycling from organic matter. 4 

Eugene V. Koonin (2020): Lytic infections (involving the replication of a viral genome) of cellular organisms, primarily bacteria, by viruses play a central role in the biological matter turnover in the biosphere. Considering the enormous abundance and diversity of viruses and other mobile genetic elements (MGEs), and the ubiquitous interactions between MGEs and cellular hosts, a thorough investigation of the evolutionary relationships among viruses and mobile genetic elements (MGEs) is essential to advance our understanding of the evolution of life 5 

Eugene V Koonin (2013): Virus killing of marine bacteria and protists largely determines the composition of the biota, provides a major source of organic matter for consumption by heterotrophic organisms, and also defines the formation of marine sediments through the deposition of skeletons of killed plankton organisms such as foraminifera and diatoms. 6 

Rachel Nuwer (2020):  If all viruses suddenly disappeared, the world would be a wonderful place for about a day and a half, and then we’d all die – that’s the bottom line. The vast majority of viruses are not pathogenic to humans, and many play integral roles in propping up ecosystems. Others maintain the health of individual organisms – everything from fungi and plants to insects and humans. “We live in a balance, in a perfect equilibrium.  In 2018, for example, two research teams independently made a fascinating discovery. A gene of viral origin encodes for a protein that plays a key role in long-term memory formation by moving information between cells in the nervous system. 7

P. Forterre (2008): Historically, three hypotheses have been proposed to explain the origin of viruses: (1) they originated in a precellular world (‘the virus-first hypothesis’); (2) they originated by reductive evolution from parasitic cells (‘the reduction hypothesis’); and (3) they originated from fragments of cellular genetic material that escaped from cell control (‘the escape hypothesis’). All these hypotheses had specific drawbacks. The virus-first hypothesis was usually rejected firsthand since all known viruses require a cellular host. The reduction hypothesis was difficult to reconcile with the observation that the most reduced cellular parasites in the three domains of life, such as Mycoplasma in Bacteria, Microsporidia in Eukarya, or Nanoarchaea in Archaea, do not look like intermediate forms between viruses and cells. Finally, the escape hypothesis failed to explain how such elaborate structures as complex capsids and nucleic acid injection mechanisms evolved from cellular structures since we do not know any cellular homologs of these crucial viral components. 

Much like the concept of prokaryotes became the paradigm on how to think about bacterial evolution, the escape hypothesis became the paradigm favored by most virologists to solve the problem of virus origin. This scenario was chosen mainly because it was apparently supported by the observation that modern viruses can pick up genes from their hosts. In its classical version, the escape theory suggested that bacteriophages originated from bacterial genomes and eukaryotic viruses from eukaryotic genomes. This led to a damaging division of the virologist community into those studying bacteriophages and those studying eukaryotic viruses, ‘phages’ and viruses being somehow considered to be completely different entities. The artificial division of the viral world between ‘viruses’ and bacteriophages also led to much confusion on the nature of archaeal viruses. Indeed, although most of them are completely unrelated to bacterial viruses, they are often called ‘bacteriophages’, since archaea (formerly archaebacteria) are still considered by some biologists as ‘strange bacteria’. For instance, archaeal viruses are grouped with bacteriophages in the drawing that illustrates viral diversity in the last edition of the Virus Taxonomy Handbook. Hopefully, these outdated visions will finally succumb to the accumulating evidence from molecular analyses. 

Viruses Are Not Derived from Modern Cells 
Abundant data are now already available to discredit the escape hypothesis in its classical adaptation of the prokaryote/eukaryote paradigm. This hypothesis indeed predicts that proteins encoded by bacterial viruses (avoiding the term bacteriophage here) should be evolutionarily related to bacterial proteins, whereas proteins encoded by viruses infecting eukaryotes should be related to eukaryotic proteins. This turned out to be wrong since, with a few exceptions (that can be identified as recent transfers from their hosts), most viral encoded proteins have either no homologs in any cell or only distantly related homologs. In the latter cases, the most closely related cellular homolog is rarely from the host and can even be from cells of a domain different from the host. More and more biologists are thus now fully aware that viruses form a world of their own, and that it is futile to speculate on their origin in the framework of the old prokaryote/ eukaryote dichotomy.

A more elaborate version has been proposed by William Martin and Eugene Koonin, who suggested that life originated and evolved in the cell-like mineral compartments of a warm hydrothermal chimney. In that model, viruses emerged from the assemblage of self-replicating elements using these inorganic compartments as the first hosts. The formation of true cells occurred twice independently only at the end of the process (and at the top of the chimney), producing the first archaea and bacteria. The latter escaped from the same chimney system as already fully elaborated modern cells. In the model, viruses first co-evolved with acellular machineries producing nucleotide precursors and proteins.

The emergence of the RNA world involves at least the existence of complex mechanisms to produce ATP, RNA, and proteins. This means an elaborated metabolism to produce ribonucleotide triphosphate (rNTP) and amino acids, RNA polymerases, and ribosomes, as well as an ATP-generating system. If such a complex metabolism was present, it appears unlikely that it was unable to produce lipid precursors, hence membranes. If this is correct, then ‘modern’ viruses did not predate cells but originated in a world populated by primitive cells. 

Viruses and the Origin of DNA 
Considering the possibility that at least some DNA viruses originated from RNA viruses, it has been suggested that DNA itself could have appeared in the course of virus evolution (in the context of competition between viruses and their cellular hosts). Indeed, DNA is a modified form of RNA, and both viruses and cells often chemically modify their genomes to protect themselves from nucleases produced by their competitor. It is usually considered that DNA replaced RNA in the course of evolution simply because it is more stable (thanks to the removal of the reactive oxygen in position 20 of the ribose) and because cytosine deamination (producing uracil) can be corrected in DNA (where uracil is recognized as an alien base) but not in RNA. 

Anyone that studies biochemistry, knows the enormous complexity of ribonucleotide reductase enzymes, that remove oxygen from the 2' position of ribose, the backbone of RNA, to transform RNA into DNA. There is no scientific explanation for how RNA could have transitioned to DNA, and the origin of the ultra-complex machinery to catalyze the needed reactions. Molecules have no goals, no foresight. They did not think about the advantage of stability if transitioning to DNA. There's nothing about inert chemicals and physical forces that say we want to become part of a living self-replicating entity called a cell at the end of a chemical evolutionary process. Molecules do not have the "drive", they do not urge or "want" to find ways to become information-bearing biomolecules, or able to harness energy as ATP molecules, become more efficient, or become part of a molecular machine, or in the end, a complex organism. There is a further hurdle to overcome. More and more biologists are now fully aware that viruses form a world of their own. Proteins encoded by bacterial viruses are not related to bacterial proteins. Modern viruses exhibit very different types of genomes (RNA, DNA, single-stranded, double-stranded), including highly modified DNA, whereas all modern cellular organisms have double-stranded DNA genomes. So the question becomes how Viruses that have a DNA genome originated since they had an independent origin from living cells. Even more: P. Forterre (2008): Many DNA viruses encode their own enzymes for deoxynucleotide triphosphate (dNTP) production, ribonucleotide reductases (the enzymes that produce deoxyribonucleotides from ribonucleotides), and thymidylate synthases (the enzymes that produce deoxythymidine monophosphate (dTMP) from deoxyuridine monophosphate (dUMP). 
That means RNR enzymes would have evolved independently, in a convergent manner, twice !! 

The replacement of RNA by DNA as cellular genetic material would have thus allowed genome size to increase, with a concomitant increase in cellular complexity (and efficiency) leading to the complete elimination of RNA cells by the ancestors of modern DNA cells. This traditional textbook explanation has been recently criticized as incompatible with Darwinian evolution since it does not explain what immediate selective advantage allowed the first organism with a DNA genome to predominate over former organisms with RNA genomes. Indeed, the newly emerging DNA cell could not have immediately enlarged its genome and could not have benefited straight away from a DNA repair mechanism to remove uracil from DNA. Instead, if the replacement of RNA by DNA occurred in the framework of the competition between cells and viruses, either in an RNA virus or in an RNA cell, modification of the RNA genome into a DNA genome would have immediately produced a benefit for the virus or the cell. It has been argued that the transformation of RNA genomes into DNA genomes occurred preferentially in viruses because it was simpler to change in one step the chemical composition of the viral genome than that of the cellular genomes (the latter interacting with many more proteins). Furthermore, modern viruses exhibit very different types of genomes (RNA, DNA, single-stranded, double-stranded), including highly modified DNA, whereas all modern cellular organisms have double-stranded DNA genomes. This suggests a higher degree of plasticity for viral genomes compared to cellular ones. The idea that DNA originated first in viruses could also explain why many DNA viruses encode their own enzymes for deoxynucleotide triphosphate (dNTP) production, ribonucleotide reductases (the enzymes that produce deoxyribonucleotides from ribonucleotides), and thymidylate synthases (the enzymes that produce deoxythymidine monophosphate (dTMP) from deoxyuridine monophosphate (dUMP). Because in modern cells, dTMP is produced from dUMP, the transition from RNA to DNA occurred likely in two steps, first with the appearance of ribonucleotide reductase and production of U-DNA (DNA containing uracil), followed by the appearance of thymidylate synthases and formation of T-DNA (DNA containing thymine). The existence of a few bacterial viruses with U-DNA genomes has been taken as evidence that they could be relics of this period of evolution. If DNA first appeared in the ancestral virosphere, one has also to explain how it was later on transferred to cells. One scenario posits the co-existence for some time of an RNA cellular chromosome and a DNA viral genome (episome) in the same cell, with the progressive transfer of the information originally carried by the RNA chromosome to the DNA ‘plasmid’ via retro-transposition. 8

What came first, cells or viruses? 
This is a classical chicken & egg problem: Gladys Kostyrka (2016): Cells depend on viruses, but viruses depend on cells as a host for replication. What came first? How could viruses play critical roles in the OL if life relies on cellular organization and if viruses are defined as parasites of cells? In other words, how could viruses play a role in the emergence of cellular life if the existence of cells is a prerequisite for the existence of viruses? 9

Virus origins: From what did viruses evolve or how did they initially arise? The answer to this question is not simple, because, while viruses all share the characteristics of being obligate intracellular parasites that use host cell machinery to make their components which then self-assemble to make particles that contain their genomes, they most definitely do not have a single origin.

Virus origins: From what did viruses initially arise?
E.Rybicki: The graphic depicts a possible scenario for the evolution of viruses: “wild” genetic elements could have escaped, or even been the agents for transfer of genetic information between, both RNA-containing and DNA-containing “protocells”, to provide the precursors of retroelements and of RNA and DNA viruses.  Later escapes from Bacteria, Archaea and their progeny Eukarya would complete the virus zoo. It is generally accepted that many viruses have their origins as “escapees” from cells; rogue bits of nucleic acid that have taken the autonomy already characteristic of certain cellular genome components to a new level.  Simple RNA viruses are a good example of these: their genetic structure is far too simple for them to be degenerate cells; indeed, many resemble renegade messenger RNAs in their simplicity. 10

Beyond Evolution: The Origin of Species by Design Bacter15

Viruses, the most abundant biological entities on earth
Steven W. Wilhelm (2012): Viruses are the most abundant life forms on Earth, with an estimated 10^31 total viruses globally. 11 

Eugene V. Koonin (2020): Viruses appear to be the dominant biological entities on our planet, with the total count of virus particles in aquatic environments alone at any given point in time reaching the staggering value of 10^31, a number that is at least an order of magnitude greater than the corresponding count of cells.  The genetic diversity of viruses is harder to assess, but, beyond doubt, the gene pool of viruses is, in the least, comparable to that of hosts. The estimates of the number of distinct prokaryotes on earth differ widely, in the range of 10^7 to 10^12, and accordingly, estimation of the number of distinct viruses infecting prokaryotes at 10^8 to 10^13 is reasonable. Even assuming the lowest number in this range and even without attempting to count viruses of eukaryotes, these estimates represent vast diversity. Despite the rapid short-term evolution of viruses, the key genes responsible for virion formation and virus genome replication are conserved over the long term due to selective constraints. Genetic parasites inescapably emerge even in the simplest molecular replicator systems and persist through their subsequent evolution. Together with the ubiquity and enormous diversity of viruses in the extant biosphere, these findings lead to the conclusion that viruses and other mobile genetic elements MGEs played major roles in the evolution of life ever since its earliest stages.   5

G.Witzany (2015): If we imagine that 1ml of seawater contains one million bacteria and ten times more viral sequences it can be determined that 10^31 bacteriophages infect 10^24 bacteria per second. 12

Eugene V. Koonin (2022):  We argue that viruses emerge on a number (even if far from astronomical) independent occasions, so that the number of realms will considerably increase from the current 6, by splitting some of the current realms, giving the realm status to some of the currently unclassified groups of viruses and discovery of new distinct groups. Viruses are often considered to be the most numerous entities in the global biosphere. The most common estimates suggest that there are on the order of 10^31 virus particle on the planet at any given moment, about an order of magnitude greater than the total number of cells. To the best of our current understanding, all organisms on earth are hosts to multiple viruses, with the possible exception of some endosymbiotic bacteria. Empirical observations on the ubiquity of viruses are buttressed by theoretical arguments on the inevitable emergence of genetic parasites in any replicator system. Virus genomes are also extremely diverse, and the ongoing metagenomic metatranscriptomic revolution reveals the vast scale of that diversity. The case of RNA viruses can serve as an apt illustration. Astonishingly, analysis of a single metatranscriptome, apparently coming from an environment rich in unicellular eukaryotes hosting RNA viruses, resulted in a twofold expansion of the known RNA virome. Three independent subsequent studies exploring thousands of metatranscriptomes from diverse environments each led to a further, several-fold increase in the number of known distinct RNA viruses (distinct, in this case, means not too closely related to each other, more specifically, clusters of genomes with similar sequences that roughly correspond to a virus species level), which combined, would amount to a more than an order of magnitude expansion. Rarefaction analysis shows that saturation of the RNA virus diversity is not yet in sight. Metagenomic studies indicate that the case of DNA viruses is similar, and expansion of some groups, for instance, tailless bacteriophages, or tailed phages of the expansive order Crassvirales has been even more dramatic.

So how many distinct viruses, or virus species, are there in the global virome altogether? Given that metagenomic and metatranscriptomic analyses (below we refer to these collectively as metaviromics insofar as applied to virus discovery) are not yet approaching saturation, this number cannot be inferred by extrapolation from available data. However, to obtain a rough, back-of-the-envelope estimate, we can take a different approach modeled over that employed previously to estimate the number of unique microbial genes. The great majority of viruses on earth are tailed and tailless phages infecting bacteria; viruses of archaea and eukaryotes are only relatively small additions. Let us conservatively assume that there are 10^6 to 10^7 bacterial species on earth (some estimates are orders of magnitude higher). Most if not all bacteria are hosts to multiple viruses. For Escherichia coli alone, about a hundred bacteriophages have been identified, whereas for Mycobacterium smegmatis mc2155, more than 10,000 individual mycobacteriophages have been isolated, although only 2,100 of these have been sequenced and thus it remains to be determined how many different virus species they represent. Furthermore, analysis of CRISPR spacers, the majority of which appear to be virus-derived but do not match known viruses, implies large, host species-specific viromes. Let us assume 10 to 100 virus species per host species as a conservative estimate. Then, the size of the global virome can be crudely estimated at 10^7 to 10^9 distinct virus species – obviously, even the low bound in this range, probably, a vast underestimate, is a huge number. The upper bound appears more realistic, so there is likely to be about a billion virus species if not more on earth – evidently, a long way to go from the currently recognized 10^4 species until we know them all. 13

Capsid-encoding organisms in contrast to ribosome-encoding organisms
Eugene V. Koonin (2014): Viruses were defined as one of the two principal types of organisms in the biosphere, namely, as capsid-encoding organisms in contrast to ribosome-encoding organisms, i.e., all cellular life forms. Structurally similar, apparently homologous capsids are present in a huge variety of icosahedral viruses that infect bacteria, archaea, and eukaryotes. These findings prompted the concept of the capsid as the virus “self” that defines the identity of deep, ancient viral lineages. This “capsidocentric” perspective on the virus world is buttressed by observations on the extremely wide spread of certain capsid protein (CP) structures that are shared by an enormous variety of viruses, from the smallest to the largest ones, that infect bacteria, archaea, and all divisions of eukaryotes. The foremost among such conserved capsid protein structures is the so-called jelly roll capsid (JRC) protein fold, which is represented, in a variety of modifications, in extremely diverse icosahedral (spherical) viruses that infect hosts from all major groups of cellular life forms. In particular, the presence of the double-beta-barrel JRC (JRC2b) in a broad variety of double-stranded DNA (dsDNA) viruses infecting bacteria, archaea, and eukaryotes has been touted as an argument for the existence of an “ancient virus lineage,” of which this type of capsid protein is the principal signature (9). Under this approach, viruses that possess a single beta-barrel JRC (JRC1b)—primarily RNA viruses and single-stranded DNA (ssDNA) viruses— could be considered another major viral lineage. A third lineage is represented by dsDNA viruses with icosahedral capsids formed by the so-called HK97-like capsid protein (after bacteriophage HK97, in which this structure was first determined), with a fold that is unrelated to the jelly roll fold. This assemblage of viruses is much less expansive than those defined by either JRC2b or JRC1b, but nevertheless, it unites dsDNA viruses from all three domains of cellular life. The capsid-based definition of a virus does capture a quintessential distinction between the two major empires of life forms, i.e., viruses and cellular life forms.    14

Beyond Evolution: The Origin of Species by Design Capsid10
Replication-expression classes of viruses and homologous, capsidless selfish elements. (A) RNA and reverse-transcribing elements. (B) DNA elements. The three shades of the blue background denote approximate relative prevalences of capsidless selfish elements in the respective Baltimore class (i.e., low for ssRNA genomes, moderate for dsDNA genomes, and high for retroelements and ssDNA genomes; so far, there are no capsidless elements with negative-strand RNA or dsRNA genomes). The abbreviations for the virus hallmark genes are as follows: RdRp, RNA-dependent RNA polymerase; S3H, superfamily 3 helicase; JRC, jelly roll capsid protein; RT, reverse transcriptase; INT, retro-type integrase; RCRE, rolling circle replication endonuclease; A-E DNA primase, archaeo-eukaryotic DNA primase; UL9-like S2H, UL9-like superfamily 2 helicase; FtsK pack-ATPase, FtsK-family packaging ATPase; ATPase suT, ATPase subunit of terminase; ppPolB, protein-primed DNA polymerase B; Ad-like Pro, adeno-like protease; and mat-Pro, maturation protease. The hallmark genes that are present in all known members of the given class are rendered in bold. For negative-strand RNA viruses, the RdRp is indicated in parentheses to emphasize the tentative relationship between the RNA polymerases of these viruses and the RdRp/RT. Helitrons are marked by an asterisk because of their distinct replication cycle: unlike other RCRE-encoding ssDNA selfish elements, helitrons are transposed as dsDNA. DdDp, DNA-dependent DNA polymerase.

Viruses with a different genetic alphabet
Stephen Freeland (2022):The genetic material of more than 200 bacteriophage viruses uses 1-aminoadenine (Z) instead of adenine (A). This minor difference in chemical structures is nevertheless a fundamental deviation from the standard alphabet of four nucleobases established by biological evolution at the time of life's Last Universal Common Ancestor (LUCA). Placed into broader context, the finding illustrates a deep shift taking place in our understanding of the chemical basis for biology. 15

What is the best explanation for viral origin?
Edward C. Holmes (2011):  The central debating point in discussions of the origin of viruses is whether they are ancient, first appearing before the last universal cellular ancestor (LUCA), or evolved more recently, such that their ancestry lies with genes that “escaped” from the genomes of their cellular host organisms and subsequently evolved independent replication. The escaped gene theory has traditionally dominated thinking on viral origins (reviewed in reference 37), in large part because viruses are parasitic on cells now and it has been argued that this must have always have been the case. However, there is no gene shared by all viruses, and recent data are providing increasingly strong support for a far more ancient origin. 16

Koonin mentions three possible scenarios for their origin. One of them: 

Eugene V. Koonin (2017) The virus-first hypothesis, also known as the primordial virus world hypothesis, regards viruses (or virus-like genetic elements) as intermediates between prebiotic chemical systems and cellular life and accordingly posits that virus-like entities originated in the precellular world. The second: The regression hypothesis, in contrast, submits that viruses are degenerated cells that have succumbed to obligate intracellular parasitism and in the process shed many functional systems that are ubiquitous and essential in cellular life forms, in particular the translation apparatus. The third, the escape hypothesis postulates that viruses evolved independently in different domains of life from cellular genes that embraced selfish replication and became infectious. 17

The second and third are questionable, in face of the fact that evolution would sort out degenerated cell parts that would harm their survival. The hypothesis that these parts would become parasites, goes detrimentally against the evolutionary paradigm, since evolution is about the survival of the fittest, and not evolving parasites that would kill the cell. Furthermore, if Viruses were not extant right from the beginning, how would ecological homeostasis be guaranteed?

Koonin agrees that the first is the most plausible. He writes:  The diversity of genome replication-expression strategies in viruses, contrasting the uniformity in cellular organisms, had been considered to be most compatible with the possibility that the virus world descends directly from a precellular stage of evolution, and an updated version of the escape hypothesis states that the first viruses have escaped not from contemporary but rather from primordial cells, predating the last universal cellular ancestor. The three evolutionary scenarios imply different timelines for the origin of viruses but offer little insight into how the different components constituting viral genomes might have combined to give rise to modern viruses.

The conclusion that can be drawn is, that Viruses co-emerged with life, and that occurred multiple times. If just emerging once is extremely unlikely based on the odds, how much more, multiple times?

Koonin continues: A typical virus genome encompasses two major functional modules, namely, determinants of virion formation and those of genome replication. Understanding the origin of any virus group is possible only if the provenances of both components are elucidated. Given that viral replication proteins often have no closely related homologs in known cellular organisms, it has been suggested that many of these proteins evolved in the precellular world or in primordial, now extinct, cellular lineages. The ability to transfer the genetic information encased within capsids—the protective proteinaceous shells that comprise the cores of virus particles (virions)—is unique to bona fide viruses and distinguishes them from other types of selfish genetic elements such as plasmids and transposons.Thus, the origin of the first true viruses is inseparable from the emergence of viral capsids. Studies on the origin of viral capsids are severely hampered by the high sequence divergence among these proteins.

Analysis of the available sequences and structures of major capsid proteins (CP) and nucleocapsid (NC) proteins encoded by representative members of 135 virus taxa (117 families and 18 unassigned genera) allowed us to attribute structural folds to 76.3% of the known virus families and unassigned genera. The remaining taxa included viruses that do not form viral particles (3%) and viruses for which the fold of the major virion proteins is not known and could not be predicted from the sequence data (20.7%). The former group includes capsidless viruses of the families Endornaviridae, Hypoviridae, Narnaviridae, and Amalgaviridae, all of which appear to have evolved independently from different groups of full-fledged capsid-encoding RNA viruses. The latter category includes eight taxa of archaeal viruses with unique morphologies and genomes, pleomorphic bacterial viruses of the family Plasmaviridae, and 19 diverse taxa of eukaryotic viruses. It should be noted that, with the current explosion of metagenomics studies, the number and diversity of newly recognized virus taxa will continue to rise. Although many of these viruses are expected to have previously observed CP/NC protein folds, novel architectural solutions doubtlessly will be discovered as well. 17

Gladys Kostyrka (2016): To french molecular biologist and microbiologist Patrick Forterre, viruses could not exist without cells because he endorses their definition as intracellular obligate parasites. However, this does not mean that viruses did not exist prior to DNA cells. On the basis of comparative sequence analyses of proteins and nucleic acids from viruses and their cellular hosts, Forterre hypothesized that viruses originated before DNA cells and before LUCA (the Last Universal Cellular Ancestor). Forterre’s hypothesis has been first formulated in the 1990s and was inspired by protein phylogenies. “Comparative sequence analyses of type II DNA topoisomerases and DNA polymerases from viruses, prokaryotes and eukaryotes suggest that viral genes diverged from cellular genes before the emergence of the last common ancestor (LCA) of prokaryotes and eukaryotes”.  At least some viruses originated not from the known cellular domains e Bacteria, Eukarya, and Archaea e but before these three domains were formed. In other words, these viruses must have originated before LUCA. 

There are several genes shared by many groups of viruses with extremely diverse replication-expression strategies, genome size and host ranges. In other words, there are several “hallmark genes”, coding for several hallmark proteins present in many viruses. Yet these genes and proteins are not supposed to be shared by viruses that do not have the same origin, given their diversity. This “key observation” of several hallmark viral genes is thus problematic. It is even more problematic if one takes into account the fact that these genes are not found in any cellular life forms.1 It is then highly improbable that these viral hallmark genes were originally cellular genes that were transferred to viruses. Koonin assumes that these genes originated in a primordial viral world and were conserved. “The simplest explanation for the fact that the hallmark proteins involved in viral replication and virion formation are present in a broad variety of viruses but not in any cellular life forms seems to be that the latter actually never possessed these genes. Rather, the hallmark genes, probably, antedate cells and descend directly from the primordial pool of virus-like genetic elements” 17

If Koonin's hypothesis were the case, these nucleotides would require foresight to assemble into genes, that later would become virions, depending on cell hosts. That's simply not tenable.  The evidence is better interpreted by the creationism model. It coincides with the hypothesis, that God created each species/kind and viruses separately. Multiple creation events by natural means and the emergence of symbiotic and parasitic relationships just mean multiplying the odds, and then naturalistic proposals become more and more untenable.

Achieving the same function through different molecular assembly routes refutes an evolutionary-naturalistic origin of viruses
Eugene V. Koonin (2015): The ability to form virions is the key feature that distinguishes viruses from other types of mobile genetic elements, such as plasmids and transposons. The origin of bona fide viruses thus appears to be intimately linked to and likely concomitant with the origin of the capsids. However, tracing the provenance of viral capsid proteins (CPs) proved to be particularly challenging because they typically do not display sequence or structural similarity to proteins from cellular life forms. Over the years, a number of structural folds have been discovered in viral CPs. Strikingly, morphologically similar viral capsids, in particular, icosahedral, spindle-shaped and filamentous ones, can be built from CPs which have unrelated folds. Thus, viruses have found multiple solutions to the same problem. Nevertheless, the process of de novo origin of viral CPs remains largely enigmatic.  18

Stephen J. Gould (1990):…No finale can be specified at the start, none would ever occur a second time in the same way, because any pathway proceeds through thousands of improbable stages. Alter any early event, ever so slightly, and without apparent importance at the time, and evolution cascades into a radically different channel.19

Fazale Rana (2001): Gould’s metaphor of “replaying life’s tape” asserts that if one were to push the rewind button, erase life’s history, and let the tape run again, the results would be completely different.  The very essence of the evolutionary process renders evolutionary outcomes as nonreproducible (or nonrepeatable). Therefore, “repeatable” evolution is inconsistent with the mechanism available to bring about biological change. 20

William Schopf (2002): Because biochemical systems comprise many intricately interlinked pieces, any particular full-blown system can only arise once…Since any complete biochemical system is far too elaborate to have evolved more than once in the history of life, it is safe to assume that microbes of the primal LCA cell line had the same traits that characterize all its present-day descendants. 21 22

Hugh M. B. Harris: (2021): Viruses are ubiquitous. They infect almost every species and are probably the most abundant biological entities on the planet, yet they are excluded from the Tree of Life (ToL). Viruses may well be essential for ecosystem diversity 23

Matti Jalasvuori (2012): Viruses play a vital role in all cellular and genetic functions, and we can therefore define viruses as essential agents of life. Viruses provide the largest reservoir of genes known in the biosphere but were not, stolen’ from the host. Such capsids cannot be of host origin. It is well accepted by virologists that viruses often contain many complex genes (including core genes) that cannot be attributed to having been derived from host genes. 24

Julia Durzyńska (2015): Many attempts have been made to define nature of viruses and to uncover their origin.   As the origin of viruses and that of living cells are most probably interdependent, we decided to reveal ideas concerning nature of cellular last universal common ancestor (LUCA).   Many viral particles (virions) contain specific viral enzymes required for replication. A few years ago, a new division for all living organisms into two distinct groups has been proposed: ribosome-encoding organisms (REOs) and capsid-encoding organisms (CEOs). 25

Eugene V. Koonin: (2012): Probably an even more fundamental departure from the three-domain schema is the discovery of the Virus World, with its unanticipated, astonishing expanse and the equally surprising evolutionary connectedness. Virus-like parasites inevitably emerge in any replicator systems, so THERE IS NO EXAGGERATION IN THE STATEMENT THAT THERE IS NO LIFE WITHOUT VIRUSES. And in quite a meaningful sense, not only viruses taken together, but also major groups of viruses seem to be no less (if not more) fundamentally distinct as the three (or two) domains of cellular life forms, given that viruses employ different replication-expression cycles, unlike cellular life forms which, in this respect, are all the same. 26

Shanshan Cheng: (2013): Viral capsid proteins protect the viral genome by forming a closed protein shell around it. Most of currently found viral shells with known structure are spherical in shape and observe icosahedral symmetry. Comprised of a large number of proteins, such large, symmetrical complexes assume a geometrically sophisticated architecture not seen in other biological assemblies. The geometry of the complex architecture aside, another striking feature of viral capsid proteins lies in the folded topology of the monomers, with the canonical jelly-roll β barrel appearing most prevalent (but not sole) as a core structural motif among capsid proteins that make up these viral shells of varying sizes. Our study provided support for the hypothesis that viral capsid proteins, which are functionally unique in viruses in constructing protein shells, are also structurally unique in terms of their folding topology. 27

Eugene V. Koonin (2020): In a seminal 1971 article, Baltimore classified all then-known viruses into six distinct classes that became known as Baltimore classes (BCs) (a seventh class was introduced later), on the basis of the structure of the virion's nucleic acid (traditionally called the virus genome):


The seven Baltimore classes (BCs): information flow. For each BC, the processes of replication, transcription, translation, and virion assembly are shown by color-coded arrows (see the inset). Host enzymes that are involved in virus genome replication or transcription are prefixed with “h-,” and in cases when, in a given BC, one of these processes can be mediated by either a host- or a virus-encoded enzyme, the latter is prefixed with “v-.” Otherwise, virus-encoded enzymes are not prefixed. CP, capsid protein; DdDp, DNA-directed DNA polymerase; DdRp, DNA-directed RNA polymerase; gRNA, genomic RNA; RdRp, RNA-directed RNA polymerase; RT, reverse transcriptase; RCRE, rolling-circle replication (initiation) endonuclease.

1. Double-stranded DNA (dsDNA) viruses, with the same replication-expression strategy as in cellular life forms
2. Single-stranded DNA (ssDNA) viruses that replicate mostly via a rolling-circle mechanism
3. dsRNA viruses
4. Positive-sense RNA [(+)RNA] viruses that have ssRNA genomes with the same polarity as the virus mRNA(s)
5. Negative-sense RNA [(−)RNA] viruses that have ssRNA genomes complementary to the virus mRNA(s)
6. RNA reverse-transcribing viruses that have (+)RNA genomes that replicate via DNA intermediates synthesized by reverse transcription of the genome
7. DNA reverse-transcribing viruses replicating via reverse transcription but incorporating into virions a dsDNA or an RNA-DNA form of the virus genome.

Evidence supports monophyly for some of the BCs but refutes it for others. Generally, the evolution of viruses and MGEs is studied with methods of molecular evolutionary analysis that are also used for cellular organisms. However, the organizations of the genetic spaces dramatically differ between viruses and their cellular hosts.

Beyond Evolution: The Origin of Species by Design Mr031010
Representation of the 6 “superviral hallmark genes” in virus genomes of the seven Baltimore classes. The “superviral hallmark proteins” are shown by ribbon diagrams of the representative protein structures. The lines connect the proteins with the viruses of BCs in which they are present. The thickness of each connecting line roughly reflects the abundance of a given “superhallmark” gene in a given BC. DJR-CP, double-jelly-roll capsid protein; RCRE, rolling-circle replication (initiation) endonuclease; RdRp, RNA-directed RNA polymerase; RT, reverse transcriptase; S3H, superfamily 3 helicase; SJR-CP, single-jelly-roll capsid protein.

Rob Phillips (2018):The origins of superviral hallmark genes VHGs appear to be widely different. In particular, RdRps, RTs, and RCREs most likely represent the heritage of the primordial, precellular replicator pool as indicated by the absence of orthologs of these proteins in cellular life-forms. At the top of the megataxonomy are the four effectively independent realms that, however, are connected at an even higher rank of unification through the super-VHG domains.

The International Committee on Taxonomy of Viruses or ICTV classifies viruses into seven orders:

Herpesvirales, large eukaryotic double-stranded DNA viruses;
Caudovirales, tailed double-stranded DNA viruses typically infecting bacteria;
Ligamenvirales, linear double-stranded viruses infecting archaea;
Mononegavirales, nonsegmented negative (or antisense) strand single-stranded RNA viruses of plants and animals;
Nidovirales, positive (or sense) strand single-stranded RNA viruses of vertebrates;
Picornavirales, small positive strand single-stranded RNA viruses infecting plants, insects, and animals;
Tymovirales, monopartite positive single-stranded RNA viruses of plants.

In addition to these orders, there are ICTV families, some of which have not been assigned to an ICTV order. Only those ICTV viral families with more than a few members present in our dataset are explored. 28

Structure and Assembly of Complex Viruses
Carmen San Martin (2013): Viral particles consist essentially of a proteinaceous capsid protecting a genome and involved also in many functions during the virus life cycle. In simple viruses, the capsid consists of a number of copies of the same, or a few different proteins organized into a symmetric oligomer. Structurally complex viruses present a larger variety of components in their capsids than simple viruses. They may contain accessory proteins with specific architectural or functional roles; or incorporate non-proteic elements such as lipids. They present a range of geometrical variability, from slight deviations from the icosahedral symmetry to complete asymmetry or even pleomorphism. Putting together the many different elements in the virion requires an extra effort to achieve correct assembly, and thus complex viruses require sophisticated mechanisms to regulate morphogenesis. This chapter provides a general view of the structure and assembly of complex viruses.

A viral particle consists essentially of a proteinaceous capsid with multiple roles in the protection of the viral genome, cell recognition and entry, intracellular trafficking, and controlled uncoating. Viruses adopt different strategies to achieve these goals. Simple viruses generally build their capsids from a number of copies of the same, or a few different proteins, organized into a symmetric oligomer. In the case of complex viruses, capsid assembly requires further elaborations. What are the main characteristics that define a structurally complex virus? Structural complexity on a virus often, but not necessarily, derives from the need to house a large genome, in which case a larger capsid is required. However, capsid or genome sizes by themselves are not determinants of complexity. For example, flexible filamentous viruses can reach lengths in the order of microns, but most of their capsid mass is built by a single capsid protein arranged in a helical pattern. On the other hand, architecturally complex viruses such as HIV have moderate-sized genomes (7–10 kb of single-stranded (ss) RNA). Structurally complex viruses incorporate a larger variety of components into their capsids than simple viruses. They may contain accessory proteins with specific architectural or functional roles or incorporate non-proteic elements such as lipids. 29

Forming viral symmetric shells
Roya Zandi (2020): The process of formation of virus particles in which the protein subunits encapsidate genome (RNA or DNA) to form a stable, protective shell called the capsid is an essential step in the viral life cycle. The capsid proteins of many small single-stranded RNA viruses spontaneously package their wild-type (wt) and other negatively charged polyelectrolytes, a process basically driven by the electrostatic interaction between positively charged protein subunits and negatively charged cargo.  Regardless of the virion size and assembly procedures, most spherical viruses adopt structures with icosahedral symmetry. How exactly capsid proteins (CPs) assemble to assume a specific size and symmetry have been investigated for over half a century now. As the self-assembly of virus particles involves a wide range of thermodynamics parameters, different time scales, and an extraordinary number of possible pathways, the kinetics of assembly has remained elusive, linked to Levinthal’s paradox for protein folding. The role of the genome on the assembly pathways and the structure of the capsid is even more intriguing. The kinetics of virus growth in the presence of RNA is at least 3 orders of magnitude faster than that of empty capsid assembly, indicating that the mechanism of assembly of CPs around RNA might be quite different. Some questions then naturally arise: What is the role of RNA in the assembly process, and by what means then does RNA preserve assembly accuracy at fast assembly speed? Two different mechanisms for the role of the genome have been proposed: (i) en masse assembly and (ii) nucleation and growth.

The assembly interfaces in many CPs are principally short-ranged hydrophobic in character, whereas there is a strong electrostatic, nonspecific long-ranged interaction between RNA and CPs. To this end, the positively charged domains of CPs associate with the negatively charged RNA quite fast and form an amorphous complex. Hydrophobic interfaces then start to associate, which leads to the assembly of a perfect icosahedral shell. Based on the en masse mechanism, the assembly pathways correspond to situations in which intermediates are predominantly disordered. They found that, at neutral pH, a considerable number of CPs were rapidly (∼28 ms) adsorbed to the genome, which more slowly (∼48 s) self-organized into compact but amorphous nucleoprotein complexes (NPC). By lowering the pH, they observed a disorder−order transition as the protein−protein interaction became strong enough to close up the capsid and to overcome the high energy barrier separating NPCs from virions. 30



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No common ancestor for Viruses

Eugene V. Koonin (2020): In the genetic space of viruses and MGEs, no genes are universal or even conserved in the majority of viruses. Viruses have several distinct points of origin, so there has never been a last common ancestor of all viruses. 33

Koonin's statement challenges the notion of a universal common ancestor for all viruses, suggesting that viruses have multiple distinct points of origin rather than arising from a single ancestral lineage.  Viruses and mobile genetic elements (MGEs) encompass an immense variety of genetic content and structures. Unlike cellular organisms, they lack a universal set of conserved genes shared across different viral lineages. This genetic diversity is a key characteristic that distinguishes viruses from cellular life forms. The absence of universally conserved genes and the vast genetic diversity in viruses make it challenging to identify a single common ancestor for all viruses. Instead, the genetic space of viruses appears to be fragmented, with multiple points of origin. Viruses display a wide range of replication strategies, depending on their genetic material and structure. For example, DNA viruses replicate using host cellular machinery, while RNA viruses often encode their own replication enzymes.  Evidence from genomic analyses suggests the existence of seven distinct lineages, each with its own distinct origins and characteristics. These seven lineages are double-stranded DNA viruses, positive-strand RNA viruses, negative-strand RNA viruses, reverse-transcribing viruses, viruses with a double-stranded RNA genome, single-stranded DNA viruses, and satellite viruses. The genetic diversity and unique replication mechanisms within each of these lineages provide evidence for independent origins rather than shared ancestry.

Viruses and the Tree of life (2009): Viruses are polyphyletic: In a phylogenetic tree, the characteristics of members of taxa are inherited from previous ancestors. Viruses cannot be included in the tree of life because they do not share characteristics with cells, and no single gene is shared by all viruses or viral lineages. While cellular life has a single, common origin, viruses are polyphyletic – they have many evolutionary origins. Viruses don’t have a structure derived from a common ancestor.  Cells obtain membranes from other cells during cell division. According to this concept of ‘membrane heredity’, today’s cells have inherited membranes from the first cells.  Viruses have no such inherited structure.  They play an important role by regulating population and biodiversity. 34

Comment: The shared characteristics among members of taxa are inherited from common ancestors. However, viruses deviate from this paradigm due to their unique properties and origins. The polyphyletic nature of viruses stems from their lack of shared characteristics with cellular organisms. Unlike cellular life forms, viruses lack a universal set of genes or structures that can be traced back to a common ancestor. This absence of consistent traits prevents viruses from fitting neatly into the tree of life. Instead, viruses are thought to have multiple, independent origins that have shaped their diverse characteristics. One key reason for the exclusion of viruses from the Tree of life is their deviation from the structural and genetic features commonly found in cellular organisms. While cellular life has a cohesive membrane structure, viruses lack such a unified inherited structure.  Despite their unconventional status, viruses play crucial roles in ecosystems by regulating population sizes and influencing biodiversity. Viral infections can control the abundance of host organisms, preventing unchecked growth and maintaining ecological balance. This ecological role highlights the essential interplay between viruses and cellular life.  Some viruses integrate their genetic material into host genomes, influencing the adaptation of host species. Others cause diseases, driving selective pressures that shape the genetic diversity of hosts.

Eugene V. Koonin (2017): The entire history of life is the story of virus–host coevolution. Therefore the origins and evolution of viruses are an essential component of this process. A signature feature of the virus state is the capsid, the proteinaceous shell that encases the viral genome. Although homologous capsid proteins are encoded by highly diverse viruses, there are at least 20 unrelated varieties of these proteins. Viruses are the most abundant biological entities on earth and show remarkable diversity of genome sequences, replication and expression strategies, and virion structures. Evolutionary genomics of viruses revealed many unexpected connections but the general scenario(s) for the evolution of the virosphere remains a matter of intense debate among proponents of the cellular regression, escaped genes, and primordial virus world hypotheses. A comprehensive sequence and structure analysis of major virion proteins indicates that they evolved on about 20 independent occasions. Virus genomes typically consist of distinct structural and replication modules that recombine frequently and can have different evolutionary trajectories. The present analysis suggests that, although the replication modules of at least some classes of viruses might descend from primordial selfish genetic elements, bona fide viruses evolved on multiple, independent occasions throughout the course of evolution by the recruitment of diverse host proteins that became major virion components. 35

Comment: The story of life is intrinsically woven with the dance of interdependence between these entities, revealing the intricate design behind their interactions. This narrative places the origins of viruses at the forefront of understanding this harmonious interplay. A key feature that distinguishes viruses is their signature capsid—the proteinaceous shell enfolding the viral genome. Astonishingly, despite their immense diversity, distinct yet homologous capsid proteins are present across a wide array of viruses. This intricate design showcases a purposeful adaptation for diverse viral species to engage with their respective hosts in meaningful ways. Viruses, intriguingly, emerge as the most populous life forms on Earth. Their vast diversity in genome sequences, replication methods, expression strategies, and virion structures underscores the brilliance of their design.   The study of evolutionary genomics in viruses has brought to light numerous unexpected connections, sparking intense debates among researchers regarding the origin of the virosphere. Within this discourse, three primary hypotheses have emerged: cellular regression, escaped genes, and the primordial virus world hypothesis. Each of these hypotheses offers a distinct perspective on how viruses supposedly originated and evolved over time. The cellular regression hypothesis suggests that viruses evolved from more complex cellular organisms that regressed to simpler forms due to parasitic or symbiotic relationships. According to this view, viruses could be considered degenerate remnants of once-independent cellular life forms. This idea stems from observations of certain viruses that exhibit genetic and structural similarities to cellular organisms, raising the possibility that these viruses could be evolutionary remnants of a bygone cellular state. The escaped genes hypothesis proposes that viruses emerged from genes that "escaped" from cellular organisms, gaining the ability to replicate and spread independently. This scenario suggests that some genetic elements within cellular genomes, originally involved in various cellular processes, acquired the necessary components for autonomous replication and encapsulation. Over time, these escaped genes could have evolved into distinct viral entities. The primordial virus world hypothesis envisions a world where viruses predate cellular life forms, representing an ancient and independent form of life. Proponents of this hypothesis suggest that viruses could have existed prior to cellular organisms and played a role in shaping early life's evolutionary trajectories. In this scenario, viruses are considered a fundamental component of the early Earth's ecosystem, potentially influencing the emergence of cellular life as we know it. To shed light on the evolution of viruses, researchers have conducted comprehensive sequence and structure analyses of major virion proteins. These analyses have revealed intriguing insights, indicating that major virion proteins have originated independently on at least 20 occasions. This suggests that viruses have experienced multiple instances of convergent origins, where similar features and functions have emerged independently in different lineages. Virus genomes are typically composed of distinct modules responsible for replication and structure. These modules frequently undergo recombination, leading to diverse evolutionary trajectories. While the replication modules of certain virus classes might have origins as primordial selfish genetic elements, the overall evolution of bona fide viruses appears to have occurred through a process of recruiting diverse host proteins. These host proteins eventually became essential components of viral particles, contributing to the viral structure and life cycle.

The importance of the admission that viruses do not share a common ancestor cannot be outlined enough. Researchers also admit, that under a naturalistic framework, the origin of viruses remains obscure, and has not found an explanation. One reason is that viruses depend on a cell host in order to replicate. Another is, that the virus capsid shells that protect the viral genome are unique, there is no counterpart in life. A science paper that I quote below describes capsids with a "geometrically sophisticated architecture not seen in other biological assemblies". This seems to be interesting evidence of design. The claim that their origin has something to do with evolution is also misleading - evolution plays no role in explaining either the origin of life or the origin of viruses. The fact that "no single gene is shared by all viruses or viral lineages" prohibits drawing a tree of viruses leading to a common ancestor.  

Evidence Indicates that Life started Polyphyletic

D M Raup (1983):  Life forms are made possible by the remarkable properties of polypeptides. It has been argued that there must be many potential but unrealized polypeptides that could be used in living systems. The number of possible primary polypeptide structures with lengths comparable to those found in living systems is almost infinite. This suggests that the particular subset of polypeptides of which organisms are now composed is only one of a great many that could be associated in viable biochemistries. There is no taxonomic category available to contain all life forms descended from a single event of life origin. Here, we term such a group, earthly or otherwise, a bioclade. If more than one bioclade survives, life is polyphyletic. If only one survives, it is monophyletic. We conclude that multiple origins of life in the early Precambrian is a reasonable possibility.36

W. Ford Doolittle (2007): Darwin claimed that a unique inclusively hierarchical pattern of relationships between all organisms based on their similarities and differences [the Tree of Life (TOL)] was a fact of nature, for which evolution, and in particular a branching process of descent with modification, was the explanation. However, there is no independent evidence that the natural order is an inclusive hierarchy, and the incorporation of prokaryotes into the TOL is especially problematic. The only data sets from which we might construct a universal hierarchy including prokaryotes, the sequences of genes, often disagree and can seldom be proven to agree. Hierarchical structure can always be imposed on or extracted from such data sets by algorithms designed to do so, but at its base the universal TOL rests on an unproven assumption about pattern that, given what we know about the process, is unlikely to be broadly true. This is not to say that similarities and differences between organisms are not to be accounted for by evolutionary mechanisms, but descent with modification is only one of these mechanisms, and a single tree-like pattern is not the necessary (or expected) result of their collective operation. Pattern pluralism (the recognition that different evolutionary models and representations of relationships will be appropriate, and true, for different taxa or at different scales or for different purposes) is an attractive alternative to the quixotic pursuit of a single true TOL.37

Comment: Darwin's assertion that all living organisms are neatly interconnected in a hierarchical framework, forming the Tree of Life (TOL), might not be as unshakeable as it initially appeared. While he championed this notion as an inherent truth underpinned by evolution's guiding hand, there exists a notable absence of autonomous proof supporting the concept of a universal and all-encompassing hierarchy. This raises questions, particularly when grappling with the inclusion of prokaryotes within this framework, which proves to be a particularly thorny concern. The evidence drawn from gene sequences, a potential foundation for constructing an encompassing hierarchy, doesn't unfailingly align. In fact, these sequences often find themselves in a state of disagreement, creating a quagmire where a unanimous consensus is elusive. Algorithms designed to impose hierarchical order upon these datasets offer a semblance of structure, but the bedrock of the universal Tree of Life rests precariously on an assumption that lacks conclusive verification. Given the known intricacies of the evolutionary process, it's plausible that this assumption might not hold true. The insistence on a solitary, tree-like pattern as the definitive result of their collective interplay might not be the most reasonable or anticipated outcome. This brings us to the notion of pattern pluralism. 

Douglas L. Theobald (2010): In all cases tried, with a wide variety of evolutionary models (from the simplest to the most parameter rich), the multiple-ancestry models for shuffled data sets are preferred by a large margin over common ancestry models (LLR on the order of a thousand), even with the large internal branches. 38

C. P. Kempes (2021): We argue for multiple forms of life realized through multiple different historical pathways. From this perspective, there have been multiple origins of life on Earth—life is not a universal homology. By broadening the class of originations, we significantly expand the data set for searching for life.  We define life as the union of two crucial energetic and informatic processes producing an autonomous system that can metabolically extract and encode information from the environment of adaptive/survival value and propagate it forward through time. We provide a new perspective on the origin of life by arguing that life has emerged many times on Earth and that there are many forms of extant life coexisting on a variety of physical substrates. The ultimate theory of life will certainly have ingredients from abstract theories of engineering, computation, physics, and evolution, but we expect will also require new perspectives and tools, just as theories of computation have.  It should be able to highlight life as the ultimate homoplasy (convergence) rather than homology, where life is discovered repeatedly from many different trajectories.

Comment: I propose a perspective that celebrates life's diversity, manifested through a multitude of historical journeys. Within this lens, life's origins exhibit a fascinating complexity – they aren't bound to a singular, universal template. This opens up the realm of possibilities, suggesting that life has sprung forth through various channels on Earth. The notion of life as an encompassing homology gets a recalibration, shifting our focus toward an array of distinct birth events. In defining life, I distill it to the convergence of two fundamental processes: a dance of energy and information. These processes collaborate to give rise to autonomous systems capable of extracting and encoding valuable survival-oriented information from their environment. This wisdom, perpetuated through time, forms the core essence of life. In the exploration of life's origins, this presents a fresh vantage point that unveils a dynamic truth – life has emerged not once, but on multiple occasions on our planet. Consequently, the spectrum of living forms extends over various physical surfaces, accommodating a medley of extant life forms. This perspective redefines the discourse on life's genesis, urging us to acknowledge the existence of a thriving tapestry of life, each thread woven through distinct trajectories. Central to this paradigm is the idea that life thrives as a recurrent masterpiece of convergence, a tapestry of existence that finds expression through myriad pathways. Rather than a mere echo of a single blueprint, life emerges independently time and again, each instance a testimony to the creative act of a powerful intelligent creator.

A science forum was held at Arizona State University in February 2011, where the following dialogue between Dawkins and Venter was reported:

Venter: I'm not so sanguine as some of my colleagues here that there's only one life form on this planet we have a lot of different types of metabolism different organisms I wouldn't call you the same life-form as the one we have that lives in pH12 base that would dissolve your skin if we drop you at it. The same genetic it will have a common anything well you don't have the same genetic code in fact the micoplasmas use a different genetic code and it would not work  in yourself so there are a lot of variations on the unit
Dawkins: But you're not saying it belongs to a different tree of life from me
Venter: I well I think the Tree of Life is an artifact of some early scientific studies that aren't really holding up so the tree you know there may be a bush of life. Bush I don't like that word written but that's only I can see that so there's not a tree of life and in fact from our deep sequencing of organisms in the ocean out of now we have about 60 million different unique gene sets we found 12 that looked like a very very deep branching perhaps fourth domain of life that obviously is extremely rare that it only shows up out of those few sequences but it's still DNA based but you know the diversity we have in the DNA world I'm not so saying what in wedding ready to throw out the DNA world. 39 40

From the Last Universal Common Ancestor, LUCA, to Eukaryotic cells

C. Woese (2002): The evolution of modern cells is arguably the most challenging and important problem the field of Biology has ever faced41

G. E. Mikhailovsky (2021): It is puzzling why life on Earth consisted of prokaryotes for up to 2.5 ± 0.5 billion years (Gy) before the appearance of the first eukaryotes. This period, from LUCA (Last Universal Common Ancestor) to LECA (Last Eucaryotic Common Ancestor), we have named the Lucacene, to suggest all prokaryotic descendants of LUCA before the appearance of LECA. The structural diversity of eukaryotic organisms is very large, while the morphological diversity of prokaryotic cells is immeasurably lower.    42

Viruses with a different genetic alphabet
Stephen Freeland (2022):The genetic material of more than 200 bacteriophage viruses uses 1-aminoadenine (Z) instead of adenine (A). This minor difference in chemical structures is nevertheless a fundamental deviation from the standard alphabet of four nucleobases established by biological evolution at the time of life's Last Universal Common Ancestor (LUCA). Placed into broader context, the finding illustrates a deep shift taking place in our understanding of the chemical basis for biology. 43

Yasemin Saplakoglu (2021): These viruses use a unique genetic alphabet not found anywhere else on the planet. The blueprint for life on our planet is typically written by DNA molecules using a four-letter genetic alphabet. But some bacteria-invading viruses carry around DNA with a different letter — Z — that may help them survive. And new studies show it is much more widespread than previously thought. A series of new papers describe how this strange chemical letter enters into viral DNA, and researchers have now demonstrated that the "Z-genome" is much more widespread in bacteria-invading viruses across the globe — and may have even evolved to help the pathogens survive the hot, harsh conditions of our early planet. DNA is almost always made up of the same four-letter alphabet of chemical compounds known as nucleotides: Guanine (G), cytosine (C), thymine (T) and adenine (A). A DNA molecule consists of two strands of these chemicals that are tied together into a double-helix shape. DNA's alphabet is the same whether it's coding for frogs, humans or the plant by the window, but the instructions are different.

In 1977, a group of scientists in Russia first discovered that a cyanophage, or a virus that invades a group of bacteria known as cyanobacteria, had substituted all of its As for the chemical 2-aminoadenine (Z). In other words, a genetic alphabet that typically consists of ATCG in most organisms on our planet was ZTCG in these viruses.  For decades, this was a head-scratching discovery — as weird as spelling apples “zpples” — and little was known about how this one-letter substitution may have impacted the virus. In the late 1980s, researchers found that this Z nucleotide actually gave the virus some advantages: it was more stable at higher temperatures, it helped one strand of DNA bind more accurately to the second strand of DNA after replication (DNA is double-stranded), and Z-DNA could resist certain proteins present in bacteria that would normally destroy viral DNA. Now, two research groups in France and one in China have discovered another piece of the puzzle: how this Z-nucleotide ends up in the genomes of bacteriophages — viruses that invade bacteria and use its machinery to replicate.

Factory Z
All three research groups, using a variety of genomic techniques, identified a part of the pathway that leads to the Z-genome in bacteriophages. The first two groups found two major proteins known as PurZ and PurB that are involved in making the Z-nucleotide. Once the cyanophage injects its DNA into bacteria to replicate itself, a series of transformations take place: Those two proteins make a precursor Z-molecule and then convert the Z precursor molecule into the Z-nucleotide. Other proteins then modify it so that it can be incorporated into DNA. The third group identified the enzyme responsible for assembling new DNA molecules from the parent DNA molecule: a DNA polymerase known as DpoZ. They also found that this enzyme specifically excludes the A-nucleotide and always adds the Z instead. For decades, the Z-genome was only known to exist in one species of cyanobacteria. "People believed that this Z-genome was so rare," Suwen Zhao, an assistant professor in the school of life science and technology at ShanghaiTech University and the senior author of one of the studies, said.  Zhao and her team analyzed sequences of the phages with the Z-genome and compared them to other organisms. They discovered that Z-genomes are actually much more widespread than previously thought. The Z-genome was present in more than 200 different types of bacteriophages.  The phages carrying this Z-genome "could be considered as a different form of life," Pierre Alexandre Kaminski, a researcher at the Institut Pasteur in France, senior author of another one of the studies and co-author on the third, said. But "it's difficult to know the exact origin," and it's necessary to explore the extent that this PurZ protein exists across bacteriophages — and maybe even organisms, he told Live Science.

Kaminski and his group analyzed the evolutionary history of the PurZ protein and discovered that it is related to a protein called PurA found in archaea that synthesizes the A-nucleotide. This "distant" evolutionary connection raises the question of whether the proteins involved in making the Z-nucleotide first arose in bacteria and were eventually adapted by viruses, or whether they occurred more frequently in preliminary lifeforms on the planet, perhaps even within cells,  PurZ and DpoZ are often inherited together, which suggests that the Z-genomes has existed alongside normal DNA since the early days of life on our planet, before 3.5 billion years ago, they wrote. What's more, an analysis conducted in 2011 of a meteorite that fell in Antarctica in 1969 discovered the Z-nucleotide alongside some standard and nonstandard nucleotides likely of extraterrestrial origin, "raising a potential role for Z in early forms of life," they wrote.

Future Z
It's possible that this Z-genome, if it existed that early in our planet's history, could have conferred an advantage to early lifeforms. "I think it's more suitable for Z-genome organisms to survive in the hot and the harsh environment" of the early planet, Zhao said.  The Z-genome is very stable. When two strands of normal DNA join together to form a double helix, two hydrogen bonds bind A to T, and three hydrogen bonds bind G to C. But when A is replaced with Z, three hydrogen bonds bind them together, making the tie stronger. This is the only non-normal DNA that modifies the hydrogen bonding, Kaminski said. But it's no surprise that the Z-genome is not widespread across species today. The Z-genome creates very stable, but not flexible, DNA, Zhao said. For many biological events, such as replicating DNA, we need to unzip the double-strand, and the extra hydrogen bond makes unzipping more difficult, she said. "I think it's more suitable for hot and harsh environments, but not this more comfortable environment right now," Zhao said.  Still, the Z-genome's stability makes it an ideal candidate for certain technologies. Now that researchers know which proteins the virus uses to make these Z-genomes, scientists can make them themselves. "Now we can produce the Z-genome on a large scale," Zhao said. 44

A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes

Dona Sleiman (2021): Cells have two purine pathways that synthesize adenine and guanine ribonucleotides from phosphoribose via inosylate. A chemical hybrid between adenine and guanine, 2-aminoadenine (Z), replaces adenine in the DNA of the cyanobacterial virus S-2L. We show that S-2L and Vibrio phage PhiVC8 encode a third purine pathway catalyzed by PurZ, a distant paralog of succinoadenylate synthase (PurA), the enzyme condensing aspartate and inosylate in the adenine pathway. PurZ condenses aspartate with deoxyguanylate into dSMP (N6-succino-2-amino-2′-deoxyadenylate), which undergoes defumarylation and phosphorylation to give dZTP (2-amino-2′-deoxyadenosine-5′-triphosphate), a substrate for the phage DNA polymerase. Crystallography and phylogenetics analyses indicate a close relationship between phage PurZ and archaeal PurA enzymes. Our work elucidates the biocatalytic innovation that remodeled a DNA building block beyond canonical molecular biology.


Bacteriophage genomes contain many modified nucleotides that are enzymatically synthesized and then incorporated by polymerization. The most conspicuous is 2-aminoadenine (hereafter referred to as Z), which was found in Synechococcus phage S-2L (1) and has also been detected in meteorites, suggesting a prebiotic existence. Z completely replaces the canonical adenine in S-2L DNA, increasing its thermostability because of a third hydrogen bond in the pair Z:T and altering the conformational properties of the double helix because of the presence of a 2-amino group in the minor groove, which renders S-2L DNA resistant to most restriction enzymes. The substitution of adenine (A) in S-2L DNA suggested an aminoadenine biosynthetic pathway encoded by the phage. This is in line with the fact that the S-2L genome encodes a putative homolog of succinoadenylate synthase PurA, which catalyzes the first step of de novo biosynthesis of adenosine 5′-monophosphate (AMP) by coupling the hydrolysis of guanosine 5′-triphosphate (GTP) with the synthesis of succinoadenylate from L-aspartate and inosine 5′-monophosphate (IMP). We identified PurZ homologs in several bacteriophages, notably in the PhiVC8 phage infecting Vibrio cholerae, whose DNA contains amino adenine instead of adenine. This prompted us to characterize the activity of the PurZ enzymes, to elucidate the biosynthetic pathway for amino adenine nucleotides, and to probe it in vivo. We first expanded our search for PurA and PurZ homologs and found candidates in 60 other phages infecting distantly related bacteria (mostly Actinobacteria, Firmicutes, and Proteobacteria). Phylogenetic analysis revealed a clear distinction between prokaryotic and eukaryotic canonical PurA sequences on the one hand and phage PurZ sequences (pink) falling into a clade embedded within archaeal PurA sequences on the other hand (green) (Fig. 1 and fig. S1). The PurZ clade also includes some bacterial homologs (blue), which could originate from phages. This evolutionary closeness is consistent with two specific deletions that are not found in bacterial and eukaryotic PurA. The evolutionary distinction between the PurZ clade and cellular PurA is also confirmed by a number of specific sequence signatures corresponding to Vibrio phage PhiVC8 amino acids S14, R230, I234, G238, L255, G256, and T262. In particular, the essential D13 residue (S14 in PhiVC8) in Escherichia coli PurA  is not conserved in PurZ sequences. 45



1. Nejc Kejzar: New Vista into Origins of Viruses from a Prototypic ssDNA Phage May 27, 2022
2. Curtis A. Suttle: Viruses in the sea  14 September 2005
3. Hugh Ross: Viruses and God’s Good Designs March 30, 2020
4. Ramesh K Goel: Viruses and Their Interactions With Bacteria and Archaea of Hypersaline Great Salt Lake 2021 Sep 28
5. Eugene V. Koonin: Global Organization and Proposed Megataxonomy of the Virus World 4 March 2020
6. Eugene VKoonin: A virocentric perspective on the evolution of life October 2013
7. Rachel Nuwer  Why the world needs viruses to function  (2020)
8. P.Forterre: Origin of Viruses 2008
9. Gladys Kostyrka: What roles for viruses in origin of life scenarios? 27 February 2016
10. Rybicki: Virus origins: from what did viruses evolve or how did they initially arise? 12th August 2015
11. Steven W. Wilhelm: Ocean viruses and their effects on microbial communities and biogeochemical cycles 2012 Sep 5.
12. G.Witzany: Viruses are essential agents within the roots and stem of the tree of life 21 February 2010
13. Eugene V. Koonin: The global virome: how much diversity and how many independent origins? 2022 Sep 12
14. Eugene V. Koonin: Virus World as an Evolutionary Network of Viruses and Capsidless Selfish Elements 2, June 2014
15. Stephen Freeland: Undefining life's biochemistry: implications for abiogenesis 23 February 2022
16. Edward C. Holmes: What Does Virus Evolution Tell Us about Virus Origins? 2011 Jun; 85
17. Eugene V. Koonin: Multiple origins of viral capsid proteins from cellular ancestors March 6, 2017
18. Eugene V. Koonin:  Evolution of an archaeal virus nucleocapsid protein from the CRISPR-associated Cas4 nuclease 2015
19. Stephen J. Gould, Wonderful Life: The Burgess Shale and the Nature of History 1990
20. Fazale Rana: Repeatable Evolution or Repeated Creation? 2001
21. J. William Schopf: Life’s Origin 2002
22. Fazale Rana: Newly Discovered Example of Convergence Challenges Biological Evolution 2008
23. Hugh M. B. Harris: A Place for Viruses on the Tree of Life 14 January 2021
24. Matti Jalasvuori  Viruses: Essential Agents of Life (2012)
25. Julia Durzyńska  Viruses and cells intertwined since the dawn of evolution  (2015)
26. Eugene V. Koonin:  The Logic of Chance : The Nature and Origin of Biological Evolution (2012)
27. Shanshan Cheng: Viral Capsid Proteins Are Segregated in Structural Fold Space February 7, 2013
28. Rob Phillips: A comprehensive and quantitative exploration of thousands of viral genomes 2018 Apr 19
29. Carmen San Martin: Structure and Assembly of Complex Viruses  19 April 2013
30. Roya Zandi: How a Virus Circumvents Energy Barriers to Form Symmetric Shells March 2, 2020
31. Viruses and the tree of life 19 March 2009
32. Arturo Becerra and Luis DelaLAye: THE UNIVERSAL ANCESTOR AN UNFINISHED RECONSTRUCTION 2016
33. Eugene V. Koonin: Global Organization and Proposed Megataxonomy of the Virus World 4 March 2020
34.  Vincent Racaniello Viruses and the tree of life 19 March 2009
35. Eugene V. Koonin: Multiple origins of viral capsid proteins from cellular ancestors March 6, 2017
36. D M Raup: Multiple origins of life. May 1, 1983
37. W. Ford Doolittle: Pattern pluralism and the Tree of Life hypothesis February 13, 2007
38. Douglas L. Theobald: A formal test of the theory of universal common ancestry 2010 
39. Youtube: Dr. Craig Venter Denies Common Descent in front of Richard Dawkins! 2011 
40. Evolution News: Venter vs. Dawkins on the Tree of Life — and Another Dawkins Whopper March 9, 2011
41. Carl R. Woese: On the evolution of cells June 19, 2002
42. George E. Mikhailovsky: LUCA to LECA, the Lucacene: A model for the gigayear delay from the first prokaryote to eukaryogenesis  1 April 2021
43. Stephen Freeland: Undefining life's biochemistry: implications for abiogenesis 23 February 2022
44. Yasemin Saplakoglu: Some viruses have a mysterious 'Z' genome April 29, 2021

45. Dona Sleiman Et al: A third purine biosynthetic pathway encoded by aminoadenine-based viral DNA genomes 2021 Apr 30



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Universal Common descent


Did life start polyphyletic, diversified, or monophyletic, with a universal common ancestor? 

In the world of scientific research, it's imperative to challenge established paradigms to ensure that our understanding of the natural world is accurate and unbiased. However, when it comes to the theory of universal common ancestry and the Tree of Life, it's concerning that dissenting voices have been stifled, and questioning the status quo is often met with resistance. Science should always be open to critical evaluation and new evidence. The problem arises when the theory of universal common ancestry is treated as an unassailable truth rather than a hypothesis that should continuously be examined and scrutinized. By accepting universal common ancestry as an unquestioned dogma, we risk overlooking alternative explanations and interpretations of the evidence. It's true that some proponents of intelligent design consider universal common ancestry as a possibility within their frameworks. However, their acceptance of this idea doesn't negate the fact that there are legitimate questions and concerns about its validity. One is the assumption that all life forms can be neatly arranged into a hierarchical tree-like structure. While the concept of a nested hierarchy is often touted as evidence for common ancestry, there are instances where the observed data doesn't fit this model. Some researchers have pointed out cases where organisms display traits that don't align neatly with the expected branches on the tree. These instances are not anomalies to be brushed aside, but rather valid points of inquiry that deserve rigorous investigation. Furthermore, the lack of transitional forms in the fossil record presents another challenge. The expected abundance of intermediate forms connecting different species is often absent. This gap in the fossil record raises questions about the gradual, step-by-step process of evolution posited by the theory of universal common ancestry. Rather than simply fitting evidence into the preconceived framework of the Tree of Life, scientific inquiry should prioritize a thorough examination of the evidence itself. If there are cases where the evidence doesn't align with the tree-like structure, it's essential to explore alternative explanations rather than ignoring or dismissing the discrepancies.

If one looks into the scientific literature, nothing is certain. O. Zhaxybayeva (2004): There is disagreement on the location of the root of the Tree of Life (e.g. different studies place the root: 

1. within the bacterial domain or on the branch that leads to the bacterial domain; 
2. within the eukaryotic domain; 
3. within the archaeal domain; 
4. yield inconclusive results. The timing of the organismal cenancestor is another unresolved question. 1

It's intriguing to note that within the scientific community itself, there exists a degree of uncertainty and debate regarding fundamental aspects of the Tree of Life. As O. Zhaxybayeva highlighted in her 2004 work, the very foundation of the tree—the location of its root—is a subject of contention. This lack of consensus on the root's placement speaks to the complexity of the evolutionary narrative. It's not just a matter of neat branches representing clear evolutionary pathways. Instead, researchers have proposed different starting points for the Tree of Life, which encompasses bacteria, archaea, and eukaryotes. The implications of these varying root placements are significant, as they shape our understanding of the relationships between these domains. Interestingly, this disagreement echoes a key concern that I and others have raised.  The issue of the timing of the organismal cenancestor—the common ancestor of all living beings—is another unresolved aspect. This uncertainty underscores the limitations of our knowledge when it comes to tracing back the origins of life. While proponents of universal common ancestry may argue that these uncertainties are just a part of the ongoing scientific process, they also provide room for alternative viewpoints.

The dismissal or questioning of the Genesis account of special creation is a topic that raises significant questions about the intersection of science, faith, and interpretation. Many argue that the Genesis narrative should not be taken literally and that it belongs to the realm of ancient myths and allegories. However, such a viewpoint might be overlooking the profound significance and depth of the biblical account. While some contend that the age and cultural context of Genesis diminishes its relevance and reliability, it's important to consider that the Bible has been a source of guidance and inspiration for countless individuals throughout history. The argument that Genesis is an ancient myth doesn't necessarily negate its potential theological and philosophical value. In fact, the Bible's capacity to convey complex truths through symbolic language is a hallmark of its enduring impact. Genesis 1:1's concise declaration, "In the beginning, God created the heavens and the earth," holds immense depth within its brevity. This single sentence encapsulates the concept of a divine creator initiating the universe's existence. In the realm of information theory, it's crucial to recognize that semantic weight extends beyond word count; it encompasses the meaning conveyed. In this sense, Genesis 1:1 stands as a powerful statement that informs us about the ultimate origin of the cosmos. In the scientific pursuit of understanding origins, a level of humility is required. The array of theories, suppositions, and hypotheses regarding the beginning of the universe, life, and biodiversity highlights the inherent complexity of these questions. The terms used by scientific investigators, such as "probably," "suppose," and "most likely," underline the ongoing nature of scientific exploration and the inherent uncertainties in understanding these monumental issues. Contrastingly, the Bible's account provides a definitive perspective on the origin of life and species. It presents a narrative that underscores the significance of life's creation from the very beginning and its subsequent diversification. From a creationism standpoint, the biblical account offers a coherent explanation for the origins of life and the universe, grounded in a divine purpose and intention.

Gen. 1.11: Then God said, "Let the land produce vegetation: seed-bearing plants and trees on the land that bear fruit with seed in it, according to their various kinds." And it was so.
Gen. 1.21: So God created the great creatures of the sea and every living and moving thing with which the water teems, according to their kinds, and every winged bird according to its kind. And God saw that it was good.
Gen. 1.24: And God said, "Let the land produce living creatures according to their kinds: livestock, creatures that move along the ground, and wild animals, each according to its kind." And it was so.
Gen. 1.26/27: Then God said, "Let us make man in our image, in our likeness, and let them rule over the fish of the sea and the birds of the air, over the livestock, over all the earth, and over all the creatures that move along the ground." 27 So God created man in his own image, in the image of God he created him; male and female he created them.

When examining the contrasting narratives of the Genesis account and the theory of evolution proposed by Darwin, we encounter a pivotal crossroads where belief and evidence intersect. The choice ultimately boils down to whether we accept the account presented in Genesis or embrace the evolutionary perspective put forth by Darwin. The Genesis account offers a comprehensive and distinct portrayal of origins. It outlines a series of events through which a transcendent Creator brought the universe, life, and diversity into existence. This narrative is not merely a random assortment of events; it carries the weight of profound theological and philosophical implications. From the creation of light to the formation of distinct species, Genesis provides a coherent framework that asserts a purposeful intent behind the universe's formation. On the other hand, Darwin's theory of evolution presents an alternative viewpoint rooted in natural processes and gradual change over immense spans of time. The theory postulates a Universal Common Ancestor from which all life forms are said to have originated. While the theory has garnered significant scientific support and has shed light on various mechanisms driving adaptation and change within populations, it does encounter certain challenges when it comes to explaining the origins of complex structures and the apparent gaps in the fossil record. When evaluating which of these accounts is most likely true, it's important to recognize that both perspectives involve an element of belief. In the case of the Genesis account, it relies on faith in a divine Creator and the authority of sacred scripture. Conversely, the theory of evolution rests on a framework built upon observations and scientific methodologies. The absence of empirical, verifiable, and replicable evidence demonstrating primary macroevolutionary transition zones of speciation and population differentiation is a point of contention that has long been raised by critics of the evolutionary paradigm. This is an issue that challenges the core principles of evolutionary theory as they relate to the macroevolutionary processes that purportedly drive significant transitions between species. Since the publication of Darwin's seminal work, "On the Origin of Species," numerous scientific papers have been published that discuss and explore various mechanisms and concepts within the framework of evolution. These papers have contributed significantly to our understanding of microevolutionary processes such as natural selection and genetic variation. However, the observed instances of microevolutionary changes, such as variations within species, do not necessarily provide direct evidence for the mechanisms driving macroevolutionary transitions. Macroevolutionary changes involve much more substantial transformations, including the emergence of new species and higher taxonomic groups. Despite the extensive research and accumulated knowledge in the field of evolutionary biology, there remains a notable absence of empirical evidence demonstrating the step-by-step mechanisms that lead to the formation of distinct new species through intermediate stages. This raises questions about the plausibility of macroevolutionary processes operating solely through naturalistic mechanisms. The complexity and information-rich nature of biological systems evidence the involvement of a guiding intelligence and purposeful design. The complexity, specified information, and irreducible structures found in living organisms raise questions about the adequacy of purely natural explanations. The challenges faced by evolutionary mechanisms in explaining certain aspects of life's development invite consideration of alternative explanations.

Alberts (2022): The living world consists of three major divisions, or domains: eukaryotes, bacteria, and archaea. The great variety of living creatures that we see around us are eukaryotes. The name is from Greek, meaning “truly nucleated”, reflecting the fact that the cells of these organisms have their DNA enclosed in a membrane-bound organelle called the nucleus. Visible by simple light microscopy, this feature was used in the early twentieth century to classify living organisms as either eukaryotes (those with a nucleus) or prokaryotes (those without a nucleus). We now know that prokaryotes comprise two of the three major domains of life, bacteria, and archaea. Eukaryotic cells are typically much larger than those of bacteria and archaea; in addition to a nucleus, they typically contain a variety of membrane-bound organelles that are also lacking in prokaryotes. The genomes of eukaryotes also tend to run much larger—containing more than 20,000 genes for humans and corals, for example, compared with 4000–6000 genes for the typical bacteria or archaea. In addition to plants and animals, the eukaryotes include fungi (such as mushrooms or the yeasts used in beer- and bread-making), as well as an astonishing variety of single-celled, microscopic forms of life. 2

Was there a First and a Last Universal Common Ancestor?

In his book, Darwin suggests that all living organisms are related by ascendency, and therefore they are all derived from ancestral species, which migrate around the world and diversify, generating the amazing biodiversity of organisms (Darwin, 1859).

K. Padian (2008): A sketch Darwin made soon after returning from his voyage on HMS Beagle (1831–36) showed his thinking about the diversification of species from a single stock (see Figure). This branching, extended by the concept of common descent, eventually formed an entire 'tree of life, developed enthusiastically by his German disciple Ernst Haeckel in the decades following the Origin. 3

Beyond Evolution: The Origin of Species by Design 41586_2008_Article_BF451632a_Figc_HTML

Charles Darwin's 1837 sketch of the diversification of species from a single stock. Credit: CAMBRIDGE UNIV. LIB./DARWIN-ONLINE.ORG.UK

This sketch, the "Tree of Life," illustrates Darwin's early conceptualization of how species could have descended from a common ancestor and diversified over time. Darwin's sketch encapsulates the essence of this idea: that the diversity of life on Earth can be explained through a process of descent with modification. The branches of the tree represent the different species that have emerged from a single ancestral species, showcasing the notion of common ancestry. This representation highlights the concept that the vast array of species we observe today is the result of gradual changes and adaptations accumulated over generations. While this sketch is a fundamental aspect of Darwin's legacy, it's important to acknowledge that the debate surrounding the Tree of Life concept continues to this day. The challenges to Darwin's theory include not only the gaps in the fossil record and the absence of direct transitional forms, as previously discussed but also questions regarding the mechanisms that can drive the complexity and diversity observed in living organisms. From an intelligent design standpoint, Darwin's Tree of Life sketch raises important considerations. 

D.Moran: Though the tree of life idea had been used to visualize taxonomy by Carl Linneaus, it became foundational as a tool for the development of Darwin’s evolutionary hypothesis.  Lines connecting groups of organism branched off to more specific and supposedly related forms.  Darwin saw that the connections made to groups and the position of species within a group were the result of shared similarities through ancestral descent.  His theory was one attempt at explaining how those relationships might have come to exist.  Ancestry was presumed to give rise to multiple lineages that diverged to create new life forms.  Natural selection was the driving force for the divergence of species from a common ancestor.  Natural variation within a type of organism was the generator of novel traits.  Together, variation and selection would prove life evolved to its current time in existence.

M.A. Ragan (2009): The rapid growth of genome-sequence data since the mid-1990s is now providing unprecedented detail on the genetic basis of life, and not surprisingly is catalyzing the most fundamental re-evaluation of origins and evolution since Darwin’s day. Several papers in this theme issue argue that Darwin’s tree of life is now best seen as an approximation—one quite adequate as a description of some parts of the living world (e.g. morphologically complex eukaryotes), but less helpful elsewhere (e.g. viruses and many prokaryotes); indeed, one of our authors goes farther, proclaiming the “demise” of Darwin’s tree as a hypothesis on the diversity and seeming naturalness of hierarchical arrangements of groups of living organisms. 4

1. Peter Gogarten Cladogenesis, coalescence and the evolution of the three domains of life 2004 Apr;2
2. B.Alberts: Molecular Biology of the Cell, 7th edition 2022
3. Kevin Padian: Darwin's enduring legacy 06 February 2008
4. Mark A. Ragan: The network of life: genome beginnings and evolution 2009 Aug 12

Reasons to Refute the Claim of  Universal Common Ancestry 
https://reasonandscience.catsboard.com/t2239-evolution-common-descent-the-tree-of-life-a-failed-hypothesis#10954



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5


Adaptation & Microevolution


Adaptation: This is a process by which organisms become better suited to their environment over time. It can also refer to the specific features or behaviors that evolve in response to environmental pressures, making an organism more fit to survive and reproduce.
Microevolution: This refers to small-scale changes in allele frequencies in a population over a few generations. These changes can lead to variation within species but don't necessarily result in the formation of new species (macroevolution).

The Mechanisms of Microevolution

Mutation: Random changes in DNA can introduce new genetic variations.
Gene Flow: Also known as migration, this occurs when individuals from different populations interbreed, causing alleles to be exchanged between populations.
Genetic Drift: This is a random change in allele frequencies due to chance events. It's more significant in smaller populations.
Natural Selection: It's the process by which traits that enhance survival and reproduction become more common in a population over generations.
Sexual Selection: A form of natural selection where individuals with certain inherited characteristics are more likely than other individuals to obtain mates.

The Role of Adaptation in Microevolution

Adaptation plays a central role in microevolution. As environmental pressures change (due to factors like climate change, predator-prey relationships, availability of food, etc.), organisms that possess traits that offer a survival advantage are more likely to survive and reproduce. Over time, these traits become more common in the population, leading to evolutionary change on a small scale. For example, if a population of beetles is exposed to a new predator that can easily spot bright-colored beetles, the darker-colored beetles might have a higher survival rate. Over time, the frequency of dark-colored beetles in the population may increase.

Beyond Evolution: The Origin of Species by Design 96456310

What is the current understanding, that drives adaptation & microevolution ?

In light of the expansive body of knowledge and burgeoning research, it's evident that the evolutionary process is not only a product of random genetic variations but also entails intricate cellular mechanisms. These cellular activities suggest a highly coordinated and precise system, alluding to a potential underlying design. Cells, the fundamental units of life, possess inherent qualities of intelligence and self-awareness. This isn't merely a theoretical assumption. In fact, recent studies demonstrate how cells use filopodia, actin-based extensions from their membranes, to coordinate tasks as complex as angiogenesis. This showcases active forms of basal perception, adaptive problem-solving, and precise time-keeping. Such sophisticated coordination and communication among cells underline the fact that these aren't mere biochemical happenstances but rather intricate, deliberate processes. These cellular processes reflect a self-referential awareness, an innate 'knowing' quality. This self-awareness is not just an abstract concept; it has concrete biological implications. For instance, the defense of 'self' is fundamental to the development of life, underpinning its immunological context. Whenever cells process and utilize information, they're essentially employing problem-solving techniques to maintain homeorhesis – dynamic states of balance supporting their vitality. Beyond the cellular level, the very fabric of multicellularity seems woven with precision. Multicellular organisms aren't just conglomerates of cells; they represent highly coordinated, interdependent networks, working in tandem. The nature of this coordination suggests not just randomness but deliberate, orchestrated action. A pivotal example is how cells collectively construct niches, optimizing their environment to promote their survival and functionality. This nuanced understanding of cellular processes and multicellularity extends our definition of cognition. Cognition entails mechanisms allowing organisms to acquire, process, store, and act on environmental information. And this doesn't just apply to higher organisms but spans all living entities, including microbes. The intricate dynamics of information processing observed in cells and multicellular entities echo human cognition, indicating that life, in all its forms, operates on a continuum of cognitive complexity.

Delving further, it becomes evident that there's an underlying structure and coordination that transcends the narrative of mere randomness. The propositions we're exploring further underline the intricate nature of biological development.

Directed Phenotypic Variations: Rather than purely random events, the variations in phenotype, as evidenced in natural cellular engineering and niche constructions, predominantly emanate from directed cellular responses. These are reactions to specific environmental and epigenetic challenges, suggesting a proactive and adaptive problem-solving approach at the cellular level.
Holobionts as Collaborative Entities: The notion that all multicellular eukaryotes are holobionts, comprised of various cellular domains (Prokaryota, Archaea, Eukaryota), offers a panoramic view of evolution. This proposes that evolutionary variance isn't the sole realm of individual entities but rather a collaborative endeavor, co-engineered with the inclusion of viral symbioses. This collective effort underlines the complexity of life and its interconnectedness.
Protection of Self-Identity through Collaboration: The intricate processes of natural cellular and genetic engineering primarily aim to safeguard the self-identity of each participating cellular entity. Interestingly, the most effective way to achieve this is through collaboration, emphasizing the inherent interdependence in the biological realm.
A Shift from Gene-Centrism to an Informational Interactome: Contrary to the gene-centric view of Neo-Darwinism, a more encompassing perspective emerges, viewing biology as an interwoven network of information-based interactions. This "informational interactome" illustrates a mutually beneficial relationship between cognitive organisms and their environments. Here, genes are not the dictators of fate but rather tools at the disposal of intelligent cells, further showcasing the proactive nature of cellular life.

Historically, the Modern Synthesis, while foundational, has not been without critiques. Many researchers have expressed the need for its evolution, especially regarding sources of adaptive variation. Despite these evolving perspectives, the bedrock of the Modern Synthesis remains - that adaptive evolution primarily arises from natural selection acting on variability originating from unintentional genetic changes. However, this does not mean that the role of epigenetic mechanisms, lateral transfers, transposable elements, and paramutations are negligible. They are recognized, albeit as secondary players in the evolutionary stage. Yet, the prevailing consensus, even in light of these contributions, underscores that changes in allele frequency, driven by natural selection, remain the principal driver of the evolution of adaptive traits. Visualized through a landscape of 'adaptive peaks' and 'phenotypic valleys', evolution in this view appears as a journey navigated by organisms over eons, influenced predominantly by random genetic fluctuations.

The Cognition-Based Evolution (CBE)

In contrast, the perspective of non-random genome editing and the intelligence-driven paradigm of cognition-based evolution challenge this stance, suggesting a more coordinated and strategic evolutionary journey. Evolution, the continuous and vast process of change in life on Earth, has long been debated, dissected, and posited through myriad frameworks, theories, and models. Neo-Darwinism, rooted in the ideas of random genetic mutations and natural selection, has been one of the most dominant narratives. However, the emergence of the Cognition-Based Evolution (CBE) model presents an intriguing pivot from traditional thinking, centering the cell as the pivotal player in the grand evolutionary scheme. 

Self-referential Cellular Dynamics: At the heart of CBE lies the idea that cells are not merely passive recipients of genetic instructions but are active participants in evolutionary processes. Each cell embodies a certain level of intelligence, manifested through its capability for self-reference – its ability to perceive, process, and act upon information in ways that prioritize its own well-being. This cellular 'self-awareness', so to speak, stands distinct from the mechanical processes that govern non-living systems. For instance, the role of filopodia in angiogenesis, as pointed out, serves as evidence of cellular communication and coordination, going beyond the mere passive processes to active problem-solving.
The Spectrum of Cognition: Grounding the discussion of cognition is the understanding that it isn't restricted to higher-order organisms alone. Basal cognition, even as its definitions vary, universally acknowledges the fundamental processes of acquiring, processing, storing, and acting on environmental information. This extends not just to animals, but to all living forms, including microbes. The assertion here, then, is that the spectrum of cognition observed across life forms is continuous, bridging the gap between the simplest single-celled organisms and complex beings like humans.
Multicellularity and Collaboration: CBE posits that multicellularity – the complexity of interdependent cells that make up multicellular organisms – isn't just a result of random genetic mutations. Instead, it is the outcome of coordinated cellular actions, problem-solving, and collaboration. As cells communicate, assess their environments, and make informed decisions, they engineer their own niches and collectively contribute to the organism's adaptation and evolution.
The Contrast with Neo-Darwinism: While Neo-Darwinism emphasizes the randomness of genetic mutations and the role of natural selection, CBE offers a more proactive narrative. Instead of viewing genes as the driving force, CBE envisions them as tools employed by intelligent cells to ensure survival and adaptation. Evolution, in this framework, is not just a passive process of survival of the fittest but an active collaboration between intelligent cellular entities, responding to and shaping their environments.

In essence, CBE underscores the vital role of cellular intelligence and coordination in evolution, a shift from the randomness emphasized in Neo-Darwinism. It paints a picture of life as an intricate dance of communication, collaboration, and coordination, where every cell plays an active role in crafting the evolutionary tale. With the increasing evidence supporting these ideas, it might be time to reframe our understanding of evolution, placing the intelligent cell at its center.

Emerging Perspectives and Challenges to the Modern Synthesis

The landscape of evolutionary biology has been marked by a series of debates, critiques, and elaborations on the Modern Synthesis (MS). The model of random genetic mutations and natural selection, while still influential, is being increasingly challenged by new insights and data. These challenges, which focus on the mechanisms underlying biological variation and the dynamics of evolution, suggest a more intricate and nuanced process than previously understood.

Beyond Randomness in Genetic Variation: The core assertion of the Cognition-Based Evolution (CBE) framework challenges the MS's foundation by suggesting that much of phenotypic variation arises from non-random cellular problem-solving. Cells, according to this perspective, are not passive entities but active participants in the evolutionary process, interacting with environmental and epigenetic factors to drive variation.
Holobionts and Co-Engineering: Another significant proposition from CBE is the idea of multicellular organisms as holobionts – complex entities formed from interactions between different cellular domains (Prokaryota, Archaea, Eukaryota) and even viruses. This co-engineering process, involving symbiotic relationships, suggests that evolutionary change is not just driven by individual genetic variations but also by collaborative efforts across cellular domains.
Genes as Cellular Tools: Moving away from the gene-centric view, CBE posits that genes are tools employed by intelligent cells to ensure survival and adaptation. This shifts the focus from genes as the primary drivers of evolution to cells as active agents employing genes to meet environmental challenges.
Biology as an Informational Interactome: Going further, CBE presents the idea that all of biology is best seen as a network of communication and interaction among organisms and their environments. Rather than a simple one-way flow of genetic information dictating outcomes, it's a complex web of interactions, feedback loops, and collaborations.
Traditional Standpoints and Their Challenges: Traditional views, epitomized by the MS, have remained steadfast in emphasizing the primacy of random genetic mutations and natural selection. While there's acknowledgment of other factors like lateral gene transfers or epigenetic mechanisms, the emphasis has primarily been on random mutations and allele frequency changes.

However, this traditional perspective hasn't gone uncontested. Notable theories challenging the steady, gradualistic view of evolution have emerged over time:

Saltational Theory: This posits that evolution takes place in large leaps or "jumps," resulting from significant mutations that give rise to entirely new species.
Punctuated Equilibrium: Gould and Eldridge's theory suggesting that evolutionary change is not gradual but marked by bursts of rapid change, followed by long periods of stasis.
Extended Evolutionary Synthesis: This calls for incorporating a broader range of mechanisms into the evolutionary framework, including epigenetic inheritance and niche construction.
Evolutionary Developmental Biology (Evo-Devo): Moczek's perspective, which critiques the idea of genes as blueprints and emphasizes the crucial role of environmental conditions in normative development.

The evolving perspectives on evolution are emblematic of the nature of science – it's dynamic, self-correcting, and always open to new data and interpretations. As more data accumulates, especially in the realms of cell biology, epigenetics, and environmental interactions, our understanding of evolution will likely continue to grow in complexity, capturing the intricate dance of life in all its facets. The Cognition-Based Evolution (CBE) framework introduces a radical shift in our understanding of evolutionary processes. Instead of viewing evolution solely as a byproduct of random genetic mutations and natural selection, CBE emphasizes the active role of cells, which possess intelligence and are capable of exchanging information with their environment and with each other.

Cells as Intelligent Measuring Units: At its core, CBE views cells as intelligent entities that actively measure and interact with their surroundings. They are not merely passive agents that change solely due to random genetic mutations. This view draws heavily from principles rooted in thermodynamics and the importance of energy and information exchange in living systems.
Beyond Randomness: Studies, such as those cited by Trerotola et al., indicate that genetic mutations or allelic polymorphisms are inadequate explanations for the full spectrum of observed heritable variation. Instead, CBE underscores that variation often arises from cellular measurements and collaborations across cellular domains, leading to co-engineered responses to environmental challenges.
Lessons from Unicellular Life: The behavior of prokaryotes (unicellular organisms without a nucleus) provides deep insights into the mechanisms underpinning biological variation.
Antibiotic Resistance: For instance, the exchange of antibiotic resistance genes in bacterial communities within biofilms demonstrates active information sharing in response to environmental threats. Biofilms are structured communities of microorganisms where cells are embedded in a matrix of self-produced polymeric substances. Within these communities, bacteria can communicate and collaborate, a phenomenon especially evident in the sharing of antibiotic resistance genes.
Quorum Sensing: A vital component of this collaborative behavior is quorum sensing, a system where bacterial cells communicate using signaling molecules. It enables collective behaviors and resource sharing among bacterial cells. In environments like biofilms, cells can indicate their ability to resist antibiotics, facilitating the transfer of resistance genes to other cells in the community.
Collaborative Gene Transfer: The method by which antibiotic resistance genes are transferred, often involving specialized structures like pili, highlights the intricacy and specificity of such interactions. This is not a random exchange; it requires mutual recognition and cooperation between donor and recipient cells. It underscores the notion that these cells possess a sense of self and can differentiate between self and non-self entities.
Re-envisioning Genes: Such interactions also emphasize that genes are not just passive units of inheritance but are tools that cells can deploy, share, and exchange in response to specific challenges. They can be seen as instruments in the toolbox of intelligent cells that actively measure, predict, and respond to their environment.

The CBE framework proposes a dynamic, collaborative, and interactive view of evolutionary biology. It emphasizes cooperation over competition, highlights the intelligence of cells, and underscores the importance of cellular interactions and information exchange in shaping evolutionary outcomes. Prokaryotes, with their complex behaviors like antibiotic resistance gene transfer, offer a glimpse into this intricate dance of mutual interactions, reinforcing the notion of biology as a collaborative co-engineering process. The rich tapestry of interactions and collaborations, from the scale of individual cells to that of multicellular organisms, underscores the need for an expanded understanding of evolutionary processes beyond the confines of traditional Neo-Darwinism.

Genetic Engineering in Nature

Across various domains of life, cells often exhibit an innate ability to engineer genetic modifications. These alterations, typically seen as responses to environmental cues, are intricate, controlled, and more than just random events, reflecting a dynamic cellular intelligence at play.

Trans-Kingdom Genetic Transfers

Agrobacterium tumefaciens: This bacterium is an example of nature's genetic engineer, with an ability to transfer genes to plant cells. The Ti plasmid within the bacterium carries the vir genes that facilitate the DNA transfer to plant cells, subsequently modifying them. The transferred genes can affect plant growth or stimulate the synthesis of compounds that the bacterium uses for its nourishment. Unlike pili-mediated transfer in some prokaryotes, this bacterium uses a complex mechanism involving membrane fibrils for cell attachment. Such a process highlights the bacterium’s capacity to sense plant-derived signals, respond with synchronization, and strategically turn off its virulence system post-infection.

Cellular Response to Environmental Stress

Pseudomonas fluorescens: Lab experiments reveal that genetically-engineered immotile strains of this bacterium, devoid of flagella due to a fleQ deletion, can redevelop flagella within a mere 96 hours. They achieve this by repurposing existing genetic pathways, boosting the expression of alternative genes. Such genetic reconfigurations aren't free from trade-offs. Enhanced motility in these strains correlates with impaired nitrogen regulation. This suggests that cells, in their drive to adapt, often strike a balance between gaining a new advantage and losing an existing one.

Accelerated Mutagenesis

Escherichia coli: This bacterium exhibits an adaptive stress response called "accelerated target mutagenesis," where mutations are clustered in specific genomic regions. Such a focused mutation pattern challenges the traditionally held view of random mutations and underscores the precision with which cells can modulate their genetic material.

Bioengineering Applications

Rapamycin Exploration: Scientists tried to bioengineer Streptomyces rapamycinicus, a bacterium, aiming to produce new forms of rapamycin. When a temperature-sensitive replicon was introduced, instead of obtaining a single expected strain, they witnessed a range of unexpected variants. This observation suggested that a single genomic change can result in a myriad of genetic adaptations.
Cellular Adaptability: The production of these varied compounds, termed rapalogs, indicates that cells can engage in rapid genetic alterations, often in a specific genetic region, when faced with a new environmental challenge. The ability of cells to produce such diverse compounds in a short time frame is reminiscent of accelerated evolutionary bioengineering.

Cells, whether prokaryotic or eukaryotic, are not passive entities simply acted upon by environmental forces. They actively sense, respond, and sometimes even anticipate environmental changes by modifying their genetic machinery. The evidence points towards an intricate, active, and strategic cellular intelligence, suggesting a more nuanced understanding of evolution, beyond the traditional Neo-Darwinian randomness. The ability of cells to engineer their own genetics, sometimes at accelerated rates, presents a blend of evolutionary biology and engineering principles, potentially rewriting our understanding of cellular adaptability.

Collective Engineering in Biofilms: An Insight into Cellular Problem-Solving

Biofilms, a predominant form of prokaryotic life, represent complex communities of microorganisms that attach to surfaces and each other, embedded in a matrix of extracellular polymeric substances. Here, cells cooperate, compete, and even specialize in tasks, showcasing an intricate form of collective engineering.

Specialized Biofilm Engineering in Bacillus subtilis

Role Specialization: Cells within the Bacillus subtilis biofilm exhibit remarkable versatility. Depending on the environmental and surface conditions, they can specialize in producing an extracellular matrix optimized either for adhesion or for mobility.
Phenotypic Diversity: These specialized roles, which differ from their free-living state, culminate in unique phenotypes, each dedicated either to adhere or to move. Such specialization is an outcome of cooperative actions where cells trade resources and some even relinquish certain functions for the greater good of the collective.

The Cellular Senome: A Comprehensive Sensory Apparatus

Environmental Cue Processing: For cells to adapt and make decisions, they must effectively receive and interpret environmental signals. This crucial function is argued to be managed by the "senome," a conceptualized entity encompassing all sensory inputs of a cell.
Cellular Homeostasis and Information Management: By processing these sensory cues, cells maintain homeorhesis (a dynamic equilibrium). This sensory information connects to adaptive behaviors through intricate sensorimotor circuits in prokaryotes. The management of such information, considered a form of intracellular engineering, is integral to a cell's decision-making processes.

Senomic Integration in Collective Cellularity

Cognitive Gateway: The senome is not just a passive recipient of sensory data. It acts as a cognitive interface where sensory memories get translated into bioactive molecules. This process is universal across cellular domains.
Common Platform for Multicellularity: In multicellular arrangements, such as biofilms or holobionts (symbiotic associations of a host with diverse microbial communities), the aggregated senomic inputs from individual cells provide a shared informational platform.

Source of Biological Variation

From Cellular Response to Phenotypic Variation: The intricate cellular reactions derived from senomic inputs should be recognized as the origin of biological variation. Every phenotypic change, ultimately, has its roots at the cellular level. By responding and adapting to environmental cues, cells can manifest variations, driving evolution at a larger scale.  Biofilms, as complex microbial communities, underscore the collaborative engineering capacities of cells. The cellular senome offers a comprehensive understanding of how cells perceive, integrate, and act upon environmental signals. This insight reshapes our understanding of biological variations, positioning the cell, with its intricate machinery and adaptive capabilities, as the primary orchestrator of evolutionary changes.



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Variations in Multicellular Organisms: An Overview of Mechanisms and Insights

Before natural selection can act upon variations, those variations must first exist. This is consistent with Darwin’s original ideas.

There are four primary mechanisms that bring about hereditary change:

- Mutational copying errors
- Epigenetics
- Symbiosis
- Hybridization
- Viruses and Genetic Transfer

Emphasis is placed on the role of viruses in several of these mechanisms, especially through horizontal genetic transfer (HGT). In eukaryotes, evolutionary transitions are linked to the activity of viral transfers and transposons, especially in gene regulatory networks. For example, these elements play pivotal roles in the origins of the immune system.

Transposons and Eukaryotic Evolution: Transposons have been posited to be foundational in eukaryotic evolution, influencing the development of regulatory genetic networks integral to eukaryotic characteristics.
‘Biased’ Mutations and Facilitated Variation: There is evidence suggesting mutations aren't purely random. Some mutations target specific 'hot spots'. Another proposition is 'facilitated variation', which posits that phenotypic changes arise from mutations in limited genetic regions, mainly regulatory elements. While this theory attempts to support Neo-Darwinian ideas, it actually suggests biased, non-random mutation patterns, contradicting traditional beliefs.
Extended Evolutionary Synthesis: The idea of 'developmental bias' has been proposed as a directed, non-random mechanism leading to phenotypic variation. It supports a broader evolutionary perspective known as the Extended Evolutionary Synthesis.
Reconceptualizing the Genome: There's a growing consensus to consider the genome not just as a static repository of genes, but as a dynamic entity. Some, like Shapiro, suggest the genome should be seen as a "Read-Write" system, where environmental cues can lead to cellular adaptations written back into the genome. This can include epigenetic changes or even changes to the DNA sequence itself.
Mobile Genetic Elements: These elements move throughout the genome, offering coordinated signals. They act as a direct mechanism for internalizing cellular stresses, leading to adaptive expression, especially through non-coding DNA and RNAs.
Biocommunication: Viruses adjust their relationship with cells through this editing process.

The mechanisms driving genetic variation in multicellular organisms are diverse and intricate. Understanding these mechanisms is crucial for a more complete grasp of evolutionary processes. As we deepen our knowledge, traditional perspectives on evolution and genetics are being broadened, leading to richer, more nuanced models of heredity and adaptation.

Variations in Multicellular Organisms: Viral-Cellular Variation and the Role of Horizontal Gene Transfer

Microevolution & Adaptation as a Dynamic Process 

Evolution can be seen as a "verb" rather than a static "noun". This highlights the ongoing, active nature of evolutionary processes, further emphasized by the ‘Read-Write’ genome concept. Here, genomes are viewed not as fixed codes, but as pliable entities co-evolving with their environments. The vast network of interactions within the cell is not confined to localized or compartmentalized genetic activities. Processes like endocytosis, where one cell engulfs another, allow the recipient cell to gain a plethora of bioactive molecules or even genetic material. This transportation of material inside the cell happens through specialized vacuoles laden with both vital information and nutrients. As an example, specific cells, like those in breast cancer, can absorb lipoproteins that influence gene expression via receptor-mediated endocytosis. Viruses have also adapted to leverage such processes, using various strategies for cellular entry. Furthermore, the concept of endosymbiosis sheds light on the origins of eukaryotic cells. Eukaryotic organelles such as mitochondria and plastids are thought to have evolved from once free-living bacteria that were ingested and later formed a mutually beneficial relationship within the host cell. Over time, much of the engulfed genetic material migrated to the host genome, showcasing horizontal acquisition's potential. Entosis provides another illustration of cellular interaction. Through this process, one cell engulfs or invades another, transferring the whole genetic architecture. Some studies suggest that such transfers can be so comprehensive that they might even transfer learned behaviors in specific organisms. Horizontal gene transfer (HGT) has emerged as a crucial factor in the evolutionary journey. Initially seen as a contentious source of genetic variation, it's now recognized that HGT is rampant among unicellular organisms, reshaping their genomes over time. Bacterial genes, in particular, have been highly influenced by HGT, with research suggesting that up to three-quarters may have experienced at least one HGT event. Interestingly, even multicellular organisms are not exempt from HGT's influence. Microbial associations, for instance, have had profound impacts on larger eukaryotic entities, introducing novel metabolic capabilities. Endogenized retroviruses have carved their niche in evolutionary development. It's not just retroviruses that undergo this endogenization; various eukaryotic viruses can become part of the host genome. The sequences from these incorporated viruses can lead to the formation of entirely new genes. Viruses have particularly had a hand in driving evolutionary change, influencing the formation of essential structures like the placenta. As these viral insertions become embedded in the genome, they can also introduce changes in gene regulation. Certain research suggests that these retrotransposition events are more than just random occurrences but may be guided by specific interactions. Endogenous retroviruses (ERVs) can be found across all vertebrates. They are remnants of ancient germ-line infections. The influence of ERVs extends to crucial areas of evolution, such as the development of mammalian placentas. HGT is also prevalent between multicellular organisms and their microbial companions. The human microbiome, for instance, plays a role in our metabolism and immunity, but new findings hint at the possibility of direct genetic transfers between humans and their microbial residents. The updated perspective on genetics sees the genome as an intricate ecosystem. It houses a myriad of transposable elements (TEs) that establish themselves in unique, non-random patterns. These TEs interact in a dynamic environment characterized by both cooperation and competition. In eukaryotes, TEs might occupy a more significant chunk of the genomic DNA compared to prokaryotes. This prevalence of TEs has led to the horizontal expansion within genomes. There's growing evidence that these TE transfers and their subsequent integration into the genome might be guided events rather than random insertions.

These RNA-mediated processes underscore the flexibility and adaptability of the cellular genetic framework. The integration of various RNA molecules into the genome serves as an avenue for innovation, allowing cells to rapidly adjust to new challenges and environmental conditions. One example of this is the emergence of novel small RNAs, which are often derived from transposable elements and retroviruses. They play pivotal roles in regulating gene expression, especially in the context of stress responses and developmental transitions. Non-coding RNAs, like long non-coding RNAs (lncRNAs), have been implicated in diverse biological processes ranging from chromatin remodeling to the regulation of transcription and post-transcriptional modifications. The diverse repertoire of lncRNAs and their specific interactions with proteins and other RNAs highlights the intricacy and finesse with which the cellular machinery operates. Their emergence from retrotransposons and other mobile elements again emphasizes the evolutionary significance of these once-termed “junk” sequences. Moreover, the role of RNAs in epigenetic regulation cannot be understated. Epigenetics, referring to heritable changes in gene expression without changes in DNA sequence, is a vital component of cellular adaptability. Various RNAs, particularly small RNAs, are intricately involved in establishing and maintaining these epigenetic states. They function to guide the cellular machinery to specific sites in the genome, leading to modifications like DNA methylation or histone modification that change the chromatin landscape and, consequently, gene expression. The interconnectedness of DNA, RNA, and protein networks provides an elegant feedback system. While DNA houses the genetic information, RNAs, both coding and non-coding, act as mediators and regulators, ensuring the appropriate proteins are produced under given conditions. The proteins then, in turn, feed back to influence DNA packaging, replication, and transcription, often guided by RNAs. This multidimensional communication system allows for swift, adaptive changes.

Furthermore, the presence of viral and transposable sequences in genomes acts as a reservoir of potential genetic novelty. Rather than being mere parasites, these sequences can be co-opted by their host organisms for beneficial purposes, often playing roles in adaptation and evolution. This co-option is evident in cases like the evolution of the mammalian placenta, which involves genes derived from endogenous retroviruses. However, while this dynamic nature of genomes and the active role of horizontal gene transfer and mobile elements might suggest a chaotic system, it's essential to recognize the underlying regulatory mechanisms that keep these processes in check. Without appropriate checks and balances, the unbridled activity of transposable elements and unchecked horizontal gene transfer could be detrimental, leading to genomic instability. However as has been observed, these processes are often under tight cellular control, ensuring that while innovation is possible, genomic integrity is maintained. The intricate landscape of genetic and epigenetic components unveils a highly sophisticated and layered system of cellular evolution, adaptation, and function. The standard model of genetics, which traditionally stresses the central role of DNA in inheritance, is being expanded upon with the understanding of a diverse range of molecular actors – from circular DNAs and RNAs to prions and the expansive influence of the microbiome. The presence of extra-chromosomal circular DNAs and the diversity of RNA forms upend the conventional understanding of genetic information and its transmission. These entities underscore the notion that genetic information and regulatory mechanisms are far more dispersed and interactive than previously thought. It's not just the direct genetic information that impacts an organism's function and adaptation. The cellular environment, shaped by a myriad of regulatory RNA molecules and proteins, determines how genes are expressed and how they respond to external stimuli. The importance of circular RNAs in regulating gene expression, for instance, is becoming clearer, highlighting the need to understand genetics from a broader perspective than just linear DNA sequences. Moreover, the adaptability of organisms isn't solely based on their genomic content. Proteins, especially those like KRAB-ZFPs and virus-interacting proteins, also play pivotal roles in determining how organisms respond to environmental challenges. Their ability to interact with various cellular elements, including transposable elements TEs and viruses, signifies their importance in facilitating rapid adaptations and in potentially leading to longer-term evolutionary changes. Structural variations in DNA and RNA architectures further add to the complexity of genetic regulation and function. Such variations, when they arise in response to environmental stressors, can lead to immediate changes in an organism's phenotype, potentially providing it with an adaptive advantage. Furthermore, prions, while best known for their role in causing diseases, exhibit properties that can be beneficial, aiding in the evolution and adaptation of organisms, as evidenced by their role in yeast. Such findings necessitate a shift in understanding about what constitutes heritable information. The vast influence of the microbiome cannot be understated. As entities living in close symbiosis with us, these microorganisms play fundamental roles in a plethora of our physiological processes. Their genetic diversity and ability to influence our metabolism, immunity, and even nervous system demonstrate that to truly understand human biology and evolution, one must consider the collective genome of the holobiont – the host and its microbiota combined. The dynamic nature of genetic and epigenetic components, their interactions, and their roles in adaptation and function paint a picture of life that is interconnected, adaptable, and continuously evolving. As research progresses, it becomes evident that the realms of genetics and epigenetics are not separate but are deeply intertwined, each influencing and being influenced by the other.

The nuanced, dynamic responses of cells to environmental stressors demonstrate that heredity is not solely defined by DNA sequences, but is rather a culmination of a plethora of cellular activities and interactions, many of which are influenced by environmental inputs. This concept of cellular information management emphasizes that cells are not passive entities merely governed by their genetic code; rather, they are proactive agents that actively manage, process, and act upon information. This underscores the concept that genomes are not static, but are in a constant state of flux, adapting, and evolving in response to environmental cues and challenges. However, the processing and management of biological information is complicated by the inherent ambiguity of the signals that cells receive. The thermodynamic limitations of energy conversion into work, the physical barriers such as cellular membranes, and the uncertainty in communication sources all contribute to this ambiguity. Yet, cells have mechanisms to mitigate these challenges and ensure survival. One fundamental principle is that living systems operate under boundary conditions, primarily facilitated by membranes. Communication among cells is not always direct or clear. Without always knowing the sender or receiver, there is inherent uncertainty, which is further complicated by potential threats from external agents like pathogens. These factors collectively introduce variability and unpredictability into cellular decision-making. Yet, despite these challenges, cells have remarkably sophisticated mechanisms to assess, process, and act upon the information they receive. They are not just passive receivers; they measure and interpret the ambiguous signals, making decisions that best ensure their survival and functionality. But why do cells go through such lengths to process this information? The answer lies in the imperfections of biological information. If cells were always presented with perfect, unambiguous signals, there would be no need for such intricate processing mechanisms. But the very nature of life, with its uncertainties and challenges, necessitates these complex information management systems. Cells are not just simple entities dictated by their genetic codes. They are dynamic, adaptable systems that continuously interact with their environment, making decisions based on a mix of imperfect information.

The complexity and intricacy of these cellular tissue ecologies provide an extended depth to our understanding of life and its myriad interactions. Each cellular unit, while preserving its self-identity, plays a critical role in forming the foundational building blocks of multicellular organisms, orchestrating the dynamic ballet of biological processes that keep us alive. This intricate dance goes well beyond mere genetic blueprints; it encompasses the exchange of biological information, intricate feedback loops, and continuous environmental interactions. Further examining the tissue ecologies, we find evidence of constant cellular communication that is both directed and received. This cellular dialogue, a blend of chemical, physical, and informational exchanges, aids cells in responding adaptively to environmental cues. Cells do not merely react passively to their environment; they actively assess, measure, and interpret the signals they receive, refining their responses over time. 1 - 7 This behavior is demonstrative of a deep-rooted cellular intelligence, one that is not solely contingent on DNA instructions but is shaped by a mosaic of interactive elements, including non-coding RNAs, extracellular matrices, and cellular senomes. The mutualistic proteome further enriches this dynamic tapestry. It represents a shared language of bioactive molecules and immunomodulators, a lexicon that cells use to foster cooperation, facilitate mutualistic relationships, and manage competition. This comprehensive molecular vocabulary ensures that the cellular community is primed for collective decision-making, harmonizing its efforts to achieve shared objectives. Reflecting upon holobionts, these superorganisms are exemplars of cooperation on an even grander scale. A holobiont isn't simply a host and its symbiotic partners; it's a unified, collaborative entity that emerges from the synchronized actions of vastly different organisms. This level of cooperation, transcending genetic boundaries, underscores the adaptability and intelligence of life. It highlights that, even without shared genetics, different species can find ways to communicate, collaborate, and cohabit. They can engage in mutual learning, evolving together in a ceaseless dance of adaptation and co-evolution. The shared appraisal of environmental cues among different organisms within a holobiont demands exceptional adaptability and coordination. This coordination cannot be dictated by a rigid genetic script but requires a dynamic, responsive system that evolves as environmental conditions change. At the heart of this system lies the principle of natural cellular engineering. The continuous efforts of cells to sustain and adapt themselves and their communities present biological ingenuity, where each cell contributes to the ever-evolving masterpiece of life. In this context, microevolution and adaptation can be seen not merely as an outcome of genetic variations but as a sophisticated strategy for optimizing the assessment and response to environmental information. Multicellularity provides a platform for collective intelligence, where cells can pool their resources, share their assessments, and collaboratively navigate the complexities of their environment. It's akin to a biological version of crowd-sourcing, where every cellular participant contributes to the collective wisdom.

Life's inherent complexity and adaptability spring from more than just its genetic code. It is a result of intricate cellular networks, dynamic feedback loops, and continuous interactions with the environment. At its core lies the principle of engineering setup in cells, making complex lifeforms remarkably abt to innovate, adapt, and thrive amidst constant change. The challenge now lies in deepening our understanding of these processes, exploring their implications, and harnessing this knowledge for a better understanding of how this exquisite complexity came to be. Every gene possesses the potential for variation, yet it is through epigenetic modifications that organisms harmonize with their surrounding environment. This underscores the assertion that, amidst the intricate web of life, the targeted use and editing of genes becomes imperative, especially when considering the need for adaptability at multiple biological scales. While it's clear that phenotype arises from cellular activities, these same activities are shaped and influenced by the phenotype itself. Within this intertwined relationship, processes like cellular engineering and the active shaping of genetic material become wellsprings of biological innovation, all the while being tethered by the ecological boundaries set by the cell itself. Rather than viewing evolutionary development as a mere consequence of randomly occurring changes at the minute level of nucleotides, one can perceive it as an intricate dance of information flow and organization spanning various scales. The primary motivation behind these processes is the ongoing quest to ensure harmony between the organism and its environment, internalizing external cues. In essence, cellular engineering serves as the tangible embodiment of the cell's sophisticated system of information management.

William B. Miller, Jr. (2021) Cognition-Based Evolution (CBE) asserts a comprehensive alternative approach to phenotypic variation and the generation of biological novelty. In CBE, evolutionary variation is the product of natural cellular engineering that permits purposive genetic adjustments as cellular problem-solving.  Evolutionary development has traditionally been attributed to random genetic mutations, specifically single-nucleotide polymorphisms. While this perspective acknowledges the role of various mechanisms of genetic variation, including epigenomics and structural genetic variations, there remains a hesitancy to embrace the idea that non-random genetic events can play a significant role in evolutionary adaptation. The common perspective holds that evolution is driven by either replication errors or induced genetic alterations. However, there are challenges to this framework. For one, rather than mutations occurring at a consistent rate, some have proposed that mutations can beget other mutations in a more erratic manner, leading to more rapid changes. This, in turn, presents its own issue: if mutations accelerate, there's the risk of uncontrollable accumulation of mutations. Hence, a strict error correction system is necessary. This poses the dilemma of how random genetic errors can feasibly give rise to beneficial biological variations, especially if increasing errors in specific genetic segments don't necessarily lead to better adaptability. 8

Commentary: William B. Miller, Jr.'s exploration into Cognition-Based Evolution (CBE) postulates a substantial and thought-provoking shift in understanding evolutionary development. This propounds that evolutionary variation is not a product of sheer randomness or haphazard genetic mutations but is a result of natural cellular engineering. This cellular problem-solving allows for intentional, purpose-driven genetic adjustments, fostering biological novelty and adaptation. In the traditional framework of evolutionary development, which attributes changes predominantly to random genetic mutations, especially single-nucleotide polymorphisms, there lies a notable hesitancy to consider the significant influence of non-random genetic events on evolutionary adaptation. The mainstream perspective leans heavily on the idea of evolution being propelled by either replication errors or induced genetic alterations, with little room for a purposefully implemented possibility of genetic modification with function. However, Miller's CBE sheds light on the limitations and challenges of this conventional view. It highlights the possible inconsistency in the mutation rate and brings attention to the fact that mutations do not always occur randomly or steadily but instigate further mutations, leading to expedited changes. This phenomenon poses significant questions. An accelerated mutation rate could lead to an uncontrollable accumulation of mutations, necessitating a rigorous error correction system. Amidst these challenges, the CBE theory emerges as a coherent explanation, suggesting that the process of evolutionary development is not solely reliant on random errors and mutations. Instead, it emphasizes the role of natural cellular engineering in permitting purposeful genetic adjustments, contributing to evolutionary variation and adaptation. This perspective underlines the significance of cellular problem-solving abilities in navigating the evolutionary landscape, potentially leading to a more robust, adaptable, and harmonious biological ecosystem. In the light of CBE, one might ponder the intricate, well-orchestrated nature of the evolutionary process. The hypothesis that evolution is an outcome of the implementation of cellular engineering, enabling purposeful and adaptive genetic modifications, points towards an intelligently designed setup. This subtly hints at the possibility of a grand design, a structured and purposeful blueprint underlying the adaptability of life, guiding its evolutionary journey through the ages.

It's clear to observe the precision, coordination, and efficiency with which these cellular mechanisms operate. Each process is governed by a specific set of instructions embedded within the molecular structures, ensuring exact outcomes. Specific sequences in the DNA facilitate the precise transfer of genetic material between organisms. The methodical nature of this process ensures that genes are correctly incorporated into the recipient genome, a precision unaccounted for by random chance. The perfect alignment and exchange of genetic material require an impeccable level of coordination, not feasibly attributed to randomness. The sequences recognize each other, align perfectly, and exchange material in a seamless fashion. The efficient movement of transposable elements within the genome is guided by specific sequences. This clear-cut mechanism functions with a high level of accuracy and purpose and highlights a structured process. Specific sites targeted for chemical modification to alter gene expression demonstrate purpose and targeted action, not explainable by random occurrences. The CRISPR system recognizes and targets viral DNA for destruction, a sophisticated defense strategy indicative of a well-organized system. The harmonious relationships established in symbiosis and endosymbiosis denote an integrated and cooperative system, ill-aligned with the concept of random evolutionary emergence. The controlled and sequenced response to external and internal signals again points towards a system operating with intent and organization. The exact regulatory role of non-coding RNAs again underlines a level of precision and directed action in contradiction with randomness. In analyzing these mechanisms, it's evident that the seamless, organized, and purposeful operations present cannot be merely brushed aside as random occurrences or accidents of nature. The intricate details, the specific sequences, and the coordinated interactions all point toward a source of origination characterized by understanding, intention, and intellect. The hypothesis of randomness fails to account for the systematic and ordered nature of these processes, leaving the door open for exploration and understanding beyond mere chance and into realms of and intentionally and intelligently designed and implemented genetic world.

Sources of Genetic Variation

"The following 86 mechanisms encompass a vast range of biological processes that underline the diversity, adaptability, and complexity of life on Earth. They range from intricate molecular interactions, such as DNA methylation, which regulates gene activity, to broader ecological and evolutionary dynamics like co-evolution, where species evolve in tandem. They reflect both the microscopic intricacies, like the role of endosymbiosis in the emergence of eukaryotic cells, and the macroscopic phenomena, like the formation of new species through allopatric speciation. These mechanisms demonstrate the ways in which organisms evolve, adapt, and interact with their environments and with one another. They show how genes can be transferred or modified, how organisms respond to environmental stresses, and how species develop and maintain their genetic diversity. Together, they provide a comprehensive view of the multifaceted interactions, changes, and processes that drive the biological world." In an overarching sense, many of these mechanisms contribute to genetic variation, which is a foundational concept in biology. Genetic variation is essential for populations to adapt, evolve, and survive in changing environments. From molecular processes like DNA methylation and alternative splicing to macroscopic events like allopatric speciation and ecological interactions, these mechanisms either directly generate, influence, or result from genetic variation within and between species. Whether through the transfer, mutation, regulation, or combination of genetic material, these processes and phenomena play a role in shaping the genetic diversity that is central to life on Earth.

The landscape of genetic adaptation and evolution in organisms is multi-faceted. While traditional Mendelian inheritance and Darwinian evolution have been the mainstay of understanding these processes, there are many more mechanisms that add layers of complexity: 


1. Adaptive Immune System: A complex system in vertebrates that can recognize and remember specific pathogens, providing long-term immunity. It relies on specialized cells such as T cells and B cells to target specific antigens.
2. Allopatric Speciation: A mode of speciation that occurs when populations of a species become geographically isolated, leading to genetic divergence and the evolution of new species.
3. Alternative Splicing: A post-transcriptional process allowing a single gene to code for multiple proteins. By splicing the pre-mRNA in various ways, different mRNA molecules are produced.
4. Antibiotic Resistance Evolution: The process by which bacteria evolve mechanisms to resist the effects of antibiotics, often due to inappropriate antibiotic use or overuse.
5. Assortative Mating: A mating pattern where individuals with similar phenotypes or genotypes mate with one another more frequently than would be expected under a random mating pattern.
6. Assumed Heritability: An estimate of the proportion of variance in a trait that can be attributed to genetic factors.
7. Balancing Selection: A form of natural selection where multiple alleles are maintained in a population because they confer a selective advantage.
8. Behavioral Plasticity: The ability of an organism to modify its behavior in response to changes in its environment.
9. Bacterial Conjugation: A method of genetic exchange in which one bacterium transfers DNA to another through a structure called the pilus.
10. Bottleneck Effect: A sharp reduction in the size of a population due to environmental events or other factors, leading to a reduction in genetic diversity.
11. Chromosomal Aberrations: Structural changes in chromosomes, such as deletions, duplications, inversions, and translocations, which can lead to genetic disorders or evolutionary novelty.
12. Climate-Driven Adaptation: Evolutionary changes in organisms in response to changing climatic conditions, like temperature or rainfall. This can involve alterations in physiology, behavior, or morphology.
13. Co-evolution: The process by which two or more species reciprocally affect each other's evolution, often seen in predator-prey or parasite-host relationships.
14. Convergent Evolution: The process by which unrelated organisms independently evolve similar traits or adaptations, usually in response to similar environmental challenges.
15. Cytoplasmic Inheritance: Inheritance of traits determined by factors present in the cytoplasm, especially mitochondrial DNA. Unlike nuclear DNA, these are often maternally inherited.
16. Directional Selection: A mode of natural selection in which one extreme phenotype is favored over other phenotypes, leading to the allele associated with the favored phenotype to increase in frequency.
17. Divergent Evolution: The accumulation of differences between closely related species or populations, leading to speciation.
18. DNA Methylation: The addition of a methyl group to the DNA molecule, often acting as a switch to turn genes on or off. This can play a role in gene expression regulation, aging, and cancer.
19. Ecological Release: The phenomenon where a species expands its habitat or range due to the reduction or absence of limiting factors such as competitors or predators.
20. Endocytosis: The process by which cells internalize molecules by engulfing them in an energy-dependent way, often involving lipid bilayer invagination.
21. Endogenized Viruses: Viruses that have integrated their genome into the DNA of host cells and are passed on to subsequent generations of the host.
22. Endogenous Retroviruses (ERVs): Sequences in the genome thought to be remnants of ancient viral infections. ERVs can influence gene expression and contribute to the host's evolutionary development.
23. Endosymbiosis: A symbiotic relationship where one organism lives inside another. For instance, mitochondria in eukaryotic cells are believed to have originated from an ancient endosymbiotic relationship between a precursor eukaryotic cell and a prokaryote.
24. Entosis: A process wherein one living cell invades another, which can lead to the death of the internalized cell. This can be seen in some tumor cells and is distinct from other forms of cell-in-cell structures.
25. Environmental Change: Alterations or fluctuations in an environment, which can be due to natural processes or human activities. These changes can drive evolutionary processes or lead to extinction events.
26. Epigenetic Impacts: Changes in gene expression or cellular phenotype, driven by mechanisms other than changes in the underlying DNA sequence. This includes modifications like DNA methylation or histone modification.
27. Epigenetic Inheritance: The passing of epigenetic markers from one generation to the next, potentially influencing phenotypes in offspring without changing the DNA sequence itself.
28. Epistasis: Interaction between two or more genes where the expression of one gene affects or masks the expression of another.
29. Founder Effect: A loss of genetic variation that occurs when a new population is established by a small number of individuals from a larger population.
30. Founder-Flush Hypothesis: A theory suggesting that rapid population growth following a bottleneck or founder event can lead to a flush of evolutionary innovation and adaptation.
31. Frequency-Dependent Selection: A selective process where the fitness of a phenotype is dependent on its frequency relative to other phenotypes in a population.
32. Gene Conversion: A process during which one DNA sequence replaces a homologous sequence, thus making them identical.
33. Gene Duplication: The generation of additional copies of a gene in the genome, often leading to novel genetic material upon which evolution can act.
34. Gene Transfer Agents (GTAs): Virus-like elements produced by some bacteria that mediate the transfer of DNA fragments from one cell to another.
35. Genetic Assimilation: The process by which a phenotype originally produced in response to an environmental condition becomes genetically encoded through natural selection.
36. Genetic Assortment: The distribution of alleles into gametes, independent of other genes during meiosis.
37. Genetic Drift: Random changes in allele frequencies in a population, particularly pronounced in small populations.
38. Genetic Redundancy: The phenomenon where multiple genes, due to duplication or other mechanisms, perform the same function. Loss of one of these genes typically has no effect on the organism's phenotype.
39. Genome Editing: Techniques like CRISPR/Cas9 that allow for targeted modifications to an organism's DNA.
40. Genome Reduction in Endosymbionts: The loss of genes in endosymbiotic organisms (organisms living inside another), often because the host provides the necessary functions.
41. Heterosis (Hybrid Vigor): The increased strength, growth, or other favorable characteristics observed in hybrid offspring.
42. Heterozygote Advantage: A situation where the heterozygote has a higher fitness than either homozygote.
43. Horizontal Gene Transfer (HGT): The transfer of genes between organisms in a manner other than traditional reproduction, common among bacteria.
44. Inbreeding: Breeding between closely related individuals, leading to an increased chance of offspring inheriting two copies of a deleterious mutation.
45. Interactions with the Human Microbiome: The dynamic relationship between the collection of microorganisms living in and on our bodies and the human host, influencing health and disease.
46. Interspecies Mating: Mating between individuals of different species, sometimes producing hybrid offspring.
47. Jumping Genes: Also known as transposons, these are sequences of DNA that move or "jump" from one location in the genome to another.
48. Kin Selection: Evolutionary strategy that favors the reproductive success of an organism's relatives, sometimes at a cost to the organism's own survival.
49. Lateral Gene Transfer: Another term for horizontal gene transfer, referring to the transfer of genes between organisms outside of reproduction.
50. Linkage Disequilibrium: The non-random association of alleles at different loci.
51. Local Adaptation: The process by which populations evolve in response to the specific conditions of their local environment, enhancing their fitness in that particular context.
52. Microbiome Influence: The impact of the collective community of microorganisms in a particular environment (like the gut) on the health, behavior, and evolution of their host organism.
53. Mimicry: A phenomenon where one species evolves to resemble another species or object, often as a protective mechanism.
54. Muller's Ratchet: A process by which the genomes of an asexual population accumulate deleterious mutations in an irreversible manner.
55. Natural Genetic Engineering: The inherent ability of organisms to re-organize their genetic structure, leading to evolutionary novelty.
56. Neutral Evolution: Evolution driven by random genetic drift rather than by natural selection.
57. Niche Partitioning: The process by which competing species use the environment differently in a way that helps them coexist.
58. Parasexual Reproduction: A form of reproduction involving genetic exchange without the full process of meiosis or the formation of gametes.
59. Phenotypic Plasticity: The ability of an organism to change its phenotype in response to changes in the environment.
60. Plasmid Exchange: The transfer of small, circular DNA fragments (plasmids) between bacteria, often conveying beneficial traits such as antibiotic resistance.
61. Point Mutations: Small genetic changes where a single nucleotide base is altered, potentially affecting protein function or expression.
62. Polygenic Inheritance: The inheritance of traits that are determined by multiple genes.
63. Predator-Prey Co-evolution: The reciprocal evolutionary changes in predators and their prey, often leading to a series of adaptations and counter-adaptations.
64. Prezygotic and Postzygotic Isolating Mechanisms: Mechanisms that prevent different species from producing offspring, either by preventing mating/fertilization (prezygotic) or by causing the hybrid offspring to be sterile or inviable (postzygotic).
65. Pseudogenization: The process by which functional genes become non-functional due to mutations.
66. Quantitative Trait Loci (QTL) Mapping: A technique used to associate specific genomic regions with observed phenotypic traits.
67. Rapid Evolution: The accelerated rate of evolutionary change, often in response to strong environmental pressures or changes.
68. Rapid Speciation: The swift emergence of new species, often due to sudden environmental changes or isolated colonization events.
69. Recombination: The process by which genetic material is mixed during sexual reproduction, leading to offspring with combinations of traits different from either parent.
70. Regulatory Sequence Evolution: The evolution of DNA sequences that control the expression of genes, affecting when and where genes are active.
71. Repeat-induced point mutation (RIP): A mechanism in fungi that mutates repetitive DNA sequences, preventing the proliferation of transposable elements.
72. RNA Editing: The alteration of RNA sequences after transcription but before translation, leading to the production of a protein variant not directly encoded by the DNA.
73. Selective Breeding (Artificial Selection): The intentional breeding of organisms to promote the occurrence of desirable traits in offspring.
74. Selective Sweep: A situation where a beneficial allele increases in frequency in a population so quickly that linked alleles also increase in frequency.
75. Sexual Reproduction: The creation of a new organism by the combination of genetic material from two parent organisms.
76. Social Structure and Cooperation: The organized patterns of relationships and interactions within social species, which can influence evolutionary pathways.
77. Stabilizing Selection: A form of natural selection that favors intermediate phenotypes and acts against extreme variants.
78. Symbiosis: A close and often long-term interaction between two or more different biological species, which can be mutualistic, parasitic, or commensal.
79. Sympatric Speciation: The process of new species evolving from a single ancestral species while inhabiting the same geographic region.
80. Targeting Regulatory Components: The act of focusing on regulatory elements in the genome, such as promoters or enhancers, to understand or influence gene expression patterns.
81. Transduction: The process by which DNA is transferred from one bacterium to another by a virus.
82. Transcriptomic Variability: Differences in RNA expression levels or patterns between cells, tissues, or organisms.
83. Transposable Elements: DNA sequences that can change their position within the genome, potentially causing mutations or affecting gene expression.
84. Transformation: The uptake and incorporation of external DNA by a cell.
85. Viral Reprogramming: The alteration of a host cell's functions by a virus, often to facilitate viral replication.
86. Whole Genome Duplication (Polyploidy): The duplication of an organism's entire genome, often leading to speciation or novel evolutionary pathways.


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6. Parent, C. A., & Devreotes, P. N. (1999). A cell's sense of direction. Science, 284(5415), 765-770. Link. (Here, the authors explore chemotaxis in cells, discussing how they can detect and move in response to chemical gradients in their environment.)
7. Dennis, P. B., Jaeschke, A., Saitoh, M., Fowler, B., Kozma, S. C., & Thomas, G. (2001). Mammalian TOR: a homeostatic ATP sensor. Science, 294(5544), 1102-1105. Link. (This paper discusses the mTOR pathway and how cells measure and react to nutrient availability, regulating their growth and proliferation.)
8. Miller, W.B. Jr., Enguita, F.J., & Leitão, A.L. (2021). Non-Random Genome Editing and Natural Cellular Engineering in Cognition-Based Evolution. Cells, 10(5), 1125. Link. (This comprehensive study delves into the intricate interplay between non-random genome editing, cellular engineering, and their implications for cognition-based evolution.)

More: 

Shapiro, J.A. (2011). Evolution: A view from the 21st century. FT Press. Link. (Discusses the ways cells edit their genome in response to environmental challenges.)
Bennett-Baker, P. E., Wilkowski, J., & Burke, D. T. (2003). Age-associated activation of epigenetically repressed genes in the mouse. Genetics, 165(4), 2055-2062. Link. (Explores the role of epigenetic changes in aging and evolution.)
Feinberg, A. P., & Irizarry, R. A. (2010). Stochastic epigenetic variation as a driving force of development, evolutionary adaptation, and disease. Proceedings of the National Academy of Sciences, 107(suppl 1), 1757-1764. Link. (Examines the role of random epigenetic changes in evolution and disease.)
Danchin, É., Charmantier, A., Champagne, F. A., Mesoudi, A., Pujol, B., & Blanchet, S. (2011). Beyond DNA: integrating inclusive inheritance into an extended theory of evolution. Nature Reviews Genetics, 12(7), 475-486. Link. (Discusses the importance of non-genetic inheritance in evolution.)
Laland, K., Uller, T., Feldman, M., Sterelny, K., Müller, G. B., Moczek, A., ... & Odling-Smee, J. (2015). The extended evolutionary synthesis: its structure, assumptions and predictions. Proceedings of the Royal Society B: Biological Sciences, 282(1813), 20151019. Link. (Presents an integrative approach to understanding evolution, incorporating insights from various fields.)



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Description of the Last Universal Common Ancestor (LUCA)

Historical Overview

The concept of a "last universal common ancestor," often abbreviated as LUCA, has deep roots in the history of evolutionary biology. While the specific terminology and detailed conception of LUCA have evolved over time, the foundational idea can be traced back to the seminal work of Charles Darwin. In his groundbreaking 1859 book, "On the Origin of Species," Darwin introduced the idea of a "tree of life" to represent the relationships between different species. Although he didn't use the term "LUCA" explicitly, the idea was implicit in his discussions. At the base of this tree, the point from which all branches diverged, one could infer the existence of a common ancestor to all living things. Darwin posited that all species, past and present, have descended from a single form of life through the process of natural selection. The term "last universal ancestor" or its variations came into more widespread use in the late 20th century, especially as molecular biology and genetics began to provide tools to study the relationships between organisms at a level of detail previously unimaginable. The concept grew more refined with the advent of molecular phylogenetics, which allowed scientists to reconstruct evolutionary relationships based on DNA and RNA sequences.

Beyond Evolution: The Origin of Species by Design Sem_dd13
Carl Woese was an American microbiologist and biophysicist renowned for discovering the Archaea, a third domain of life distinct from Bacteria and Eukaryotes. His pioneering work in molecular phylogenetics using ribosomal RNA revolutionized our understanding of the evolutionary relationships among organisms.

Carl Woese (Late 20th Century):  One of the key figures in this modern exploration of LUCA was Carl Woese. In the 1970s, Woese and his colleagues used ribosomal RNA (a type of RNA present in all cells) to construct a new "tree of life." His work revealed the existence of a third domain of life, the Archaea, distinct from the previously known Bacteria and Eukarya. Woese's tree also hinted at the existence of a universal common ancestor from which all three domains sprang. Over the last few decades, the quest to understand LUCA has continued, using ever more sophisticated genetic and bioinformatic tools. Scientists today view LUCA not necessarily as a single entity, but potentially as a community or population of early life forms that shared genetic material. This sharing, possibly through horizontal gene transfer, could have led to a pooled set of genetic innovations and adaptations that became foundational for all subsequent life on Earth.

Perception of the First Life Form from Darwin's Time to Today

1. Darwin's Era (19th Century)

In the 19th century, during what is now referred to as Darwin's Era, our understanding of life's origins was still in its infancy. The mysterious emergence of life on Earth was a topic that both fascinated and puzzled scientists, scholars, and the general public alike. Early notions about the origins of life were deeply rooted in the concept of spontaneous generation. This idea was built on the everyday observation that organisms, seemingly out of nowhere, could emerge from non-living materials. For instance, the appearance of maggots on rotting meat was often attributed to the meat itself spontaneously generating life. Though this concept might appear rudimentary to our modern understanding, it was a genuine attempt in those days to grapple with the enigma of life's emergence. Meanwhile, Charles Darwin, the era's most prominent biologist, offered a more nuanced perspective. Though he was best known for his work on the origin of species, Darwin once mused about the beginnings of life itself. He postulated that life might have taken root in a "warm little pond" filled with a mix of chemicals. Such environments, he theorized, could provide the necessary conditions for life's precursors to form and perhaps, in time, lead to the first living organisms. Yet, even as these speculations were being made, the nature of these first life forms remained a matter of debate. There was a common sentiment that life, in its earliest form, must have been exceedingly simple. These primordial beings were imagined as basic entities, perhaps nothing more than gelatinous blobs of protoplasm, drifting in the early oceans or shallow ponds. The 19th century, with its limited technological and biochemical insight, could only offer these preliminary guesses and hypotheses. However, these ideas laid the groundwork for future scientific inquiries. As our tools and techniques advanced, so did our ability to probe deeper into the question that has captivated humanity for centuries: How did life begin? As we now venture into this deep past, we find ourselves piecing together clues from geology, chemistry, and biology, endeavoring to understand the conditions and processes that sparked the emergence of life on Earth.

2. Early to Mid 20th Century

In the early 20th century, as scientific understanding and methodologies developed, new theories about the origins of life began to take shape. Among these was the Oparin-Haldane Hypothesis, which marked a significant departure from earlier theories. The hypothesis, independently proposed by scientists Alexander Oparin and J.B.S. Haldane, posited that the early Earth's atmosphere, rich in methane, ammonia, and water vapor, might have played host to a "primordial soup" of organic molecules. These molecules, they theorized, could accumulate in the oceans over time, gradually increasing in complexity. The role of external energy sources, such as ultraviolet radiation from the sun or the electric spark from lightning, was highlighted as potential catalysts to trigger the necessary reactions leading to life. This idea shifted the perspective from individual spontaneous occurrences to a more gradual, global process, where the early Earth's conditions played a pivotal role in fostering life's emergence. Validating the possibilities proposed by the Oparin-Haldane Hypothesis was the groundbreaking Miller-Urey Experiment in 1953. Stanley Miller, under the supervision of Harold Urey, set out to recreate the early Earth's conditions in a laboratory setting. By simulating the proposed "primordial soup" and introducing electric sparks to mimic lightning, they were astounded to find that amino acids, the building blocks of life, could indeed form in such an environment. This experiment was a landmark moment, offering the first tangible evidence that life's basic components could emerge from the conditions believed to be present on the early Earth. Parallel to these chemical explorations, the biological perspective of the first life forms began to refine as well. Instead of picturing vague, undifferentiated blobs of protoplasm, scientists started to envision the first organisms as prokaryotes. These simple, unicellular life forms lacked a distinct nucleus and specialized organelles, representing a rudimentary stage in cellular evolution. Their simplicity, however, was their strength, allowing them to thrive and multiply in the diverse and often challenging environments of the early Earth. Together, these theories and discoveries painted a clearer, more detailed picture of life's origins. They emphasized the interconnectedness of chemistry, environment, and biology in the intricate dance that eventually led to the emergence of life. As we continue to unravel this narrative, each new discovery adds depth to our understanding, offering a window into the distant past and the marvels of life's inception.

3. Late 20th Century to Early 21st Century

In the latter half of the 20th century, as research delved deeper into the molecular intricacies of life, a fresh wave of theories began to shape the discourse around life's origins. The vast puzzle of how life started saw new pieces added, each offering a novel dimension to our understanding. Central to these newer perspectives was the RNA World Hypothesis. Unlike the earlier notion that life started with proteins or simple cellular forms, this theory placed RNA molecules at the heart of the narrative. Proposed as an alternative to the DNA-first viewpoint, it suggested that RNA, due to its dual capacity to carry genetic information and act as a catalyst, might have been the linchpin of early life. In this proposed scenario, RNA molecules took on the role of both genes and enzymes, facilitating the necessary biochemical reactions that set the stage for the complexity that was to follow. Meanwhile, the question of where life might have originated received a new contender: the deep-sea hydrothermal vents. The Thermal Vent Theory highlighted these underwater chimneys, spewing mineral-laden water, as potential cradles of life. The rich chemical milieu around these vents, combined with the constant supply of heat, offered a unique environment. This theory proposed that the gradients of temperature and chemical concentration at these sites might have provided the energy and conditions required for the assembly of organic molecules, eventually leading to life's first tentative steps. Building on the complexities of life's emergence, another perspective began to take shape, challenging the earlier notion of a singular Last Universal Common Ancestor (LUCA). This perspective proposed that the earliest life forms might not have been isolated entities, but rather members of intricate early communities. In such communities, instead of rigid boundaries and distinct lineages, there was an abundance of horizontal gene transfers. This scenario suggested a meshwork of early life forms, frequently sharing and swapping genetic material. Such exchanges could enhance adaptability, allowing these communities to navigate the challenges of the early Earth and lay the foundation for the diverse tree of life we observe today. These theories, each shining a light on different facets of life's story, underscore the intricate and multifaceted journey of life's beginnings. As science continues its relentless quest, the story of our origins becomes ever more nuanced, showcasing the incredible tapestry of processes and conditions that came together to birth life on our planet.

4. Current Understanding (Based on Synthesis)

  - Advanced Genetic Machinery: LUCA had a comprehensive genetic system, potentially DNA-based, with advanced translational mechanisms.
  - Metabolic Sophistication: Emphasis on chemoautotrophy and a unique metabolism centered on geochemical processes and hydrogen-based systems.
  - Cellular Complexity: Possibility of LUCA having precursors to eukaryotic cell structures, bridging the gap between simple and complex life forms.
  - Community Dynamics & Evolutionary Framework: LUCA perceived as part of a complex network or community, challenging the traditional linear tree of life.

Evolution of Perception through Advancing Science
 
In the unfolding story of our understanding of life's origins and complexities, technology and scientific methodology have played starring roles. Each era of discovery was deeply interwoven with the tools of its time, and each shift in perspective was enabled by advancements that allowed us to see the world in new ways. In the days of Darwin, the instruments at hand painted a picture of life's simplicity. The microscopes of the 19th century, though groundbreaking for their time, were primitive by today's standards. They revealed cells as mere blurry entities, leading to the overarching belief in the rudimentary nature of early life forms. However, as the calendar pages turned to the 20th century, a new wave of exploration began. The burgeoning field of organic chemistry came to the fore, and with it, the potential to understand life's origins from a chemical standpoint. The landmark Miller-Urey experiment, simulating early Earth conditions, produced amino acids, hinting at the complex dance of molecules that could have set the stage for life. The world started to appreciate the intricate choreography of chemical reactions that might have birthed living organisms. But the true revolution was still on the horizon. The latter half of the 20th century was marked by a molecular renaissance. Molecular biology pulled back the curtain on the detailed inner workings of cells. As DNA sequencing technologies emerged and microscopy techniques advanced, the long-held belief in the absolute simplicity of prokaryotic cells began to erode. They were not mere sacs of chemicals; they were intricate factories of life. The dawn of the new millennium brought with it a wave of genomic exploration. The sequencing of entire genomes became a reality, and suddenly, the life story written in the code of DNA was accessible. Comparative genomics took center stage, offering glimpses into evolutionary histories previously shrouded in mystery. The presumed simplistic LUCA was put under the microscope, revealing hints of a complexity that few had imagined. The early years of the 21st century saw the melding of advanced imaging techniques with the power of computational analysis. With this fusion, scientists could visualize and dissect life at unprecedented resolutions. Each pixel of an image and each byte of data added depth to our understanding of early life forms. The once-assumed simplistic LUCA was now viewed in a new light, not as a mere footnote in the annals of evolution but as a complex entity that might hold the secrets to life's grand journey. In this tale of discovery, one thing remains clear: as our tools and methodologies evolve, so too does our understanding of the intricate tapestry of life.

Reflecting on the Progression
 
Our quest to unravel the mysteries of life has been akin to a journey from the vast expanses of the cosmos to the infinitesimal dance of atoms. Initially, our gaze was fixed on the observable, the tangible - life forms we could see, touch, and describe. The macroscopic world was our canvas, filled with diverse creatures, each weaving its own tale of existence. Yet, with every stride of technological advancement, our focus shifted, revealing a hidden universe within the microcosm. The marriage of disciplines brought forth a renaissance in our understanding. No longer was biology confined to its silo, nor chemistry to its lab. The boundaries blurred as physics offered its insights into the atomic ballet, and computational sciences illuminated patterns in vast pools of data. This convergence of disciplines provided a panoramic lens through which we began to perceive the intricate mosaic of life. What once seemed simple in isolation became a complex symphony when viewed as part of a larger ensemble. The deeper we delved, the more a paradox emerged. From the apparent simplicity of primordial chemicals, an intricate tapestry of life was woven. Our early beliefs, which painted a picture of life's simple beginnings, were juxtaposed with a newfound appreciation of its complexity. We realized that, perhaps, life's journey was not a linear path from simplicity to complexity but a dynamic interplay of both. The basic building blocks might have been simple, but the blueprint they followed was grand, steering life towards the multifaceted marvels we witness today. This journey of understanding is a testament to human curiosity and our innate drive to seek answers. From the macroscopic landscapes to the microscopic realms, we've unraveled layers of the living world, each layer revealing a story more intricate than the last, and each discovery leading us closer to the essence of life itself.

Looking Forward
 
The horizon of our understanding of life is constantly shifting. As we tread deeper into the 21st century, we find ourselves on the cusp of a new era marked by the emergence of fields such as systems biology and synthetic biology. These disciplines beckon us to perceive life not as isolated entities but as interconnected and synergistic networks, much like an elaborate symphony where each note complements the other. Systems biology, with its holistic approach, seeks to discern the relationships and interactions between various components of a biological entity. By studying these interactions, we aim to fathom the underlying principles governing life's vast networks. It's akin to understanding the rhythm and harmony behind a musical piece, ensuring every instrument plays its part in perfect cohesion. Concurrently, synthetic biology dares to venture into uncharted territories, pushing the boundaries of what we consider "natural." It offers a unique promise – to not just understand life but to recreate and reshape it. This endeavor, while audacious, is more than just a testament to human ingenuity; it's a profound exploration into the very essence of life. The tools at our disposal today are unparalleled in their sophistication. They offer the tantalizing prospect of recreating scenarios from eons past, allowing us to revisit the dawn of life with newfound precision. Imagine the ability to glimpse the pivotal moments when life, in all its nascent beauty, struck a balance between the realms of simplicity and complexity. By recreating these ancient scenarios, we might just refine our grasp on the subtle interplay that gave rise to the diverse life forms we see today. Indeed, our quest is far from over. With every stride in our understanding, we are reminded of the vastness of what remains unknown. Yet, the journey itself is exhilarating, for with every discovery, we inch closer to the heart of life's grand enigma.

Intracellular Systems

As we seek to decipher the mystery of life's inception, the concept of LUCA, or the Last Universal Common Ancestor, comes forth as a beacon in the dark expanse of our planet's history. This ancient entity, in its primeval form, has been thought to carry within it the seeds of all life that would eventually flourish on Earth. One can envision LUCA as a being of immense potential, bearing a genomic blueprint. While not as refined as the DNA sequences we see today, this genetic material would have been pivotal, encoding essential instructions that guided LUCA's existence. It laid down the pathways for its survival, growth, and replication, ensuring the continuity of life in its most rudimentary form. Even in such nascent stages, life is imagined to have displayed an incredible penchant for adaptation and self-sustenance. LUCA, though rudimentary, was believed to have possessed metabolic pathways. These weren't the sophisticated systems we observe in contemporary organisms but were functional enough to harness the raw materials of the young Earth. They would have allowed LUCA to transmute available substances into vital energy, a testament to life's innate drive to persist against the odds. Perhaps one of the most intriguing aspects of LUCA's existence would have been its semblance of structure. While it may not have resembled the sophisticated cellular entities of today, there's evidence to suggest that LUCA had achieved a form of primitive compartmentalization. This is envisioned as a lipid boundary or a simple membrane, delicately demarcating its internal sanctum from the vast external universe. This rudimentary boundary served as a sanctuary, encapsulating and nurturing the vital metabolic reactions that occurred within.

Extracellular Interactions

In our quest to uncover the mysteries of life's beginnings, the LUCA stands as a pivotal figure, a bridge between the inanimate and the animate. Though the comfort of imagining a singular, solitary ancestor for all life has its allure, newer scientific revelations compel us to view the landscape with a broader lens. LUCA, if it existed, would have been an entity of resilience and adaptability. The environment it is thought to have occupied was a far cry from the nurturing cradle many might envision. Hypothesized to dwell in the intense environs of hydrothermal vents, LUCA had to be equipped not just to survive, but to thrive. These were realms of extreme temperatures, where life, as we traditionally understand it, would be challenged to its core. But for LUCA, it might have been home. In such a setting, LUCA would have had mechanisms to extract sustenance, deriving nutrients from an environment that was both its habitat and its test. Yet, the story of LUCA is not just about survival, but also about interaction. Every interaction it had with its surroundings posed challenges, nudging it, shaping it, and compelling it to adapt. Even if we steer clear of attributing these changes to classical evolutionary explanations, it's undeniable that the pressures from the environment would influence LUCA, guiding its path and perhaps setting the stage for the myriad life forms we observe today.  LUCA, would not have been a definitive entity but a hypothetical consortium of life forms. This hypothesized community would have been a dynamic entity, responding to the world around it, perhaps even changing it in return. The early Earth presented a medley of conditions, a myriad of niches, each carrying its challenges and opportunities. Within these niches, different proto-life forms would have found their foothold, establishing territories and perhaps, in some cases, forming alliances.

LUCA: Deciphering the Root of the Universal Tree of Life

Within the diverse realm of life on Earth, the scientific community posits the existence of LUCA or the Last Universal Common Ancestor. This entity stands not as an organism fossilized in ancient rock but rather as a theoretical construct inferred from comparative genomics and molecular biology. Representing a shared lineage for all extant life forms, the characterization of LUCA provides a glimpse into early evolutionary paradigms. It's generally postulated that LUCA thrived between 3.5 to 3.8 billion years ago, based on molecular clock analyses and ancient fossil evidence. However, LUCA does not mark life's origin; instead, it signifies a state of molecular maturity, underscoring a plethora of biological processes already in operation. Comparative genomics offers insights into the potential genomic framework of LUCA. This progenitor would have housed genes pivotal for RNA synthesis, DNA replication, protein production, and rudimentary metabolic processes. Such molecular mechanisms form the foundation for the vibrant thriving of life we observe today. A core feature believed to be present within LUCA's cellular machinery is its capacity for nucleic acid synthesis and maintenance. Contrary to a simplistic model, the genetic machinery of LUCA would be competent, enabling DNA replication and repair, akin to a seasoned maestro overseeing a complex orchestra. The DNA polymerases of LUCA, far from rudimentary, would have deftly decoded genetic blueprints, creating coherent genetic narratives. The debate regarding LUCA's cellular structure persists. While some assert its resemblance to contemporary prokaryotic entities, others argue for a cellular architecture that might have been more rudimentary, yet uniquely adapted to its primordial environment. The crux of LUCA's existence rests not merely in its DNA or RNA, but in its overarching biochemical machinery. Envision a cellular system already equipped to harness energy, process nutrients, and maintain genetic fidelity, preparing the groundwork for life's subsequent diversification. Beyond its genetic prowess, LUCA would have navigated challenges like sourcing energy and maintaining an internal milieu. The potential metabolic pathways it utilized are hoped to offer windows into early adaptations. As the scientific community delves deeper into LUCA's attributes and significance, it stands as a beacon, illuminating life's early constitution.  To comprehend LUCA is to appreciate a pivotal juncture and starting point for an evolutionary narrative. While not representing life's genesis, LUCA demarcates a state where foundational molecular systems were operational, paving the supposed way for the evolutionary dance that would have sculpted the diverse biosphere we now observe.

The Primordial Stage: Scrutinizing Earth's Early Environment

The quest to understand life's genesis has pointed the scientific community towards diverse environments ranging from deep-sea hydrothermal vents to surface pools rich in prebiotic compounds. Positioned in the depths of oceans, hydrothermal vents, with their mineral-rich emissions and gradients of temperature, are postulated as potential cradles of life. These environments offer a blend of chemicals and the requisite energy that might favor prebiotic reactions. However, several questions remain. How would delicate organic molecules, crucial for life, withstand the intense conditions and extreme pressures at these depths? Additionally, the rapid dilution of any synthesized compounds in vast ocean volumes may challenge the accumulation of critical biomolecules. The concept of the primordial "soup" evokes visions of surface pools teeming with a mix of organic compounds, possibly driven by lightning and ultraviolet (UV) radiation. Yet, the constant exposure to UV rays also poses a conundrum. While they may catalyze some reactions, they could also degrade sensitive organic compounds. The balance between creation and destruction in such scenarios is a subject of scrutiny. External events and conditions have been implicated in possibly steering the pathways leading up to life. Yet, were these events truly deterministic, nudging a non-living world toward the brink of life? Meteorites, laden with organic compounds, have been suggested as external donors that might have seeded Earth with prebiotic molecules. However, the journey through Earth's atmosphere subjects these compounds to extreme temperatures. Would these meteoritic compounds truly survive and remain unaltered after such a fiery descent? The early Earth's atmosphere, believed to be reducing in nature, might have facilitated the synthesis of organic compounds. But, the exact composition and its implications for the formation of biomolecules remain subjects of debate. Was the atmosphere truly conducive, or do we yet grapple with understanding its nuances?
Given the myriad conditions and hypotheses presented, the question arises: Were these circumstances sufficiently deterministic to conclude life's inevitable emergence? While it's acknowledged that certain conditions might favor the synthesis of organic compounds, progressing from simple molecules to complex, functional cellular machinery presents a wider chasm. A mere assemblage of molecules doesn't equate to life. How, then, did the leap from chemistry to cellular complexity transpire? Life's machinery hinges on synchronized interactions between biomolecules. The orchestration of these interactions in the absence of a guiding cellular framework stands as a considerable challenge to our understanding. In examining the potential birthplaces of life and the external factors influencing it, it's clear that the narrative is far from complete. While certain conditions may favor the synthesis of biomolecules, the progression to a functional, self-replicating system remains enigmatic. As we venture further into this domain, it's pivotal to approach these hypotheses with a discerning lens, appreciating the nuances and seeking clarity amidst the complexities.

From Molecules to Life: Delving into the Enigma of Biopolymer Emergence

At the most fundamental level, life's machinery is driven by a suite of molecules that serve as building blocks: amino acids, nucleotides, and lipids, to name a few. While laboratory experiments have shown that certain basic molecules can form under simulated early Earth conditions, there are still lingering questions about the yield, purity, and stability of these molecules. For instance, the Miller-Urey experiment famously produced amino acids. Yet, it's worth asking: Were the conditions used in such experiments reflective of early Earth? Furthermore, in a prebiotic setting devoid of enzymatic guidance, how were the right molecules selectively synthesized and maintained amidst a plethora of unwanted byproducts?

Natural selection did not operate during the prebiotic era on Earth

In the primeval environment, directed selection mechanisms were absent. Complex systems in contemporary organisms produce the building blocks of life.  Before life as we know it flourished, the early Earth was a blank canvas, devoid of the guiding hand of natural selection. Imagine a world where meticulously orchestrated molecular symphonies of the present day did not exist. Instead of precise, deliberate formations of nucleic acids and the twenty amino acids, there existed a cacophonous chaos of molecules. Within the sophisticated cellular machinery of modern life, missteps such as right-handed amino acids are meticulously corrected. Nucleobases, phospholipids, and carbohydrates, now with such definite roles, were lost amidst a sea of countless molecular contenders. One must wonder: in a world teeming with chemical randomness, how did unguided processes sift through and pick the molecular elite that constitutes life today?

What Do Recent Scientific Papers Reveal About LUCA's Constitution?

While this offers a comprehensive view into the possible nature of LUCA, it is crucial to understand that these are based on current research, and the true nature of LUCA, if there was one, might remain elusive 
In essence, these papers provide a portrait of LUCA as a complex entity with a sophisticated metabolism, likely living in extreme conditions such as hydrothermal vents, and possessing some of the building blocks for eukaryotic complexity. The emphasis is also on the RNA world hypothesis and the role of horizontal gene transfer in shaping early life. The lineage of life on Earth, when traced back billions of years, converges to the Last Universal Common Ancestor, often referred to as LUCA. Piecing together scientific insights, we can infer the potential genetic and metabolic systems LUCA would have had. Genetically, LUCA would have been equipped with a comprehensive suite of machinery necessary for life's basic processes. This machinery would have comprised enzymes like DNA Polymerases for DNA synthesis, DNA Gyrase for managing supercoiling, and DNA Ligase for mending breaks in the DNA backbone. The presence of RNA Polymerases and Ribosomal Proteins indicates a well-defined apparatus for transcription and translation, reflecting the intricate genetic interplay of LUCA. RNA would not have merely been a passive player in LUCA's cellular narrative. According to current research, RNA would have performed a multitude of functions beyond just being intermediaries for protein synthesis. Roles might range from RNA polymerase synthesizing RNA from ribonucleotides to Ribozymes acting as catalysts, emphasizing the centrality of RNA in LUCA's life processes. Diving into LUCA's metabolism, scientific investigations suggest that LUCA would have had a chemoautotrophic nature. Such a metabolism implies a reliance on inorganic substances and geochemical processes, perhaps in hydrogen and metal-rich environments. Enzymes like Hydrogenases, vital for managing molecular hydrogen, and ATP synthase, crucial for energy production, would have played a foundational role in LUCA's metabolic landscape. From an ecological viewpoint, LUCA would have exhibited remarkable adaptability. Its existence in extreme environments, particularly hydrothermal vents, resonates with its likely thermophilic nature. Adaptations for such environments would have included specialized proteins like Heat Shock Proteins for enduring high temperatures and Sulfide-utilizing enzymes for harnessing energy from hydrothermal vent environments. Regarding cellular complexity, LUCA would have showcased an array of structures and systems suggestive of a bridge between the simplicity of prokaryotes and the sophistication of eukaryotes. Proto-cytoskeleton elements for structural support and primitive endomembrane systems hint at the budding complexity within LUCA's cellular framework. While the exact nature of LUCA remains a topic of scientific exploration and debate, the insights garnered from extensive research paint a picture of an organism that would have been a marvel of early life, laying down the genetic, metabolic, and cellular foundations for the vast tree of life that would follow.

Genetic Machinery: The Last Universal Common Ancestor (LUCA) likely had a sophisticated genetic apparatus. Ancient duplications of aminoacyl-tRNA synthetases in LUCA imply an intricate genetic structure, alluding to a well-established translation system. The consensus points towards a DNA-centric genome, emphasizing the significance of DNA in genomic structures and replication processes ([1] Brown & Doolittle 1995, [3] Forterre 2002).
RNA World Hypothesis and LUCA: LUCA might have predominantly relied on RNA, reinforcing the pivotal role RNA played not merely in protein creation but also in other fundamental cellular operations during life's nascent stages ([7] Becerra et al. 2007).
Metabolism: LUCA's metabolic systems were presumably advanced. Chemoautotrophy, a mechanism where organisms extract energy from inorganic materials, could be a hallmark trait. This infers that LUCA capitalized on energy from the Earth's geochemical reactions in an environment abundant with hydrogen and metals ([6] Martin & Russell 2003, [14] Sousa et al. 2016).
Ecology and Environment: Environments like hydrothermal vents deep within oceans are considered likely habitats for LUCA, complementing a hydrogen-fueled metabolism. There's also discourse on LUCA's thermophilic attributes, indicating it might have flourished in high-temperature surroundings ([15] Weiss et al. 2016 ).
Cellular Complexity: Delving into LUCA's cellular makeup remains a puzzle. However, investigations on Asgard archaea offer insights, indicating that LUCA may have had the rudiments or foundations of eukaryotic cell intricacy, providing a connection between early life's simplicity and eukaryotic complexities ([18] Zaremba-Niedzwiedzka et al. 2017).
Evolutionary Framework: LUCA's placement in the evolutionary lineage is crucial. Rather than seeing it as a singular entity, contemporary theories suggest that LUCA might encompass a consortium of initial life forms, with frequent horizontal gene exchanges marking their interactions. This perspective shifts the view of life's genesis from a linear tree to a more interconnected web ([2] Woese 1998). The potential rise of eukaryotes from archaea also hints at a LUCA with a richer genomic and cellular backdrop ([12] Williams et al. 2013).
Community Dynamics:
Considering LUCA as not just an individual organism but a collective of proto-cells that engaged in extensive horizontal gene transfer offers a fresh lens. This perspective portrays early life as a genetic continuum rather than distinct species boundaries ([2] Woese 1998).
Life's Emergence and LUCA: LUCA, when placed in the larger context of life's dawn, appears to be a key transitionary form that straddled the realms of non-living geochemistry and the commencement of biological mechanisms. The evolution from geochemical reactions to chemoautotrophic prokaryotes captures the essence of life's beginnings, with LUCA as a central character in this evolutionary narrative ([6] Martin & Russell 2003).

This synthesis, derived from various research papers, offers a multi-faceted view of LUCA.

1. Brown & Doolittle (1995). Ancient gene duplications and the genomic makeup of LUCA. Proceedings of the National Academy of Sciences, 92(7), 2441-2445. Link. (This study provides insights into the complex genetic machinery of LUCA through the lens of aminoacyl-tRNA synthetases.)
2. Woese, C. (1998). The universal ancestor. Proceedings of the National Academy of Sciences, 95(12), 6854-6859. Link. (Carl Woese introduces the concept of LUCA as a community of early organisms involved in rampant horizontal gene transfer.)
3. Forterre, P. (2002). The origin of DNA genomes and DNA replication proteins. Current Opinion in Microbiology, 5(5), 525-532. Link. (Emphasizes the DNA-based genetic system in LUCA.)
4. Koonin, E. V. (2003). Comparative genomics, minimal gene-sets and the last universal common ancestor. Nature Reviews Microbiology, 1(2), 127-136. Link. (Through comparative genomics, Koonin attempts to map LUCA's genome complexity.)
5. Harris, J.K., et al. (2003). The genetic core of the universal ancestor. Genome Research, 13(3), 407-412. Link. (Highlights conserved genes in LUCA, emphasizing its genomic intricacy.)
6. Martin, W., & Russell, M.J. (2003). On the origins of cells: a hypothesis for the evolutionary transitions from abiotic geochemistry to chemoautotrophic prokaryotes, and from prokaryotes to nucleated cells. Philosophical Transactions of the Royal Society B: Biological Sciences, 358(1429), 59-83. Link. (Proposes LUCA as a chemoautotrophic prokaryote, integrated with geochemical processes.)
7. Becerra, A., Delaye, L., Islas, S., & Lazcano, A. (2007). The very early stages of biological evolution and the nature of the last common ancestor of the three major cell domains. Annual Review of Ecology, Evolution, and Systematics, 38(1), 361-379. Link. (This research focuses on the possibility of LUCA being an RNA-based organism.)
8. Glansdorff, N., Xu, Y., & Labedan, B. (2008). The last universal common ancestor: emergence, constitution, and genetic legacy of an elusive forerunner. Biology Direct, 3(29). Link. (Explores LUCA's potential adaptation to extreme environments, suggesting thermophilic characteristics.)
9. Fournier, G.P., & Gogarten, J.P. (2010). Rooting the ribosomal tree of life. Molecular Biology and Evolution, 27(8 ), 1792-1801. Link. (An investigation into ribosomal RNA to decipher LUCA's characteristics.)
10. Williams, T.A., Foster, P.G., Cox, C.J., & Embley, T.M. (2013). An archaeal origin of eukaryotes supports only two primary domains of life. Nature, 504(7479), 231-236. Link. (This paper delves into the relationship between archaea and eukaryotes, pointing towards a complex LUCA.)
11. El Baidouri, F., Venditti, C., Suzuki, S., Meade, A., & Humphries, S. (2020). Phenotypic reconstruction of the last universal common ancestor reveals a complex cell. bioRxiv. Link. (Sheds light on LUCA's phenotypic structure, suggesting a level of complexity previously unrecognized.)
12. Spang, A., Saw, J.H., Jørgensen, S.L., Zaremba-Niedzwiedzka.... (2015). Complex archaea that bridge the gap between prokaryotes and eukaryotes. Nature, 521(7551), 173-179. Link. (The paper provides evidence of complex archaeal lineages closely related to LUCA, reinforcing the archaeal roots of eukaryotes.)
13. Raymann, K., Brochier-Armanet, C., & Gribaldo, S. (2015). The two-domain tree of life is linked to a new root for the Archaea. Proceedings of the National Academy of Sciences, 112(21), 6670-6675. Link. (A revision of the tree of life showing the Archaea domain branching out separately, suggesting its distinct nature from LUCA.)
14. Sousa, F.L., Thiergart, Lane, N., & Martin, W.F. (2016). Early bioenergetic evolution. Philosophical Transactions of the Royal Society B: Biological Sciences, 368(1622), 20130088. Link. (The study delves into LUCA's potential bioenergetic systems, focusing on processes like chemiosmotic coupling.)
15. Weiss, M.C., Sousa, S., Roettger, M., Nelson-Sathi, S., & Martin, W.F. (2016). The physiology and habitat of the last universal common ancestor. Nature Microbiology, 1(9), 16116. Link. (Details the habitat and metabolic processes of LUCA, providing insights into its life characteristics.)
16. Da Cunha, V., Gaia, M., Gadelle, D., Nasir, A., & Forterre, P. (2017). Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes. PLoS Genetics, 13(6), e1006810. Link. (Challenges the role of Lokiarchaea in bridging the evolutionary gap between prokaryotes and eukaryotes, but highlights its relation to LUCA.)
17. Caetano-Anollés, G., & Caetano-Anollés, D. (2020). An evolutionary biochemistry perspective on the last universal common ancestor. Journal of Molecular Evolution, 88(6), 516-539. Link. (Uses biochemistry as a lens to investigate the possible protein domains and structures present in LUCA.)
18. Zaremba-Niedzwiedzka, K., Caceres, E.F., Saw, J.H., Bäckström, D...., (2017). Asgard archaea illuminate the origin of eukaryotic cellular complexity. Nature, 541(7637), 353-358. Link. (Introduces Asgard archaea, a key lineage connected to LUCA that gives clues about the evolutionary origins of eukaryotic cellular complexity.)



Last edited by Otangelo on Tue Sep 19, 2023 9:03 am; edited 29 times in total

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LUCA was supposedly a chemolithoautotroph

The hypothesis that LUCA was a chemolithoautotroph (an organism that derives energy from inorganic compounds and uses carbon dioxide as its main carbon source) is based on several lines of evidence and reasoning. The core metabolic pathways that are conserved across the three domains of life (Bacteria, Archaea, and Eukaryota) provide insights into the metabolism of LUCA. The presence of certain pathways, like the Wood-Ljungdahl pathway (a CO₂-fixation pathway), in both Bacteria and Archaea suggests that LUCA had an autotrophic metabolism. Molecular studies have shown that many of the genes related to autotrophic CO₂ fixation are ancient and widely distributed across the tree of life. Their early appearance and widespread distribution suggest that these metabolic capabilities were present in LUCA. The RNA world hypothesis proposes that before the evolution of DNA and proteins, early life forms had RNA that played roles in both genetics and catalysis. RNA molecules, or ribozymes, would have been central to early metabolism. In this context, chemolithoautotrophy provides a plausible mechanism for the synthesis of organic molecules needed by these early RNA-based life forms. Chemolithoautotrophy harnesses energy from inorganic compounds. Early Earth's environment is believed to have been replete with inorganic substrates like hydrogen, iron, and sulfur. These substrates could serve as energy sources for primitive metabolic reactions without the need for light or organic molecules. Earth's early atmosphere lacked oxygen, making it reducing in nature. This would have promoted reactions that derive energy from the oxidation of inorganic molecules, which is the basis for chemolithoautotrophy. The metabolic pathways associated with chemolithoautotrophy are some of the most ancient and fundamental, suggesting they could have been among the earliest metabolic systems to evolve. They are found across various extremophiles and are considered ancient metabolic strategies. Many scientists theorize that life began at hydrothermal vents deep in the ocean. These environments are rich in inorganic molecules like hydrogen, methane, and sulfur compounds, which can serve as energy sources for chemolithoautotrophic processes. This makes the idea of RNA life forms utilizing such a mechanism even more plausible. For the RNA world hypothesis to be viable, the primordial environment would need to continuously supply ribonucleotides and other precursors to RNA. Chemolithoautotrophic reactions could produce the necessary organic compounds, such as formaldehyde and cyanide, that can be involved in the prebiotic synthesis of ribonucleotides.

Geological evidence suggests that Earth's atmosphere was anoxic (lacking oxygen) until about 2.4 billion years ago, which is after the time when LUCA is thought to have existed. In such an environment, aerobic metabolism would not have been possible, making anaerobic and chemolithoautotrophic metabolisms more likely for early life forms. One theory about the origin of life places it near hydrothermal vents in the deep ocean, where mineral-laden water provides a rich source of chemicals. The organisms found in these environments today are often chemolithoautotrophs, using the inorganic compounds spewing from the vents (like hydrogen and reduced sulfur compounds) to produce organic matter. The conditions at these vents are seen as a plausible setting for life's origins, making a chemolithoautotrophic metabolism a logical candidate for early organisms, including LUCA. Autotrophy is a simple and direct way to produce organic molecules from abundant inorganic precursors like CO₂, H₂, and nitrogenous compounds. Such a metabolism would be well-suited to the early Earth, where organic molecules might have been sparse. While the chemolithoautotrophic hypothesis for LUCA is compelling based on current data, it's essential to recognize that our understanding of early life is continually evolving. As more evidence is gathered from fields like biochemistry, geology, and astrobiology, our picture of LUCA and the early conditions of life on Earth might be refined further. Regarding nitrogen sources, while there is evidence for the presence of nitrogen in the early Earth's atmosphere and in extraterrestrial bodies (like comets and meteorites), the exact mechanisms by which this nitrogen would have been made biologically available to LUCA or its predecessors are, indeed, more speculative.

1. Genetic Machinery

Nucleotide Synthesis and Recycling

At the heart of this machinery were the biosynthetic enzymes. These molecules were not just simple catalysts; they were the maestros of early life, responsible for crafting the very building blocks of genetic information: purine and pyrimidine nucleotides. Every strand of DNA, and every fragment of RNA that exists today can trace its lineage back to these enzymes' diligent work. Accompanying these biosynthetic enzymes in this ancient biochemical ballet were the nucleotide diphosphate kinases. Their role was equally pivotal. Acting as the great interchangers, these enzymes ensured that nucleotides were in their right forms, ready to participate in the great genetic dance that would lead to life as we know it. It's an awe-inspiring thought. Every piece of genetic material, every thread of DNA in every cell of every organism, owes its existence to these early processes and molecules. This intricate dance of enzymes and nucleotides set the stage for the vast and varied pageant of life. This paints a picture of LUCA not as a single point but as a bustling hub of molecular activity, laying down the blueprint for all life to come.

DNA replication

A fundamental element of LUCA's machinery would have been the processes surrounding nucleic acid polymerization and maintenance. Imagine enzymes like DNA polymerases, master builders, meticulously constructing the DNA strand by adding one deoxyribonucleotide at a time. These enzymes would ensure the faithful replication of LUCA's genetic material, passing on its instructions with precision. Yet, DNA is more than just a static string of information; it's a dynamic entity. To manage the stresses and strains of this double helix, enzymes like DNA gyrase and topoisomerases would have come into play. They'd act like skilled artisans, ensuring the DNA doesn't become overly twisted or tangled during its operations. The dance wouldn't stop there. DNA ligase, akin to a craftsman, would seal any breaks in the DNA backbone, ensuring continuity. Meanwhile, ribonucleotide reductase would labor in the background, producing the essential building blocks needed for DNA synthesis. But what happens when the DNA needs to replicate, when it needs to unwind and reveal its secrets? Enter DNA helicase, the unsung hero, tirelessly working to unzip the helix, making the genetic code accessible for replication. And to set the stage for this replication, primase would take its place, laying down RNA primers to signal where the process should begin. This portrayal of LUCA's genetic machinery paints a picture of a sophisticated and coordinated system. While the simplicity of a solitary ancestor holds appeal, the depth and complexity of the molecular world suggest something grander. If LUCA were indeed a consortium of life forms, the combined genetic tools, and mechanisms they might have shared provide a window into the vast potential and adaptability of early life.

Transcription (from DNA to RNA)

LUCA is thought to have possessed the process of transcription which stands as a fundamental pillar. At the heart of this procedure lies the RNA Polymerase, a diligent enzyme that takes on the task of converting the information coded within DNA into RNA. Acting much like a skilled scribe, it reads the genetic instructions and crafts a complementary RNA strand, ensuring that the story of life can be relayed to the next stages of cellular function. Yet, the process isn't left unchecked. Transcription factors, akin to editors, step into the scene. These proteins are crucial in determining which sections of DNA get transcribed and when. They serve to fine-tune gene expression, making certain that the right genes are active at the right times, orchestrating a harmonious performance within the cell. Together, RNA Polymerases and transcription factors represent a vital duo in the dance of genetics, mirroring the legacy of LUCA in the living world today.

Translation (from RNA to Protein)

Imagine translating RNA to protein, an essential process ensuring life's continuity. Central to this were the ribosomes, those cellular marvels made up of ribosomal RNAs and proteins. They stand as the stage upon which the drama of protein synthesis unfolds. Playing a starring role in this spectacle are the transfer RNAs (tRNAs), the diligent couriers ferrying amino acids to the ribosome, ensuring that each protein strand is crafted accurately. Yet, to ensure the tRNAs carry the right amino acid for the task, the aminoacyl-tRNA synthetases serve a pivotal role. Think of them as meticulous matchmakers, ensuring each tRNA finds its perfect amino acid partner. The entire process, from its dramatic beginning to its concluding act, is guided by initiation, elongation, and termination factors. These factors ensure that protein synthesis starts with precision, proceeds with care, and concludes with finesse. The dance of LUCA's genetic machinery, as we understand it, showcases a coordinated performance, reflecting a time when life, though young, was incredibly adept. It beckons us to dive deeper into the mysteries of the early Earth, urging us to unravel the intricate interplays that birthed life amidst ancient terrains. Each discovery draws us nearer to piecing together the grand puzzle of life's earliest moments.

Protein Folding and Post-translational Modifications

Ponder on the subsequent fate of proteins. The proteins, once constructed, face another set of challenges: assuming the right form and maintaining their functionality. Here, LUCA's story introduces us to chaperones, the unsung heroes that ensure proteins fold correctly. Much like a sculptor ensuring the clay bends and molds just so, these chaperones would have guided proteins to assume their functional shapes, ensuring the smooth operation of cellular processes. With the wisdom injected into nature, there were also contingency plans. Enter the proteases, the guardians of cellular quality control. Whenever proteins erred in their ways, taking on forms that could be detrimental or simply became redundant, proteases would have been on standby. Acting with precision, these enzymes dismantled the misfolded or unneeded proteins, ensuring the cell's milieu remained unperturbed. The subtle dance of protein folding and modification paints a vivid image of LUCA: not just a passive recipient of life's whims but an active participant, navigating challenges with tools both delicate and decisive. As we delve deeper into the early Earth's conditions, the environments that birthed these mechanisms, and the interplays of fledgling life forms, our journey becomes an exploration, one where every revelation nudges us closer to understanding the profound beginnings of life.

Repair and Protection

Enter the DNA repair enzymes. These vigilant sentinels roamed the nascent genetic landscape, constantly on the lookout for damages and anomalies. Like artisans delicately mending a tapestry, these enzymes meticulously worked to repair any faults, ensuring the preservation of the precious genetic information. But even with the best artisans at work, there might be occasional inconsistencies. This is where the mismatch repair system played its part. It functioned as a quality control mechanism, proofreading the freshly replicated DNA. If it found any errors - even the minutest discrepancies - it promptly rectified them, ensuring that the DNA's message remained clear and accurate for generations to come. Yet, life, even at its earliest, wasn't just about preserving the old; it was also about creating the new. The recombination proteins were the harbingers of novelty. They orchestrated a dance of genes, weaving together strands of DNA in new and unique patterns. This process of genetic recombination allowed for a blending of information, a molecular melding that brought forth new possibilities and potentials. Together, these systems and proteins worked in harmony, safeguarding the genetic treasures of LUCA. They formed the pillars that held up the grand edifice of life, ensuring its continuity while allowing for the birth of diversity. Through their ceaseless endeavors, the ancient narrative of life was not just preserved but also enriched, setting the stage for the myriad forms that would later populate our world.

Other Proteins and Complexes

The RNA degrading enzymes ensured that the RNA molecules didn't overstay their welcome. Acting as efficient molecular custodians, they decomposed RNA once its part was played, ensuring that the cellular environment remained orderly and efficient. But while RNA played its fleeting role, DNA's story was a longer, more intricate saga. To replicate this archive of life's instructions, an ensemble of sophisticated machinery was required. Among them were the protein complexes designed specifically for DNA replication. The sliding clamps were the anchors, holding the DNA polymerase in place, allowing it to read and replicate long stretches of DNA without interruption. Like a skilled craftsman using a steady hand to draw a straight line, these clamps ensured precision in the replication process. And, of course, no tool is of use if not positioned correctly. The clamp loader proteins were the unsung heroes, adeptly placing the sliding clamps at their rightful positions on the DNA. They ensured the process ran smoothly, coordinating each phase of replication like a master conductor leading an orchestra. Together, these entities, both the RNA degrading enzymes and the protein complexes, played their part in the elegant dance of life inside LUCA. They bore witness to the primal symphony of creation, where information flowed, was used, and was faithfully replicated, ensuring the continuation of life's grand narrative.

2. RNA's Role 

Given the potential that LUCA existed in an RNA-dominated phase, it's conceivable that RNA performed various central cellular functions beyond just protein synthesis. Here's an overview of the protein machinery LUCA might have had to support RNA's diverse roles.

RNA Synthesis and Maintenance

In LUCA's bustling molecular metropolis, RNA Polymerases were the master builders. These diligent enzymes meticulously assembled strands of RNA, one ribonucleotide at a time. Like skilled artisans crafting a tapestry, they worked with precision, ensuring that the resulting RNA molecules mirrored the blueprint set by the DNA. But crafting was just one part of the narrative. Enter RNA Helicase. Picture a librarian sorting through a tightly packed shelf of ancient scrolls. The RNA Helicase, with its unwinding prowess, made sense of coiled and knotted RNA structures, ensuring they were readable and usable. Whether aiding in the delicate process of RNA splicing, ensuring the smooth operation of translation, or assisting in the grand assembly of the ribosome, the RNA Helicase was an unsung hero, working behind the scenes to maintain order and functionality. These two, the RNA Polymerases and the RNA Helicase, were central figures in LUCA's life story, shaping the flow of genetic information and ensuring the smooth orchestration of cellular processes that made life possible.

RNA Processing and Modification

The RNase P, akin to a seasoned sculptor, took to its role with finesse. Tasked with the responsibility of shaping tRNA precursors, it ensured the birth of mature tRNA molecules, essential players in the symphony of protein creation. On the sidelines, the RNA Editing Enzymes acted with precision and delicacy. Their role can be likened to that of editors, diligently amending RNA sequences after their transcription, ensuring the narrative remained coherent and true to its purpose. Lastly, the Pseudouridine Synthases and Ribose Methyltransferases, the adept artisans of LUCA's realm, embellished the ribosomal and transfer RNAs. These modifications, subtly introduced, optimized the function and structure of these RNA molecules, akin to a jeweler adding the final touches to a masterpiece. These components, in their specialized roles, collectively weaved the complex tapestry of LUCA's RNA world.

RNA's Role in Protein Synthesis

Foremost among them, Ribosomal RNAs (rRNA) stood tall. Partnered with ribosomal proteins, they crafted the ribosome's heart and soul. This collaboration was pivotal, forming the very stage upon which the dance of protein synthesis would be choreographed. Transfer RNAs (tRNAs) were the interpreters of this dance. With a grace all their own, they read the intricate notes of mRNA sequences. Their role was clear: discern the rhythm, and bring forth the precise amino acids that would set the tempo for protein creation. In this orchestra, Messenger RNAs (mRNA) held a crucial role. Like messengers delivering scrolls of ancient lore, they carried the tales written in the DNA and relayed them to the ribosome. Theirs was the language that told what song the protein would sing. And behind the scenes, tRNA-modifying Enzymes worked tirelessly. These meticulous maestros introduced subtle tweaks into the tRNAs, ensuring that the rhythm of protein synthesis remained accurate and flawless. Their touch ensured that every note played in the grand symphony of life was pitch-perfect.

RNA in Catalysis and Other Functions

Enter the Ribozymes, not just any RNA molecules, but those gifted with the power of catalysis. Among them, standouts like the ribosomal peptidyl transferase center and self-splicing introns, exhibited their unique ability to accelerate chemical reactions, akin to the role enzymes play. They remind us that RNA isn't just a passive transmitter of genetic instructions but can take on dynamic, active roles in the cell. Then there are the mysterious influencers of the RNA world: Small Interfering RNAs (siRNAs) and microRNAs (miRNAs). Quietly, they weave their magic, guiding RNA interference and overseeing the regulation of genes after transcription. These small yet mighty molecules influence the genetic narrative, dictating which stories get amplified and which remain hushed. And amidst this bustling RNA city, RNase MRP finds its niche. Specializing in the meticulous task of ribosomal RNA processing, it ensures the ribosomes are equipped and ready for the essential task of protein synthesis. With each of these molecular players in place, LUCA's world becomes a mesmerizing dance of life's earliest processes.

RNA Protection and Degradation

RNA Chaperones are the meticulous conductors. With grace and precision, they ensure that RNA strands fold correctly, setting the stage for optimal function. These chaperones ensure that every RNA molecule assumes its intended shape, facilitating the many processes they partake in. And then, in this delicate balance of creation and degradation, enter the Ribonucleases. Their task may seem destructive, but it's essential. Like vigilant overseers, they ensure that the cellular realm isn't flooded with unwanted or damaged RNA. By controlling both the quality and quantity of RNA, they maintain harmony, allowing the cell to function without being overwhelmed. Together, these entities represent the yin and yang of the RNA world within LUCA, striking a balance between formation and dissolution, and setting the rhythm for life's earliest beats.

3. Metabolism

Given LUCA's speculated chemoautotrophic nature, it likely harnessed energy from inorganic substances and geochemical processes in an environment rich in hydrogen and metals. Here's a comprehensive list of the protein machinery LUCA might have utilized for its metabolic needs:

Energy Generation and Conservation

In LUCA's metabolic functions, Hydrogenases take center stage. These enzymes, essential in both the creation and usage of molecular hydrogen, drive vital reactions that breathe energy into early life processes. Their actions, seamlessly weaving into the larger metabolic tapestry, shape the foundational energy exchanges of life. Next, we have the Iron-sulfur proteins. These aren't just mere participants; they are vital connectors in the flow of life's energy. Engaged in the critical tasks of electron transport, they act as bridges, channeling electrons efficiently and ensuring that the energy processes run smoothly. But no discussion of LUCA's energetic functions would be complete without mentioning the master performer: ATP synthase. In an environment where every bit of energy matters, ATP synthase acts like a powerhouse, deftly converting ADP to ATP, the primary energy currency, leveraging the potential of a proton gradient. Its role is analogous to a skilled craftsman, meticulously generating the very fuel that powers the dynamism of early life. Together, these components shed light on the incredible machinery that must have buzzed within LUCA, guiding and energizing the earliest chapters of life's story.

LUCA's gas fixation mechanisms

Carbon Fixation and Assimilation: Deep within LUCA's metabolic orchestra, two notable enzymes emerge, playing pivotal roles in carbon fixation — a process vital for harnessing carbon's potential to fuel life. First, there's the Carbon monoxide dehydrogenase/acetyl-CoA synthase or CODH/ACS. This enzyme duo doesn't just participate; it leads a central act in the Wood-Ljungdahl pathway. Their primary role? To capture carbon dioxide and craftily weave it into the fabric of organic molecules. Their handiwork ensures that carbon dioxide, abundant in early Earth, is efficiently utilized, acting as a linchpin in LUCA's carbon harnessing mechanism. Then, there's the famed Ribulose-1,5-bisphosphate carboxylase/oxygenase, more commonly known as RuBisCO. Taking center stage in the Calvin cycle, its reputation is well-earned. With meticulous precision, RuBisCO assists in capturing and converting carbon dioxide, laying the groundwork for the synthesis of sugars — life's essential energy stores. These two enzymes, each with its unique role, offer a glimpse into LUCA's metabolic prowess, exemplifying how this ancient entity adeptly maneuvered the carbon-rich environment to pave the path for life's progression.
Hydrogen (H₂): Abundant near Earth's early hydrothermal vents, hydrogen stands out as a pivotal player in ancient biochemical pathways. Acting as an electron donor, hydrogen facilitates the reduction of carbon dioxide, resulting in the formation of organic molecules. This energy-harnessing reaction not only underscores hydrogen's pivotal role in early metabolic processes but also highlights its potential in supporting nascent life forms.
Methane (CH₄): Produced primarily through the biological activity of methanogenic archaea, methane's emergence stems from methanogenesis—a key metabolic process. However, the intricate web of early Earth's chemistry beckons a closer inspection of methane. While its current metabolic role is understood, methane's significance in primordial biochemistry still poses intriguing questions for researchers.
Hydrogen Sulfide (H₂S): Another compound enriched near hydrothermal vents, hydrogen sulfide served as an electron donor for certain life forms. By oxidizing this compound, organisms could tap into a vital energy source. Hydrogen sulfide's abundance and potential utility make it a candidate molecule in the search for the origins of early life's energy transactions.
Sulfur Dioxide (SO₂) and Elemental Sulfur (S⁰): Some microbes display a unique metabolic flexibility, utilizing these sulfur compounds in diverse ways. Depending on the metabolic avenue, these compounds can act either as electron donors or terminal electron acceptors. Their varied roles in microbial metabolism showcase the adaptability and diversity of life's biochemical toolkits.
Oxygen (O₂): A scarce entity in early Earth's atmosphere, oxygen's presence, even in trace amounts, may have shaped the trajectory of nascent life. With the emergence of oxygenic photosynthesis in cyanobacteria, the Earth underwent a profound atmospheric shift, reshaping the biological landscape and setting the stage for complex life forms.
Carbon Monoxide (CO): Beyond its toxic reputation, carbon monoxide assumes a vital role in some microbial metabolisms. Certain microorganisms harness this molecule for energy by oxidizing it to carbon dioxide. This ability exemplifies the myriad ways life can extract energy from seemingly inhospitable molecules.
Phosphine (PH₃): Recent buzz surrounding its potential presence on Venus has catapulted phosphine into the limelight as a prospective biosignature. While its footprint on early Earth remains speculative, some theories propose its involvement in prebiotic chemistry, hinting at a yet undiscovered chapter in the story of life's origins.

The myriad compounds and their roles in the early Earth paint a dynamic picture of the planet's ancient biochemistry. Each molecule, with its unique properties and interactions, contributes to the grand narrative of life's emergence. Delving deeper into their individual and collective roles offers not just a look back into our primordial past but also insights into life's potential beyond our planet.

Metabolism of Inorganic Substrates

Next, we encounter an ensemble of enzymes and proteins that perform an intricate task, reflecting the mastery of nature's elemental play. At the forefront are the sulfur reductases. These diligent workers don't simply handle sulfur; they transform it. Their primary task? To elegantly reduce sulfate, converting it into sulfide. This transformation captures the essence of LUCA's ability to tap into Earth's elemental resources, utilizing sulfur's potential in processes essential for life. Parallel to this, nitrogenases take the limelight. With atmospheric nitrogen as their stage, these enzymes showcase a remarkable act. They work tirelessly, reducing the ambient nitrogen—a gas that remains largely inert—to ammonia, a compound teeming with potential. Through this transformation, they pave the way for incorporating nitrogen, an essential building block, into the living world. Yet, LUCA's metabolic symphony wouldn't be complete without the unsung heroes: the metal transporters. Their role might seem humble, but it's crucial. These proteins act as vigilant gatekeepers, ensuring the uptake of metals like iron, zinc, and copper. Each metal, with its unique properties, is integral for various biochemical reactions, and these transporters ensure they reach where they're most needed. Together, these components illustrate LUCA's profound adaptability, weaving a narrative of life's early mastery over the elemental realms.

Electron Transfer Processes

Enter the cytochromes. These proteins are more than just molecular entities; they are the maestros of electron movement. Stationed strategically in the electron transport chain, they facilitate the careful handoff of electrons, ensuring that energy is harnessed efficiently, driving processes essential for survival. In tandem with the cytochromes, quinones take the stage. These aren't mere molecules; they are the couriers of the cellular world. As they move within the confines of the cellular membrane, they adeptly shuttle electrons. Acting in concert, they serve as a bridge, linking various components of the electron transport process and ensuring a smooth flow of energy. This coordinated dance between cytochromes and quinones paints a vivid picture of LUCA's sophisticated energy management system, a testament to life's early ability to capture and utilize energy in a world teeming with challenges.

Synthesis and Degradation of Biomolecules

In LUCA, the rise of molecular craftsmen took center stage, shaping the intricate narrative of life's early playbook. First up, the amino acid biosynthesis enzymes. These aren't just your run-of-the-mill proteins; they're the artisans of the cellular realm, meticulously crafting amino acids. Just as an artist shapes clay, these enzymes brought forth the essential building blocks of proteins, laying down the very foundations upon which the intricate machinery of life would be built. But what's a machine without its protective casing? Enter the fatty acid synthesis enzymes. Their role was undeniably crucial. Tasked with producing fatty acids, these enzymes sculpted the primary constituents of cellular membranes, ensuring a protective barrier for the delicate operations within. Last, but certainly not least, the nucleotide synthesis enzymes took their bow. Masters of molecular architecture, they were responsible for creating purine and pyrimidine nucleotides. These nucleotides are the keystones of the genetic world, vital for storing and transmitting the coded instructions that drive the cell. Together, this trio of enzymes carved out a harmonious existence, weaving together the foundational fabrics of life. Their collaborative efforts not only set the stage for LUCA's complex biochemical ballet but also hinted at the magnificence that life would eventually achieve.

4. Ecology and Environment

LUCA's existence is speculated to have been marked by its ability to thrive in extreme environments. Given the geological conditions and chemical processes of early Earth, hydrothermal vents located deep in the sea are often highlighted as the likely habitats. LUCA's possible thermophilic nature suggests it could have thrived in high-temperature zones. Here's an overview of LUCA's potential environmental characteristics and adaptive features:

Adaptation to Extreme Environments

Amidst LUCA's vibrant biochemical tapestry, certain proteins were paramount in ensuring survival in challenging environments. Think of a bustling city during a heatwave; just as the city's infrastructure has to adapt to the sweltering heat, so too did LUCA's internal machinery. Enter the Heat Shock Proteins, the heroes of the high-temperature realm. Their specialty? Ensuring that, even in the face of searing heat, proteins maintained their proper form. They're the unsung protectors, stepping in when temperatures soar, ensuring that the cell's machinery doesn't falter or break down. But the intricacies of a cell's inner workings aren't governed by these proteins alone. The chaperones, aptly named, are like the patient instructors of the cellular world. Whether it's assisting in the careful folding of new proteins or guiding the graceful dance of macromolecular assembly and disassembly, chaperones are there, ensuring each process unfolds seamlessly. Together, these guardians of the cellular realm serve as both protectors and facilitators, ensuring the smooth operation of life's most vital processes. They remind us that, even in the earliest chapters of life's story, there existed a level of sophistication and resilience, a testament to the marvel that is the living cell.

Deep-sea Hydrothermal Vents Adaptations

In the profound depths of the ocean, where the weight of the water above creates an environment of incredible pressure, life thrives in ways unimaginable to those living on the surface. Here, amongst the pitch-black, where sunlight is a mere myth, life has devised its own unique methods to persist. Consider the Pressure-resistant Proteins. They are like the deep-sea divers of the cellular world, built to withstand and function under the colossal pressures of the abyss. When other proteins might falter and lose their shape under such intense conditions, these proteins remain steadfast, ensuring that the cell's operations continue unhindered. Deep below, where hydrothermal vents spew forth sulfurous clouds, another set of remarkable molecules come into play: the Sulfide-utilizing Enzymes. In a world where sulfides are plentiful, these enzymes have evolved to harness this compound, deriving energy from what would be toxic for many surface-dwellers. They represent the epitome of adaptability, turning a challenge into an opportunity. But life's ingenuity in these depths doesn't stop there. Given the rich metal content surrounding hydrothermal vents, life has taken a metallic turn. The Metal-binding Proteins emerge as the expert metallurgists of the cellular domain. Binding and utilizing metals, they've turned the metallic bounty of the vents into a tool, facilitating various vital cellular functions. Together, these molecular innovations showcase life's tenacity and adaptability. Deep in the ocean's abyss, where the environment is as harsh as it is alien, life has not only found a way to survive but to thrive, painting a vivid picture of resilience and evolution at work.

Thermophilic Adaptations

In the blistering heat of extreme environments, where many molecules would denature and lose their function, certain champions of adaptability emerge, ensuring life's persistence amidst scorching conditions. The Thermosome is one such marvel. Found primarily within the mysterious realm of archaea, these unique chaperonins undertake the Herculean task of assisting in protein folding. Imagine a meticulous craftsman, working diligently to mold and shape in an inferno, ensuring that proteins achieve their correct configurations. Under conditions where most proteins would lose their shape, the thermosome ensures continuity and function. But it's not just proteins that face the wrath of extreme heat. DNA, the blueprint of life, needs stability. Enter the DNA Gyrase. This ingenious enzyme adds twists, introducing negative supercoils to DNA. Much like twisting a rubber band to store energy, these supercoils impart stability to the DNA's double helix, allowing it to withstand high temperatures that would otherwise wreak havoc on its structure. And as for the machinery of protein synthesis, the challenge of high heat is met head-on by Thermostable Ribosomal RNA. This isn't your typical rRNA. Evolved to endure, these molecules remain both stable and functional even when the thermometer soars. They serve as a testament to nature's ability to adapt, ensuring that the vital process of protein synthesis continues uninterrupted. Such molecular adaptations paint a picture of life's resilience, reminding us that even in the harshest of conditions, life finds a way, backed by an arsenal of specialized tools and mechanisms.

5. Cellular Complexity

LUCA represents a unique intersection in the history of life, posited to contain the precursors to both prokaryotic and eukaryotic cellular structures. Although the exact cellular architecture of LUCA remains speculative, it is thought that it may have had complexities bridging the gap between the simplicity of prokaryotes and the intricacy of eukaryotes. Here's an overview of LUCA's potential cellular features and the building blocks hinting at future eukaryotic developments:

Cellular Structures and Components

Delving into the early epochs of life's narrative,  we surmise the existence of rudimentary mechanisms and structures. Though elementary, these primordial components set the stage for the cellular masterpieces we observe in modern organisms. Picture the Proto-Cytoskeleton Elements — these are believed to not be the sophisticated networks of contemporary eukaryotic cells. Rather, envision them as basic scaffolds, offering structural anchorage and a hint of morphology during the nascent phases of life. These elements are thought to be the harbingers, setting a trajectory for the advanced cytoskeletons that modulate cell shape, motility, and intercellular exchanges today. Yet, the dawn of cellular advancements wasn't solely in structural domains. Inside the cell, early signs of compartmentalization are believed to have manifested with the Primitive Endomembrane Systems. Far from the adept organelles of modern cells, these systems are considered the first glimmers of intracellular organization. They hint at what might have been the early renditions of structures like the endoplasmic reticulum and the Golgi apparatus. Their emergence is thought to have prefigured the compartmentalized sophistication that epitomizes today's cells. And as these ancient cells are believed to have matured, the imperative of conveying molecules between these nascent compartments would have arisen. Thus, it's posited that the Protein Transport Systems came into play. These proto-transporters, the unsung heroes of the foundational cell, would have ensured that molecules were duly dispatched to their designated locales. Their believed existence accentuates the budding intricacies within early cells and the importance of regimented molecular conveyance for cellular equilibrium. Such ancestral components, in their conjectured simplicity, seem to distill the very spirit of life's progression — an unyielding stride towards refinement and adeptness, continually building upon the precursors. They serve as a reminder that the intricate cellular machinery we know today is thought to have originated from more fundamental, yet undeniably pivotal, beginnings.

Cellular Complexity Indicators

While many envision LUCA as a solitary organism, a singular point of commencement, scientific discourse, and exploration suggest a more nuanced scenario. The machinery that governed LUCA's cellular functions would likely be a testament to both simplicity and nascent complexity. Central to this machinery is the idea of Compartmentalized Biochemical Reactions. It is hypothesized that even in those early times, cellular reactions didn't just occur haphazardly. Instead, there might have been designated areas, primitive compartments if you will, where certain biochemical processes took precedence. Such compartmentalization would have been critical, offering the cell an opportunity to conduct vital reactions without interference, ensuring a semblance of order in a world that was largely chaotic. Further diving into LUCA's cellular constitution, one would surmise the significance of Lipid Diversity. Though it's challenging to pinpoint the exact nature of these lipids, it's believed that they weren't just a monotonous ensemble. There might have been a diverse range of lipids, each with potential roles, possibly suggesting a level of specialization. Could this diversity hint at the early foundations of specialized cellular membranes or the rudiments of membrane-bound entities? While definitive answers remain elusive, such lipid variance would likely have been crucial for LUCA's survival, offering flexibility and adaptability in a dynamic environment. Lastly, no discussion about LUCA would be complete without contemplating its interactions with its surroundings. The idea of Symbiotic Relationships surfaces here. It's postulated that LUCA might not have been entirely self-reliant. Perhaps, in the vast expanse of primordial Earth, LUCA engaged in beneficial interactions with other entities. These interactions, mutualistic in nature, could set the stage for what we recognize today as symbiotic relationships. While one could only speculate, such interactions might foreshadow the intricate relationships that later organisms would develop, such as the endosymbiotic theories surrounding mitochondria and chloroplasts. Piecing together LUCA's life story is akin to assembling a puzzle with many of its pieces still buried, waiting to be unearthed. While our understanding remains fragmented, every hypothesis and postulation adds another layer to this captivating narrative. Delving into LUCA's world reminds us of the enduring quest for knowledge, a journey to understand the very roots of life's grand narrative.

6. Evolutionary Framework

LUCA stands as a pivotal entity in the evolutionary chronicle, with debates around whether it was a singular organism or a representation of an early biological network. The nature of LUCA's existence has implications for understanding the fluidity and complexity of early life evolution, especially considering the intricate genomic and cellular landscape. Here's a breakdown of the conceptualizations around LUCA within the evolutionary framework:

Community Over Singular Entity

Within the vast spectrum of life's origins, the traditional portrayal of the Last Universal Common Ancestor (LUCA) as a solitary sentinel has undergone a profound transformation. Emerging from the depths of scientific inquiry is the concept of the Community-Based LUCA. Instead of envisioning LUCA as a lone forerunner, it is now postulated that LUCA could embody a collective—a consortium of early organisms interconnected by shared genetic and metabolic pathways. This perspective casts LUCA not as a singular pinpoint in the vastness of life's timeline but rather as a bustling commune, a confluence where primordial life forms coexisted and possibly collaborated. Accompanying this revised portrayal of LUCA is the idea of Horizontal Gene Transfers. Beyond the conventional perspective of genetic inheritance, which visualizes lineage as a linear tree with branches diverging from a common trunk, the realm of horizontal gene transfers introduces a more interconnected, web-like pattern. It's hypothesized that in the early epochs of life, genetic material wasn't just passed vertically from ancestor to offspring. Instead, organisms engaged in extensive genetic exchanges with one another. This fluidity in genetic sharing suggests a web of life, where genetic boundaries were more porous, and organisms could acquire and integrate genetic innovations from their neighbors. Together, these concepts—of a community-based LUCA and the widespread nature of horizontal gene transfers—challenge and enrich our understanding of early life on Earth. They paint a picture of a primordial world defined not by isolation but by collaboration and interconnectedness, where the flow of genetic information wove a complex tapestry of relationships. This evolving narrative reminds us that life's origins might be even more intertwined and multifaceted than previously thought.

Evolutionary Implications

The annals of biology, when charting the course of life's descent, have often depicted its journey as a branching tree—a visual metaphor where life diverges from common points of origin into myriad species. Yet, with the advent of modern genomic studies and deeper insights into early life, this tree-based model finds itself sharing space with a newer paradigm: Network-Based Evolution. Instead of portraying life's trajectory as a simple bifurcation from common nodes, this novel concept envisions it as a dense web of connections. The implication is profound: early organisms might not have strictly diverged but rather intermingled their genetic destinies, forming an intricate network of shared genes, pathways, and evolutionary trajectories. Amidst this lattice of connections emerges another intriguing observation: the Archaeal and Eukaryotic Bridge. As researchers delve into the attributes of LUCA, they've hypothesized the presence of shared characteristics between archaea and the antecedents of eukaryotes. Rather than viewing these domains of life as distinct evolutionary avenues, it's postulated that they may have once shared a common platform, with shared genomic and cellular features. This bridge, metaphorically speaking, could serve as a testament to the ancient collaborations or convergences in the primordial world. Such revelations reshape our comprehension of early life on Earth. The portrait of life's genesis is no longer just about discrete paths diverging from singular points but also about the interconnected paths that organisms might have journeyed together. In this revised narrative, life's early phase is not merely a tale of separation but also one of convergence and collaboration, underscoring the complexity and dynamism of Earth's primeval biosphere.

7. Community Dynamics

LUCA's existence remains a topic of intrigue, especially when pondering its potential representation. Instead of being a single, well-defined entity, LUCA might have symbolized a community marked by genetic fluidity. This community-centric perspective reshapes our understanding of early life's dynamics, especially in the context of rampant genetic exchanges. 

Genetically Fluid Community

Within the vast expanse of life's historical record, the question of LUCA's nature has been a tantalizing enigma. The Fluid Genetic Representation adds another layer to this riddle. Rather than viewing LUCA as a stable, well-defined genetic entity, this hypothesis presents it as an ever-changing community of organisms, characterized by malleable genetic traits. Imagine a dynamic mosaic of life, where individual organisms are not bound by rigid genetic blueprints but are part of a collective that continually shares and reshapes its genetic repertoire. In this scenario, LUCA represents not a pinpointed snapshot of early life but a broader, evolving tableau. This fluidity offers a captivating explanation: that early life was not about rigid boundaries but about adaptability and cooperation, allowing organisms to navigate the challenges of a nascent Earth. Such a community-based perspective transforms our understanding of LUCA from a fixed progenitor to a dynamic consortium of early organisms. Instead of being a mere stepping stone in life's lineage, LUCA emerges as a vibrant ecosystem, reflecting the adaptability and resilience that have been hallmarks of life throughout its journey on Earth. Through this lens, the genesis of life gains a dimension of fluidity and interconnection, painting a picture of an ancient world teeming with collaborative potential.

Horizontal Gene Transfers

Enter the concept of Rampant Genetic Exchanges. The term paints a picture of a bustling market, not of goods and wares, but of genetic material. In the ancient arenas of primordial Earth, early proto-cells weren't isolated entities safeguarding their genetic treasures. Instead, they appeared to be part of an open consortium, freely exchanging genetic codes. Such an idea suggests that the dawn of life was not characterized by rigid cellular individualism but by an interconnected community, where the lines between one organism and another were blurred. This ongoing genetic dialogue among proto-cells presents a world where survival and adaptability were communal endeavors. As challenges arose, solutions weren't just the products of individual innovation but were born from the collective wisdom of many, transferred through horizontal gene transfers. In this vibrant genetic bazaar, attributes beneficial to survival could quickly disseminate, not just through direct descent but across unrelated organisms. Such a scenario reshapes our understanding of early life. It was not an arena of isolated competitors but a cooperative landscape, where success was shared, and challenges were tackled collaboratively. The idea of Rampant Genetic Exchanges underscores the profound interconnectedness that might have characterized life's initial steps, emphasizing cooperation over competition in navigating the primal challenges of ancient Earth.

8. Life's Emergence and LUCA

LUCA's significance isn't solely rooted in its position as a possible ancestral organism. Its existence also points towards a critical juncture in the evolution of life on Earth. This nexus, potentially bridging non-biological geochemical processes with the intricate world of living entities, underlines LUCA's paramount role in the narrative of life's emergence. Let's explore these intersections more deeply:

Abiotic Geochemistry and Biological Processes

Embarking on a journey to uncover life's origins inevitably leads us to a delicate intersection, where the solid grounds of geology blend seamlessly with the fluid realm of biology. This is the realm of the Geo-Biological Nexus, and LUCA - the Last Universal Common Ancestor - is its emblematic harbinger. Imagine the early Earth, a swirling crucible of dynamic geochemical processes. Volcanic eruptions spewing molten rock, vast oceans churning with primordial brews, and an atmosphere filled with gases that seem alien to us today. But in this chaotic environment, where every rock and every droplet was abuzz with chemical reactions, a transition was taking place. Simple geochemical processes, governed by the laws of physics and chemistry, were giving rise to something more organized, something that started to hint at the rhythms and cycles of life. LUCA, in this grand tableau, was not just an organism or even a community of organisms. It stood as a beacon, marking the point where the planet's geochemistry began to give birth to the earliest biological processes. Here, in this nexus, molecules born from simple geochemical reactions began to assemble in ways that mimicked the patterns of life. They started forming chains, networks, and cycles, echoing the metabolic pathways we associate with living organisms. The Geo-Biological Nexus challenges our understanding of what life truly is. It suggests that life's emergence was not a singular, magical event, but a gradual transition. It was a spectrum, with geochemistry at one end and biology at the other, and LUCA was somewhere in between, capturing the essence of both worlds. Through the lens of LUCA and the Geo-Biological Nexus, we are compelled to reevaluate our understanding of life's inception. It becomes evident that our planet's geological and biological narratives are deeply intertwined, each shaping the other in an eternal dance, tracing back to the very dawn of time.

Evolutionary Transition

In the vast timeline of Earth's history, few moments are as profound as the transition from the geochemical to the biological. Here, amidst the primordial cauldron of organic molecules, stirred and shaped by the relentless forces of geochemical processes, the semblance of life supposedly began to emerge, and LUCA - the Last Universal Common Ancestor - would have been at the heart of this monumental shift. Visualize the young Earth, a realm governed by geochemical might. Oceans rich with molecular concoctions, skies heavy with unbridled energy, and a landscape continually reshaped by the planet's volatile temperament. In these turbulent waters, a myriad of organic molecules, synthesized by the forces of nature, would have begun to gather. These molecules, initially a byproduct of Earth's geochemical dynamism, slowly began to find harmony amongst themselves. Driven by chance, and the intrinsic chemistry of their being, they would have started to form more complex structures, establishing the first hints of molecular order. LUCA stands as a sentinel at this pivotal juncture, embodying the transition from mere chemistry to the earliest inklings of biology. It is thought that within LUCA, or perhaps within the community it represented, organic molecules, once passive products of the planet's geochemical fervor, began to actively orchestrate processes that mirrored life. They formed rudimentary cycles, networks, and chains, processes that would lay the groundwork for the more intricate dance of life that would follow. The narrative of "From Geochemical to Biological" is not just the story of LUCA or of life's origins; it's a hypothesized testament to the adaptability and resilience of matter itself. In the face of Earth's early chaos, molecules found a way to coalesce, cooperate, and eventually create. And in this transformative journey, they laid the first, crucial steps from the geochemical realm towards the rich tapestry of biology.

Journey from Non-Life to Life

Based on our current understanding, LUCA (Last Universal Common Ancestor) appears to be far too complex to reasonably infer that it could have arisen solely from unguided random events. The intricate molecular machinery, genetic information, and intricate cellular structures found even in supposedly "simple" life forms challenge the notion that such complexity could emerge without a guiding intelligence. The rapid progression of scientific knowledge, from limited microscopic insight to advanced imaging and bioinformatics, has highlighted the profound intricacies of life at various levels. This complexity aligns with the perspective of Intelligent Design, which suggests that the intricacy and precision observed in biological systems are better explained by an intelligent agent than by purely natural processes.



Last edited by Otangelo on Tue Sep 19, 2023 12:02 pm; edited 23 times in total

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Perception of the First Life Form from Darwin's Time to Today

1. Darwin's Era (19th Century)

  - Spontaneous Generation: Early theories proposed that life arose spontaneously from non-living matter, like the belief that maggots arose from decaying meat.
  - Warm Little Pond Hypothesis: Darwin once speculated that life might have begun in a "warm little pond" with the right combination of chemicals.
  - Simple Beginnings: The first life forms were often imagined as extremely simple entities, possibly just blobs of protoplasm.

2. Early to Mid 20th Century

  - Oparin-Haldane Hypothesis: Proposed that life began in a "primordial soup" of organic molecules, possibly stimulated by lightning or ultraviolet radiation.
  - Miller-Urey Experiment (1953): Simulated early Earth conditions in a lab, producing amino acids, showing that life's building blocks could form under these conditions.
  - Simple Prokaryotes: The first life forms were imagined as basic prokaryotic cells without a nucleus or organelles.

3. Late 20th Century to Early 21st Century

  - RNA World Hypothesis: Proposed that RNA molecules played a central role in the early forms of life, serving both as carriers of genetic information and as catalysts.
  - Thermal Vent Theory: Speculations that life might have started at hydrothermal vents in the deep ocean, providing the necessary conditions and chemicals.
  - Complex Early Communities: Theories suggesting LUCA might not be a single organism but rather a community with frequent horizontal gene transfers.

4. Current Understanding (Based on Synthesis)

  - Advanced Genetic Machinery: LUCA had a comprehensive genetic system, potentially DNA-based, with advanced translational mechanisms.
  - Metabolic Sophistication: Emphasis on chemoautotrophy and a unique metabolism centered on geochemical processes and hydrogen-based systems.
  - Cellular Complexity: Possibility of LUCA having precursors to eukaryotic cell structures, bridging the gap between simple and complex life forms.
  - Community Dynamics & Evolutionary Framework: LUCA perceived as part of a complex network or community, challenging the traditional linear tree of life.

Evolution of Perception through Advancing Science
 
Limited Microscopic Insight: During Darwin's era, rudimentary microscopes provided limited visual insight into cells, leading to the perception of simplicity in the first life forms.
Chemical Investigations & Organic Chemistry: As the 20th century dawned, the growth of organic chemistry and experiments like Miller-Urey's opened doors to understanding the potential chemical origins of life. This period was marked by an increased appreciation for life's chemical complexity.
Molecular Biology Revolution: The late 20th century witnessed a seismic shift with the advent of molecular biology, DNA sequencing, and advanced microscopy. It became apparent that even "simple" prokaryotic cells harbored intricate molecular machinery, signaling a departure from earlier simplistic views.
Genomics & Comparative Genomics: The turn of the millennium saw a surge in genome sequencing projects. Comparative genomics allowed scientists to trace back evolutionary histories, revealing LUCA's potential complexity and refuting the notion of its absolute simplicity.
Advanced Imaging & Bioinformatics: With cutting-edge microscopy and computational tools, the early 21st century allowed for visualization and analysis at unprecedented resolutions. This provided insights into the complex community dynamics and intricate cellular structures of early life forms, reinforcing the idea of LUCA's complexity.

Reflecting on the Progression
 
From Macro to Micro: Our journey of understanding started at a macroscopic level and delved deeper into the microscopic and molecular realms, mirroring the transition from observing visible organisms to understanding life at the atomic level.
Interdisciplinary Convergence: Over time, biology, chemistry, physics, and computational sciences converged, offering holistic perspectives. This interdisciplinary approach fueled the transition from viewing life forms as simple entities to understanding their multifaceted complexity.
The Paradox of Complexity from Simplicity: As we advanced in our understanding, it became evident that while life's origins might have started from simple chemical reactions, the evolutionary processes quickly navigated towards complexity, challenging initial simplistic perceptions.

Looking Forward
 
Systems Biology & Synthetic Biology: As we move further into the 21st century, fields like systems biology aim to understand life as integrated and interacting networks, while synthetic biology attempts to recreate life, further pushing the boundaries of our understanding.
Revisiting Origins with Modern Tools: Modern investigative tools might soon allow us to recreate early life scenarios more accurately, refining our understanding of how the balance between simplicity and complexity was achieved in early life forms.

Intracellular Systems

Genomic Blueprint: LUCA had genetic material, which was most likely DNA. This encoded the necessary instructions for its survival, growth, and replication.
Primitive Metabolic Pathways: While not as refined as modern organisms, LUCA had rudimentary metabolic systems in place to convert available materials into energy.
Protocell Compartmentalization: It's suggested that LUCA had some form of rudimentary membrane or lipid boundary. This would separate its internal environment, housing its metabolic reactions, from the external milieu.

Extracellular Interactions

Environmental Adaptations: Given that LUCA is believed to have possibly thrived in high-temperature zones like hydrothermal vents, it would have had mechanisms to harness nutrients from its surroundings and possibly withstand extreme conditions.
Evolutionary Pressures: LUCA would have interacted with its environment in a way that exposed it to evolutionary pressures, driving it to adapt and eventually give rise to the diverse lineages we see today.


Constitution of the Last Universal Common Ancestor (LUCA)

1. Genetic Machinery 

Based on the data from studies and the inherent necessities of a genetic system, LUCA's genetic machinery would have likely included the following:

Nucleotide Synthesis and Recycling
  • Various biosynthetic enzymes: Involved in synthesizing purine and pyrimidine nucleotides.
  • Nucleotide diphosphate kinases: Enzymes that help in nucleotide interconversion.

DNA replication
  • DNA Polymerases: Enzymes that synthesize DNA from deoxyribonucleotides.
  • DNA Gyrase and Topoisomerases: Enzymes that manage DNA supercoiling.
  • DNA Ligase: Enzyme that joins breaks in the DNA backbone.
  • Ribonucleotide Reductase: Enzyme that produces deoxyribonucleotides for DNA synthesis.
  • DNA Helicase: Enzyme that unwinds the DNA helix during replication.
  • Primase: Synthesizes RNA primers for DNA replication initiation.

Transcription (from DNA to RNA)

  • RNA Polymerases: Enzymes that synthesize RNA.
  • Transcription Factors: Proteins that regulate gene expression.

Translation (from RNA to Protein)

  • Ribosomal RNAs (rRNA) and Ribosomal Proteins: Components of ribosomes, the protein synthesis machinery.
  • Transfer RNAs (tRNAs): Molecules that bring amino acids to the ribosome for protein synthesis.
  • Aminoacyl-tRNA Synthetases: Enzymes that charge tRNAs with their respective amino acids.
  • Initiation, Elongation, and Termination Factors: Proteins involved in starting, continuing, and ending protein synthesis.

Protein Folding and Post-translational Modifications

  • Chaperones: Assist in proper protein folding.
  • Proteases: Enzymes that degrade misfolded or unneeded proteins

Repair and Protection

  • DNA Repair Enzymes: Responsible for repairing DNA damage.
  • Mismatch Repair System: Corrects errors made during DNA replication.
  • Recombination Proteins: Involved in genetic recombination processes.

Other Proteins and Complexes

  • RNA Degrading Enzymes: Break down RNA molecules.
  • Protein Complexes for DNA Replication: Including sliding clamps and clamp loader proteins.

2. RNA's Role 

Given the potential that LUCA existed in an RNA-dominated phase, it's conceivable that RNA performed various central cellular functions beyond just protein synthesis. Here's an overview of the protein machinery LUCA might have had to support RNA's diverse roles.

RNA Synthesis and Maintenance
  • RNA Polymerases: Enzymes responsible for synthesizing RNA from ribonucleotides.
  • RNA Helicase: Proteins that unwind RNA structures, aiding in processes like RNA splicing, translation, and ribosome assembly.

RNA Processing and Modification
  • RNase P: Processes tRNA precursors to produce mature tRNA molecules.
  • RNA Editing Enzymes: Modify RNA sequences post-transcriptionally.
  • Pseudouridine Synthases and Ribose Methyltransferases: Enzymes that introduce modifications into ribosomal and transfer RNAs.

RNA's Role in Protein Synthesis
  • Ribosomal RNAs (rRNA): Along with ribosomal proteins, they form the core of the ribosome, facilitating protein synthesis.
  • Transfer RNAs (tRNAs): Molecules that decode mRNA sequences and bring appropriate amino acids for protein synthesis.
  • Messenger RNAs (mRNA): Convey genetic information from DNA to the ribosome.
  • tRNA-modifying Enzymes: Introduce specific modifications into tRNAs to ensure accurate and efficient protein synthesis.

RNA in Catalysis and Other Functions
  • Ribozymes: RNA molecules with catalytic activity. Examples include ribosomal peptidyl transferase center and self-splicing introns.
  • Small Interfering RNAs (siRNAs) and microRNAs (miRNAs): Involved in RNA interference and post-transcriptional gene regulation.
  • RNase MRP: Involved in ribosomal RNA processing.

RNA Protection and Degradation
  • RNA Chaperones: Assist in proper RNA folding and function.
  • Ribonucleases: Enzymes that degrade RNA, managing RNA quality and quantity in the cell

3. Metabolism

Given LUCA's speculated chemoautotrophic nature, it likely harnessed energy from inorganic substances and geochemical processes in an environment rich in hydrogen and metals. Here's a comprehensive list of the protein machinery LUCA might have utilized for its metabolic needs:

Energy Generation and Conservation

  • Hydrogenases: Enzymes that play a key role in oxidation and production of molecular hydrogen (H2).
  • Iron-sulfur proteins: Involved in electron transport processes.
  • ATP synthase: Produces ATP from ADP in the presence of a proton gradient across the membrane.


Key Gases in Early Earth and Their Significance
Besides carbon dioxide and nitrogen, early life forms, including the putative LUCA, may have needed to interact with and potentially fix other gases from the environment. Some of these gases include:

Hydrogen (H₂)
  • Abundance: Thought to have been prevalent in the early Earth, especially near hydrothermal vents.
  • Role in Early Life: Used as an electron donor to reduce CO₂, possibly aiding in producing organic molecules.

Methane (CH₄)
  • Production: Biologically produced by methanogenic archaea via methanogenesis.
  • Significance: Its role in early Earth's biology and chemistry is still under study.

Hydrogen Sulfide (H₂S)
  • Abundance: Believed to be abundant near hydrothermal vents, similar to hydrogen.
  • Biological Usage: Utilized as an electron donor by certain organisms.

Sulfur Dioxide (SO₂) and Elemental Sulfur (S⁰)
  • Metabolism: Some microorganisms can process these sulfur compounds in various metabolic pathways.

Oxygen (O₂)
  • Atmospheric Levels: Extremely low levels in the early Earth atmosphere.
  • Evolutionary Impact: Its increase, due to oxygenic photosynthesis in cyanobacteria, had a significant impact on Earth's atmosphere and biology.

Carbon Monoxide (CO)
  • Biological Role: Used by some microorganisms as an energy source.

Phosphine (PH₃)
  • Recent Interest: Its potential presence on Venus has sparked discussions about its role as a biosignature.
  • Early Earth Relevance: Its role in early Earth remains speculative, but it might have been important in prebiotic chemistry.

Gas Fixation in Early Life
  • CO₂ and N₂ Fixation: Gas fixation required energy and specific catalysts. Modern cells achieve this with complex proteins or protein assemblies.
  • Early Life Challenges: How these processes operated without the advanced machinery of modern cells is a topic of active research.

Carbon Fixation and Assimilation

  • Carbon monoxide dehydrogenase/acetyl-CoA synthase (CODH/ACS): Key enzymes in the Wood-Ljungdahl pathway to fix carbon dioxide.
  • Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO): Enzyme involved in the Calvin cycle for carbon fixation.

Metabolism of Inorganic Substrates

  • Sulfur reductases: Enzymes that reduce sulfate to sulfide.
  • Nitrogenases: Involved in nitrogen fixation, reducing atmospheric nitrogen (N2) to ammonia (NH3).
  • Metal transporters: Proteins responsible for the uptake of metals like iron, zinc, and copper.

Electron Transfer Processes

  • Cytochromes: Proteins involved in electron transfer in the electron transport chain.
  • Quinones: Small molecules involved in electron transport, shuttling electrons within the cellular membrane.

Synthesis and Degradation of Biomolecules

  • Amino acid biosynthesis enzymes: For producing amino acids.
  • Fatty acid synthesis enzymes: Involved in the production of fatty acids, key components of cellular membranes.
  • Nucleotide synthesis enzymes: Involved in the production of purine and pyrimidine nucleotides.

4. Ecology and Environment

LUCA's existence is speculated to have been marked by its ability to thrive in extreme environments. Given the geological conditions and chemical processes of early Earth, hydrothermal vents located deep in the sea are often highlighted as the likely habitats. LUCA's possible thermophilic nature suggests it could have thrived in high-temperature zones. Here's an overview of LUCA's potential environmental characteristics and adaptive features:

Adaptation to Extreme Environments

  • Heat Shock Proteins: These proteins assist in maintaining proper protein folding under high-temperature conditions.
  • Chaperones: Proteins that help in the folding or unfolding and the assembly or disassembly of other macromolecular structures.

Deep-sea Hydrothermal Vents Adaptations

  • Pressure-resistant Proteins: Proteins evolved to function under the immense pressure of deep-sea environments.
  • Sulfide-utilizing Enzymes: Enzymes capable of deriving energy from the abundant sulfides present in hydrothermal vent environments.
  • Metal-binding Proteins: Proteins that bind and utilize metals, abundant in hydrothermal vents, for various cellular functions.

Thermophilic Adaptations

  • Thermosome: A type of chaperonin found in archaea that assists in protein folding under extreme temperature conditions.
  • DNA Gyrase: An enzyme that introduces negative supercoils to DNA, which can help stabilize the DNA double helix at high temperatures.
  • Thermostable Ribosomal RNA: rRNA molecules that are adapted to remain stable and functional at elevated temperatures.

5. Cellular Complexity

LUCA represents a unique intersection in the history of life, posited to contain the precursors to both prokaryotic and eukaryotic cellular structures. Although the exact cellular architecture of LUCA remains speculative, it is thought that it may have had complexities bridging the gap between the simplicity of prokaryotes and the intricacy of eukaryotes. Here's an overview of LUCA's potential cellular features and the building blocks hinting at future eukaryotic developments:

Cellular Structures and Components

  • Proto-Cytoskeleton Elements: Precursors to the complex cytoskeleton found in eukaryotes, providing structural support to the cell.
  • Primitive Endomembrane Systems: Possible early versions of the endoplasmic reticulum and Golgi apparatus, hinting at compartmentalization within the cell.
  • Protein Transport Systems: Proteins aiding in the transport of molecules across cellular compartments.

Cellular Complexity Indicators

  • Compartmentalized Biochemical Reactions: Suggesting areas within the cell where specific reactions occurred in isolation.
  • Lipid Diversity: A variety of lipids that could hint at specialization of cellular membranes or membrane-bound organelles.
  • Presence of Symbiotic Relationships: Interactions with other entities, potentially setting the stage for the evolution of organelles like mitochondria and chloroplasts via endosymbiosis.

6. Evolutionary Framework

LUCA stands as a pivotal entity in the evolutionary chronicle, with debates around whether it was a singular organism or a representation of an early biological network. The nature of LUCA's existence has implications for understanding the fluidity and complexity of early life evolution, especially considering the intricate genomic and cellular landscape. Here's a breakdown of the conceptualizations around LUCA within the evolutionary framework:

Community Over Singular Entity

  • Community-Based LUCA: The notion that LUCA might represent a community of organisms rather than just a single entity.
  • Horizontal Gene Transfers: Extensive genetic exchanges between organisms, implying a web of life rather than a strict tree.

Evolutionary Implications

  • Network-Based Evolution: Conceptualizing early life evolution as a network, challenging the traditional tree-based model.
  • Archaeal and Eukaryotic Bridge: LUCA's genomic and cellular attributes could hint at shared characteristics between archaea and the precursors to eukaryotes.

7. Community Dynamics

LUCA's existence remains a topic of intrigue, especially when pondering its potential representation. Instead of being a single, well-defined entity, LUCA might have symbolized a community marked by genetic fluidity. This community-centric perspective reshapes our understanding of early life's dynamics, especially in the context of rampant genetic exchanges. 

Genetically Fluid Community

  • Fluid Genetic Representation: The hypothesis that LUCA was not a singular entity but rather symbolized a community with flexible genetic characteristics.

Horizontal Gene Transfers

  • Rampant Genetic Exchanges: Frequent horizontal gene transfers among early proto-cells, suggesting a shared and interconnected genetic landscape during the early phases of life.

8. Life's Emergence and LUCA

LUCA's significance isn't solely rooted in its position as a possible ancestral organism. Its existence also points towards a critical juncture in the evolution of life on Earth. This nexus, potentially bridging non-biological geochemical processes with the intricate world of living entities, underlines LUCA's paramount role in the narrative of life's emergence. Let's explore these intersections more deeply:

Abiotic Geochemistry and Biological Processes

  • Geo-Biological Nexus: LUCA stands as a testament to the fine line between abiotic geochemistry and biological processes, highlighting the transformative phases of Earth's early history.

Evolutionary Transition

  • From Geochemical to Biological: LUCA represents the evolutionary transition where organic molecules, influenced by geochemical processes, began to exhibit characteristics of life.

Journey from Non-Life to Life

  • Pivotal Role of LUCA: As the bridge between non-life and life, LUCA emphasizes the fluidity of early evolutionary processes, playing a key role in shaping the narrative of life's inception.



Last edited by Otangelo on Tue Sep 19, 2023 12:36 pm; edited 6 times in total

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Unresolved issues and open questions related to LUCA

In the grand narrative of life's genesis, the Last Universal Common Ancestor, often abbreviated as LUCA, stands as a pivotal moment, a starting point for the diverse branches of life we see today. Yet, peeling back the layers of time to truly understand LUCA is a daunting endeavor. Contemplate an organism, the wellspring from which all extant life has sprung. Many facets of LUCA, notably its genomic composition, baffle our scientific minds. We're drawn to theories like the RNA World Hypothesis, which posits that in a time before our current biological framework, LUCA was predominantly reliant on RNA, using it to fulfill roles that today are apportioned between DNA and proteins. While this theory has its allure, it's not devoid of pitfalls. RNA's inherent instability is a major concern. Unlike DNA, which provides a stable genetic platform, RNA is susceptible to rapid degradation. Given the probably volatile environments of early Earth, how could RNA reliably store the genetic blueprint of nascent life? And while it's evident that RNA plays myriad roles in contemporary cells, ribozymes - those RNA variants with enzymatic activities - have their limits. The multitude of processes required to maintain even the simplest life forms seem overwhelming for ribozymes. Would they be adept enough to navigate the maze of life's chemical intricacies? Transitioning from an RNA-dominated world to the DNA-protein framework we recognize today adds another layer of complexity. This isn't just about swapping one molecule for another. It's a significant evolutionary leap. Crafting DNA from RNA involves a series of sophisticated processes, often necessitating advanced enzymes. Take ribonucleotide reductase as an example. This enzyme, crucial for the RNA-to-DNA transition, has a multifaceted structure and function, seemingly incongruent with a rudimentary RNA-dominated realm. How did such evolved proteins come to be in a world where RNA held the reins? This brings us to another obstacle: the establishment of the detailed biosynthesis pathways pivotal to life. Developing these pathways, where each phase is so dependent on the next, casts doubt on the RNA World Hypothesis, and indeed on our broader understanding of life's beginnings. As we explore these hypotheses, it's essential to remain critical, scrutinizing every aspect. Dig deeper into LUCA's cellular machinery. Picture its cellular framework. What shielded its internal components? Today, many cells are encased in lipid membranes, but we cannot confidently state LUCA had the same protective layer. Delving into its cellular interior, did LUCA have rudimentary organelles or specialized compartments? Reflect on LUCA's existence. How did it sustain itself? Was it an autonomous unit, crafting its own sustenance? Alternatively, might it have relied on its surroundings, drawing in organic molecules to nourish itself? Theories abound about LUCA's preferred habitat, with some suggesting it thrived near hydrothermal vents deep in the primordial seas. Such speculations lead to another intriguing query: Was our primeval forerunner adapted to extreme conditions, or did it favor milder climes? As we consider its genetic machinery, we must ask: Did LUCA interpret genetic codes as modern organisms do? The precise codon-to-amino acid mappings we see today, were they a part of LUCA's genetic language? The origins of LUCA, its precursor environments, and possible predecessors remain profound puzzles. As we navigate the evolutionary landscape, we're faced with a pressing query: Was LUCA a lone entity, a singular starting point? Or, in the vast expanse of evolutionary history, could there have been multiple ancestral forms, each contributing to the tree of life in its unique way?

The understanding of LUCA, the Last Universal Common Ancestor, oscillates between the simplistic idea of a single primordial entity and the intricate possibility of a collective of primordial organisms. While the allure of a lone progenitor remains strong, recent scientific probes paint a multifaceted portrait. For starters, the intricate web of metabolic processes and cellular machinery seen in present-day life forms is a challenge to trace back to a singular source. Numerous pathways integral to life bear the imprints of time, pointing to an ancient lineage, and it's arguable whether a solitary ancestor could give rise to such profound complexity. This diversity in life's mechanics hints at the likelihood of multiple early life forms that possibly swapped and merged genetic blueprints. Horizontal gene transfer (HGT), a process by which genes are exchanged outside the parent-offspring relationship, emerges as a central player in this narrative. Given its prevalence among modern microbes and its role in facilitating rapid adaptation, envisioning LUCA as a dynamic consortium of microbes engaged in HGT isn't far-fetched. This consortium, with its shared genetic pool, could have birthed the extensive repertoire of life's functions we see today. However, this view, while solving some puzzles, ushers in a host of fresh questions. If we lean into the idea of an early consortium, it begs the question: How did this ancient community come into being? The birth of such a collective necessitates conditions favoring the spontaneous emergence of varied life forms. The early Earth, a patchwork of diverse micro-environments, could it have harbored various life precursors that eventually coalesced where circumstances allowed? The dynamics among these nascent life forms, a mixture of cooperation and competition, could have forged the proposed LUCA consortium.  This line of reasoning rests on a bedrock of assumptions about early Earth, abiogenesis mechanisms, and ancient ecosystems, each of which is a research frontier of its own. The LUCA model, despite its appeal, is fraught with complexities and uncertainties.

The challenge of understanding the transition from non-living to living entities has long intrigued scientists. Imagine trying to replicate life's beginnings by introducing a mixture of raw materials—some vital for life and others not—into a controlled environment, and then observing the interplay of natural forces. Such an experiment, relying on purely unguided processes, has yet to be attempted, let alone achieved. John von Neumann was a Hungarian-American mathematician, physicist, and computer scientist, widely regarded as one of the foremost mathematicians of the 20th century. He made seminal contributions to a variety of fields, including functional analysis, quantum mechanics, computer science, and game theory. Among his diverse achievements, von Neumann delved into the concept of self-replicating machines, which are theoretical constructs capable of autonomously reproducing themselves using raw materials from their environment. These ideas not only laid foundational concepts for future studies in robotics and artificial intelligence but also posed intriguing questions about the nature of life and the potential for machines to mimic biological processes.



Beyond Evolution: The Origin of Species by Design Von_ne10

He reflected deeply on the complexity of life, positing that the mere existence of memory-stored controls that can convert symbols into physical states is nothing short of a wonder. John von Neumann's musings on the complexity of life, particularly on the memory-stored controls converting symbols into physical states, were deeply rooted in his studies on self-replicating machines and the burgeoning field of computer science. When von Neumann spoke of "memory-stored controls," he was alluding to the way that information, stored in a specific format or code, can be translated into actionable commands or physical processes. This principle is readily apparent in both modern computers and biological systems. For instance, a computer translates binary code (a series of 1s and 0s) into complex operations, graphics, and processes. Similarly, in biological systems, the genetic code stored in DNA is transcribed and translated to produce proteins, which are the workhorses of the cell. Von Neumann marveled at this intricate dance of information storage, retrieval, and transformation. He considered it a marvel because it encapsulates a foundational concept: that abstract symbols, whether in binary or genetic code, can give rise to tangible, physical realities. In the case of computers, this means software giving rise to specific operations and outputs. In biology, it means genetic information giving rise to organisms with specific traits. His reflections underscored the profundity and complexity of both designed systems, like computers, and living systems, like biological cells. He implicitly raised questions about the origins and nature of such systems, emphasizing the awe-inspiring aspect of the existence of coded information directing the operation of cells, and its transformative power.

Paul Davies, too, marveled at life's complexity, pondering how seemingly basic atoms could, on their own, generate intricate information systems. The prevailing understanding suggests no known physical law can generate complex information from mere nothingness. At the cellular level, this marvel manifests itself in the transformation of genetic blueprints into tangible, three-dimensional forms. The digital data within genes gets converted, with precision, into its analog counterpart, a true-to-form physical representation. Drawing parallels from human-made systems, Joyce and Orgel emphasized the complexity of this transformation. Consider a vehicle's blueprint: on its own, it's incapable of producing a car. The blueprint, while detailed, requires a coordinated assembly process—much like how RNA, with all its instructions, needs the orchestration of various cellular components to produce proteins. This raises a profound question: where does the cause of such orchestrated functionality originate? Just as a machine's design is conceived in an engineer's mind, might there be a guiding principle or intelligence behind the intricate workings of life? As emphasized by Jack W. Szostak, the riddle of how cellular machinery, particularly protein-centric enzymes, could have spontaneously emerged remains one of the most profound questions in our quest to understand life's origins.

Natural selection did not operate during the prebiotic era on Earth

In the primeval environment, directed selection mechanisms were absent. Complex systems in contemporary organisms produce the building blocks of life.  Before life as we know it flourished, the early Earth was a blank canvas, devoid of the guiding hand of natural selection. Imagine a world where meticulously orchestrated molecular symphonies of the present day did not exist. Instead of precise, deliberate formations of nucleic acids and the twenty amino acids, there existed a cacophonous chaos of molecules. Within the sophisticated cellular machinery of modern life, missteps such as right-handed amino acids are meticulously corrected. Nucleobases, phospholipids, and carbohydrates, now with such definite roles, were lost amidst a sea of countless molecular contenders. One must wonder: in a world teeming with chemical randomness, how did unguided processes sift through and pick the molecular elite that constitutes life today?

The Origin and Organization of Life's Fundamental Molecules

The four principal molecules of life—DNA, RNA, proteins, and lipids—serve as the cornerstone for cellular function and replication. Understanding their origin is paramount in our quest to grasp the inception of life on Earth. The chemical milieu of early Earth, without the frameworks of cellular life and hereditary systems, lacked a discernible mechanism for choosing or giving preference to one molecule over another. This, indeed, raises intricate questions about how such sophisticated and information-laden molecules emerged from a prebiotic environment. The concept of self-organization or autocatalysis, where molecules spontaneously order themselves into structured arrangements or catalyze their formation, has been posited by many in the scientific community. Such a notion would imply that under specific conditions, certain molecules possess an inherent propensity to organize or catalyze reactions that would lead to life's building blocks. Yet, the emergence of molecules as information-rich as DNA and RNA requires a context in which specificity and order are paramount. The inception of proteins, with their vast array of potential amino acid sequences and configurations, needs more than mere random chance. Moreover, the lipid molecules that form cellular barriers are not just simple hydrophobic chains but are involved in vital cellular functions and signaling. Considering these complexities, one would have to infer that the early Earth had to present conditions where specificity was not just possible but probable. The environments of this primordial world, with its myriad of micro-niches, would have to offer a wide array of physical and chemical favorable conditions. It would have to be conceived that in such a diverse landscape, the formation of life's basic building blocks was not a solitary event, but a series of events, each fine-tuned by the particular conditions of its niche. The notion of molecules with inherent properties that drive them towards life-promoting configurations suggests a level of precision and sophistication in their design. 

Andrew H. Knoll (2012):  The emergence of natural selection: Molecular selection, the process by which a few key molecules earned key roles in life’s origins, proceeded on many fronts. (Comment: observe the unwarranted claim) Some molecules were inherently unstable or highly reactive and so they quickly disappeared from the scene. Other molecules easily dissolved in the oceans and so were effectively removed from contention. Still, other molecular species may have sequestered themselves by bonding strongly to surfaces of chemically unhelpful minerals or clumped together into tarry masses of little use to emerging biology. In every geochemical environment, each kind of organic molecule had its dependable sources and its inevitable sinks. For a time, perhaps for hundreds of millions of years, a kind of molecular equilibrium was maintained as the new supply of each species was balanced by its loss. Such equilibrium features nonstop competition among molecules, to be sure, but the system does not evolve. 1

Alan W. Schwartz (2007): A problem that is familiar to organic chemists is the production of unwanted byproducts in synthetic reactions. For prebiotic chemistry, where the goal is often the simulation of conditions on the prebiotic Earth and the modeling of a spontaneous reaction, it is not surprising – but nevertheless frustrating – that the unwanted products may consume most of the starting material and lead to nothing more than an intractable mixture, or -gunk.. The most well-known examples of the phenomenon can be summarized quickly: Although the Miller –Urey reaction produces an impressive set of amino acids and other biologically significant compounds, a large fraction of the starting material goes into a brown, tar-like residue that remains uncharacterized; i.e., gunk. While 15% of the carbon can be traced to specific organic molecules, the rest seems to be largely intractable  Even if we focus only on the soluble products, we still have to deal with an extremely complex mixture of compounds. The carbonaceous chondrites, which represent an alternative source of starting material for prebiotic chemistry on Earth, and must have added enormous quantities of organic material to the Earth at the end of the Late Heavy Bombardment (LHB), do not offer a solution to the problem just referred to. The organic material present in carbonaceous meteorites is a mixture of such complexity that much ingenuity has gone into the design of suitable extraction methods, to isolate the most important classes of soluble (or solubilized) components for analysis. Whatever the exact nature of an RNA precursor which may have become the first selfreplicating molecule, how could the chemical homogeneity which seems necessary to permit this kind of mechanism to even come into existence have been achieved? What mechanism would have selected for the incorporation of only threose, or ribose, or any particular building block, into short oligomers which might later have undergone chemically selective oligomerization? Virtually all model prebiotic syntheses produce mixtures. 2

A.G.Cairns-Smith (1985):  It is one of the most singular features of the unity of biochemistry that this mere convention is universal. Where did such agreement come from? You see non-biological processes do not as a rule show any bias one way or the other, and it has proved particularly difficult to see any realistic way in which any of the constituents of a 'prebiotic soup' would have had predominantly 'left-handed' or right-handed' molecules. It is thus particularly difficult to see this feature as having been imposed by initial conditions. 3

A.G.Cairns-Smith (1985): genetic takeover, page 70: Suppose that by chance some particular coacervate droplet in a primordial ocean happened to have a set of catalysts, etc. that could convert carbon dioxide into D-glucose. Would this have been a major step forward towards life? Probably not. Sooner or later the droplet would have sunk to the bottom of the ocean and never have been heard of again. It would not have mattered how ingenious or life-like some early system was; if it lacked the ability to pass on to offspring the secret of its success then it might as well never have existed. So I do not see life as emerging as a matter of course from the general evolution of the cosmos, via chemical evolution, in one grand gradual process of complexification. Instead, following Muller (1929) and others, I would take a genetic View and see the origin of life as hinging on a rather precise technical puzzle. What would have been the easiest way that hereditary machinery could have formed on primitive Earth? 4

William Dembski (2002): The problem is that nature has too many options and without design couldn’t sort through all those options. The problem is that natural mechanisms are too unspecific to determine any particular outcome. Natural processes could theoretically form a protein, but also compatible with the formation of a plethora of other molecular assemblages, most of which have no biological significance. Nature allows them full freedom of arrangement. Yet it’s precisely that freedom that makes nature unable to account for specified outcomes of small probability. Nature, in this case, rather than being intent on doing only one thing, is open to doing any number of things. Yet when one of those things is a highly improbable specified event, design becomes the more compelling, better inference. Occam's razor also boils down to an argument from ignorance: in the absence of better information, you use a heuristic to accept one hypothesis over the other. 5

Fry, Iris. (2010): How successful are the RNA-first, RNA-later, metabolism-first, and, preparatory metabolism theories in elucidating the emergence of life as an evolutionary process? So far, none of these paradigms can claim decisive experimental support. 6

Koonin, E. V. (2012): The emergence of the first replicator system, which represented the “Darwinian breakthrough,” was inevitably preceded by a succession of complex, difficult steps for which biological evolutionary mechanisms were not accessible.  The Logic of Chance: The Nature and Origin of Biological Evolution. 7

Commentary: The fabric of life, as understood through current scientific analysis, displays an intricate orchestration of molecular machinery. The Fundamental Biomolecules are not simple assemblages of atoms; they are sophisticated entities operating in highly coordinated metabolic pathways. When we contemplate the early Earth environment, it becomes a formidable challenge to envision how such specified complex molecules would be readily available. They would have needed to form naturally, without the mediation of enzymes, and amass in considerable amounts at a singular site, ready to contribute to the foundation of life. 

1. The intricate dance of life hinges upon a finite collection of detailed biomolecules, united in a universally recognized convention. This core consortium comprises the quintessential building blocks: RNA, DNA, amino acids, phospholipids, and carbohydrates. With remarkable precision, cells leverage these elements through meticulously coordinated metabolic pathways, paths seemingly absent in Earth's early stages. Considering the principle of abiogenesis, it's imperative these biomolecules existed in a naturally occurring state, formed without enzyme mediation. Furthermore, they would have required organization to lay down the foundation for the inception of the first living cells. An abundance of these biomolecules, concentrated at a singular focal point, would have been essential.
2. Creation with an endpoint in mind necessitates a directional intent. This premise raises challenges when addressing naturalistic propositions concerning life's genesis. On the ancient Earth, a vast molecular expanse would have precluded any systematic competition or selection, making the isolation of life-essential molecules from non-essential counterparts seemingly implausible. To attribute the entirety of life's organized structure, its preservation, and its evolutionary progression from non-living entities solely to selection appears to be an oversimplified assertion. Suggesting that selection is the sole orchestrator of life's grand symphony might miss nuances essential to our understanding.
3. From our observations, a series of random events without direction is highly improbable to produce components with distinct purposes, particularly when looking at large integrated systems. Analogously, bricks don't self-assemble from raw materials nor position themselves to form walls. There’s a guiding hand behind their formation. Similarly, phospholipids, vital for cell membranes, don't spontaneously arise from their basic components. Their formation and subsequent organization hint at an overarching guidance. The question that beckons: could there be an architect behind these marvels?

Essential Biomolecules: Beyond the Realm of Selection

Regarding the selection and specificity of RNA and DNA in the prebiotic context:

1. Purity of Starting Molecules: Amidst a vast primordial concoction, how did the critical purity necessary for RNA and DNA synthesis emerge so distinctly? Such purity, considering the vastness and randomness of molecular mixtures present, points towards a potential guidance mechanism, suggesting an overarching blueprint may have been guiding this synthesis against all odds.
2. Nucleobase Selection: In an environment teeming with molecular candidates, it's perplexing how only five distinct nucleobases became prominent. This remarkable selection precision, amidst a probable sea of molecular candidates, resonates with the idea of a process that might have been intelligently choreographed rather than a product of sheer happenstance. The hydrogen bond strength in DNA is finely tuned to ensure stability and specificity in the double helix formation with adenine pairing with thymine and guanine pairing with cytosine. Correct tautomeric forms of nucleotide bases are crucial for maintaining the appropriate hydrogen bonding patterns, ensuring the accurate replication and transmission of genetic information. While numerous possible analog structures for nucleotide bases exist, only specific bases are employed in biological systems due to their unique chemical properties and base pairing specificity.
3. Structural Specificity of Purines: The intricate two-ring structure of purines, which emerged as dominant, is fascinating given the countless molecular configurations possible. Purines, with their specific double-ring structure, were selected for their unique ability to form stable and specific hydrogen bonds with their complementary pyrimidines in DNA, ensuring accurate genetic information storage and transmission. Their particular atomic arrangement and functional groups provide the necessary chemical properties and base pairing specificity crucial for the integrity and function of DNA within biological systems. This striking structural consistency, especially in primitive conditions, seems to advocate for a purposeful structural blueprint.
4. Structural Specificity of Pyrimidines:  How did pyrimidines, with their single ring made up of 4 carbon and 2 nitrogen atoms, emerge as the preferred structure, given the innumerable potential configurations? Pyrimidines, with their distinct single-ring structure, were chosen because they can establish specific and stable hydrogen bonds with their complementary purines in DNA. This specific structure and the associated functional groups ensure precise base pairing, which is essential for the accurate storage and transmission of genetic information in living organisms. The very emergence of such distinct structural specificity hints towards a possible intentional molecular choreography.
5 Base Separation in Complex Mixtures: Amidst the plethora of similar molecules that could have formed, how were the functional nucleobases of DNA and RNA selectively isolated? The capability to filter out the essential from the non-essential implies a system that favors precision.
6 Ribose Ring Selection: Why does life predominantly use ribose with its 5 carbon sugar ring in the backbone of RNA and DNA, even though other configurations like 4 or 6 carbon rings could have formed, but are non-functional? This specificity hints at an optimized design.
7 Correct Atom Linkage: How were the right nitrogen atom of the base and the appropriate carbon atom of the sugar pinpointed and linked, especially when various connections are possible? Such accuracy in molecular bonding demonstrates the intricate design in foundational biochemistry.
8 Homochirality in RNA and DNA: In a world that could produce both left and right-handed molecules, how did life come to exclusively use the right-handed configurations of RNA and DNA, particularly ribose in its D form? The consistent selection of certain chiral forms over others remains a profound mystery, suggesting a precise orchestration in the genesis of life.
9 Absence of Prebiotic Selection Mechanism: Without the machinery of life in place, how would the prebiotic environment have favored the formation of RNA and DNA molecules over others? The lack of a natural selection mechanism prior to life presents a conundrum in accounting for their emergence.
10 RNA's Dual Role in Information and Function: Given that RNA can serve as both an information carrier (like DNA) and a catalyst (like proteins), how did it come to acquire this dual role without a pre-existing selection mechanism? The multi-functionality of RNA seems to defy a simple, undirected origin.
11 Specificity of Nucleotide Pairing: Adenine always pairs with Thymine (or Uracil in RNA), and Cytosine with Guanine. How did this highly specific base pairing evolve without a mechanism to favor correct pairings over incorrect ones?
12 Origin of Replication Mechanism: How did the mechanism for the replication of RNA and DNA molecules come into being, given that the replication process itself seems to require some form of selection? Without an error-correction mechanism, the fidelity of replication would be compromised.
13 Transition from RNA to DNA World: If life began with an RNA world, as some suggest, how did the transition to the more stable DNA occur, especially in the absence of prebiotic selection mechanisms to guide such a transition?
14 Lack of Stable Prebiotic Environment: Given the potential instability and reactive nature of early Earth, how could delicate molecules like RNA and DNA form and be preserved without a stable environment and without specific mechanisms to protect and favor them?
15 Problem of Initial Functionality: How did the first RNA and DNA molecules gain the functionality necessary for them to be advantageous and subject to any form of selection, given that they would need to have some level of utility from the outset?

The challenges enumerated, especially when considered in their cumulative effect, make it clear why the origin of life is one of the most daunting and debated questions in both the fields of biology and philosophy. When we dive deep into the minutiae of molecular configurations and the specificity required for functional nucleic acids, it becomes evident that a multitude of highly specific conditions and sequences of events would have been necessary for life to emerge naturally. Many of the problems highlight the sheer specificity required at multiple stages — from selecting the right nucleobases to forming the right bonds and achieving functional sequences. This specificity seems to be at odds with random, unguided processes. The early Earth environment was not as conducive to life as it is today. High UV radiation, lack of protective atmosphere, and a plethora of reactive molecules would make the survival and formation of delicate RNA/DNA chains incredibly challenging. The importance of catalysts in modern biological systems is evident. In their absence during the prebiotic era, achieving the right reaction speeds becomes another monumental hurdle. At this prebiotic stage, the mechanisms of natural selection, which guide the evolution of life forms, weren't operational. Natural selection acts on functional, replicating entities. If you don't yet have a functional, replicating entity (like the first RNA/DNA molecules), you can't have natural selection. Given the combined weight of these challenges, it makes the idea of life emerging from purely naturalistic and unguided processes highly improbable.

Regarding the selection and specificity of amino acids and proteins in the prebiotic context:

1. Optimal Amino Acid Selection: Given that there are over 500 naturally occurring amino acids on Earth, why are only 20 of them specifically utilized in life's proteins? This unique selection seems to go beyond mere chance, pointing towards a deliberate arrangement tailored to these 20 amino acids' exceptional properties.
2. Bifunctional Monomer Preference: How is it that bifunctional monomers, those with two functional groups, became dominant in protein formation when unifunctional monomers could disrupt the process? This preference highlights the importance of structure in the creation of functional polymers.
3. Homochirality Mystery: Why do life forms chiefly use left-handed amino acids and right-handed sugars, especially when non-chiral precursors could lead to either form? The exclusive use of certain chiral forms speaks to a specificity in biological design.
4. Natural Amino Acid Choice: Considering the vast number of naturally occurring amino acids, how is it that life on Earth primarily utilizes a consistent subset for protein construction? This consistency underscores the idea of a finely-tuned selection for optimal function.
5. Avoidance of Unwanted By-Products: What mechanism ensures that the synthesis of biological amino acids does not result in undesired or irrelevant by-products? The precision in this process suggests a higher level of orchestration.
6. β, γ, δ Amino Acid Sorting: How were non-alpha amino acids filtered out in the primordial soup, given their potential presence? This filtering hints at a process that prioritizes functionality and efficiency.
7. Addressing Homochirality: How could an environment with achiral precursors lead exclusively to left-handed amino acids? This phenomenon remains one of the great mysteries of biochemistry.
8. NH3 Accumulation: How did ammonia, essential for amino acid synthesis, amass on the early Earth despite its short lifetime due to photochemical dissociation? This suggests conditions were somehow optimal for the emergence of life.
9. Organosulfur Compound Formation: How did early Earth processes generate the organosulfur compounds necessary for certain amino acids, considering the state of sulfur in nature? The existence of these compounds implies a pathway that was conducive to life.
10. Enzymatic Transition: How did the shift from prebiotic enantiomer selection to enzymatic reactions like transamination take place, given its necessity for life's emergence? This intricate transition speaks to the complexity and finesse in biological systems.
11. Amino Acid Suitability: How is it that the chosen amino acids are perfectly suited for forming structures with tight cores, enabling binding pockets within proteins? The optimal nature of these amino acids hints at purposeful design.
12. Unique Amino Acid Set: Why does the set of amino acids used by life seem to be near-optimal in properties like size, charge, and hydrophobicity, especially compared to millions of alternatives? This optimization suggests a design geared for maximal functionality.
13. Emergence of Synthesis Regulation: How did the regulation of amino acid synthesis pathways emerge, ensuring supply meets demand? Such regulation indicates a system that is not just complex but also adaptive.
14. Metabolic Pathway Transition: How did the shift from prebiotic synthesis to metabolic pathway-based amino acid synthesis occur, especially given the numerous enzymes involved? This complex transition emphasizes the intricacies in the development of life's systems.

From the selection of the right building blocks (amino acids) to the formation of complex three-dimensional structures (proteins), each step poses significant challenges to naturalistic explanations for the origins of life. These problems not only require answers for individual steps but also necessitate an understanding of how these steps might sequentially and synergistically come together. While research in the field of abiogenesis is ongoing and some strides have been made, the cumulative weight of these challenges often leads to intense debates among scientists, philosophers, and theologians regarding life's origins.

Regarding the selection and specificity of phospholipids in the prebiotic context:

1. Hydrocarbon Chain Selection: In the midst of prebiotic conditions, how did processes naturally select hydrocarbon chains of precisely 14 to 18 carbons in length? Given the lack of any physical directive, chains could have formed in a variety of lengths, raising the question of specificity in the emergence of cellular membranes. The specificity required in the length of hydrocarbon chains is nothing short of fascinating. The early Earth's environment would have been a tumultuous mix of various elements and compounds. The emergence of such precision amidst chaos challenges our understanding of spontaneous order. If chains of any length were plausible, the consistent development of this exact range seems beyond mere coincidence.
2. Phospholipid Composition: Cellular membranes aren't made up of a singular type of phospholipid. How did random events lead to the development of membranes comprising diverse phospholipid species, often combined with sterols like cholesterol? The pathway for the selection and synthesis of this intricate mixture remains puzzling in a prebiotic context. The intricate mixture of phospholipid species in cellular membranes is another testament to the precision implemented in nature. In a setting without directed guidance or cellular machinery, achieving such a refined composition raises significant questions about the prebiotic processes at play.
3. Formation of Bilayers: Phospholipids in cell membranes naturally form bilayers, a critical structure for cell integrity and function. How did spontaneous events promote the consistent formation of bilayers in the absence of cellular machinery or directives? Bilayers are integral to cell functionality. Their spontaneous formation in a prebiotic setting, devoid of cellular directives, seems like a formidable hurdle. The inherent organization this requires is a profound mystery in understanding the genesis of life, unless one posits intelligent design. 
4. Molecular Symmetry: Phospholipids display a head and two fatty acid tails, implying a certain degree of symmetry. How were the conditions favorable to consistently produce this dual-tailed structure, as opposed to other possible configurations? The symmetry displayed by phospholipids, with a head and two tails, implies an underlying order. Achieving this structure consistently in early Earth's turbulent conditions speaks to processes and phenomena that remain enigmatic unless they were instantiated with intent.
5. Specific Phospholipid Functions: Different phospholipids serve distinct roles within cellular membranes, influencing fluidity, curvature, and interaction with proteins. How did prebiotic conditions facilitate the formation of a wide variety of phospholipids, each with its unique function? Beyond their formation, each phospholipid serves a unique role, contributing to the membrane's properties. How prebiotic conditions produced such functional diversity remains a major puzzle in the understanding of life's origins, unless one infers design. 
6. Environmental Stability: Given the dynamic and potentially harsh conditions of the early Earth, how were phospholipids stabilized? Without the protective environment of a cell, these molecules could be degraded by various factors. Phospholipids, vulnerable to degradation, faced the harsh and variable conditions of early Earth. Their persistence and eventual dominance in cellular membranes suggest mechanisms of stability and protection that could only be implemented with foresight and intent.
7. Concentration and Assembly: For bilayers to form, a sufficient concentration of phospholipids would be required. How were these concentrations achieved and maintained amidst the vast prebiotic "soup"?  The formation of any structured entity requires a threshold concentration of its components. How phospholipids achieved such concentrations in the vastness of prebiotic environments raises profound questions about the early dynamics of molecular assembly.
8. Integration of Other Membrane Components: Membranes also consist of proteins, cholesterol, and other components. How did the early membranes incorporate these elements in the right proportions and configurations for functionality? Modern membranes are complex mosaics of various components. The harmonious integration of these components, each contributing to membrane function, points to an inherent sophistication that challenges simplistic, undirected origin models.
9. Functional Asymmetry: Modern cell membranes display asymmetry, with different phospholipids in the inner and outer leaflets of the bilayer. How was such a complex arrangement achieved in the absence of enzymes and transporters? Asymmetry in cell membranes is not a mere structural detail; it's fundamental to function. Achieving this intricate arrangement without enzymes or transporters adds another layer of complexity to the origin puzzle.
10. Selective Permeability: One of the vital functions of the membrane is to regulate the passage of substances. In the absence of specialized proteins, how did early membranes achieve any semblance of selective permeability? The ability to regulate substance passage is vital for any proto-cell. The emergence of selective permeability, especially in the absence of specialized proteins, remains one of the most intriguing questions about the early stages of life.

In essence, these challenges, especially when viewed cumulatively, present significant hurdles to simplistic, undirected narratives of life's origins. Each question underscores the sophistication and specificity inherent in even the most basic components of life. Understanding these intricacies not only deepens our appreciation for the wonder of life but also reinforces the enormity of the quest to unravel its genesis.

Regarding the selection and specificity of carbohydrates in the prebiotic context:

1. Emergence of Vital Sugars: In the vast prebiotic landscape, how did essential sugars like glucose and ribose distinctively form? The precision and specificity of these simple sugars in life's matrix hint at an intentional blueprint underpinning their presence.
2. Pentose Sugar's Role: Amidst the countless molecular structures, what guided the consistent selection of pentose sugars for RNA's backbone? Such a unique choice in the early molecular dance suggests an underlying design.
3. Evolution of Polysaccharides: The progression from simple monosaccharides to complex polysaccharides seems more than mere molecular serendipity. Their formation and function in early life forms indicate a pre-conceived architectural plan.
4. Glycosidic Bond's Precision: In an environment devoid of sophisticated enzymes, how did the accurate glycosidic bonds between sugars emerge?  Glycosidic bonds refer to the covalent linkages that connect monosaccharide units in disaccharides, oligosaccharides, and polysaccharides. In other words, they are the bonds that link individual sugar molecules together in larger carbohydrate structures.  It's likely that LUCA had some rudimentary form of a protective exterior, possibly incorporating simple carbohydrates or carbohydrate-like structures to maintain cellular integrity and mediate interactions with its environment.The meticulous nature of these bonds alludes to an inherent design principle.
5. Carbohydrates in Energy Storage: The primordial role of carbohydrates like glycogen and starch in energy storage seems beyond random. Their precise structures and functions in LUCA's descendants suggest a blueprint aimed at energy optimization.
6. Cell-Surface Carbohydrate Code: How did the complex carbohydrate patterns on cell surfaces, crucial for cell recognition and signaling, come into existence? Their intricate design suggests an intentional matrix for early cellular communication.
7. Origin of Glycolysis: The glycolytic pathway, central to most life forms, exhibits a remarkable sequence of reactions. How did this elegant process, vital for energy extraction from glucose, originate? Its precision hints at a designed mechanism pivotal to early life's sustenance.
8. Chirality in Sugars: With multiple chiral configurations possible, what determined the dominance of specific orientations in biological carbohydrates? The selectivity of D-sugars in life implies an underlying design strategy.

Carbohydrates, being central to numerous life processes ranging from energy storage to cell signaling, indeed present a myriad of challenges when it comes to explaining their origins. The way they precisely bond, their chiral preferences, their unique roles in various cellular pathways, and their consistent structures across numerous life forms raise compelling questions about how such order and complexity could arise in a presumably chaotic prebiotic environment. The focus on LUCA (Last Universal Common Ancestor) also brings forth the idea that even the most primitive life forms exhibited remarkable molecular precision and complexity, suggesting that the foundational principles of life are rooted in a deep-seated order and design.

Beyond Evolution: The Origin of Species by Design Image115

1. Fundamentals of Geobiology Editor(s): Andrew H. Knoll, Donald E. Canfield, Kurt O. Konhauser Published: 30 March 2012 Print ISBN: 9781118280812 | Online ISBN: 9781118280874 | DOI: 10.1002/9781118280874
2. Schwartz, A.W. (2007). Intractable mixtures and the origin of life. Chem Biodivers, 4(4), 656-64. Link. (This paper delves into the complexities surrounding mixtures and their implications for the origins of life.)
3. Cairns-Smith, A.G. (Reprint Edition). Seven Clues to the Origin of Life: A Scientific Detective Story (Canto). Link. (This book takes a detective's approach to unraveling the mysteries behind the origins of life.)
4. Cairns-Smith, A. G. (1982). Genetic Takeover: And the Mineral Origins of Life 1st Edition. Cambridge University Press. Link. (This book delves into the theory of life's origins through mineral processes.)
5. Dembski, W.A. (2002). Naturalism’s Argument from Invincible Ignorance: A Response to Howard Van Till. Intelligent Design. Link. (This article offers a response to Howard Van Till's "E. coli at the No Free Lunchroom" and delves into the debate surrounding intelligent design and naturalism.)
6. Fry, Iris. (2010). The Role of Natural Selection in the Origin of Life. Origins of Life and Evolution of Biospheres, 40(2). Link.
7. Koonin, E. V. (Updated Edition). The Logic of Chance: The Nature and Origin of Biological Evolution (paperback). Amazon.



Last edited by Otangelo on Tue Oct 17, 2023 7:31 am; edited 2 times in total

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Does time inherently promote the progression in molecular complexity to get to life?

The ticking clock of the prebiotic world wasn't necessarily an ally. While modern enzymes act as time-benders, accelerating vital reactions to breakneck speeds, their ancient counterparts lacked such luxury. Think of the OMP decarboxylase enzyme, a temporal miracle worker that hastens a pivotal reaction to make RNA and DNA from a 78 million-year marathon to mere moments. In an era without such enzymatic marvels, the likelihood of stumbling upon the right chemical reaction could easily dwarf even the grandiosity of the universe's atom count.

Beyond Evolution: The Origin of Species by Design G95210

On Molecular Precision and Life's Origins:

The vast complexities and intricacies inherent within molecular structures and systems present an enigma when considering life's origins. When we examine the highly specific sequences within nucleic acids or the precision demanded in enzymatic reactions, it becomes clear that the margin for error is minimal. Such specificity and precision seem contradictory to the inherent tendencies of random molecular assemblies. The challenge becomes even more evident when considering the propensity of organic systems to form complex, disorganized mixtures when left to spontaneous processes. This is juxtaposed against the exactness and purposefulness exhibited by biological entities. Life, as we understand it, operates with a degree of precision and consistency that's unparalleled. Such meticulous orderliness isn't just a mere luxury; it's a requisite for survival. Taking into account the propensity of molecules toward randomness and the observed precision in living systems, we're faced with a profound question: How did such precision arise amidst a backdrop of molecular chaos? Purely stochastic processes seem insufficient to bridge this divide. The leap from disordered molecular assemblies to the intricate systems of life appears to require mechanisms or processes beyond mere chance. Furthermore, it's worth noting that life, in its myriad forms, operates not just with molecular precision but with an evident purpose. Cells function with a clear goal: to survive, replicate, and respond to their environment. Such purposefulness, paired with molecular precision, hints at a guiding force or design behind life's complexity. The true origins of life, while remaining a subject of debate, demand a multifaceted approach. However, given the challenges and mysteries inherent in purely naturalistic explanations, it's worth considering that the origins of life might be rooted in a design, a purposeful blueprint that facilitated the emergence of the complex systems we observe today.

Ilya Prigogine (1972): The probability that at ordinary temperatures a macroscopic number of molecules is assembled to give rise to the highly ordered structures and to the coordinated functions characterizing living organisms is vanishingly small. The idea of spontaneous genesis of life in its present form is therefore highly improbable, even on the scale of the billions of years during which prebiotic evolution occurred. 1

Steven A. Benner (2015):: The Asphalt Paradox: An enormous amount of empirical data have established, as a rule, that organic systems, given energy and left to themselves, devolve to give uselessly complex mixtures, “asphalts”. The theory that enumerates small molecule space, as well as Structure Theory in chemistry, can be construed to regard this devolution a necessary consequence of theory. Conversely, the literature reports (to our knowledge) exactly zero confirmed observations where “replication involving replicable imperfections” (RIRI) evolution emerged spontaneously from a devolving chemical system. Further, chemical theories, including the second law of thermodynamics, bonding theory that describes the “space” accessible to sets of atoms, and structure theory requiring that replication systems occupy only tiny fractions of that space, suggest that it is impossible for any non-living chemical system to escape devolution to enter into the Darwinian world of the “living”. Such statements of impossibility apply even to macromolecules not assumed to be necessary for RIRI evolution. Again richly supported by empirical observation, material escapes from known metabolic cycles that might be viewed as models for a “metabolism first” origin of life, making such cycles short-lived. Lipids that provide tidy compartments under the close supervision of a graduate student (supporting a protocell first model for origins) are quite non-robust with respect to small environmental perturbations, such as a change in the salt concentration, the introduction of organic solvents, or a change in temperature. 2

Rob Stadler (2021):  Even in a very short DNA of just two nucleotides, there are dozens of incorrect possible arrangements of the components, and only one correct arrangement. The probability of consistent arrangement decreases exponentially as the DNA lengthens. If natural processes could polymerize these monomers, the result would be chaotic “asphalt,” not highly organized, perfectly consistent biopolymers. Think about it — if monomers spontaneously polymerized within cells, the cell would die because all monomers would be combined into useless random arrangements. 3

Deamer, D. (2017): It is clear that non-activated nucleotide monomers can be linked into polymers under certain laboratory conditions designed to simulate hydrothermal fields. However, both monomers and polymers can undergo a variety of decomposition reactions that must be taken into account because biologically relevant molecules would undergo similar decomposition processes in the prebiotic environment.4

Luisi, P. L. (February 2014) Attempts to obtain copolymers, for instance by a random polymerization of monomer mixtures, yield a difficult-to-characterize mixture of all different products. To the best of our knowledge, there is no clear approach to the question of the prebiotic synthesis of macromolecules with an ordered sequence of residues. 5

Timothy R. Stout (2019):  Prebiotic processes naturally randomize their feedstock. This has resulted in the failure of every experimentally tested hypothetical step in abiogenesis beginning with the 1953 Miller-Urey Experiment and continuing to the present. Not a single step has been demonstrated that starts with appropriate supply chemicals, operates on the chemicals with a prebiotic process, and yields new chemicals that represent progress towards life and which can also be used in a subsequent step as produced. Instead, the products of thousands of experiments over more than six decades consistently exhibit either increased randomization over their initial composition or no change. We propose the following hypothesis of Abiogenetic Randomization as the root cause for most if not all of the failures: 1) prebiotic processes naturally form many different kinds of products; life requires a few very specific kinds. 2) The needs of abiogenesis spatially and temporally are not connected to and do not change the natural output of prebiotic processes. 3) Prebiotic processes naturally randomize feedstock. A lengthy passage of time only results in more complete randomization of the feedstock, not eventual provision of chemicals suitable for life. The Murchison meteorite provides a clear example of this. 4) At each hypothetical step of abiogenesis, the ratio of randomized to required products proves fatal for that step. 5. The statistical law of large numbers applies, causing incidental appearances of potentially useful products eventually to be overwhelmed by the overall, normal product distribution. 6) The principle of emergence magnifies the problems: the components used in the later steps of abiogenesis become so intertwined that a single-step first appearance of the entire set is required. Small molecules are not the answer. Dynamic self-organization requires from the beginning large proteins for replication, metabolism, and active transport. Many steps across the entire spectrum of abiogenesis are examined, showing how the hypothesis appears to predict the observed problems qualitatively. There is broad experimental support for the hypothesis at each observed step with no currently known exceptions. Just as there are no betting schemes that allow a person to overcome randomness in a casino, there appear to be no schemes able to overcome randomness using prebiotic processes. We suggest that an unwillingness to acknowledge this has led to the sixty plus years of failure in the field. There is a large body of evidence—essentially all experiments in abiogenesis performed since its inception sixty plus years ago—that appear to be consistent with the hypothesis presented in this paper. Randomization prevails. 6

Beyond Evolution: The Origin of Species by Design Matter11

Further unsolved hurdles of the Origin of Life by unguided means

1. Purity Dilemma: Unlike the controlled environments of labs that use pure substances, the early Earth likely presented an impure chemical setting.
2. Energy Conundrum: Prebiotic entities would need innovative methods to acquire Gibbs free energy, essential for entropy reduction.
3. Activation Processes: Monomers require activation for polymerization to transpire, enabling the synthesis of amino acid chains and genetic material.
4. Information: Genes store complex, specific information in digital form, guiding the assembly of molecular machines.
5. Polymerization: The spontaneous polycondensation of amino acids and nucleotides in early Earth's diverse solutions presents a puzzle.
6. Eigens Paradox: This paradox challenges the conception of the origins of life, questioning the size limits of self-replicating molecules.
7. Muller's Ratchet: It posits that smaller asexual populations will inevitably accrue detrimental mutations due to genetic drift.
8. Protected Environments: UV exposure, temperature extremes, or incorrect atmospheric conditions could jeopardize chemical reactions.
9. Reaction Sequence: Cellular metabolic pathways necessitate properly sequenced enzymes. Spontaneous events must have guided this organization.
10. Order from Chaos: How did the chaotic prebiotic environment transform into organized systems exhibiting characteristics like growth and evolution?
11. Irreducible Complexity: Cells, as life's minimal units, possess components that are functional only when integrated.
12. Homeostasis: Managing metabolism is vital for life, and disruptions to this balance can result in various pathologies.
13. The condensation problem: There is a difficulty in prevital synthesis of biopolymers: all the major biopolymers are metastable in aqueous solution in relation to their (deactivated) monomers. Left to itself in water, a polypeptide will hydrolyze to its constituent amino acids.
14. The Nuances of Organic Chemistry The intricate steps and precise conditions essential for organic chemistry work-ups challenge the notion that such complex processes could spontaneously arise in primitive geological settings without deliberate orchestration.


Obstacles in Probability Assessment 

To gauge the likelihood of a specific event occurring, it's crucial to discern which odds are significantly low to rule out mere chance as the cause. Evaluating the odds becomes especially pertinent when discussing the probability of an outcome with minimal chances of success. Prebiotic synthesis presents multiple challenges that render the spontaneous emergence of life through undirected processes highly implausible.

1. Getting Pure Materials 

Imagine the pristine labs of today, replaced with the tumultuous environment of the ancient Earth. Instead of neatly labeled bottles of pure chemicals, we'd be presented with a swirling mix of countless compounds. This untamed molecular wilderness, far from the controlled settings of modern laboratories, was where the first inklings of life had to take root. It wasn't just about finding the right molecules to react; it was about these molecules identifying each other amidst a sea of distractions. Think of it as a cosmic dance, where partners needed to find each other in a room crowded with countless other dancers, all moving to their rhythms. It wasn't just the dance; it was about finding the right partner to make the dance meaningful. In understanding the genesis of life, it's imperative to acknowledge this chaotic, cluttered backdrop. It wasn't just the right reactions that were crucial but the sheer tenacity of molecules to find their counterparts against overwhelming odds. This raw, untamed scenario presents a compelling backdrop for the emergence of life, emphasizing not just the beauty of chemistry but the resilience and persistence of the earliest molecules in their journey toward life.

2. Getting Free Gibbs Energy

Today's scientific understanding is deeply rooted in the principles of thermodynamics. The behavior of every atom and molecule, every star in a galaxy, follows these universal laws. Central to these is the Gibbs free energy concept, which essentially dictates whether a reaction will proceed spontaneously. Underlying this is the ever-present balance between the energy that a system holds and the disorder or randomness (entropy) within it. Imagine a vast, open landscape dominated by towering mountains and deep valleys. In this landscape, molecules are akin to wanderers. Naturally, a wanderer would opt for the path of least resistance, traversing downhill rather than struggling uphill. But the chemistry that underpins life isn't so straightforward. It's akin to these wanderers, against all logic, choosing to climb treacherous peaks rather than sauntering down the gentle slopes. The dawn of life on Earth had to contend with this thermodynamic puzzle. The raw ingredients present faced a choice: to merely follow the easy path as dictated by Gibbs free energy or to marshal the necessary resources and carve out new, unprecedented routes. These early molecular entities had to ingeniously tap into the vast energy reservoirs of their environment, be it from the sun's radiance, geothermal vents, or other sources, and repurpose this energy with finesse and strategy.
This wasn't just about obtaining energy. It was about crafting the very mechanisms to judiciously utilize this energy, channeling it towards forming complex structures and intricate pathways. It laid the groundwork for a future where cells could harness sunlight to fuel their needs or mitochondria could adeptly manage power for multicellular giants. This saga of early molecules underpins the elegance and tenacity of life's precursors, painting a picture of resilience, innovation, and the undying urge to evolve beyond the ordinary.

3. Activation and Repetitive Processes 

The very birth of life's long chains, be they amino acid strands or genes, hinges on a dance of activation and repetition. While contemporary cells boast sophisticated machinery, like the RNA or DNA polymerase protein complexes, to orchestrate this dance, their primeval predecessors lacked such luxury. They faced the daunting task of consistently and accurately binding monomers, all without the refined tools and structures of modern biology. It's a mystery that remains unsolved: how, in the vast expanse of early Earth, did the first molecules manage this monumental feat?

4. Instructional Information, and the Genetic Code

The origin of biological Information, and the genetic code remains enshrouded in mystery. Picture this: a cause trying to architect a factory complex housing over a thousand unique machines, executing 1,500 reactions concurrently. This cause lacks engineering intellect and is devoid of directed energy, relying solely on raw natural forces. The statistical odds for such a system to emerge by sheer chance are staggeringly low, akin to hitting a singularly marked molecule among all molecules representing the universe's atoms.

Statistical Challenge: In the vast expanse of the molecular world, proteins emerge as fascinating architectures of life, sculpted with precision according to the script laid out by DNA. The depth of this design is such that the exact sequence of amino acids determines the functional three-dimensional folds of these proteins. This orchestration lies at the intersection of sheer improbability and meticulous specification, a crossroads that has sparked numerous debates regarding the likelihood of such a phenomenon arising by chance. Venturing into the world of the minuscule, we encounter the simple yet fascinating bacterium, Pelagibacter ubique. Despite its modest stature, this organism stands as a testament to nature's efficiency. With a streamlined genetic content of about 1,300 genes and just over 1.3 million base pairs, it codes for 1,354 proteins, each playing a unique role in the dance of life. This bacterium, in its simplicity, manages to cover the complete biosynthetic pathways for all 20 amino acids. Broadening our perspective to encompass the wider biological realm, it emerges that the average protein length hovers around 400 amino acids for both prokaryotic and eukaryotic cells. Now, this brings us to a realm of astronomical probabilities. Each position in a protein chain can be filled by any of the 20 amino acids, leading to an almost unfathomable number of permutations. The odds of randomly assembling a functional protein from this vast sea of possibilities is akin to 1 in a staggering 10^520. Considering the breadth of proteins needed to construct even the most rudimentary free-living cell, this probabilistic challenge amplifies. The mathematics of chance thus pushes us into realms far beyond comprehension. If one were to accumulate the number of amino acids required for a basic cell, you'd be dealing with over half a million amino acids. These would need to be sequenced perfectly, with the added complexity of choosing only left-handed amino acids, further stretching the odds to an unimaginable 10^722,000,000. Even when imagining multiple universes, each teeming with planets shuffling sequences continuously for eons, the likelihood remains infinitesimal. To further illustrate this, let's consider Mycoplasma genitalium, another contender for the title of the simplest organism. Despite being deemed 'simple', its genome encompasses a substantial 580,000 base pairs. This organism, with its 470 genes, codes for proteins that average 347 amino acids in length. The odds stacked high against the random emergence of just a single protein of this length. As we extend our calculations to encompass the entire array of proteins this bacterium needs, the probabilities continue to defy comprehension. This narrative paints a picture of a molecular realm where randomness seems an unlikely architect, given the staggering complexities and precise requirements of life's building blocks. The mathematical tapestry woven around the emergence of life pushes our understanding and challenges us to reflect deeper on the nature of our origins.

5. The Precision of Polymerization: A Purposeful Ballet

In the vast ocean of early Earth, a multitude of molecular actors - amino acids and nucleotides - stood poised for connection. This was not a mere playground of random encounters. Each bond and linkage represented a marvel of exactitude, suggestive of a purpose beyond mere chance. Polymerization, the art of molecular connection, appears almost miraculous when studied in isolation from the sophisticated mechanisms we know today. Consider the peptides and phosphodiester bonds that stitch amino acids and nucleotides, respectively. In modern cellular environments, specific enzymes and machines facilitate these processes with impeccable precision. But on the ancient Earth, devoid of these intricate facilitators, how did such precision emerge? Perhaps there's more to the story than sheer accident. The molecular actors may have had predisposed affinities, guided by an inherent set of rules or principles. Mineral surfaces, with their unique configurations, might have served as meticulous templates, enabling amino acids and nucleotides to align in just the right manner. The varying cycles of tidal pools could have played a strategic role, in concentrating and positioning the molecules for optimal interaction. Even the volatile elements from deep-sea vents or atmospheric discharges might have had a specific role to play, not merely as agents of chaos but as purposeful interveners. For every successful bond formed, numerous other attempts might have faltered. Yet, those successful sequences that did emerge had properties far beyond mere stability. They showcased the capability to catalyze, replicate, and exhibit functional behaviors, a hint towards a greater order in play. These were not just random sequences but carefully orchestrated arrangements, leading to the foundational molecules of life. The origin of these molecular ballets poses profound questions. Was it merely the result of random permutations, or is there a purposeful order underlying the chaos? Delving deeper into the chemistry and physics of the early Earth environment, one can't help but ponder upon the unseen guiding principles that facilitated the emergence of life's foundational molecules. This purposeful assembly, viewed through the lens of the ancient Earth, beckons us to appreciate the remarkable precision and design underpinning the genesis of life.

6. The Enigma of Eigen's Paradox

The vast genetic encodings of life present a puzzle that perplexes even the most astute minds. Eigen's Paradox emerges from the very foundation of molecular biology, shedding light on the theoretical conundrums faced by early self-replicating molecules. These molecules, theoretically, should be limited in length, perhaps to just a few hundred digits, given the constraints of the error threshold. Yet, life as we observe it reveals a story rich with extensive genetic information, far surpassing these modest lengths. Herein lies a core mystery: The accuracy of genetic replication is maintained by a fleet of error-correcting enzymes. These sentinels of genetic fidelity ensure that DNA's vast repository of information remains uncompromised. But, paradoxically, the instructions to construct these enzymes reside within the expansive genome they guard. This presents a scenario that teases the logical mind: which preceded the other? To appreciate the depth of this riddle, one must consider the nuanced coordination required. A molecule with the capacity for replication would need to not only maintain the integrity of its genetic code but also develop mechanisms to correct any deviations. Such precision, especially in the absence of the very enzymes designed to maintain it, is both awe-inspiring and baffling. Akin to a timepiece that requires an intricate assembly of gears and springs to function, but also includes within it the blueprint for its own construction, the relationship between expansive genomes and their protective enzymes highlights a sophisticated interdependence. It pushes us to ponder on the origin of such a precise system. Was it a product of myriad chance events, or does it hint at an underlying principle or set of principles guiding its formation? Probing deeper into molecular biology and the conditions of early Earth, scientists face the formidable task of unraveling this mystery. The precise dance between extensive genetic encodings and their vigilant overseers is but one facet of the fascinating journey to understand life's enigmatic origins.

7. Muller's Ratchet and the Genesis of Life

Muller's Ratchet presents a formidable challenge to understanding the origins of early life. Small, asexual populations would invariably face an escalating threat from the accumulation of harmful mutations. As these mutations accumulate, they exert an intensifying downward pressure, amplifying their susceptibility to genetic drift and, subsequently, the addition of further detrimental mutations. This cycle, referred to as the mutational meltdown, seemingly traps these populations in a narrowing corridor, pushing them toward potential extinction. Given this scenario, the emergence of life demands deeper contemplation. A mere isolated organism would be insufficient. The dawn of life would have seemingly necessitated a diverse assemblage of microbes, each equipped with its unique genetic toolkit. They would need the capability to compartmentalize, to engage in sophisticated genetic exchanges, and to adroitly navigate the challenges of their primordial habitat. This delicate balance between collaboration, competition, and innovation becomes central to enduring the early Earth's challenges. One can't help but marvel at the precise mechanisms that would need to be in place for life to thrive amidst such adversities. Such a diversified framework, rich in potential for both genetic exchange and recombination, underscores the meticulous nature of these early life forms. These conditions raise significant questions about how the initial microbial consortium could harmoniously coexist, adapt, and pave the way for the remarkable complexity and diversity seen in today's biosphere. To truly appreciate this scenario, one must delve deeper into the conditions and mechanisms of the early Earth. Each finding adds to our understanding of how these primordial communities might have come to be, moving us forward in our quest to grasp the profound origins of life.

8. Critical Environments for Biogenesis

The early Earth's environment imposed stringent conditions for biochemical reactions central to the origin of life. Excessive UV radiation, extreme temperature oscillations, and rapid pH changes could readily disrupt or preclude the necessary molecular processes. As highlighted by Shapiro in 2006, understanding the genesis of life extends beyond individual chemical reactions. It demands a suitable environment, one that can sustain the continuity of these reactions. While laboratory experiments can simulate isolated processes in controlled settings, the real challenge is understanding how these processes could coalesce into a unified framework amidst the dynamic conditions of the primordial Earth.

9. Ordered Catalytic Processes

In contemporary cells, an intricate cascade of enzymatic reactions is observed, with each enzyme proficiently processing a specific substrate and handing it off to the subsequent enzyme. In the absence of these sophisticated enzymes, early Earth would have depended on rudimentary catalysts such as clay or specific ions. This presents a conundrum: how were reactions orchestrated in the necessary sequence for life under these rudimentary conditions? The likelihood of random processes achieving the requisite order, synchrony, and progression for these foundational reactions appears extremely low.

10. Systematic Convergence in Primordial Conditions

In the context of early life, it's not merely the presence of individual compounds, but the structured assembly of these components that captures our attention. Faced with an environment potentially abundant with countless varied molecules at low concentrations, the emergence of organized systems capable of growth, replication, and information processing is a conundrum. The pressing question arises: What mechanisms or conditions drove these myriad molecules to align, self-assemble, and embark on the intricate journey towards the initial hallmarks of life?

11. Functional Wholeness

At the heart of life's design, there is an evident principle of cohesion and interrelation. Isolated components are reminiscent of disassembled segments of machinery — purposeful only when integrated into a larger system. A protein, beyond its constituent amino acids, necessitates a particular order and length to assume functionality. Similarly, the nature of a living cell extends beyond the mere presence of molecules; it represents an intricate system engineered for energy production, information processing, and sustained operability. This intricate unity of the cell presents a significant scientific inquiry: How did these individual elements come into existence when their true utility and purpose manifest predominantly within the organized and unified complexity of the full system?

12. Homeostatic Precision

Life demonstrates an exceptional attribute of maintaining equilibrium – homeostasis. In the midst of external variables, cellular entities exhibit a profound ability to keep their internal processes stable, facilitating a continuity of life processes. Achieving this equilibrium is no small feat. Any deviation from this delicate balance can lead to detrimental consequences. The question then arises: How did initial cellular entities establish such a precise balance? A piecemeal emergence of this equilibrium seems unlikely given the intricate nature of homeostasis. The inherent ability of life to sustain this stability implies an inherent complexity from its inception, which poses questions regarding a gradual emergence. The inception of life, in light of this, seems to necessitate a comprehensive and precise foundation.

13. The condensation problem

The synthesis of biopolymers in pre-life conditions presents a notable conundrum. A core challenge is that biopolymers, such as polypeptides, are metastable when immersed in an aqueous environment. Given time, without external intervention, a polypeptide will revert through hydrolysis to its foundational amino acids. This inherent instability suggests that the initial formation and persistence of biopolymers in primordial conditions would require specific circumstances or catalysts to prevent their immediate degradation. The question arises: How were these complex molecules stabilized long enough to play their role in the advent of life, given their natural inclination towards decomposition in water? This scenario implies an inherent precision and specificity in the early processes that led to life.

14. The Nuances of Organic Chemistry 

Organic chemistry is marked by its intricacies and precision. Often, the post-reaction procedures, termed as 'work-up', present the most significant challenges. This involves several steps such as pH adjustments, solvent extractions, chromatography, and evaporation, among others. While one might postulate that primitive geological conditions could inadvertently carry out these processes, it's essential to consider the complexity involved. Each stage of the work-up is critical. For instance, the mere transfer of a solution, a washing step, or an evaporation process could significantly influence the outcome. Moreover, many of these procedures must occur in a specific sequence and under particular conditions. Even slight deviations can be the determinant between a successful chemical synthesis and an unusable mixture. In the hands of a chemist, these steps are meticulously planned, often relying on their expertise to make real-time decisions — like determining the exact duration after a pH adjustment to commence filtration. Given the multifaceted nature of organic synthesis, the assumption that such precision could arise from spontaneous geochemical processes seems ambitious. The harmony and sequence required for these reactions underscore the need for a thoughtful orchestration, raising questions about the inherent mechanisms that facilitated these processes during the Earth's formative years.



1. Prigogine, I., Nicolis, G., & Babloyantz, A. (1972). Thermodynamics of evolution. Physics Today, 25(11), 23-28. Link. (This paper delves into the thermodynamics of living systems, particularly how they reconcile with the Second Law of Thermodynamics.)
2. Benner, S. A. (2014). Paradoxes in the origin of life. Orig Life Evol Biosph, 44(4), 339-343. Link. (This paper discusses paradoxical aspects related to the origins of life.)
3. Rob Stadler (2021): A Strikingly Unnatural Property of Biopolymers
4. Deamer, D. (2017). The Role of Lipid Membranes in Life’s Origin. Life (Basel), 7(1), 5. Link. (This article explores the significance of lipid membranes in the early stages of life's origin.)
5. 1. Adamala, K., Anella, F., Wieczorek, R., Stano, P., Chiarabelli, C., & Luisi, P. L. (February 2014). OPEN QUESTIONS IN ORIGIN OF LIFE: EXPERIMENTAL STUDIES ON THE ORIGIN OF NUCLEIC ACIDS AND PROTEINS WITH SPECIFIC AND FUNCTIONAL SEQUENCES BY A CHEMICAL SYNTHETIC BIOLOGY APPROACH. Link. (This research paper investigates the chemical origins of nucleic acids and proteins using a synthetic biology approach.)
6. Stout, T. R., & Matzko, G. (2018, October 3). A Natural Origin of Life. https://doi.org/10.31219/osf.io/p5nw3

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Richard Dawkins, evolutionary biologist and author, is well-known for his advocacy of atheism and secularism, often framed within the context of evolutionary biology. Dawkins declared that the theory of evolution by natural selection,  established by Charles Darwin, offered a comprehensive explanation for the diversity of life on Earth, negating the need for supernatural interpretations of the complexity and design apparent in living organisms. Dawkins posited that a deep understanding of evolutionary mechanisms enabled one to see the natural world in a new light, one that did not require the invocation of a divine creator. This perspective was presented in his book, "The Blind Watchmaker," where he contended that natural selection, an unconscious, automatic, and non-random process, could account for the complex forms of life, effectively removing the necessity for an intelligent designer. By advocating that evolution provided a complete explanation for the biological world, Dawkins challenged traditional views that saw God as an essential part of understanding life's complexity. Dawkins' assertion that evolution led him to become an "intellectually satisfied atheist" was grounded in the belief that the theory of evolution offers a more coherent and intellectually fulfilling framework for understanding the natural world than explanations based on intelligent design. This stance became a central theme in his broader mission to promote atheism and disbelief in God. 

Since the publication of Richard Dawkins's  "The Blind Watchmaker," in 1986, the field of biological sciences, and particularly molecular biology, has undergone transformative changes. The advancements in these fields over the past decades have not only deepened our understanding of life at its most fundamental levels but have also revolutionized the way we approach questions about evolution, genetics, and the complexity of life as Dawkins once explored.
The scientific community has witnessed a series of landmark discoveries that have expanded our knowledge and capabilities in unprecedented ways. One of the most significant milestones was the completion of the Human Genome Project in 2003. This monumental achievement provides a 'blueprint' of human DNA that has paved the way for advancements in medicine, anthropology, and evolutionary biology.   Moreover, the advancements in imaging and microscopy have provided unparalleled insights into the microworld of cells and molecules. Techniques such as cryo-electron microscopy, which won the Nobel Prize in Chemistry in 2017, have allowed scientists to visualize proteins and other biological molecules at atomic resolution, revealing the intricate machinery of life. These images serve as a powerful reminder of the complexity and elegance of evolutionary processes that Dawkins marveled at, now laid bare in exquisite detail. The field has also seen significant advances in computational biology, leveraging the exponential growth in computing power to analyze and interpret vast datasets. Bioinformatics, the application of computer technology to the management of biological information, has become an indispensable tool in decoding complex genetic information, modeling evolutionary processes, and understanding the regulatory networks that dictate cellular function. This computational revolution has expanded our ability to test evolutionary theories, simulate the dynamics of natural selection, and uncover the genetic underpinnings of phenotypic traits.

The exploration into the depths of the molecular world, empowered by the remarkable advancements in biological sciences since the late 20th century, has unveiled a landscape of life far more intricate, complex and diverse than previously imagined. This newfound understanding challenges the simplicity with which life's complexity was once viewed, suggesting a tapestry woven with a myriad of genetic, biochemical, and physiological threads that defy a singular narrative of origin. At the heart of this revelation is the discovery of alternative DNA structures, which extend beyond the iconic double helix to include quadruplexes and other complex configurations, each playing unique roles in genetic regulation and stability. Such diversity in the very fabric of life's code underscores the variability and adaptability inherent in biological systems. Moreover, the influence of viruses, once considered mere parasitic entities, has been reevaluated to reveal their profound impact on the function of host genomes. Viruses have been shown to act as agents of horizontal gene transfer, facilitating the spread of genetic material across diverse life forms and contributing to the genetic mosaic that characterizes many organisms. This interplay between viruses and hosts adds a layer to the complexity of biological dynamics, suggesting mechanisms that encompass more than the gradual accumulation of mutations envisaged by traditional neo-Darwinian frameworks.

The notion of polyphyly, which posits that life diversified from multiple independent origins rather than a single common ancestor, gains traction in light of such discoveries. The existence of distinct biological systems, from the myriad forms of cellular architecture to the vast array of metabolic pathways, speaks to a biological realm that is not the product of linear, tree-like evolution, but separate, distinct creation events. This perspective is further supported by the observation of 33 variations of genetic codes and over 223 distinct epigenetic, manufacturing, and regulatory codes and biological languages, each contributing to the unique identity and functionality of different life forms. The architecture of multicellular organisms, with its staggering complexity, arises from the orchestration of at least 47 key developmental processes. These processes are regulated through an elaborate network of signals and interactions, embodying a level of systemic complexity that surpasses the capabilities of unguided natural processes. The coordination of hundreds of signaling networks, which facilitate functional communication and integration among cellular and extracellular components, hints at an underlying order and purposefulness reminiscent of intelligent design. This perspective posits that the multifaceted mechanisms underlying life's diversity and complexity, from the molecular to the organismal level, may not be fully accounted for by natural selection and random mutations alone. Instead, they indicate the presence of an intelligent cause, a guiding force that imbued the natural world with the initial conditions, information, and integrated complexity, necessary for life to flourish in its manifold forms.

The picture that emerges is one of staggering complexity, marked by interdependent systems and processes that defy simple explanations. This complexity, coupled with the evidence of multiple origins of life's building blocks, suggests a narrative of life's origins and adaptation that is far richer and more nuanced than previously conceived. It invites a reevaluation of the mechanisms and forces that have shaped the living world, pointing towards an intelligence that imbued matter with the potential for life's astonishing diversity. Louis Pasteur, a pioneering figure in microbiology and chemistry, is often associated with the quote, "A little science estranges men from God; a lot of science brings them back to Him." This statement reflects a nuanced view of the relationship between scientific inquiry and faith in God, suggesting that the pursuit of scientific knowledge can have different impacts on one's belief in and relationship with the divine, depending on the depth and breadth of that pursuit. In the initial stages of scientific exploration, the mechanics of the natural world might seem to provide straightforward, empirical explanations for phenomena that were previously attributed to the supernatural or divine. This could lead to a sense of estrangement from God, as the mysteries and wonders that once pointed to a higher power are seemingly demystified. The allure of empirical evidence and the tangible results of scientific inquiry can, at first glance, diminish the perceived need for spiritual explanations and thus distance one from faith. However, Pasteur suggested that as one delves deeper into the complexities of the natural world, the scale, intricacy, and elegance revealed by advanced scientific research can inspire a renewed sense of awe and wonder. This profound appreciation for the natural world and its complexity might lead one to acknowledge a greater intelligence or design, thus bringing someone closer to God. The more one learns about the natural world, from the vastness of space to the intricacies of molecular biology, the more one might be inclined to see the hand of a creator behind the intricate order and harmony. This perspective aligns with the views of many scientists and theologians who see science and faith not as conflicting, but as complementary ways of understanding the world. The idea is that science provides the tools to understand how the universe operates, while spirituality offers a context for understanding why it exists and what its existence means for humanity. Pasteur's statement encapsulates the journey from seeing the world through solely empirical evidence, which might limit the scope of understanding to what is directly observable, to a broader, more integrated view that encompasses both the tangible and the transcendent. It's a reminder that the pursuit of knowledge can lead to diverse interpretations of the world around us and that for some, deeper scientific understanding can enhance, rather than diminish, spiritual belief. Molecular Biology, and scientific investigation into the microworld, have permitted me to become a more intellectually satisfied theist.

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