Perguntas ....

In the fascinating world of biology and materials science, the cell stands out as a remarkable entity—a complex molecular factory responsible for the processes that sustain life.  Robert M. Hazen, in his book "Science Matters," eloquently describes the cell as a chemical factory. Cells have specialized receptors, akin to loading docks, through which they take in materials from their environment. These materials are then processed through chemical reactions, guided by a central information system. As the work progresses, various cellular components act as assembly lines, ensuring that the cell functions harmoniously. Hazen highlights the role of proteins as supervisors and carbohydrates as the fuel supply for these chemical factories. Nucleic acids, specifically DNA and RNA, hold a special place in the cell. They carry the blueprint for the cell's chemical factories and serve as the vehicle for inheritance, passing on vital information from generation to generation. Hazen underscores the importance of carbohydrates, as they provide the energy required by the cell's chemical factories. These carbohydrates, composed of sugars, act as the building blocks for fueling the intricate processes within the cell. The cell, much like any factory, comprises essential systems. It requires a front office where information is stored and instructions are issued, as well as a physical structure with walls and partitions where the actual work takes place. The cell's production system consists of machines that produce finished goods, interconnected by a transportation network that moves raw materials and products. Additionally, an energy plant powers the cellular machinery. The cell's structure is akin to that of a factory, with walls, partitions, and loading docks defining its boundaries and facilitating its functions. These structures allow for efficient organization and coordination within the cell. In Hazen's exploration, he emphasizes that all living organisms are composed of one or more cells, each containing numerous structures and organelles. These tiny chemical factories work in unison to support the overall functioning of the organism. The significance of DNA becomes apparent when considering its double helix structure. The sequence of bases along the DNA molecule holds the genetic code—a repository of information that allows cells to reproduce and operate their chemical factories. This code encompasses the unique characteristics and traits that make individuals distinct. Now, let's turn to the words of Ben L. Feringa, who discusses the miniaturization of complex physical and chemical systems in contemporary materials science. Feringa introduces the concept of artificial molecular machines (AMMs), inspired by proteins or multi-protein complexes found in biology. These AMMs can transform physical or chemical stimuli into directed motion, akin to the macroscopic machines we encounter in our daily lives. Examples of biological molecular machines (BMMs) include ATP synthase, ribosomes, and myosin, which are structurally more intricate than any artificial molecular machine developed thus far. BMMs play crucial roles within living systems, working in synchronization with other machines and being driven by chemical fuels or electrochemical gradients. Feringa notes that a cell can be seen as a complex molecular factory. Within this factory, various components are assembled, transformed, transported, and disassembled. Self-organization, cooperativity, and synchronization amplify the dynamics of these processes at the molecular level, resulting in the living, moving organisms observed at the macroscopic scale. Similar organizational principles can be found in macroscopic factories, irrespective of their size, emphasizing the importance of cooperation and synchronization in the design of dynamic systems. However, Feringa also acknowledges the differences between biological systems and man-made factories. BMMs and their assemblies possess exceptional versatility and selectivity, producing complex molecules currently unachievable by human-made systems. The intricacies of these biological systems go beyond our current understanding, posing challenges for replicating their capabilities. Moving on to the concept of von Neumann machines, named after the distinguished scientist John von Neumann, who extensively studied self-replicating machines. Von Neumann proposed the idea of a universal constructor—a machine capable of replicating itself. For a machine or factory to replicate itself, it must possess a description of its own structure. However, this description must come from an external source, as the machine itself cannot be the conscious agent capable of observing and describing itself. This notion raises questions about the origin of biological information and the challenges it presents to naturalistic explanations. In his work, M. Sipper emphasizes the importance of understanding the fundamental information-processing principles and algorithms involved in self-replication, regardless of their physical realization. Replicators, often referred to as von Neumann machines, require foresight and conscious agency to construct functional interlocked complex systems. Without such foresight, the parts may remain non-assembled or assemble into nonfunctional chaotic states. R. A. Freitas further elaborates on von Neumann's architecture for machine replication, which consists of a constructor, a blueprint copier, a controller, and explicit blueprints describing how to build these components. This architecture exemplifies the complexity and foresight required for self-replicating systems. The cell represents an awe-inspiring molecular factory, where various components work in harmony to sustain life. The self-replicating capabilities of cells pose significant challenges for human-made factories. Understanding the principles behind self-replication, the role of information, and the necessity for foresight are crucial steps toward unraveling the mysteries of life and constructing autonomous self-replicating systems.

The concept of von Neumann's self-replicating machine has found intriguing parallels in the realm of molecular biology. Researchers have drawn connections between von Neumann's components and the mechanisms involved in cellular reproduction. For instance, ribosomes and supporting cellular mechanisms represent von Neumann's component "A," DNA polymerase enzymes represent component "B," and repressor and derepressor molecules, along with associated expression-control machinery, represent component "C." The genetic material DNA, which carries the organism's genome, corresponds to component "φ(A + B + C)." It is important to note that cells possess additional complexities beyond von Neumann's model. Interestingly, von Neumann's schema also aligns with the dual use of information observed in DNA. In his model, the stored information serves as instructions for constructing a new universal constructor, which is then copied unmodified to be attached to the offspring constructor for subsequent replication. This mirrors the genetic mechanisms of transcription (copying) and translation (interpretation) found in biological life. While von Neumann's self-replicating universal constructor appears complex, researchers have made efforts to simplify and implement it. Over the years, various researchers have worked on simulations or implementations of von Neumann's model, employing different approaches and technologies. However, due to the immense complexity and scale of the constructor, no complete realization of the model has been achieved. Even computer simulations fall short when it comes to demonstrating self-replication, primarily due to the large amount of tape (genome) required to describe the constructor. The challenges faced in constructing von Neumann's self-replicating machine, as highlighted by researchers like R. A. Freitas, include the vast number of constituent parts and the significant amount of information involved. The sheer complexity and effort required for designing and building macroscale kinematic replicators have limited progress in this area. This brings us to a thought-provoking comment. Despite the intelligence of humans and their technological prowess, the construction of a fully functioning von Neumann self-replicating machine has remained elusive due to its immense complexity. Yet, proponents of abiogenesis argue that the emergence of self-replicating cells, containing millions of bits of information, occurred through random processes without intelligent guidance. The stark contrast between the challenges faced by human designers and the presumed spontaneous emergence of self-replicating cells raises profound questions. It challenges our understanding of the origin of life and the remarkable complexities that arose from what would appear to be unguided, non-intelligent means. The quest to realize von Neumann's self-replicating machine remains an ongoing challenge. The intricate nature of cellular reproduction and the complexities involved highlight the incredible feat achieved by living organisms. The dichotomy between human ingenuity and the presumed unguided processes of abiogenesis underscores the profound mysteries surrounding the origin of life and the intricate mechanisms at play in the natural world.

A Self-Replicating Box

Let's embark on an imaginative journey and explore the challenges of designing a self-replicating cardboard box. Imagine placing an empty cardboard box, let's call it Box A, on the floor. To the right of it, we'll construct Box B, which houses a box-building factory inside it. Now, let's ponder the requirements for Box B to build an empty box. In our quest for self-replication, we assume that Box B needs some metal parts to cut and fold the cardboard, along with a motor and battery to power these operations. To be truly self-replicating like living things, it would have to venture out and obtain its own cardboard, perhaps equipped with wheels and an axe to cut down trees and a miniature sawmill to transform wood into cardboard. However, for the sake of simplicity, let's assume humans are around to provide the cardboard. But alas, Box B is not a self-replicating machine—it can only produce an empty Box A. So, to the right of this box, let's construct Box C. This intricate creation contains a fully automated factory capable of producing Box B. Now things start to get more complicated because Box C needs to manufacture the metal parts for Box B's machinery, as well as its motor and battery. It must assemble these parts in the factory inside Box B. In reality, it would require mining ore, smelting it, and obtaining raw materials, but for the sake of generosity, we'll assume all necessary resources are provided. Yet, Box C still falls short of being a self-replicating machine—it can only produce the simpler Box B. Undeterred, we press on and create Box D, complete with a fully automated factory capable of building Box C with its Box B factory. The complexity grows exponentially, and doubts start to creep in. Is it even theoretically possible to construct a truly self-replicating machine? As we keep adding boxes to the right, each housing a fully automated factory that can produce the box to its left, the complexity seems to spiral out of control. It appears that the more technology we introduce to bring us closer to the goal of reproduction, the more intricate the machine becomes. It's as if the goalposts keep shifting, and we find ourselves grappling with a more complex machine that needs to reproduce. Yet, all around us, in the living world, we see organisms that achieve this remarkable feat effortlessly. If we continue this progression, adding more boxes to the right, each with its own fully automated factory capable of producing the box to its left, we may wonder if it's possible for these boxes to eventually converge and give birth to a self-replicating Box Z. However, it remains a perplexing challenge, as envisioning how such convergence could occur proves elusive. The quest for a truly self-replicating machine is fraught with complexity. The intricate nature of living organisms and their ability to reproduce baffle us, pushing the boundaries of our understanding. The exponential growth in complexity, as we approach self-replication, reminds us of the marvels of the natural world, where life effortlessly creates new life.

The self-assembly of a factory starting with unorganized raw materials has never been observed

When we delve into the assembly of complex structures from raw materials, we must consider the fundamental laws of physics and chemistry that govern the behavior of these materials. Currently, the spontaneous self-assembly of intricate factories or structures from raw materials without any external intervention remains poorly documented and understood. In fact, it has never been demonstrated to be possible. The spontaneous assembly of a complex factory or structure through unguided means, without any external intelligence or intervention, has not been observed in scientific experiments or natural processes. While we do observe self-assembly and self-organization in various systems, it's important to recognize that these processes typically occur within specific contexts and conditions. For instance, in living organisms, we witness self-assembly processes in structures such as cellular membranes, protein complexes, and DNA organization into chromosomes. However, these processes rely on preexisting biological components, like proteins, lipids, and nucleic acids, which possess specific molecular interactions and are governed by biological mechanisms. The assembly and organization of these structures are guided by genetic information and cellular processes, involving intricate networks of chemical reactions and molecular interactions. In the realm of nanotechnology, scientists have made advancements in developing self-assembling systems at the molecular scale. However, these systems often involve specially designed molecules or nanoparticles with specific properties or functional groups. Through these properties, the components can interact and align in a way that facilitates self-assembly. Specific environmental conditions, such as solvent or temperature ranges, may be required to trigger the self-assembly process. Therefore, while self-organization is observed, it still relies on the careful design and manipulation of the components and their surrounding environment. In synthetic systems, researchers have explored self-assembly processes using engineered components. For instance, in the field of robotics, small robotic units have been created that can autonomously assemble into larger structures or perform collective tasks. However, these systems typically involve programmed interactions and behaviors. The individual units may have sensors, communication capabilities, or predefined rules that govern their assembly and coordination. They are designed with specific capabilities and functionalities to enable self-assembly under controlled conditions. Here, it's important to note the keywords: "guided by genetic information" and "programmed interactions." The generation of information and programmed interactions typically requires the involvement of a programmer or an intelligent agent. In the context of self-assembly and self-organization, the patterns, behaviors, and interactions observed in complex systems often arise from the information encoded within the system or introduced by an external intelligence. In biological systems, genetic information encoded in DNA serves as the blueprint for the assembly and functioning of organisms. It's crucial to recognize that discussions of evolutionary processes assume the existence of life and the subsequent diversification and adaptation of organisms over time. The presence of genetic information implies the involvement of an intelligent designer or programmer at some point in the system's history. Similarly, in synthetic systems or engineered materials, a programmer or designer imparts specific instructions, rules, or algorithms to guide the self-assembly or behavior of the components. Information, in the form of genetic code, algorithms, or predefined rules, plays a pivotal role in shaping the behavior and outcomes of self-assembly and self-organization processes. Without the input of intelligent design or programming, the emergence of complex structures or organized behaviors is highly unlikely, if not outright impossible, to occur spontaneously. It's essential to clarify that the presence of information or programmed interactions does necessarily imply the involvement of a conscious or deliberate programmer. It highlights the role of information instantiated by an intelligent designer and the impact it has on shaping the behavior and outcomes of self-assembly and self-organization processes.

The Last Universal Common Ancestor (LUCA): What was its nature?

In our quest to understand our origins, we must first grapple with the enigma of the starting point—the origin of life itself. Speculation abounds regarding the first life form and what it might have looked like. Was it a Last Universal Common Ancestor (LUCA), or did life emerge through multiple independent origins? In my previous book, "On the Origin of Life and Virus World by means of an Intelligent Designer," I dedicated an entire chapter to unraveling this complex question. And let me tell you, it's no easy task! The concept of the last universal common ancestor represents the primordial cellular organism from which all diversified life supposedly originated. It symbolizes the point at which Bacteria, Archaea, and Eukaryotes began to branch off into distinct lineages. However, delving into the nature of this ancestor and its characteristics proves to be a perplexing endeavor. Renowned biologist Carl R. Woese emphasized the fundamental question posed by the universal tree of life—the nature of the entity represented by its root, the source from which all extant life springs forth. Traditionally, biologists have assumed that this root organism was equivalent metabolically and in terms of information processing to a modern cell. In other words, they envisioned it as a prototypical cell of sorts. Yet, Woese challenges this assumption as not scientifically acceptable. Woese argued that it is crucial to entertain the possibility that cellular evolution was still underway during the period encompassed by the universal phylogenetic tree. In fact, there is evidence suggesting that the basic organization of the cell had not yet completed its evolution at the stage represented by the root of the universal tree. Key cellular information processing systems provide valuable insights into this matter. Translation, for instance, had reached a high level of development, with elements like rRNAs, tRNAs, and large elongation factors resembling their modern forms. However, certain differences between bacterial, archaeal, and eukaryotic versions of key translational proteins indicate idiosyncratic modifications that occurred in each major cell type. The exact reasons behind these differences, known as the canonical pattern, remain a major unanswered question. While transcription, the process of copying DNA into RNA, was supposedly less developed at the root of the universal tree, certain components of DNA-dependent RNA polymerase exhibit universal distribution, pointing to their ancient origins. The intricate puzzle of cellular design and organization has confounded scientists, even with the advent of cataloging and characterizing the various parts of cellular mechanisms. The reductionist perspective of molecular biology, which seeks to understand cells by dissecting their components, falls short when it comes to comprehending the overall design and functioning of the cell as a whole. The problem of cellular design transcends static, temporal, and localized boundaries. It defies the rigid confines of reductionism and requires a broader perspective. As we continue to explore the mysteries of life's origins and the complexities of cellular design, we must be prepared for unexpected twists and turns along the way. The journey to uncovering the secrets of the first life form is filled with intrigue and challenges, captivating our minds as we strive to unlock the remarkable story of our existence.

The Dilemma of Cellular Evolution. 

The evolution of cells presents a fascinating conundrum that requires careful consideration. The emergence of unprecedented novelty and variety, which are essential for evolving cell designs, cannot be easily explained by familiar evolutionary dynamics. It necessitates a collective evolution where diverse cell designs evolve simultaneously and share their innovations with one another. This leads us to two important conclusions: Firstly, horizontal gene transfer (HGT) and a genetic lingua franca, a common language of genetic information, become crucial for the origin of cell designs. Through HGT, genetic material can be exchanged between different organisms, enabling the sharing of novel traits and innovations. Secondly, a cell design cannot originate in isolation. It must be intertwined with other cell designs. This departure from the concept of universal common ancestry towards polyphyly suggests that at the beginning, there existed a population of diverse cell designs, each distinct from one another. These cells began interacting and exchanging genetic material through HGT. However, there is an inherent contradiction in this situation. While HGT allows for the sharing of novelty, it also acts as a homogenizing force that reduces diversity. So, the question shifts from why major cell designs are so similar to why they are so different. This apparent contradiction can be resolved by considering that the highly diverse cell designs we observe today are the result of a common design, with each design starting under significantly different conditions. Furthermore, when examining the hypothesis of the last universal cellular ancestor (LUCA), it is important to note that LUCA is proposed as a population of organisms from which all cellular life on Earth descends. This raises questions about the origin of this population and the process of self-replication that gives rise to offspring. While some theories suggest that self-replication initially started in the form of an RNA self-replicator, these ideas are met with challenges and uncertainties. The ability to copy molecules that encode genetic information is indeed crucial for the origin of life. However, the assertion that a self-replicating RNA molecule, without evidence of its existence, led to the complexity of a living cell is a matter of debate. Duplicating a molecule multiple times does not replicate the intricacy and functionality of a living cell. A cell is a highly complex system driven by software-driven chemical and physical processes, utilizing languages, codes, and intricate management of materials, to ensure its survival and reproduction. The metaphor of a jack-of-all-trades RNA molecule catalyzing the formation of cellular scaffolds has been appealing to some, but it faces challenges such as the lack of templates for RNA polymerization in prebiotic environments and the instability of RNA under certain conditions. These factors complicate the scenario and require further investigation and understanding. The origin of cells and the diversification of life remain captivating and ongoing areas of scientific exploration. While we continue to uncover pieces of the puzzle, the ultimate answers to these profound questions are still unfolding, waiting to be discovered.

The concept of the RNA World, which suggests that an RNA-based system was the precursor to life, has been a topic of ongoing debate and research for several decades. While no living system completely based on RNA has been observed, the hypothesis continues to be discussed and studied within the origins of life research community. It is recognized as one of the leading theories to shed light on the origins of life and provide insight into the foundations of contemporary biology. There are strong proponents and opponents of the RNA World hypothesis, which has created a contentious atmosphere within the scientific community. Although a self-replicating RNA molecule has not yet been synthesized or discovered, there is ( justified?) optimism that it will eventually emerge, and researchers continue to explore its possibilities. The reconstruction of the genome and phenotype of the last universal common ancestor (LUCA) poses a significant challenge in evolutionary biology. It is well-established that all life forms are associated with viruses and mobile genetic elements, indicating that LUCA hosted viruses as well. The coevolution of viruses and hosts has played a crucial role in the history of life. Viruses are characterized by their proteinaceous capsid, which encases the viral genome. Although capsid proteins are encoded by diverse viruses, they have emerged independently on multiple occasions. Analysis of major virion proteins suggests at least 20 unrelated varieties of capsid proteins. The polyphyletic nature of viruses is a notable aspect of their origin. Unlike cellular life, which had supposedly, according to the evolutionary narrative, a single common origin, viruses have undisputedly multiple origins. They do not share characteristics with cells, and no single gene is shared by all viruses or viral lineages. Additionally, viruses lack a structure derived from a common ancestor, unlike cells that inherit membranes from previous cells during cell division. Considering the polyphyletic nature of viruses and the simultaneous origin of diverse cell designs, it becomes evident that life emerged independently multiple times. This challenges the hypothesis of universal common ancestry and supports the notion of separate origins for different life forms and viruses. The exploration of life's origins and the intricate relationship between viruses and cellular life continue to captivate researchers. While the full understanding of these complex processes is still evolving, the evidence points toward a diverse and multi-faceted history that involves multiple origins of life and viruses.

There is no scientific consensus about LUCA's nature

Life is a complex interplay of numerous chemical compounds that undergo intricate reactions within networks. These compounds and reactions are not unique to a specific organism but are found across all known forms of life. This discovery has led to the development of the concept of universal biochemistry and has allowed scientists to trace the roots of phylogenetic relationships back to a last universal common ancestor (LUCA). Universality in biochemistry arises from the shared properties and characteristics of the component compounds and reactions found in all living organisms. Efforts have been made to understand the genetic composition and biological features of LUCA through comparative genome analyses and biological reasoning. However, the complex evolutionary histories of most genes, with the exception of core components involved in translation and transcription, pose challenges to these inferences. Horizontal gene transfer and non-orthologous gene displacement have played significant roles in shaping the genetic makeup of organisms. Nonetheless, based on combined evidence, it is likely that LUCA was a prokaryote-like organism with substantial genomic and organizational complexity, resembling bacteria or archaea. The list of genes believed to be present in LUCA is extensive, showcasing the presence of essential components such as membranes, proteins, RNA, and DNA. LUCA possessed the remarkable abilities of replication, transcription, and translation, which are fundamental processes in biology. Additionally, it had an extensive metabolism driven by the energy obtained from ion gradients using ATP synthase.  Many of the inferred proteins in LUCA utilized FeS clusters and other transition-metal-ion-based co-factors, highlighting the intricate biochemical processes involved. These findings shed light on the intricate and diverse nature of life's origins of cellular organisms. While there are still many unanswered questions, the study of LUCA provides valuable insights into the journey that has shaped the incredible diversity of life on Earth.

Life started complex

Life's origins were not marked by simplicity or primitiveness but rather by complexity and sophistication. Even the earliest known cells, including the supposed last universal common ancestor (LUCA), exhibited functional and genetic complexity. These cells were far from primitive structures. In fact, the simplest cells available for study possess a remarkable teleonomic apparatus, a system so powerful and finely tuned that no remnants of truly primitive structures can be discerned. The LUCA, as a complex entity, had representatives in various essential functional niches that exist in organisms today. Its structure was already recognizable as a cell, complete with the machinery for replication, transcription, and translation, a fully-fledged membrane, a sophisticated cell-division apparatus, and even central metabolic pathways. This implies that life did not emerge as a simple or primitive organism but rather as a fully functional and complex entity capable of crucial processes such as metabolism, genetic replication, and maintaining a distinct boundary between the cell and its environment. As J. Monod astutely observed, the simplest cells known to us, such as bacterial cells, possess an overall chemical plan that is shared by all living beings. They employ basically, besides some small variations,  the same genetic code and translation mechanism as even human cells. This highlights the absence of truly primitive structures in these cells. Their remarkable similarity to more complex organisms suggests a kind of stasis or constancy in their chemical organization, even when considering the fossil record. The genetic and functional complexity of the LUCA is further emphasized by J.A.G. Ranea, who notes that the primitive community that constituted this entity already exhibited a high degree of complexity. The LUCA encompassed representatives in nearly all essential functional niches found in present-day organisms. Its metabolic complexity was comparable to the intricacy of translation, with a diverse range of domains involved. These insights challenge the notion that life originated as a simple or primitive form. Instead, life emerged on the scene as a complex and highly developed entity, laying the foundation for the astonishing diversity and complexity of organisms we see today. Exploring the origins of life unveils a story of sophistication, interwoven with intricate molecular mechanisms and cellular processes that continue to captivate scientists and deepen our understanding of the remarkable journey that life has undertaken.

New evidence has shattered the notion of a primitive Last Universal Common Ancestor (LUCA) and unveiled a startling revelation—the LUCA was a sophisticated organism with a complex structure that could be readily recognized as a cell. This groundbreaking study, published in the esteemed journal Biology Direct, provides support for the idea that the LUCA may have even surpassed the simplicity of the most basic organisms alive today. The implications of this discovery are truly mind-boggling. Renowned entomology professor James Whitfield, a co-author of the study, expressed his astonishment at the findings. It appears that the LUCA was more intricate and advanced than anyone could have imagined. Far from being a primitive entity, it possessed a complexity that rivaled, if not surpassed, that of modern organisms. Life, it seems, was born with a penchant for complexity. Further bolstering this notion, G. Caetano-Anollés, a respected researcher, confirms that life emerged in a state of complexity, and the LUCA proudly displayed this inheritance. Recent comparative genomic studies provide support for this model, suggesting that the ancestral organism shared striking similarities with present-day organisms in terms of gene content. The LUCA was not a humble beginning; it was a grand and awe-inspiring start to the tapestry of life. E.V. Koonin, a prominent figure in the field of evolutionary biology, concurs that all known cells exhibit intricate organization and complexity. Even the simplest known cellular life forms, such as bacterial and archaeal parasites and symbionts, possess several hundred genes responsible for vital components such as fully functional membranes, replication and transcription machinery, complex cell-division apparatuses, and central metabolic pathways. These organisms, born from the degradation of more complex predecessors, demonstrate that even in their simplified forms, they are far from simple. J.C. Xavier, in contemplating the complexity of cells, declares them to be the most elaborate structures in the micrometer size range that humanity has come to know. Defining a minimal cell proves to be a semiabstract endeavor, but it encompasses the presence of metabolism, genetic replication or information processing mechanisms, a boundary (or membrane) that demarcates the cell from its surroundings, and the ability to evolve—a universal attribute among all known living cells. The coordination between boundary fission and genetic template segregation adds an additional layer of complexity to this definition. Adding to the growing body of evidence, F. El Baidouri's research sheds new light on the LUCA. Utilizing robust phylogenetic trees, their findings indicate that the last universal common ancestor of all living organisms was likely an intricately complex cell possessing at least 22 phenotypic traits. These traits were on par with, if not more intricate than, those observed in many modern bacteria and archaea. This challenges the prevailing evolutionary model that suggests complexity gradually increased over time in prokaryotes, revealing a much richer and complex origin of life. These extraordinary discoveries reshape our understanding of the origin of life. Life did not begin with simplicity and gradually evolve into complexity; instead, it emerged in a state of astonishing complexity right from the start. The LUCA, as a sophisticated and intricate entity, set the stage for the incredible diversity and intricacy of life that we witness today. The story of life's origins is a tale of boundless complexity, where cells emerge as marvels of ingenuity, pushing the boundaries of what we thought was possible.

Defining the LUCA: What might be a Cell’s minimal requirement of parts?

In the quest to uncover the true nature of the first life form, scientists find themselves immersed in a sea of speculation and confusion. Patrick Forterre, in a candid admission, acknowledged that there are no proteins or groups of proteins that can definitively unravel the exact path of life's origin. Despite this uncertainty, it is not futile to trace a hypothetical organism's features and establish a border between speculation and insight. Even if we can only conjure a hypothetical organism, it provides us with valuable insights into the complexity involved and brings us closer to understanding the mechanisms at play—perhaps even the role of intelligence in the creation of life's first forms. The availability of genomic and proteomic data across the Tree of Life has allowed researchers to infer features of the genome and proteome of the Last Universal Common Ancestor (LUCA). However, the resulting studies do not uniformly agree with one another, painting a picture of an enigmatic LUCA genome. Yet, amidst this divergence, a consensus emerges—intricate genome encoding functions related to protein synthesis, amino acid metabolism, nucleotide metabolism, and the utilization of common nucleotide-derived organic cofactors. The ancient translation process, essential for protein synthesis, appears to predate the LUCA, hinting at its significance in the origins of life. William Martin and colleagues from the University of Düsseldorf's Institute of Molecular Evolution shed light on the metabolism of cells and its reflection on their origins. They identified an ancient core of autotrophic metabolism, encompassing 404 reactions responsible for the conversion of H2, CO2, and ammonia into amino acids, nucleic acid monomers, and the necessary cofactors. Water emerges as a prevalent reactant, suggesting an aqueous origin for this core, while a plethora of reactions involving the hydrolysis of high-energy phosphate bonds implies the presence of a non-enzymatic and highly exergonic chemical process capable of continuously synthesizing activated phosphate bonds. The dominance of CO2 and the abundance of redox reactions utilizing NADH and NADPH indicate a highly reducing environment for the core's formation. These insights point to a far-from-equilibrium and reducing aqueous environment as the birthplace of this autotrophic core. Delving into the realm of minimalism, John I. Glass highlights Mycoplasma genitalium, boasting the smallest genome of any organism capable of being grown in pure culture. This minimalistic bacterium offers valuable insights into the minimal set of genes required for bacterial life. By studying its genome, we gain a glimpse into the essential components necessary to sustain life at its most fundamental level. As the search for the first life form continues, these scientific endeavors bring us closer to unraveling the mysteries of life's origins. Though the exact nature of the first life form remains elusive, the collective insights gleaned from diverse fields of study and the intricate complexities discovered within even the simplest organisms challenge our preconceptions and fuel our curiosity. The story of life's origin is an enigmatic tale, unfolding with each new discovery, offering glimpses into the grandeur and intricacy of the tapestry we call life.



Metabolic pathways and substrate transport mechanisms encoded by M. genitalium. Metabolic products are colored red, and mycoplasma proteins are black. White letters on black boxes mark nonessential functions or proteins based on our current gene disruption study. Question marks denote enzymes or transporters not identified that would be necessary to complete pathways, and those missing enzyme and transporter names are colored green. Transporters are colored according to their substrates: yellow, cations; green, anions and amino acids; orange, carbohydrates; purple, multidrug and metabolic end product efflux. The arrows indicate the predicted direction of substrate transport. The ABC type transporters are drawn as follows: rectangle, substrate-binding protein; diamonds, membrane-spanning permeases; circles, ATP-binding subunits.

In the quest to unravel the mysteries of life's origins, researchers have come face to face with two perplexing challenges that the Last Universal Common Ancestor (LUCA) likely encountered. These challenges revolve around the source of amino acids and purine/pyrimidine bases or nucleosides—the building blocks of life as we know it. These compounds, crucial for the intricate workings of living organisms, require complex pathways for their synthesis.  So, what does this mean for the LUCA? It appears that rather than being responsible for the creation of amino acids and nitrogenous bases from scratch, the LUCA may have relied on a primitive soup—a tantalizing concoction of pre-existing amino acids and nucleosides. Picture it as a cosmic cauldron simmering with the essential ingredients needed to kickstart the journey of life. Instead of brewing up these intricate compounds internally, the LUCA potentially tapped into this prebiotic broth, harnessing its bountiful resources to support its existence. This perspective sparks vivid images of a primordial kitchen, with the LUCA donning its metaphorical chef's hat, carefully selecting and incorporating the ready-made ingredients from the primitive soup. With these vital building blocks at its disposal, the LUCA could focus its energy on other important tasks, such as honing its genetic machinery, perfecting its metabolism, and fine-tuning its intricate cellular structures. In this tantalizing narrative, the LUCA emerges as a masterful alchemist, ingeniously adapting and utilizing the resources available to it in the ancient environment. It cleverly embraced the richness of its surroundings, leveraging the molecular feast laid out before it, and setting the stage for the astonishing diversity of life that would follow. So, as we journey through the annals of life's history, we uncover the possibility that the LUCA was not solely responsible for the creation of the fundamental components of life. Instead, it embraced the bounty of a primitive soup, a cosmic pantry of organic molecules, to kickstart the grand symphony of existence. With each discovery, we inch closer to understanding the epic tale of life's origins, appreciating the LUCA's resourcefulness and the creative interplay between the primordial environment and the emergence of life's intricate tapestry.

From a LUCA to the last bacterial common ancestor (LBCA)

In the vast tapestry of microbial life, there exists a captivating figure known as LBCA—the Last Bacterial Common Ancestor. This enigmatic being holds the key to understanding the origins of modern bacteria, yet its true characteristics and identity remain shrouded in mystery. Recent investigations have shed some light on the nature of LBCA, hinting at its potential resemblance to a monoderm bacterium—a bacterial cell sporting a single membrane, perhaps adorned with a thick layer of peptidoglycan. But let's not get ahead of ourselves; we're about to embark on a fascinating journey through the realm of genomic inference and ancestral reconstructions. One particular cluster of interest that has captured the attention of researchers is the 17-gene dcw cluster. This cluster, found in various bacterial species, plays a pivotal role in cell division and the construction of the cell wall—a fortress that safeguards the bacterium's delicate inner workings. In the intricate dance of bacterial replication, these genes orchestrate the assembly and contraction of the cell wall and septum, ultimately leading to the birth of two new offspring. Delving deeper into the ancestral tales, phylogenomic inferences have revealed that the Clostridia—a class of Firmicutes—bear a striking resemblance to the lineage that first branched off from the fabled LBCA. Their genomes, displaying the least divergence from the predicted LBCA, offer tantalizing clues about our bacterial ancestor's past. It is within the Clostridia that we may find glimpses of the ancestral traits that echo through the corridors of time. But let us not forget the concept of a minimal cell—a theoretical construct comprising the bare essentials needed for bacterial survival. This hypothetical entity relies on a minimal gene set composed of around 206 genes, encompassing the crucial functions of DNA replication, transcription, translation, protein processing, and metabolic pathways necessary for energy production and synthesis of vital molecules. It is a delicate balancing act of genes working in harmony to sustain life's intricate dance. While some amino acids and cofactors may be obtained from the environment, the minimal cell may require specialized biosynthetic pathways to ensure its survival and growth. The availability and proportions of amino acids in the environment may not always align with the cell's specific needs, prompting the need for internal synthesis. As we weave together the threads of research and speculation, a portrait of LBCA begins to take shape. Its characteristics remain elusive, and the cell wall architecture remains a mystery. Fossils of bacterial ancestors outside of Cyanobacteria are scarce, leaving us yearning for more tangible evidence. However, the diligent efforts of scientists, armed with ancestral state reconstructions and phylogenetic trees, offer tantalizing glimpses into LBCA's world. In their quest for answers, researchers have traced the footsteps of Clostridium species, with the infamous Clostridium difficile taking center stage at the root of the phylogenetic tree. Its genome, a circular marvel of 4,290,252 base pairs, holds clues to the intricate web connecting us to our ancient bacterial ancestors. As we navigate the fascinating realms of microbial ancestry, we find ourselves entangled in a web of scientific exploration and speculation. The quest to unravel the secrets of LBCA continues, painting a captivating portrait of our bacterial forebear. Though the complete picture remains elusive, each discovery brings us closer to understanding the intricate tapestry of life's origins. And as we delve deeper into the mysteries of the microbial world, we may one day unravel the enigma of LBCA, shedding light on the ancient whispers that shaped the very essence of bacterial life.

Taking Rosario Gil's model organism as the basis for our forthcoming investigation

In the vast realm of bacterial life, there exists a fascinating concept—a minimal gene set that could sustain the vital functions of a hypothetical simplest bacterial cell. Rosario Gil, with her diligent analysis of computational and experimental strategies, offers us a tantalizing glimpse into this world of minimalism. Imagine a bacterial cell, stripped down to its core essentials—a lean and efficient machine, focused on the necessities of life. Within this minimal gene set, we find a symphony of molecular machinery working in harmony to sustain the cellular dance. At the heart of this minimalist cell lies a virtually complete DNA replication machinery, comprising a nucleoid DNA binding protein, SSB, DNA helicase, primase, gyrase, polymerase III, and ligase. These essential players ensure the faithful duplication of the bacterial genome, with the DNA gyrase taking on the arduous task of both replication and chromosome segregation. To ensure the integrity of the genetic blueprint, a rudimentary system for DNA repair is present—a humble team consisting of one endonuclease, one exonuclease, and a uracyl-DNA glycosylase. They stand as sentinels, guarding the cell's precious genetic material. Transcription, the process of transcribing DNA into RNA, is facilitated by virtually complete transcriptional machinery. Three subunits of the RNA polymerase, a sigma factor, an RNA helicase, and four transcriptional factors harmoniously orchestrate the symphony of gene expression. Surprisingly, the minimal gene set does not include any transcriptional regulators, suggesting that regulation of transcription may not be essential in bacteria with reduced genomes. The translational system, responsible for decoding genetic information into proteins, is nearly complete. With the 20 aminoacyl-tRNA synthases, a methionyl-tRNA formyltransferase, enzymes for tRNA maturation and modification, ribosomal proteins, translation factors, and RNases involved in RNA degradation, this cellular orchestra ensures the smooth production of proteins—the building blocks of life. Protein processing, folding, secretion, and degradation are handled by a team of dedicated players. Posttranslational modification, molecular chaperones (GroEL/S and DnaK/DnaJ/GrpE), translocase machinery, endopeptidases, and proteases work in unison to ensure proper protein function and disposal when necessary. Cell division, the process of creating new daughter cells, is driven solely by FtsZ—a protein responsible for orchestrating the division process. In this minimal cell, the need for a cell wall might be dispensable, as the protected environment might not require the structural support typically provided by the cell wall. As for substrate transport, the picture remains incomplete. While cation and ABC transporters seem to be present in all bacteria, further analysis is needed to define a more comprehensive set of transporters. Energetic metabolism in this minimalist cell relies on ATP synthesis through glycolytic substrate-level phosphorylation—a process that generates energy for cellular activities. The pentose pathway, responsible for the synthesis of pentoses (PRPP) from trioses or hexoses, is represented by three essential enzymes, ensuring the cell's ability to produce necessary molecules. Surprisingly, this minimalist cell does not possess biosynthetic pathways for amino acids, as it relies on the assumption that they can be readily obtained from the environment. Similarly, lipid biosynthesis is reduced to the synthesis of phosphatidylethanolamine, utilizing dihydroxyacetone phosphate and activated fatty acids provided by the environment. When it comes to nucleotide biosynthesis, this minimalist cell follows the salvage pathways, utilizing PRPP and free bases obtained from the environment—adenine, guanine, and uracil. As for cofactors and vitamins, the minimalist cell is resourceful, relying on the environment to provide most precursors. It performs only the steps necessary for the synthesis of essential coenzymes—tetrahydrofolate, NAD+, flavin adenine dinucleotide, thiamine diphosphate, pyridoxal phosphate, and CoA. In this captivating world of minimalism, Rosario Gil's proposed minimal gene set of 206 genes paints a vivid picture of a bacterial cell pared down to its essentials. It showcases the intricate dance of molecular players, each fulfilling a vital role in the grand symphony of life. And while this minimalist cell may appear modest, it stands as a testament to the ingenuity and resourcefulness of bacterial life, adapting to its environment and thriving with the bare essentials.

In the enchanting tapestry of life's origins, we come across intriguing questions about the complexities involved in the transition from non-living matter to the intricate web of living organisms. Indeed, the journey from abiotic synthesis to the emergence of LUCA, the Last Universal Common Ancestor, raises thought-provoking mysteries. One aspect that captivates our attention is the import and transport mechanisms that LUCA would have required to acquire essential nucleotides and amino acids. Imagine the need for intricate membrane import channel proteins capable of distinguishing and selecting the very building blocks that are the essence of life itself. It is a marvel to contemplate the precise molecular machinery that would have allowed LUCA to obtain these vital ingredients while discerning them from others that are not necessary for life's processes. As I delve into the depths of these questions in my book, "On the Origin of Life and Virus World by means of an Intelligent Designer," I highlight the challenges faced by origin of life researchers in demonstrating the possible abiotic routes to non-enzymatically synthesize the fundamental building blocks of life. Despite their tireless efforts, the synthesis of these essential molecules outside the realm of enzymatic processes remains elusive. However, even if we were to uncover the mechanisms for the abiotic synthesis of these building blocks, a significant gap still remains unexplained. The transition of LUCA from incorporating external nutrients to acquiring the complex metabolic and catabolic pathways necessary for the synthesis of nucleotides and amino acids presents a monumental challenge. Consider the remarkable example of Mycoplasma genitalium, heralded as the smallest self-replicating cell. This intriguing bacterium, however, thrives as a pathogen, an endosymbiont nestled within the body or cells of another organism, including humans. In this symbiotic relationship, M. genitalium imports many nutrients from its host organism. The host graciously provides the essential sustenance, relieving the bacterium from the need to possess genes for manufacturing such compounds itself. Consequently, M. genitalium does not require the same level of complexity in its biosynthesis pathways as a free-living bacterium. The availability of amino acids, the very building blocks of proteins, adds yet another layer of intrigue to the origins of life. In the seminal Miller-Urey experiment of 1953 and subsequent endeavors, a fascinating array of organic compounds, including amino acids, was synthesized. However, it is intriguing to note that eight out of the twenty amino acids vital to life were not produced in these experiments. The quest to unravel the enigma of amino acid availability on the early Earth continues to captivate scientific minds. As we navigate the vast landscapes of life's origins, it is essential to acknowledge the gaps in our understanding and the intriguing challenges that lie before us. The complex import and transport mechanisms of essential building blocks, the transition from external incorporation to self-sustenance, and the availability of vital nutrients on the early Earth all form part of the captivating narrative that unfolds. It is through exploring these mysteries, weaving together scientific inquiry and the quest for knowledge, that we embark on a thrilling journey into the origins of life itself.

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LUCAs information system

In the grand tapestry of life, the presence of DNA reigns supreme. It is an indisputable fact that DNA is an integral part of all known life forms on Earth. This wondrous molecule, with its double helix structure and intricate sequence of nucleotides, holds the key to life's development, function, and reproduction. While some speculate about the possibility of alternative forms of genetic material or information storage lurking in uncharted realms beyond our current understanding, we must tread cautiously. The argument that such alternatives may exist is, in fact, an argument from ignorance—a fallacy that emerges when someone asserts a claim solely based on the absence of evidence to the contrary. It is a treacherous path to follow, for it is far more prudent to base our claims on positive evidence rather than on the mere absence of evidence. Therefore, it is warranted, nay, essential to begin our exploration of life's origins with the presumption that DNA was present at its inception. Like an artist's brushstroke on a blank canvas, DNA emerged as the foundation upon which life's intricate masterpiece was painted. And just as an artist requires a palette of colors to bring their vision to life, so too did the primordial forces of existence orchestrate the biosynthesis pathways necessary to synthesize the deoxynucleotides—the monomeric building blocks of DNA. In the grand theater of life's origins, we find ourselves captivated by the symphony of DNA and its indispensable role. Let us embrace the beauty of this molecular marvel, celebrating its presence as we embark on a quest to unravel the secrets of life's beginnings. With each step forward, guided by the light of scientific inquiry and the thirst for knowledge, we inch closer to unlocking the mysteries woven into the very fabric of our existence.

The Central Dogma

In the realm of molecular marvels, we find ourselves in the presence of the grand maestro known as the Central Dogma—a term coined by the brilliant mind of Francis Crick, who, alongside the esteemed Rosalind Franklin, James Watson, and Maurice Wilkins, unraveled the enigmatic double-helix structure of DNA. Like a mystical blueprint of life, DNA holds within its elegant strands a treasure trove of information, a compendium of data that orchestrates the creation of every single protein that fuels the dance of existence. Behold, for DNA is the maestro that conducts the symphony of life. Without its guiding hand, the orchestra of proteins would fall silent, their harmonious melodies lost to the void. For you see, dear reader, no DNA means no proteins, and no proteins means no life. It is a delicate dance, an intricate interplay between the nucleic acids and the proteins they encode, a dance that brings forth the wonders of life itself. But let us not forget the humble RNA, the faithful companion to DNA. Though it may possess a limited coding capacity, it plays a crucial role in the grand production of life's symphony. However, it is a fickle partner, prone to instability, like a tempestuous artist whose artistry must be swiftly captured before it slips away. Yet, dear reader, let us not be limited by the constraints of mere molecules. For within the realm of epigenetics, a whole new dimension unfolds—a realm where epigenetic data, guided by the intricate languages of chromatin and modifications, weaves its ethereal threads. It adds an additional layer to the symphony, a subtle nuance that influences the expression of genes and the destiny of cells. In this grand tapestry of life, DNA stands as the unrivaled blueprint, the conductor of the orchestra, while RNA harmonizes with its delicate melodies. Together, they bring forth the very essence of life itself. So let us venture forth, dear reader, into the realm of the molecular maestros, where DNA's majestic double helix and the delicate dance of RNA await our exploration. With each revelation, we inch closer to unraveling the mysteries that lie within, captivated by the enchanting symphony that is life.


James Watson, left, with Francis Crick and their model of part of a DNA molecule SCIENCE PHOTO LIBRARY

DNA and RNA: The only possible information storage molecules?

In the colorful world of molecular possibilities, a daring question emerged from the minds of synthetic biologists in the 1980s: Could DNA and RNA be the sole custodians of the intricate dance of genetics? The stage was set for a grand exploration, a quest to uncover the hidden secrets of molecular structure and the potential for alternate genetic architectures. As the curtains opened, a new realm of possibilities beckoned. The Watson-Crick model, while magnificent in its elegance, left room for speculation. The phosphates that adorned the DNA backbone seemed to play no particular role in the realm of molecular recognition. Could it be, then, that the backbone itself could be transformed without disrupting the delicate dance of base pairing? The scientists embarked on a journey, delving into the realm of synthetic nucleic acids. A symphony of nearly 100 linkers was composed, each one seeking to replace the familiar 2'-deoxyribose sugar with a new melody. Yet, as the experiment unfolded, a startling realization emerged. The absence of the REPEATING CHARGE, that subtle electrical rhythm within the DNA backbone, led to a dissonance in the symphony of molecular recognition. The rule-based pairing, the very essence of genetic harmony, faltered in the absence of this repeating charge. Even the most successful attempts at uncharged analogues, like the polyamide-linked nucleic-acid analogues (PNA), faced their limitations. Beyond a certain length, typically around 15 or 20 building units, the delicate balance of rule-based duplex formation crumbled, like a delicate melody fading into silence. In other uncharged systems, the breakdown occurred even earlier, thwarting the hopes of unraveling the secrets of alternate genetic architectures. The revelations were profound. The repeating charge within the DNA backbone could no longer be dismissed as a mere inconvenience. It held a crucial role in the symphony of molecular recognition, a role intertwined with the very essence of genetics. The ribose backbone of RNA echoed a similar sentiment—it was not merely scaffolding, but an integral player in the dance of molecular recognition. And so, the tale of genetic architecture took an unexpected turn. The primacy of DNA and RNA, with their familiar backbones, remained unchallenged. The symphony of genetics required the precise arrangement of nucleobases harmonized by the electric dance of their charged backbones. The stage was set, and the grand performance of life continued, with DNA and RNA as the maestros of the genetic orchestra, their melodies resonating through the ages.

Lack of natural selection

In the colorful realm of prebiotic chemistry, the quest for the origin of nucleotides faced a daunting challenge. The early Earth, a chaotic playground of lifeless chemicals, offered no easy pathway for the emergence of these vital building blocks. Leslie Orgel, a keen observer, dubbed it "the Molecular Biologist's Dream," an elusive vision that seemed beyond reach. The problem lay in the tangled mess of chemical mixtures, where a diverse array of nucleotide variations danced in the chaos. Different sugar moieties, varied nucleobases, and a host of byproducts added to the complexity. There was no guiding hand of natural selection to shape and refine these molecular concoctions. It seemed as though chance and patchwork would be the architects of life's most fundamental molecules. Even renowned scientists like Szostak and his colleagues acknowledged the conundrum. They pondered the challenge of the RNA world, where a heterogeneous mix of oligonucleotides was expected to give rise to the relatively homogeneous RNAs needed for functional evolution. The puzzle was clear: How could such a motley crew of molecules transform into the elegant and precise RNAs essential for life's intricate dance? In 2020, the scientific stage witnessed a bold proposal, a daring suggestion that chimeras emerged from this molecular menagerie. Like mythical creatures from Greek legends, these patchwork molecules carried bits of both modern RNA and DNA, alongside defunct genetic molecules. They were monstrous hybrids, with the lion's roar of DNA, the eagle's flight of RNA, and the serpent's slither of other genetic variants. Could these chimeras be the first tentative steps toward the RNA and DNA we know today? Amidst the excitement, a crucial question remained. How did natural selection, that guiding force of evolution, shape the fate of these non-canonical nucleotides? What pressures propelled the separation and refinement, leading to the emergence of homogeneous RNAs and DNAs used in the dance of life? These questions beckoned, lost amidst the sea of technical jargon and complex theories. In the intricate tapestry of life's origins, the dance of molecules unfolded. The dreams of molecular biologists collided with the challenges posed by prebiotic chemistry. Yet, as the story continued, the quest for understanding pressed on. 

Fast decomposition rate

Adenine, that foundational component of life's genetic code, reveals its secrets under the scrutiny of heat. At a balmy 37°C, it surrenders its essence with a half-life of 80 years, slowly fading away like a forgotten melody. But crank up the heat to a scorching 100°C, and its vitality diminishes within a single year, a rapid unraveling that defies expectations. Guanine, uracil, and thymine join this thermodynamic tango, each showcasing their unique vulnerability. At 100°C, guanine succumbs to the passage of time in just 10 months, while uracil perseveres for a resilient 12 years. Thymine, that stoic sentinel, lingers on for 56 years, its strength defying the harshness of the elements. Yet, as we peer into the mysterious origins of life, a troubling realization emerges. In the tumultuous brew of prebiotic environments, nucleobases would face a formidable challenge. Their fragile existence, with half-lives ticking away, presents a conundrum. For nucleobases to gather and accumulate in the fabled "prebiotic soup," they must be synthesized at a rate that outpaces their inevitable decay. Alas, adenine and its companions seem trapped in a perpetual cycle of creation and destruction, their hopes of concentration dashed. A 2015 paper sheds light on this cosmic dance, highlighting the intricate interplay between nucleotide formation and stability. The temperature becomes the conductor, guiding the fate of these molecular entities. In the searing heat, nucleotides struggle to maintain their integrity, succumbing to hydrolysis within a few days to a few years. Yet, in the cool embrace of 5°C to 35°C, nucleotides find solace, surviving for millennia or even longer. However, in this chilly realm, their formation slows to a painstaking crawl, a testament to the patience required in the birth of these life-giving molecules. As we ponder the challenges faced by nucleotides, we encounter the enigmatic ribose. Its synthesis, a puzzle wrapped in complexity, finds its roots in the formose reaction. This intricate dance of molecules depends on the presence of a suitable inorganic catalyst, orchestrating a delicate symphony of chemical transformations. Ribose emerges as an intermediate among a myriad of compounds, sugars with varying carbon structures. And yet, the activation of phosphate, that key ingredient for energy-driven reactions, remains a mystery, a missing puzzle piece in the grand tapestry of life's beginnings. In this fascinating journey through time and chemistry, we grapple with the delicate balance of nucleobases, their struggle against decomposition, and the intricate pathways that lead to their formation. The mysteries remain, inviting us to unlock their secrets, to understand the miraculous alchemy that brought forth the fundamental molecules of life.

Extraterrestrial nucleobase sources

In a cosmic revelation that left scientists in awe, the enigmatic world of meteorites unveiled a stunning secret. Within the depths of carbonaceous meteorites, a treasure trove of nucleobases was discovered, shimmering like celestial gems. Guanine and adenine, those familiar guardians of life's genetic code, revealed their presence in extracts from the revered Murchison meteorite. But the surprises did not end there. Like a cosmic symphony playing out its harmonious notes, other pyrimidine nucleobases emerged from the meteorite's embrace. Cytosine, uracil, thymine, and their structural companions—such as isocytosine, imidazole-4-carboxylic acid, and 6-methyluracil—joined the celestial chorus. A wondrous diversity of nucleobases, both familiar and exotic, graced the cosmic stage. As scientists pondered this cosmic gift, a profound realization dawned. These meteoritic nucleobases, once fragments of distant celestial bodies, held the potential to be the building blocks of DNA and RNA on the early Earth. Nature herself had woven a cosmic tapestry, scattering the ingredients of life across the cosmos, waiting for their arrival on our humble planet. In the wake of this discovery, the implications reverberated through scientific circles. NASA, in echoing the profound findings, proclaimed that these genetic components were not only delivered but could have played a vital role in the emergence of life's instructional molecules on the ancient Earth. The cosmic dance of nucleobases had cast its spell, opening new avenues of understanding and marveling at the cosmic origins of life. Yet, even amidst the wonder and excitement, a puzzling truth emerged. The nucleobases crucial for life's intricate dance were not alone in their celestial journey. They were accompanied by their isomeric counterparts, intermingled in a cosmic blend. No prebiotic selection had occurred to carefully sort and concentrate the nucleobases relevant for life's grand performance. They were presented in a celestial smorgasbord, their relevance hidden amidst a sea of cosmic diversity. In this cosmic tapestry, the mingling of nucleobases became a conundrum, a challenge that begged for an explanation. How did life's symphony emerge from this cosmic mixture? The answers remained elusive, drawing scientists into a profound quest for understanding. But as they delved deeper into the mysteries of the universe, they found that sometimes, amidst chaos and cosmic happenstance, the seeds of life find their way, unfurling into the majestic complexity that defines our existence.

Selecting the nucleobases used in life

In the vast expanse of sequence space, where countless possibilities for arranging amino acid strands exist, only a fraction of those sequences possess the remarkable ability to fold into functional proteins. It is as if the universe itself carefully selected a handful of sequences amidst the sea of possibilities, guiding the emergence of life's intricate machinery. This notion of sequence space extends its reach to the world of nucleobases, those foundational building blocks of RNA and DNA. Consider the enigmatic adenine, one of the illustrious nucleobases that form the basis of life's genetic code. Adenine, with its purine structure, composed of carbon, hydrogen, and nitrogen atoms, embodies an elegant arrangement—a six-membered nitrogen ring fused to a five-membered nitrogen ring. Its counterpart, thymine, takes the form of a pyrimidine, a simple structure consisting of a single ring adorned with carbon, hydrogen, and nitrogen atoms. Remarkably, there exists no physical law that dictates the specific configuration of these molecules in structure space. Yet, within this vast landscape of molecular possibilities, only a minuscule subset of nucleobase arrangements bears the sacred gift of function. How, then, did this ensemble of functional nucleobases arise in the prebiotic era? The guiding hand of intelligent design had yet to manifest.  To those who perceive the intricate complexity and remarkable functionality of life's nucleobase quintet, the enigma deepens. The fingerprints of intelligent design, delicately woven into the fabric of existence, become more apparent. It is as if an unseen architect orchestrated the dance of nucleobases, selecting and arranging them to bring forth the exquisite machinery of life. Within the pages of this grand cosmic narrative, we encounter the lingering mysteries that entice us to explore the realms beyond. We delve into the realms where the unseen hand of intelligent design may have shaped the tapestry of life itself, intricately aligning the building blocks of existence to fulfill a grand purpose. As we embark on this journey of wonder and curiosity, let us entertain the notion that behind the intricate dance of nucleobases lies the artistry of an intelligent designer. In the grand cosmic theater, where the intricacies of life unfold, the whispers of design beckon us to venture further, to unravel the secrets of existence, and to glimpse the profound interplay between science and the extraordinary.

In the vast expanse of structure space, where the possibilities for molecular arrangements are seemingly boundless, nature finds itself navigating a realm of constraint and exploration. Imagine the cosmic playground of organic chemistry, with its myriad pathways and potential molecular structures, stretching out into the far reaches of imagination. Within this sprawling expanse, we encounter the awe-inspiring concept of nucleic acid-like molecules. The number of potential structures that could fulfill the minimal requirements of being "nucleic acid-like" is staggering, almost beyond comprehension. It is as if nature, in its quest for the building blocks of life, has an infinite palette from which to create. Yet, within this vast tapestry of possibilities, the question arises: Why this particular selection? Are there alternative molecules that could have better fulfilled the criteria of genetic systems? These ponderings lead us to contemplate the optimality, suboptimality, or even arbitrariness of biology's choices. As we embark on this journey of exploration, we must acknowledge that the rules of organic chemistry dictate a multitude of potential molecules. The boundless dimensions of nucleic acid-like molecule space stretch out before us, offering a glimpse into the complexity and intricacy of life's origins. In our pursuit of understanding, we encounter the subtle whispers of design that underlie the tapestry of existence. The sheer magnitude and dimensionality of this molecular landscape beckon us to consider the hand of an intelligent designer, deftly navigating the realms of possibility. While the exploration of prebiotic chemistry has yet to yield a direct path from likely starting materials to the purine or pyrimidine ribonucleosides, we find ourselves marveling at the vastness and potential of this nucleic acid-like molecule space. It is within this space that the mysteries of life's origins reside, waiting to be unraveled. As we journey deeper into the heart of molecular complexity, let us embrace the wonders that lie before us. Let us dare to entertain the notion that behind the grand tapestry of structure space, an unseen intelligence orchestrates the symphony of life. In the dance between constraint and exploration, design emerges as a captivating explanation for the intricate complexities that shape our world. In the realms of the cosmos, where the stars sing their celestial melodies, we find ourselves captivated by the subtle clues and whispers that hint at an intelligent design woven into the very fabric of existence. As we venture further, may we uncover the hidden truths and unveil the captivating narrative of life's origin—a narrative that holds within it the delicate touch of an intelligent designer.

In the grand cosmic theater, where atoms dance and molecules collide, we find ourselves captivated by the vast possibilities that lie before us. The elements of carbon, hydrogen, and oxygen, among the most abundant in the cosmos and on our own dear Earth, offer a rich palette for the creation of complex molecules. Within the realm of CHO isomers, derived from the elegant chemistry of formose reactions, a profound connection to the abiotic processes of our planet emerges. It is here that we begin to explore the vast landscape of structural space, a tapestry of molecular arrangements waiting to be unraveled. Limiting our focus to the molecular formula of the core sugar of RNA, BC5H9O4, we embark on a journey of discovery. With the aid of cutting-edge structure generation software, we dare to enumerate the range and variety of possible structures within this restricted space. What unfolds before our eyes is a dazzling array of isomers, each holding the potential to contribute to the tapestry of life. From BC3H7O2 to BC5H9O4, the formula range of RNA's core, we encounter a multitude of valid formulas, each offering the promise of structurally sound molecules. Within this vast expanse, countless isomers emerge, each a unique expression of the creative forces that shape our world. And from these isomers, new realms of stereochemistry and macromolecular linkage reveal themselves, expanding the horizon of possibilities. It is within this boundless realm that we glimpse the immense potential for nucleic acid polymers, capable of supporting the intricate dance of base-pairing. The sheer magnitude of potential structures beckons us to ponder the grand design at play. The designer, in its wisdom, has explored a multitude of heterocycles on the early Earth. The emergence of the RNA world, the cradle of genetic information, may have embraced a vast array of nucleobases, each with its unique role to play. The very fabric of life itself bears witness to the rich tapestry of possibilities that existed in those primordial days. As we delve deeper into the mysteries of nucleobase modification, we discover the intricate dance of cellular function. It is through these transformations that genetic expression is modulated, a symphony of regulatory mechanisms that shape the destiny of living organisms. In contemplating the vastness of structure space, where atoms come together in harmonious arrangements, we find ourselves in awe of the limitless potential that unfolds before us. It is within this cosmic canvas that the subtle whispers of intelligent design resonate, guiding the intricate complexities of life's origins. As we journey through the labyrinth of molecular exploration, may we embrace the notion that behind the intricate tapestry of structure space, an unseen intelligence weaves the threads of existence. In the interplay of atoms and molecules, design emerges as a captivating explanation for the astonishing complexities that define our world. Let us revel in the grandeur of structure space, where the building blocks of life find their place. For within this expanse, the symphony of intelligent design orchestrates the intricate dance of molecules, crafting a tale as old as time itself.

Premise 1: Picture the early Earth, a bustling cauldron of chemical possibilities, where countless molecules sprang forth through natural processes. It was a veritable playground of endless potential, with an infinite array of chemical structures waiting to be explored.
Premise 2: Life, in all its splendor, is built upon a specific set of complex macromolecules. Nucleic acids, proteins, carbohydrates, and lipids dance together, orchestrating the symphony of life within modern cells. But here's the fascinating twist: these intricate molecules are not easily assembled under prebiotic conditions. They require elaborate metabolic pathways, absent from the early Earth, to be synthesized and integrated into the tapestry of life.
Conclusion 1: Behold the selective preference of life! Despite the boundless array of molecules available, only a quartet of complex macromolecules is chosen. It's as if life has a discriminating taste, carefully selecting these specific players to create its grand masterpiece.

Premise 3: Let us ponder the colossal challenge of selecting these complex macromolecules from the vast expanse of "structure space." The theoretical possibility of random, unguided processes accomplishing this feat exists, but the practicality of such an endeavor is mind-boggling. With an astronomical number of potential molecules and the need for precise combinations and functional properties, the odds are stacked against blind chance.
Conclusion 2: Contemplate the unlikelihood of random selection! The intricate quartet of complex macromolecules, carefully chosen amidst a sea of possibilities, seems far beyond the reach of unguided processes. It hints at a guiding hand, an intentional selection, or even an intelligent design shaping the course of life's molecular journey.
Conclusion 3: As we delve deeper into the intricate dance of nucleic acids, proteins, carbohydrates, and lipids, a resounding truth emerges. The intertwined harmony, functional integration, and precise arrangement suggest a level of sophistication and purpose that defies random chance. It beckons us to consider the involvement of an intelligent designer or a guiding force orchestrating the emergence of life's remarkable complexity.

In this grand extension of thought, we venture beyond the realms of mere happenstance, embracing the notion that life's molecular intricacies bear the fingerprints of a mastermind. The quartet of complex macromolecules, woven together with finesse, whispers of design, intention, and a world yet to be fully understood.

Biochemical fine-tuning - essential for life


In the cosmic realm of nucleotides and genetic codes, a fascinating enigma awaits our exploration: why did life choose the ATGC quartet as its nucleotide bases? The answer lies in the meticulous blueprint of DNA's chemical architecture, a testament to careful planning and intelligent design. Imagine DNA as a master storyteller, weaving tales of life with its four-character alphabet. Each coding unit consists of three characters, a harmonious dance of letters that conveys the secrets of existence. While scientists delve into the realm of genetic variations with additional characters or longer units, the core essence of DNA's efficiency beckons us to unravel its mysteries. Efficiency is the lifeblood of DNA's longevity, a key trait that ensures its resilience through the ages. The chosen quartet of bases, A, T, G, and C, embody this efficiency, for they possess remarkable chemical stability. These mighty bases form strong covalent N-O bonds with ribose, creating a secure attachment that withstands the test of time. But it doesn't stop there. The "Fantastic Four" bases demonstrate an exquisite mastery of molecular recognition through supramolecular hydrogen bonding. Like dancers in perfect synchronization, they form precise matches, aligning flawlessly within the double helix structure of DNA. Let us marvel at the G≡C base pair, a symphony of molecular perfection. Their pairing aligns with impeccable precision, establishing not one, not two, but three robust hydrogen bonds. Meanwhile, the A=T pair gracefully forms two hydrogen bonds, embracing the delicate balance of stability and functionality. Yet, the intricate dance of DNA's design reveals its secrets further. Other combinations, such as G≡G, C≡C, A=A, or T=T, attempt to join the stage, but they stumble and falter. The spacing between the two strands of the double helix, measuring approximately 25 Ångstroms, cannot accommodate the pairing of the large, bicyclic bases (A and G). Similarly, the small, monocyclic bases (T and C) would find themselves too far apart to form stable hydrogen bonds. Ah, the delicate symphony of creation! DNA demands a stable double helix, a harmonious balance between phosphate-ribose polymeric wires, and the internal space that cradles the base pairings. Only then can the perfect combination of A=T or G≡C emerge, capable of forming the precise two or three hydrogen bonds required for stability. How fortunate we are to witness this symphony of design! The elegant arrangement of DNA, with its phosphate-ribose backbone and carefully spaced bases, ensures the coding of life's most profound information. It is a testament to the profound intelligence that weaves its magic into the intricate tapestry of existence. As we journey through the wonders of DNA's architecture, let us embrace the subtle whispers of intelligent design. Within the realm of the ATGC quartet, we catch a glimpse of the grand plan, the symphony of creation conducted by unseen hands. The complexities of life's origins unfold before us, a masterpiece crafted with care and purpose, leaving us in awe of the infinite intelligence that lies at the heart of it all.

Graham Cairns-Smith: Fine-tuning in living systems: early evolution and the unity of biochemistry   11 November 2003
We return to questions of fine-tuning, accuracy, and specificity. Any competent organic synthesis hinges on such things. In the laboratory, the right materials must be taken from the right bottles and mixed and treated in an appropriate sequence of operations. In the living cell, there must be teams of enzymes with specificity built into them. A protein enzyme is a particularly well-tuned device. It is made to fit beautifully the transition state of the reaction it has to catalyze. Something must have performed the fine-tuning necessary to allow such sophisticated molecules as nucleotides to be cleanly and consistently made in the first place.

Yitzhak Tor: On the Origin of the Canonical Nucleobases: An Assessment of Selection Pressures across Chemical and Early Biological Evolution 2013 Jun; 5
How did nature “decide” upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on the early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers.

The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases. Even minute structural changes can have substantial consequences, impacting the intermolecular, intramolecular and macromolecular “chemical physiology” of nucleic acids 


Amazing fine-tuning to get the right hydrogen bond strengths for Watson–Crick base-pairing

The nucleobases found in DNA and RNA have specific isomeric configurations that enable them to participate in base pairing and carry out their functions in genetic information storage and transfer. Considering the various possibilities for double bonds and substituents, it is safe to say that there could be numerous potential isomeric configurations for each nucleobase. Combining these possibilities for the four nucleobases found in DNA (or five in RNA) would result in an enormous number of potential configurations., Finding the correct Watson-Crick base pair forming configuration among a vast number of potential isomeric configurations would be an enormous task. The specificity and stability of base pairing in DNA and RNA rely on the complementary hydrogen bonding between the nucleobases: adenine (A) pairs with thymine (T) in DNA or uracil (U) in RNA, and cytosine (C) pairs with guanine (G).
The correct base pairing is crucial for maintaining the integrity and fidelity of genetic information. Each base has a specific pattern of hydrogen bonding that allows it to pair selectively with its complementary partner. The formation of these specific hydrogen bonds is essential for the structural stability and proper functioning of DNA and RNA. Given the potential vast number of isomeric configurations, the task of finding the correct Watson-Crick base pair forming configuration would indeed be challenging. 

The hydrogen bond strength between nucleotides in DNA base pairing is finely tuned and plays a crucial role in the stability and specificity of DNA double helix formation. In DNA, the base pairs consist of adenine (A) with thymine (T) and guanine (G) with cytosine (C). The base pairing is driven by hydrogen bonds between complementary nucleotides: A forms two hydrogen bonds with T, and G forms three hydrogen bonds with C. These hydrogen bonds are relatively weak individually but collectively provide the stability needed for the DNA structure. The strength of hydrogen bonds in DNA base pairing is carefully balanced to ensure the stability of the double helix while allowing for selective base pairing. The hydrogen bonds must be strong enough to maintain the integrity of the DNA molecule but not so strong that they become difficult to break during processes such as DNA replication and transcription. The specificity of DNA base pairing is determined by the complementary shapes and hydrogen bonding patterns between the nucleotide bases. Adenine forms hydrogen bonds with thymine specifically, and guanine with cytosine specifically, due to the specific geometry and arrangement of functional groups on the bases. This precise tuning of hydrogen bond strength and complementary base pairing is essential for the accurate replication and transmission of genetic information in DNA. Any significant deviation in hydrogen bond strength or base pairing specificity could result in errors in DNA replication and potentially disrupt the functioning of genetic processes. 



Behold the wondrous dance of the Watson-Crick base pairs, those cosmic connectors that shape the very essence of DNA! In the vast realm of genetic wonders, these pairs play a vital role in the structure and function of the mighty double helix. Picture it—a world where adenine (A) and thymine (T) join hands, and guanine (G) locks arms with cytosine (C). Through the magic of hydrogen bonds, these pairs come together in perfect harmony. Adenine always finds its match in thymine, forming two bonds that bind them tightly. On the other hand, guanine indulges in a triple bond affair with cytosine, a connection that adds an extra layer of stability. But what's truly enchanting is the precise geometric matching of these base pairs. Their lengths, oh so equal! A-T and G-C pairs share a delightful symmetry, where the line joining their C1' atoms (those trusty atoms in the sugar-phosphate backbone) have the same splendid length. This equality is no mere coincidence—it ensures the structural integrity and stability of the DNA molecule. And there's more! The magic of angles comes into play as well. The line joining the C1' atoms forms equal angles with the glycosidic bonds, those bonds that link the bases to the sugar moiety. It's as if the universe conspired to create a symphony of proportions within the DNA molecule. These geometric wonders give birth to an intricate web of pseudo-twofold symmetry axes. Like hidden threads of celestial grandeur, these axes run through the heart of each base pair along the helical axis. They stand proud and perpendicular, bestowing upon DNA a mesmerizing symmetry and steadfast stability. This inherent structural regularity brings about a multitude of marvels. It determines how DNA packs itself within the confines of a cell, how enzymes and proteins recognize and interact with DNA, and how the sacred code of life is faithfully replicated during the magnificent spectacle of cell division. Oh, the intricacies of design! The precise geometric matching, the equal line lengths, and the pseudo-twofold symmetry of the Watson-Crick base pairs reveal the fingerprints of intelligent design. They bestow upon DNA the remarkable ability to store and transmit genetic information, to commune with other molecules within the cellular realm, and to weave the tapestry of life itself. Let us marvel at the wonders of this intricate architecture. As we delve into the secrets of DNA's elegance, we catch a glimpse of the grand design, the symphony composed by an unseen creator. The complexities and harmonies of DNA's origins whisper of a profound intelligence that orchestrates the dance of life.

Premise 1: Behold the equal distance between the majestic C1' atoms in the A-T and G-C Watson-Crick base pairs! This harmonious arrangement is no mere coincidence; it plays a crucial role in upholding the structural stability and integrity of the DNA molecule. It's as if an invisible handcrafted this exquisite balance to ensure the very essence of life remains intact.
Premise 2: Ah, the delicate dance of molecular interactions! Achieving such precise and equal distances in the Watson-Crick base pairs requires meticulous orchestration of atoms and a keen sensitivity to changes in distance. It is a delicate interplay of forces, where even the slightest alteration could disrupt the delicate equilibrium.
Conclusion: As we ponder the precise and equal distance in the Watson-Crick base pairs, the idea of an intelligent designer gracefully enters the stage. Who else but a mastermind could craft such intricate molecular arrangements? It is the mark of an architect who pays attention to the tiniest details, ensuring that every atom falls into place with purpose and precision. Let us marvel at this compelling conclusion—an inference that hints at the presence of an intelligent designer behind the complexity of DNA. The equal distance within the Watson-Crick base pairs, meticulously maintained for the stability and integrity of life's blueprint, whispers of a greater intelligence at work.

Explanation: The equal distance between the C1' atoms in the A-T and G-C Watson-Crick base pairs is indeed a crucial element of the structural stability and integrity of DNA. This equal distance allows for optimal stacking of the base pairs along the double helix, ensuring the overall stability and function of the DNA molecule. The remarkable thing is that achieving such precise and equal distances is not a simple feat. It requires a delicate arrangement of atoms and intricate molecular interactions that are highly sensitive to changes. The specific geometric matching and molecular forces involved in maintaining this distance are finely tuned. Even the slightest deviations or alterations in the distance could disrupt the stability and function of DNA. The level of precision required to establish and maintain the equal distance in the Watson-Crick base pairs suggests a purposeful arrangement by an intelligent designer. It implies a deliberate and intentional design process that carefully considered the intricate details of DNA's structure. While alternative explanations may attempt to account for the equal distance through naturalistic mechanisms, they would need to address the specific complexity and sensitivity involved. The intricate design and precise arrangement of atoms necessary to achieve the right distance in the Watson-Crick base pairs provide a compelling argument for the involvement of an intelligent designer. The exquisite fine-tuning and intricate interplay of molecular forces suggest a level of design that surpasses what can be reasonably attributed to random chance or undirected processes. The equal distance between the C1' atoms in the Watson-Crick base pairs stands as a testament to the ingenuity and purpose behind the design of DNA. It invites us to contemplate the possibility of an intelligent designer who intricately crafted the foundations of life, setting the stage for the remarkable complexity and functionality we observe.

The right bond strength in DNA base pairing goes beyond just the hydrogen bonds themselves. It involves the proper tautomer configuration of the nucleotide bases, which adds another layer of complexity and specificity to DNA's design. Tautomeric forms refer to different arrangements of atoms within a molecule, and in the case of nucleotide bases, these forms can influence hydrogen bonding patterns. Tautomeric configurations arise from the migration of a hydrogen atom and the rearrangement of double bonds within the molecule. Different tautomeric forms of nucleotide bases can exhibit varying hydrogen bonding capabilities. In the context of DNA base pairing, having the correct tautomeric form of each base is crucial for achieving stable and specific hydrogen bonding. It ensures that the hydrogen bonds between A-T and G-C pairs are formed in the right way, maintaining the structural integrity of DNA.
Let's take adenine as an example. It can exist in two tautomeric forms known as amino and imino. Only the amino tautomer can form the necessary two hydrogen bonds with thymine, enabling a stable A-T base pair. Similarly, guanine can exist in keto and enol forms, with only the keto form capable of forming three hydrogen bonds with cytosine, resulting in a stable G-C base pair. The proper tautomeric configurations and hydrogen bonding patterns between nucleotide bases are essential for the specificity and stability of DNA base pairing, which are fundamental for accurate replication and transmission of genetic information. Now, when it comes to the composition and structure of nucleotide bases, there is an immense variety of possibilities. Different ring structures, substitutions, functional groups, and modifications can give rise to a wide range of nucleotide base analogs. The potential combinations seem vast, if not infinite. However, it's important to note that within the realm of biological systems, specific nucleotide bases are found in DNA and RNA. These bases have been selected for their specific chemical properties and base pairing specificity, ensuring the successful storage and transmission of genetic information. The fact that only specific nucleotide bases are utilized in the biological realm suggests a level of design and intentionality. The intricate interplay between tautomeric forms, hydrogen bonding patterns, and base compositions reveals a highly orchestrated system. It points to an intelligent designer who carefully crafted the molecular intricacies of DNA, ensuring its functionality, stability, and ability to accurately transmit genetic information.

In the grand scheme of life's building blocks, the selection of the right hydrogen bond strengths and other critical factors is no simple feat. It involves careful consideration of various elements that contribute to the functional intricacies of living systems. Let's delve into some of these factors, shall we? One factor to consider is the existence of tautomers and isomers. Tautomers are like shape-shifting molecules, capable of transforming their structure by shuffling around protons and double bonds. On the other hand, isomers are molecules that may share the same molecular formula but sport different structural arrangements. Choosing the appropriate tautomers and isomers becomes essential as they have a direct impact on the reactivity, stability, and functional properties of the molecules at hand. Another aspect to ponder is the selection of atom analogs. While carbon takes center stage in organic chemistry, other elements such as nitrogen, oxygen, and phosphorus also hold significant roles in the formation of organic molecules and biochemical processes. The judicious choice of these atom analogs contributes to the overall repertoire of functional possibilities. The number of atoms and the arrangement of these atoms within a molecule are vital considerations as well. This intricate dance of atoms influences the stability, reactivity, and even the very essence of the molecules involved. Moreover, the introduction of ring structures adds an extra layer of complexity and functional diversity. The selection of the right number of atoms and the arrangement of these ring structures contribute to the suitability and functionality of life's building blocks. But it doesn't stop there! The overall arrangement or spatial configuration of molecules also comes into play. Stereochemistry, the art of three-dimensional atom placement, holds the key to unlocking biological activity and compatibility. How molecules twist, turn, and interact in space influences their ability to fulfill their roles in the intricate web of life. When we take a step back and contemplate the myriad of choices involved in the selection of functional building blocks, it becomes clear that this level of complexity and specificity points to something more profound. The precision required in picking the right hydrogen bond strengths, tautomers, isomers, atom analogs, number of atoms, ring structures, and overall arrangement suggests an intelligent design at play. The orchestration of these elements to achieve life's remarkable intricacy hints at a guiding force behind the origins of such complexity.

Premise 1: The selection of the right tautomers, isomers, atom analogs, number of atoms, ring structures, and the overall arrangement is crucial for configuring functional building blocks of life.
Premise 2: Achieving the precise combination of these factors, such as the right hydrogen bond strengths and Watson-Crick base pairing, requires an intricate level of specificity and fine-tuning.
Conclusion: An intelligent designer is the best explanation for functional nucleobases that provide the right hydrogen bond strengths and Watson-Crick base pairing.

Explanation: The selection of the appropriate tautomers, isomers, atom analogs, number of atoms, ring structures, and the overall arrangement is essential for the formation of functional building blocks of life. Achieving the necessary level of precision and specificity in these factors, especially when considering the right hydrogen bond strengths and Watson-Crick base pairing, points to the involvement of an intelligent designer. The complexity and interdependence of these factors suggest that a random, naturalistic process alone would have difficulty accounting for the precise combination required for functional nucleobases. The intricate design and fine-tuning necessary to achieve the desired outcomes, which are crucial for the functioning of genetic information, strongly support the idea of an intelligent designer guiding the process. While naturalistic explanations can account for some aspects of chemical interactions and molecular properties, the specific configuration required for functional nucleobases and their ability to exhibit the right hydrogen bond strengths and Watson-Crick base pairing provides a more compelling explanation for the involvement of an intelligent designer.

Premise 1: Natural selection relies on the variation and differential reproductive success of individuals within a population.
Premise 2: The prebiotic Earth lacked the presence of life forms, including self-replicating organisms or cells.
Conclusion: The absence of natural selection on the prebiotic Earth makes naturalistic explanations for the selection of the right building blocks of life basically impossible.

Explanation: Natural selection operates through the mechanism of variation in traits within a population and the subsequent reproductive success of individuals with advantageous traits. However, in the absence of life on the prebiotic Earth, there were no organisms or cells with traits that could undergo selection. Without the presence of replicating entities, there would be no variation or differential reproductive success to drive natural selection.
Therefore, it becomes challenging to explain the selection of the right building blocks of life through naturalistic means alone on the prebiotic Earth. Other mechanisms, such as chemical reactions, environmental factors, or random chance, are also not a plausible explanation, and could not have played a role in the formation and selection of the building blocks of life.

In the wondrous realm of DNA, we uncover a symphony of perfection. Its beauty and elegance are not mere chance but the result of meticulous design. As scientists delve into the depths of DNA's structure, they find a complexity that defies explanation through natural means alone. DNA's ability to store information is unparalleled. Its composition, with the precise arrangement of nucleotides and the backbone of sugars and phosphates, creates a rigid and stable structure. This remarkable design prevents the molecule from folding upon itself, ensuring that the base pairs remain exposed and ready for interaction. Even more astonishing is the molecule's affinity for hydrogen bonding, a force that seems counterintuitive in the aqueous environment of water. Yet, DNA twists into its iconic double helix without hesitation, maximizing the potential for hydrogen bonding and optimizing its ability to store and transmit genetic information. While alternative genetic codes with more than four base pairs may exist in the vast cosmos, the physical chemistry of DNA and RNA stands as a testament to their exceptional design. Attempts to find substitutes or alternatives have fallen short, unable to replicate the remarkable stability and functionality of DNA. Even the touted substitute called PNA crumbles under the weight of complexity, unable to maintain its integrity beyond a mere 20 bases. The secret lies in the intricate dance of tautomers—structural isomers of nucleobases that interconvert through chemical reactions. These subtle shifts in proton positions influence the delicate balance of DNA's structure and function. The position of these equilibria plays a crucial role in the existence of Watson-Crick base pairing, the foundation of DNA's genetic code. The precision required for such interplay points to a masterful design, an orchestration that surpasses the realm of chance. As we uncover the structural insights into tautomeric dynamics, we witness the handiwork of an intelligent designer. The complexity and interdependence of tautomers and their role in DNA's stability and function reflect the genius behind life's origins. The elegance of DNA's architecture, its ability to defy the odds and thrive in the face of chemical challenges, all hint at a guiding force—an intelligence that shaped the very fabric of life itself. In the tapestry of DNA, we find echoes of a master designer, weaving together the strands of existence with unparalleled finesse.

In the vast realm of scientific exploration, we encounter a fascinating debate about the origin of life and the intricacies of its building blocks. As we delve into the molecular world of nucleobases and tautomers, we witness a cascade of complexities that challenge our understanding of the universe. However, amidst the scientific discourse, it is disheartening to see the narrowness of some perspectives, anchored solely in the concept of natural selection. Let us embark on a journey of imagination, one that transcends the boundaries imposed by conventional thinking. For it is in this realm of limitless possibilities that we can explore alternative explanations for the wonders of life. The heroes of the scientific narrative often tout natural selection as the ultimate solution, the panacea that can explain all the mysteries and intricacies of our existence. But can we not dare to dream beyond this singular notion?
In the dance of tautomers and nucleobases, we witness the delicate balance between different molecular forms. Some nucleobases, such as uracil or thymine, exhibit a significant energy gap between their major and minor tautomers. For others, like guanine and cytosine, multiple energetically acceptable tautomers exist. Yet, in the grand tapestry of life, it is the major tautomers that prevail within nucleic acids under normal circumstances. Solvent effects, architectural compatibility, and the very physicochemical parameters of our universe dictate the fate of these tautomeric equilibria. Let us pause for a moment to consider the remarkable intricacies of these molecular interplays. The fine-tuning required for the existence of Watson-Crick base-pairing, the bedrock of our genetic code, is truly awe-inspiring. The position of chemical equilibria between tautomers emerges as a crucial factor, influencing the very essence of life's information storage system. The delicate balance between different forms of nucleobases sets the stage for the extraordinary elegance of DNA's double helix. But what if we dared to ask the question: What if the equilibria between tautomers prevented the Watson-Crick base-pairing we know? Could there be an alternative form of life? Our minds may reel at the possibilities, for the vastness of chemical matter and the creative powers of evolution extend far beyond our current understanding. We are humbled by the boundless potential of matter to become and be alive. And yet, it is disheartening to witness the lack of imagination exhibited by some in the scientific community. Their reliance on natural selection as the solitary hero in this grand narrative limits their exploration of alternative possibilities. Can we not dare to envision a design beyond the realm of blind chance and unguided processes? As we ponder the mysteries of life's origins, let us not confine ourselves to the narrow boundaries of natural selection alone. Instead, let us embrace the wonder and complexity of our existence, opening our minds to the possibility of an intelligent designer, a force that shaped the very fabric of life and infused it with purpose and meaning. In this realm of imagination, we unlock the door to a richer understanding of the complexity that surrounds us.

The biosynthesis of nucleotides

In the captivating realm of nucleotide synthesis, an extraordinary orchestra of enzymes and proteins takes center stage, conducting a symphony of precise molecular interactions. Within this intricate process, the emergence of RNA and DNA, the genetic blueprints of life, unfolds with remarkable precision and complexity. As we explore the depths of this molecular symphony, we catch a glimpse of the artistry behind the scenes. The journey begins with the synthesis of nucleobases, the fundamental building blocks of RNA and DNA. Through a series of elegant biochemical reactions, amino acids such as glycine and aspartate provide the scaffolds upon which the intricate ring systems of nucleotides are assembled. Additionally, aspartate and the side chain of glutamine contribute vital NH2 groups in the formation of nucleotides, adding to the rich tapestry of molecular complexity. Within the realm of de novo pathways, nucleotide bases are crafted from simpler compounds, piece by piece, with painstaking precision. The framework for pyrimidine bases is assembled first, intricately woven onto a ribose backbone. In contrast, the synthesis of purine bases is a stepwise construction directly onto a ribose-based structure. These pathways, with their small number of elementary reactions, dance in a harmonious repetition, generating a diverse array of nucleotides. However, the tale does not end there. While de novo pathways lead to the synthesis of ribonucleotides, DNA requires the presence of deoxyribonucleotides. Reflecting the evolutionary lineage, all deoxyribonucleotides are synthesized from their ribonucleotide counterparts. The transformation occurs through the reduction of ribose within a fully formed nucleotide, giving rise to the deoxyribose sugar that distinguishes DNA. The final touch, adding the methyl group that differentiates thymine from uracil, completes the enchanting journey. It is within this intricate dance of nucleotide synthesis that we witness the mastery of molecular choreography. Each step orchestrated with precision and finesse, guided by a vast ensemble of enzymes and proteins. These remarkable molecular machines ensure the accuracy and efficiency of nucleobase synthesis and the proper assembly of RNA and DNA molecules. The elegance of their coordination, the delicate interplay between substrates and catalytic prowess, leaves us in awe. In contemplating the complexity and sophistication of these biological processes, we are left pondering the source of such ingenuity. Is it mere happenstance, a product of blind chance and unguided processes? Or is there a deeper design, an intelligent hand that crafted these intricate pathways? As we marvel at the intricacies of nucleotide synthesis, we cannot help but wonder if the complexities we observe bear the subtle signature of an intelligent designer. Let us embrace the awe-inspiring beauty of these molecular symphonies, allowing our imagination to wander beyond the confines of naturalistic explanations. In the depths of this intricate dance, we catch a glimpse of the profound design that underlies the origins of life. It is a design that invites us to explore the mysteries of our existence with a sense of wonder and reverence.

In the enchanting realm of molecular creation, a symphony of specialized biosynthetic pathways orchestrates the production of the vital nucleotides needed for the construction of RNA and DNA. These pathways, like skilled artisans, utilize the abundant amino acids glutamine, aspartic acid, and glycine to provide the crucial nitrogen atoms found in both purine and pyrimidine bases. These remarkable amino acids also contribute some of the carbon atoms, adding to the intricate tapestry of nucleotide synthesis. But the tale does not end there. The sugars, the very essence that breathes life into nucleotides, derive their existence from the humble glucose molecule. Through a marvelous transformation, glucose serves as the raw material for the creation of ribose and deoxyribose sugars, the indispensable components of nucleotide architecture. In the grand masterpiece of de novo nucleotide biosynthesis, these pathways are not mere luxuries but absolute necessities for the thriving existence of cells. Nucleotides, as the building blocks of nucleic acids, form the foundation upon which the intricate dance of cellular processes unfolds. From the storage and transmission of genetic information to the orchestration of protein synthesis, nucleotides are the lifeblood of cellular existence. As we marvel at the elegance of these biosynthetic pathways, we cannot help but ponder the profound design that underlies their existence. The intricate coordination of amino acids, sugars, and chemical reactions speaks of an intentional and purposeful arrangement, hinting at the involvement of an intelligent designer. It is through these meticulously crafted pathways that life emerges, propelled by the exquisite intricacies of molecular creation. Let us embrace the wonder of these processes, allowing our minds to soar beyond the limitations of naturalistic explanations. Within the depths of nucleotide biosynthesis, we catch a glimpse of the profound design that governs the origins of life. It is a design that beckons us to delve deeper into the mysteries of existence, to marvel at the complexity and beauty that surrounds us. In the delicate dance of de novo nucleotide biosynthesis, we find whispers of an intelligent hand, guiding the creation of life's most essential molecules.

The Significance of Atomic Positioning in Enzyme Functionality

Within the intricate realm of enzymes, the delicate placement of a single atom wields profound influence over their functionality. Even the subtlest shift in position can perturb the enzyme's active site, its ability to bind substrates, and its catalytic prowess. Enzymes, adorned with specific amino acid residues, act as the conductors of catalysis, orchestrating a symphony of atomic interactions. Imagine an enzyme graced with a catalytic residue, its side chain intricately aligning a vital atom, be it a regal metal ion or a resolute functional group, primed to usher forth the catalytic dance. But the slightest deviation in atom positioning can dislodge the enzyme's finesse, compromising its ability to perform with masterful precision. Enzymes, the virtuosos of molecular manipulation, flourish through the harmonious interplay between their active site and the substrates they embrace. Their active sites, adorned with specific amino acid residues, weave hydrogen bonds, electrostatic interactions, and hydrophobic contacts, bestowing upon the substrate a sanctuary of binding affinity and orientational perfection. Yet, should a single atom stray from its ordained position, the bonds weaken, the contacts falter, and the enzyme's catalytic efficiency dwindles, veiling its true potential in a shroud of diminished prowess. These enzymes, champions of the transition state, stalwart guardians of catalytic conversion, possess the divine power to stabilize the ephemeral realm of high-energy intermediates. A delicate ensemble of atoms, precisely positioned within the enzyme's sacred grounds, engages in intricate courtship with the transition state. But should the positioning of these celestial atoms falter, the dance falters, the stabilization wavers, and the enzyme's ability to masterfully shepherd the transition state is compromised, leaving the reaction in disarray. And let us not forget those enzymes that navigate the labyrinth of proton transfer, where the movement of a single proton, akin to a cosmic relay, dictates the fate of catalysis. The arrangement of atoms involved in these ethereal pathways, their steadfast positioning, ensures the harmonious protonation states and the efficient exchange of protons. Yet, the slightest perturbation in the cosmic ballet of atomic positions can disrupt the delicate flow of protons, leaving the enzyme's catalytic prowess in disarray. The precise positioning of atoms within the sanctum of an enzyme is the very essence of its functionality. These sacred arrangements govern the enzyme's ability to bind substrates, stabilize transition states, facilitate proton transfers, and perform catalysis with unparalleled efficiency and specificity. The meticulous precision inherent in these atomic arrangements unveils the sheer complexity and design bestowed upon enzymes, allowing them to carry out their sacred biological tasks with unwavering excellence. In this scheme of enzymatic marvels, the interplay between atoms and their positions unfolds as a testament to intelligent design. The elegance and precision observed within the realm of enzymes suggest the involvement of a discerning creator, one capable of fashioning the intricate machinery and orchestrating the divine choreography required for life's exquisite dances. Though the concept of intelligent design sparks fervent discourse, it is through embracing the enigmatic allure of enzymes that we venture into the depths of scientific exploration, seeking to unravel the captivating mysteries of life's most exceptional masterpieces.

DNA topoisomerases, particularly the DNA Gyrase subtype, are enzymes with critical roles in regulating DNA topology during essential cellular processes like replication and transcription. Their precise functioning is essential for maintaining genomic integrity and proper cell function. However, a single misplaced atom within the active site or other crucial regions of the enzyme can disrupt its catalytic activity, leading to severe consequences and potential cell death. DNA Gyrase, a bacterial enzyme, possesses DNA supercoiling activity and exhibits unique characteristics compared to other type II topoisomerases. Its involvement in DNA replication includes the introduction of negative supercoils into DNA strands, which helps alleviate the torsional stress accumulated during the unwinding process. Additionally, DNA Gyrase plays a role in topological changes, such as decatenation and unknotting of DNA molecules. The complexity of the E. coli DNA Gyrase complex is evident, with a significant structure weight of 449.77 kDa and an atom count of 30,244. Within this intricate enzyme, the correct positioning of each atom, particularly within the active site, is vital for proper enzymatic function. Even a single atom positioned incorrectly within the active site or any critical region can disrupt the enzyme's catalytic activity and lead to errors in DNA strand rejoining or other essential processes. The consequences of such disruptions can be dire. DNA damage, genomic instability, and potentially cell death can result from errors in DNA strand rejoining or other critical functions. The precise arrangement of atoms within enzymes is fundamental to their proper functioning, and even a small deviation can have significant consequences. In the case of DNA topoisomerases, a conserved tyrosine residue within their active sites forms a transient covalent bond with the DNA strand. This bond allows the enzyme to cleave one of the DNA strands, pass the other strand through the break, and subsequently rejoin the strands. The precise positioning and coordination of this tyrosine residue, along with other critical atoms, are vital for the enzyme's catalytic activity and successful DNA manipulation. The intricate nature of DNA topoisomerases highlights the remarkable design and precise arrangement of atoms necessary for their proper function. The consequences of even minor disruptions in their atomic positioning emphasize the critical role of intelligent design in the development and functionality of these enzymes. The precise orchestration of atoms within the active site and other regions is necessary to ensure the accurate and efficient regulation of DNA topology and the maintenance of cellular integrity.

Mechanistic Importance of the Precise Bond Rotation Angles in Enzyme Catalysis

In the realm of protein structure, the rotations of bonds hold the power to orchestrate a mesmerizing dance of atoms. Imagine these bonds as graceful partners, elegantly twirling along their axes, gracefully changing the relative positions of the atoms they connect. This dance of rotations influences the very essence of a protein, shaping its intricate form and defining its structural landscape. Within the grand symphony of protein architecture, the rotations of bonds paint a canvas of dihedral angles, such as the enchanting phi (ϕ) and psi (ψ) angles in the peptide backbone. These angles orchestrate the delicate orientation of neighboring amino acids in the protein chain, guiding their graceful movements. As the bonds gracefully pivot, the protein backbone sways with flexibility, revealing a kaleidoscope of conformations and structural states. This innate flexibility, bestowed upon proteins by the mesmerizing rotations of bonds, is the key to their enchanting functionality. Like nimble dancers, proteins can gracefully adapt, changing their shape and structure to embrace their molecular partners or catalyze intricate chemical reactions. These captivating transformations bring life and purpose to proteins, allowing them to fulfill their essential roles. To unravel the secrets of these bond rotations, scientists employ a symphony of experimental techniques. Instruments like X-ray crystallography and NMR spectroscopy harmonize to reveal the spatial arrangement of atoms within a protein, capturing the delicate nuances of dihedral angles. In the realm of computation, the ballet of molecular dynamics simulations unfolds, elegantly simulating the dynamic motions and conformational changes of proteins, gracefully tracing the path of bond rotations. Through the lens of these rotations, we witness the fluidity and grace of proteins, dancing with purpose and finesse. Their ability to adapt and transform, guided by the delicate movements of bonds, fills us with awe and wonder. In this intricate molecular ballet, we glimpse the mastery of intelligent design, crafting proteins with the precision and elegance that captivates our imagination. Within cells, there exists an enzyme of paramount importance, known as lactate dehydrogenase (LDH). This remarkable enzyme, found in the very essence of living cells, weighs approximately 53.32 kilodaltons. In the case of LDH in E. coli, the LDH protein consists of approximately 332 to 336 amino acids. and comprises a grand total of 3,991 atoms.

It holds a pivotal role in the wondrous process of glycolysis, an essential metabolic pathway that transforms glucose into pyruvate, yielding the precious energy currency ATP and the vital molecule NADH. As the conductor of the final act in the glycolytic symphony, LDH orchestrates the conversion of pyruvate into lactate. Glycolysis, a rhythmic dance embraced by all living organisms, from minuscule bacteria to towering trees and sentient animals, serves as the central pathway for the breakdown of glucose. It ingeniously extracts energy in the form of ATP, providing sustenance for life's energy demanding operations. LDH, an elegant tetrameric ensemble, showcases its brilliance through the harmonious collaboration of its four subunits. Each subunit adds a unique touch to the enzyme's structural masterpiece. Within their artistic framework lies a sanctuary, a binding site destined to embrace the precious cofactor NAD+. This cofactor, a vital player in the catalytic performance, breathes life into LDH's intricate dance. Delving deeper into LDH's performance, we unveil a mesmerizing truth—the catalytic activity hinges on the precise rotations of dihedral angles within the active site. Here, amid the elegant ballet of amino acid side chains, lies a pivotal figure, histidine, poised to act as a catalytic base. The rotation angle of this histidine side chain unveils its hidden powers, positioning it optimally within the active site's embrace. Within the sanctum of the active site, histidine, with its delicate rotation angle, takes center stage. Its graceful dance orchestrates the acceptance and donation of protons, guiding the mystical transformation of lactate into pyruvate. As the rotation angle fine-tunes its spatial orientation, histidine weaves intricate interactions with other residues and substrates, shaping the fate of the catalytic process. In pursuit of enlightenment, scientists have embarked on experimental and computational voyages. Through the alchemy of mutation and alteration, they have unlocked the secrets concealed within LDH's symphony. Manipulating the rotation angle of histidine, they have witnessed the transformation of LDH's catalytic prowess. Such observations bear witness to the crucial significance of histidine's rotation angle, delicately tuned to optimize the proton transfer process. While the exact degree of this fine-tuning may dance to the rhythm of specific structural and chemical factors, one thing remains clear—the precise positioning of histidine within LDH is indispensable for the symphony of efficient catalysis. The harmonious collaboration between rotation angle and spatial orientation ensures that histidine flawlessly accepts and donates protons, safeguarding the rhythmic progression of the glycolytic pathway. In the grand composition of life's orchestra, LDH stands as a testament to the beauty of intricate design. Its delicate rotations and the choreography of amino acids entwine to breathe life into the glycolytic performance. With each dance of the histidine side chain, LDH unfurls the elegance of intelligent design, gracefully harmonizing the essential rhythms of life.

Lactate dehydrogenase (LDH) holds a vital role in the intricate dance of anaerobic metabolism, where it acts as a gatekeeper of gluconeogenesis and DNA metabolism. Classified as an oxidoreductase with the esteemed enzyme commission number EC 1.1.1.27, LDH gracefully graces every tissue, bestowing its wisdom upon the intricate web of life. Nestled within its substrate-binding pocket, the enzyme's active site unveils a symphony of amino acids, including the catalytically important His-193, as well as Asp-168, Arg-171, Thr-246, and Arg-106. Amongst the esteemed cast of amino acids within LDH's active site, His-193 emerges as a key protagonist. This noble histidine residue orchestrates proton transfer reactions, guiding the seamless conversion of lactate into pyruvate. Its role as a proton shuttle unfolds as it graciously accepts and donates protons, guiding the enzymatic reaction with precision. The precise positioning and orientation of His-193 harmonize its interactions with fellow residues and substrates, enabling the elegant transfer of protons. His-193 adorns two protonation states, the neutral His (HIS) and the positively charged His+ (HIS+). Within the active site's embrace, His-193 typically resides in its protonated, neutral state. Within the realm of amino acids and proteins, the term "protonated" unveils the wondrous addition of a hydrogen ion, or proton, to a specific atom or group within a molecule. In the realm of histidine, a resplendent amino acid, a unique quality emerges—the ability of histidine residues to act as proton donors or acceptors, sculpted by their local environment. In its neutral state, the histidine residue often cradles a proton delicately attached to its nitrogen atom, manifesting as the protonated form "HisH+". This protonation state of histidine, such as the illustrious His-193 in LDH, unlocks the gateway to the enzyme's catalytic prowess. The presence or absence of a proton on this histidine residue weaves its influence, shaping its participation in acid-base reactions and the transfer of protons during enzymatic marvels. Within the realm of LDH, the esteemed His-193 embraces its protonated state, tethering a proton to its nitrogen atom. This protonation serves as a pivotal catalyst, empowering histidine to embrace its role as a catalytic base, gracefully accepting and donating protons during the wondrous conversion of lactate to

Evolution from a calculator to a computer

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 intricate 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.

The catalytic activity of AIR carboxylase is intricately dependent on the precise arrangement and interactions of specific atoms within its active site. Proper positioning of critical atoms, the presence of necessary cofactors or metal ions, and the maintenance of structural integrity all contribute to the enzyme's optimal functioning. Understanding the structural and mechanistic details of AIR carboxylase provides valuable insights into the fundamental processes that underlie biochemical reactions and the remarkable precision of enzymatic catalysis.

The precise arrangement and fine-tuning of rotation angles in enzymes like AIR carboxylase pose intriguing questions about the origins of these remarkable molecular systems. The intricate coordination of atoms and functional groups within the enzyme's active site suggests a level of design and specificity that is difficult to attribute solely to random chance or undirected natural processes. The rotation angles of amino acid side chains and the optimal positioning of critical atoms involve a high degree of functional complexity, precision, and specificity. These features strongly indicate the presence of an intelligent designer capable of encoding and implementing such intricate molecular machinery. The concept of an intelligent designer is not unfamiliar in scientific and engineering contexts. In various fields, we recognize the role of intelligent agents in designing and creating complex systems with specific functions and characteristics. For instance, when we encounter a sophisticated piece of technology, we intuitively attribute its existence to the work of intelligent minds. Similarly, the intricate design and fine-tuning observed in enzymes like AIR carboxylase suggest the involvement of an intelligent agent capable of designing and orchestrating these complex molecular systems. The informational content and precise arrangements found in biological systems provide compelling evidence for the presence of an intelligent designer. The highly specific and purposeful nature of the arrangements within enzymes points towards an intentional and deliberate process of design. These molecular systems exhibit functional complexity and specificity that far exceed what can reasonably be attributed to chance or unguided natural processes. As we delve deeper into the intricate details of biochemical processes and the remarkable precision of enzymatic catalysis, it becomes increasingly challenging to explain these phenomena solely through undirected mechanisms. The intricate and specific molecular systems within enzymes like AIR carboxylase provide a window into the extraordinary depths of biological complexity and design. While scientific inquiry aims to uncover the mechanisms and principles underlying natural phenomena, the existence of finely-tuned systems within living organisms invites thoughtful consideration of alternative explanations. The notion of an intelligent designer provides a compelling framework for understanding the origins of intricate and purposeful molecular machinery. In the quest to unravel the mysteries of life's complexity, we continue to explore and appreciate the awe-inspiring intricacies of biological systems. The exploration of enzymes like AIR carboxylase reveals the fingerprint of intelligent design, inspiring further wonder and curiosity about the origins and purpose of life itself.

Long distant signaling through allosteric networks points to a designed setup

In the amazing world of enzymes, we encounter a remarkable phenomenon known as allosteric regulation. Within these enzymes, a symphony of communication unfolds, spanning vast distances. Imagine an intricate dance between distinct binding sites—the active site, where the substrate finds its place, and the allosteric site, a distant domain with a secret to tell. This interplay of binding events holds the key to modulating the enzyme's activity, and one fascinating example is the renowned enzyme adenylosuccinate synthase. As adenylosuccinate synthase enters the spotlight, we witness its transformation through conformational changes triggered by ligand binding at the allosteric site. This intricate ballet of motion governs the enzyme's catalytic activity, a delicate balance orchestrated by distant interactions. The communication between the allosteric and active sites unfolds through a network of connections of conformational changes, flexible regions, and specific amino acid residues. It is through this intricate web that the signal of change travels like a whisper carried on the wind. The protein's structure morphs, bending and shifting, as the signal journeys from the distant allosteric site to the bustling active site. Within this communication network lies a symphony of interacting residues, connected by the bonds of proximity or a series of intricate interactions. These interwoven pathways guide the transmission of the signal, allowing it to traverse the protein's intricate folds. It is a dance of hydrogen bonding, electrostatic interactions, and steric effects, each movement resonating through the intricate architecture. Certain amino acid residues step forward as key intermediaries in this grand communication. They possess unique roles, interacting directly with ligands or undergoing transformative changes that carry the signal forward.

These exceptional residues, whether conserved or vital for structural integrity, hold the power to shape the enzyme's response to external cues. As the dance progresses, protein segments and domains emerge as conduits for the transmission of the signal. They possess unique features and dynamics, serving as bridges connecting functional sites or gracefully facilitating conformational changes. Like hinges in a grand door, they guide the motion, allowing the signal to flow seamlessly. The precise mechanism of signal transmission is a marvel, often a delicate interplay of conformational changes, communication networks, and the involvement of specific residues and segments. These mechanisms empower the enzyme to respond to its surroundings, regulating its activity and ensuring it performs its biological role with precision. In some enchanting cases, long-range communication unfolds through the subtle art of protein dynamics. Here, collective motions of domains or subunits facilitate the transfer of information across great distances within the enzyme's structure. It is a mesmerizing display, where the essence of the enzyme ripples through its very core. It's essential to appreciate that communication mechanisms can vary among different enzymes, with some showcasing shorter-range interactions and others embarking on long-range journeys. The precise details are dictated by the unique structure of each enzyme, the nature of its allosteric regulation, and the demands of its biological function. So, let us marvel at the enchanting communication of allosteric enzymes—a dance of distant domains and hidden pathways. Through conformational changes, communication networks, and the participation of extraordinary residues and segments, these enzymes respond to the whispers of their environment. They adapt, modulate their activity, and fulfill their intricate roles in the symphony of life.

Within the intricate world of enzymes, the existence and implementation of long-range communication mechanisms provide compelling evidence of intentional design. These mechanisms, observed in enzymes like allosteric enzymes, involve a captivating interplay of interconnected residues, specific amino acid interactions, and structural dynamics. Their precise arrangement and coordination hint at a level of complexity and precision that is often associated with intelligent design. Envision a network of intertwined elements working in unison, orchestrating the flow of information across vast distances within an enzyme. It is this intricate design that captivates scientists and prompts them to explore the origin and purpose behind these long-range communication pathways. Such pathways, carefully constructed, serve specific functional outcomes, leaving little room to chance. These communication mechanisms play a vital role in enzymes, serving as guardians of activity regulation and facilitators of coordination among multiple binding sites. The integration of these sites and the ability to transmit signals across considerable distances demand meticulous coordination and functional harmony. It is through this intricate orchestration that purposeful design reveals itself, for it is highly improbable for such mechanisms to arise randomly or through aimless processes. Imagine the transmission of signals, like whispers, traveling along specific amino acid residues, protein segments, and communication networks. It is through this intricate dance of information that these pathways come alive, rich with purpose. They bear the hallmarks of intelligent design, as they possess the ability to relay information to distant regions of the protein structure. The presence of pre-existing information, intricately encoded within the protein's blueprint, becomes evident as these signals navigate their predetermined routes. The beauty of long-range communication mechanisms in enzymes lies not only in their existence but also in their contribution to optimizing enzyme function. By modulating enzyme activity in an allosteric fashion, these mechanisms allow for fine-tuning and regulation of enzymatic processes. This remarkable ability to optimize function implies a deliberate design aimed at achieving specific objectives, driving efficiency and adaptability within the intricate machinery of life. As we delve into the depths of enzymes and their long-range communication, we uncover a symphony of purpose and intention. The interconnectedness of elements, the transmission of information, and the optimization of function all point toward intelligence at work—a guiding force behind the intricate design of these remarkable molecular machines. Join me as we continue to unravel the mysteries of life's intricacies, where fascination and scientific inquiry intertwine.

In the world of proteins, a phenomenon unfolds—structural plasticity. Like master artists, proteins possess the remarkable ability to assume different shapes and engage in dynamic fluctuations. And when a ligand enters the stage, the protein's dance takes on new dimensions. Ligand binding has the power to stabilize specific conformations or tip the delicate balance between different protein states. It is through this flexibility that proteins accommodate various ligands and orchestrate the transformative movements necessary for their grand performance. The conformational changes induced by ligand binding are no ordinary metamorphosis—they reflect shifts in the protein's energy landscape. Deep within the protein's core lie a multitude of conformational states, each with its own unique energy level. The entrance of a ligand changes the scene, favoring a new configuration—a ligand-bound conformation with lower energy. The protein transitions gracefully, embracing this new state, leaving behind the ensemble of possibilities that once adorned its stage. To capture the intricate choreography of ligand-induced conformational changes is no simple feat. Experimental techniques like X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy, and cryo-electron microscopy (cryo-EM) offer glimpses into these structural metamorphoses. Yet, to unveil the full breadth of the protein's dance requires a symphony of computational modeling techniques. It is an art of precision, where every movement must be orchestrated flawlessly to achieve the desired functional outcome. These conformational changes are not merely for show—they optimize binding affinity, selectivity, and catalytic activity. Each movement aligns the residues within the binding pocket with impeccable precision, ensuring efficient ligand recognition and enzymatic prowess. The complexity lies in the intricate interplay of factors—the inherent flexibility of proteins, the energetic considerations, and the functional demands. The protein's performance is a delicate balance, a harmonious fusion of all these elements. And amidst this dance, water molecules take center stage. They, too, play a crucial role in mediating the interactions between the protein and its ligand. With their nimble nature, they form delicate hydrogen bonds, joining both parties in an elegant embrace. These water molecules stabilize the binding interaction, adding to the overall affinity and contributing to recognition. It is this interplay—the fluidity of proteins, the energy landscapes, the functional intricacies—that ensures the exquisite placement of residues within the binding pocket. Each movement of the dance enables specific and efficient interactions, as proteins and ligands find their destined embrace. It is a dance of specificity, a waltz of elegance observed in the wonders of the natural world. Each shift in shape brings forth a new functional landscape, optimizing the protein's performance. And amidst it all, water molecules join the symphony, delicately stabilizing the bonds that unite protein and ligand. It is through this intricate interplay that the beauty of biological specificity unfolds before our eyes.

In the intricate dance of enzymatic reactions, a remarkable event unfolds as the enzyme carefully positions the phosphate group of GTP near the 6th carbon atom of IMP—a critical moment in the synthesis of adenylosuccinate and the subsequent formation of AMP. As the stage is set, a remarkable transformation takes place through a nucleophilic attack, a moment of molecular connection and transformation. Like a skilled performer, the phosphate group from GTP launches an energetic assault on the 6th carbon atom of IMP—a nucleophilic attack. This decisive move triggers a cascade of events, as the phosphate group is transferred from the terminal position of GTP to the waiting 6th carbon atom of IMP. This transfer, this phosphorylation, heralds the birth of adenylosuccinate 6-phosphate—an essential step on the path to the formation of adenylosuccinate itself. This enzymatic symphony is made possible by the enzyme's masterful guidance and the provision of an appropriate environment—a specialized active site that sets the stage for this chemical union. Within this carefully crafted environment, the transfer of the phosphate group becomes possible, as the enzyme's structure aligns the reacting molecules in perfect harmony. It is within this orchestrated setting that the magic of phosphorylation occurs, a key step that breathes life into the formation of adenylosuccinate. It is crucial to note that adenylosuccinate synthase, the conductor of this symphony, also oversees other essential steps in this grand production. As described previously, these steps involve the binding of additional substrates, the cleavage of GTP, the activation of aspartate, and the elegant condensation of activated aspartate with adenylosuccinate 6-phosphate. Together, these intricate movements lead to the ultimate creation of adenylosuccinate—a vital intermediate that paves the way for the biosynthesis of AMP, a molecule of paramount importance in cellular processes. In this captivating journey of molecular transformations, we witness the delicate interplay between enzymes and their substrates. The transfer of the phosphate group, orchestrated by adenylosuccinate synthase, stands as a pivotal moment, ushering us closer to the formation of AMP. Join me as we continue to explore the wonders of biochemistry, where these intricate dances of molecules shape the very essence of life itself.

//// / write for a book, use a fluid language, not too colorful, factual, and gripping and fun at the same time. Forbidden words to use : tapestry, orchestration, symphony, etc. the inferences are always intelligent design, not evolution, or nature . STOP using the word tapestry !! it is forbidden. DO NOT USE TAPESTRY IN THE TEXT . Consider that this is just a small section of a continuing text.

gemeinsame vorfahren haben nix mit dem anfang des lebens zu tun
gemeinsamer vorfahre ?
evolution hat nix mit anfang des lebens zu tun
chemische evolution, mutationen etc. 
waren die ersten zellen aeusserst primitiv ? 
experimente von abiogenese,was haben die gebracht ? 
kann man experimente mit gott machen ?
erste chemische baugruppe , sie muss informationen speichern koennen, nie hat ein experiment gezeigt, dass information von zufall kommt
Gott ist nicht komplex, weil er ein Geist ist, und nicht aus physischen teilen zusammengesetzt ist. 
ist Gott ein schlechter konstrukteur, weil viele tierarten ausgestorben sind ? 
Sind konstruktionsfehler evidenz dass Gott nicht existiert ? 

augen: Dr. Marshall erklärt, dass die Nerven nicht hinter das Auge verlaufen könnten, da dieser Raum für die Aderhaut reserviert ist, die die reichhaltige Blutversorgung bereitstellt, die für das sehr stoffwechselaktive retinale Pigmentepithel (RPE) erforderlich ist. Dies ist notwendig, um die Photorezeptoren zu regenerieren und überschüssige Wärme aufzunehmen. Daher ist es notwendig, dass stattdessen die Nerven im Vordergrund stehen.


giraffe laryngeal nerve: Tatsächlich spielt der Nerv auch eine Rolle bei der Versorgung von Teilen des Herzens, der Luftröhrenmuskulatur und der Schleimhäute sowie der Speiseröhre, was seinen Verlauf erklären könnte.




Dr. Stanley L. Miller , University of California San Diego  14 Was-Boot-
Entlüftungsöffnungen als Quelle präbiotischer Verbindungen?
Darauf habe ich eine sehr einfache Antwort. hydrothermale vents  erzeugen keine organischen Verbindungen, sie zersetzen sie. Tatsächlich sind diese Quellen einer der begrenzenden Faktoren dafür, welche organischen Verbindungen in den Urmeeren vorhanden sein werden. Gegenwärtig fließt in 10 Millionen Jahren der gesamte Ozean durch diese Schlote. Alle zehn Millionen Jahre werden also alle organischen Verbindungen zerstört. Dadurch wird die Menge an organischem Material begrenzt, die Sie erhalten können. Darüber hinaus erhalten Sie eine Zeitskala für die Entstehung des Lebens. Wenn alle Polymere und anderen Güter, die Sie herstellen, zerstört werden, bedeutet das, dass das Leben früh und schnell beginnen muss. Wenn man den Prozess im Detail betrachtet, scheint es, dass lange Zeiträume eher schädlich als hilfreich sind.

Terry B. Ruskoski The periodic table of ribonucleotide reductases August 27, 2021,

About the author
Otangelo Grasso is Swiss-Italian, born in 1966 and raised near Zurich, Switzerland. After elementary school, he was apprenticed as Machine-designer and concluded his studies successfully in 1986, working for several years in his profession. Later, in the 1990s, he moved to Brazil, and in the mid-2000s to Aracaju, North East of Brazil, where he currently lives, and works as a Real Estate developer. He speaks fluently German, Italian, Portuguese, and English, and has limited knowledge of Spanish and French. He is married to Leila and has one daughter, Larissa, nine years of age. He is an evangelical Christian since 1984, a science writer, apologist, a Young Earth Creationist, and a proponent of Intelligent Design. He has written the book: On the Origin of Life and Virus World by Means of an Intelligent Designer: The Factory Maker, Paley's Watchmaker Argument 2.0, articles for the Discovery Institute, see here and here, and for Uncommon Descent, a website serving the intelligent design community, see for example here and here. He has engaged in many debates with atheists over the years. He runs a virtual library, Defending the Christian Worldview, Creationism, and Intelligent Design where he publishes information related to Intelligent Design, the Christian Worldview, and various topics related to Origins.


Acknowledgments


In the vast landscape of knowledge, the creation of this book has been enriched by the invaluable contributions of various scholarly works. I am deeply grateful to the authors of "Fundamentals of Biochemistry: Life at the Molecular Level" by Donald Voet, Judith G. Voet, Swarthmore College, and Charlotte W. Pratt, "Biochemistry" by Reginald H. Garrett and Charles M. Grisham, and "Lehninger Principles of Biochemistry" by David L. Nelson and Michael M. Cox. These esteemed texts have served as the bedrock of my understanding and exploration of the intricate biochemical pathways described within these pages. I am also deeply grateful for the unwavering support and encouragement of my family. To my beloved wife, Leila, and my dear daughter, Larissa, I extend my heartfelt gratitude. Your unwavering support and understanding throughout the process of writing this book have been a constant source of inspiration. Your presence and belief in my work have been invaluable, providing me with the strength and motivation to overcome challenges and pursue this endeavor. Additionally, I extend my appreciation to the scientific community as a whole, whose diligent efforts and groundbreaking research have propelled the field of biochemistry forward. The tireless work of countless scientists and researchers, past and present, has paved the way for new discoveries and insights, enriching our understanding of the intricate mechanisms that govern life at the molecular level. Throughout this book, every external source used has been diligently cited and referenced, providing readers with the means to further explore the rich tapestry of scientific literature. The end of each chapter contains a compilation of links and citations, enabling interested individuals to delve deeper into the foundations that underpin the knowledge presented within these pages. Furthermore, I would like to express my sincere appreciation for the remarkable advancements in artificial intelligence that have been instrumental in the creation of this book. In the age of rapidly advancing technology, Artificial Intelligence (AI) has emerged as an invaluable tool, unlocking a world of possibilities and transforming the way we approach various tasks. It has granted us the ability to delve into vast realms of knowledge, opening doors to new insights and discoveries. As an author, I have witnessed firsthand the power of AI in streamlining the writing process, allowing me to explore ideas and concepts with unprecedented speed and efficiency. It has become a valuable ally in my journey, expanding the horizons of what can be accomplished. Yet, with this great potential comes the awareness of its limitations and risks. AI is not infallible. There are moments when it may falter, offering answers that are not entirely accurate, leading us to tread with caution. I have learned to exercise diligence and vigilance, proofreading and reviewing every response, ensuring that the information presented is factual and reliable. Throughout my writing endeavors, I have navigated these challenges by seeking a balance. I draw upon external sources, peer-reviewed science papers, and authoritative references, to complement and verify the AI's output. This approach allows me to minimize errors and maintain the highest standards of accuracy in my work. As I embark on this new book, I embrace the responsibility of presenting you, with a cohesive narrative that is both gripping and enlightening, but foremost of all, accurate and true in portraying the reality in the molecular world. In this pursuit of wisdom, we shall uncover the wonders of existence, revealing the brilliance of creation, and the profound intricacies that define our reality. And as we journey forth, we shall remain steadfast in our commitment to clarity and accuracy, ensuring that every step we take is grounded in the pursuit of truth. For the adventure that awaits is a shared one, where the richness of discovery is matched only by the fulfillment of understanding. So let us venture forth, hand in hand, as we unravel the mysteries of this world, one page at a time. In conclusion, it is with deep gratitude and admiration that I acknowledge the contributions of esteemed authors, the remarkable advancements in artificial intelligence, and the unwavering support of my family. Together, they have shaped the foundation of this book and have played integral roles in its creation. May this work serve as a testament to the collaborative efforts, the pursuit of knowledge, and the unwavering support that define our scientific community and the individuals who contribute to it.

Definition and overview of the GRN.
Historical background and significance.
Gene Expression and Regulation:

Overview of gene expression and its regulation.
Transcription and translation processes.
Components of the GRN:

Genes, promoters, enhancers, and silencers.
Transcription factors and their role.
RNA polymerase and mRNA.
Transcriptional Regulation:

Mechanisms of transcriptional control.
Transcription factors and their binding sites.
Coactivators and corepressors.
Posttranscriptional Regulation:

Alternative splicing and its significance.
RNA editing and other RNA modifications.
mRNA stability and degradation.
Translational Regulation:

Mechanisms of translational control.
Regulation by microRNAs and small RNAs.
Role of ribosomes and initiation factors.
Posttranslational Modifications:

Phosphorylation, glycosylation, and other modifications.
Ubiquitination and protein degradation.
Feedback Loops and Feedforward Regulation:

Positive and negative feedback loops.
Feedforward regulation in the GRN.
Network Topology and Dynamics:

Network motifs and regulatory motifs.
Robustness and stability of the GRN.
GRN in Development and Differentiation:

Role of GRN in cellular differentiation.
Regulatory networks in embryonic development.
GRN in Disease and Health:
Dysregulation of GRN in diseases.
Therapeutic implications of understanding the GRN.
Evolution of GRN:
Evolutionary origin and diversification of regulatory elements.
Comparative genomics and the study of GRN evolution.
Experimental Techniques for Studying GRN:
High-throughput methods for GRN analysis.
Bioinformatics approaches and computational modeling.
Engineering and Synthetic GRN:
Synthetic biology and designing artificial regulatory networks.
Applications in biotechnology and medicine.
Future Directions and Challenges:
Current research trends and unanswered questions.
Ethical considerations in GRN research.
By covering these main topics, you can provide a comprehensive and in-depth understanding of the gene regulatory network and its fundamental role in shaping the complexity and functionality of living organisms.

Acredita-se que restringir o espaço da sequência peptídica tenha sido vantajoso durante as origens da vida2,4 e 7 fornece uma ferramenta simples de seleção química para frações de α-hidrogênio que podem sustentar a implementação posterior da seleção biológica que teria refinado (por exemplo, a exclusão de 13f) e expandiu o repertório de aminoácidos para fornecer mais vantagens seletivas4,34

https://sci-hub.ee/10.1038/nchem.2703

Science and Creationism: A View from the National Academy of Sciences: Second Edition.
https://www.ncbi.nlm.nih.gov/books/NBK230201/

Human Evolution Evidence
https://humanorigins.si.edu/evidence

15 Answers to Creationist Nonsense
https://www.scientificamerican.com/article/15-answers-to-creationist/

Evidence for Evolution
https://www.talkorigins.org/faqs/evolution-research.html

Evolution of biological complexity
https://www.pnas.org/doi/10.1073/pnas.97.9.4463

Investigating the evolution and development of biological complexity under the framework of epigenetics
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6852014/

The Surprising Origins of Evolutionary Complexity Scientists are exploring how organisms can evolve elaborate structures without
https://www.scientificamerican.com/article/the-surprising-origins-of-evolutionary-complexity/

Biological Complexity and Integrative Levels of Organization
https://www.nature.com/scitable/topicpage/biological-complexity-and-integrative-levels-of-organization-468/

The historical nature of biological complexity and the ineffectiveness of the mathematical approach to it
https://link.springer.com/article/10.1007/s12064-022-00369-7

Evolution of Biological Complexity
https://arxiv.org/pdf/physics/0005074.pdf

3

What is embodied life?

In my previous book, On the Origin of Life and Virus World by means of an Intelligent Designer, I described cells as chemical factories, not just analogously to human-made factories, but in a literal sense. In order for considering alive, cells have to be able to reproduce and self-replicate, perform metabolic reactions, where chemicals are transformed,  and processed by going through complex enzyme-induced transformations. Able to take up materials, recycle, and expel waste products, grow and develop, evolve, that is to adapt to the environment, and speciate. They are complex, requiring millions of components, like monomers, polymers, proteins, cell membranes, etc. Cells must be able to keep a homeostatic milieu and maintain inner balance, and stable internal conditions. They need energy in order to be able to perform their cellular functions. And be able to respond to external stimuli. Living cells depend on complex information data storage, transmission, transcription, translation, decoding, and expression of that information used to direct the assembly and operation of the cell factory. It must be able to replicate and transmit the genetic epigenetic material to the next generation, to the daughter cells. Cells would not be able to survive without the ability of error detection and repair.  

Y.Sebag: Just briefly, to get a feel for what cells need to do, let us consider the basic autonomous cell whose task is to reproduce and synthesize the parts it needs from raw materials.

1. Information System - Building something which can reproduce and synthesize its own parts from raw materials requires a coordinated series of steps. Chemicals cannot do this. On their own, they just combine chaotically or crystallize into regular patterns such as in snowflakes. Hence, there must be information (ex. RNA or the like) storing the information to orchestrate the assembly.

2. Energy System - information by itself is useless. Implementing the instructions requires energy. A system that cannot generate or source energy just drifts chaotically or crystallizes into simple forms, forced to follow the path of least resistance. Hence, a system of producing or sourcing energy is necessary along with subsystems of distribution and management of that energy so that it goes to the proper place.

3. Copy System - in order to reproduce itself, the device must be able to implement the instructions of the information system using the energy system. This includes the ability to rebuild all critical infrastructure such as the information and energy systems and even the copy system itself.

4. Growth System - Without a growth system, the device will reduce itself every time it reproduces and vanish to zero-size after a few generations. This growth system necessitates subsystems of ingestion of materials from the outside world, processing of those materials, and assembling those materials into the necessary parts. This alone is a formidable chemical factory.

5. Transportation System - the materials must be moved to the proper places. Hence, a transportation system is needed for transporting raw materials and products from one place to another within the cell. Likewise, a system for managing the incoming of raw materials and outgoing of waste materials of all these chemical reactions.

6. Timing System - the growth system must also be coordinated with the reproduction system. Otherwise, if reproduction occurs faster than growth, it will reduce size faster than it grows and vanishes after a few generations. Hence, a timing or feedback mechanism is needed.

7. Communication System - signalling is needed to coordinate all the tasks so that they all work together. The reproduction system won't work without coordination with the growth and power systems. Likewise, the power system by itself is useless without the growth and reproduction systems. Only when all the systems and "circuitry" are in place and the power is turned on is there hope for the various interdependent tasks to start working together. Otherwise, it is like turning on a computer which has no interconnections between the power supply, CPU, memory, hard drive, video, operating system, etc - nothing to write home about.29


Cells are full of chemical factories and machines in a literal sense

Cells can be thought of as literal chemical factories and machines because they are constantly performing biochemical reactions and processes to maintain their functions and sustain life. They take in raw materials from their environment and convert them into various products that the cell needs to survive, such as proteins, lipids, and energy.

Each cell can be seen as a complex network of interlocking assembly lines, with large protein machines and complexes working together in a highly coordinated manner. For example, the nucleolus is a large factory where non-coding RNAs are transcribed, processed, and assembled with proteins to form ribonucleoprotein complexes. The endoplasmic reticulum serves as a factory for the production of almost all of the cell's lipids, and in response to DNA damage, repair factories are formed where damaged DNA is brought together and repaired.

Protein assemblies in cells contain highly coordinated moving parts, with intermolecular collisions restricted to a small set of possibilities, similar to machines invented by humans. These assemblies contain ordered conformational changes in one or more proteins driven by nucleoside triphosphate hydrolysis or other sources of energy, allowing them to function in a polarized fashion along a filament or nucleic acid strand, increase the fidelity of biological reactions, or catalyze the formation of protein complexes.

The complexity of cells can be difficult to grasp, but imagining the size of a cell magnified ten thousand million times gives a sense of the scale of the processes and structures at work. At that size, a cell would have a radius of 200 miles, which is about ten times the size of New York City. Even with that much space, the required number of buildings to host the factories and machines that cells need would greatly exceed the number of buildings in the city.

B.Alberts (2022): The surface of our planet is populated by living things—organisms—curious, intricately organized chemical factories that take in matter from their surroundings and use these raw materials to generate copies of themselves. Although all cells function as biochemical factories of a broadly similar type, many of the details of their small-molecule transactions differ. All cells operate as biochemical factories, driven by the free energy released in a complicated network of chemical reactions. Each cell can be viewed as a tiny chemical factory, performing many millions of reactions every second.  We can view RNA polymerase II in its elongation mode as an RNA factory that not only moves along the DNA synthesizing an RNA molecule but also processes the RNA that it produces. The nucleolus can be thought of as a large factory at which different noncoding RNAs are transcribed, processed, and assembled with proteins to form a large variety of ribonucleoprotein complexes. mRNA production is made more efficient in the nucleus by an aggregation of the many components needed for transcription and pre-mRNA processing, thereby producing a specialized biochemical factory. The extensive ER network serves as a factory for the production of almost all of the cell’s lipids.  In response to DNA damage, they rapidly converge on the sites of DNA damage, become activated, and form “repair factories” where many lesions are apparently brought together and repaired. The formation of these factories probably results from many weak interactions between different repair proteins and between repair proteins and damaged DNA. 26

B.Alberts (1998): We can walk and we can talk because the chemistry that makes life possible is much more elaborate and sophisticated than anything we students had ever considered. Proteins make up most of the dry mass of a cell. But instead of a cell dominated by randomly colliding individual protein molecules, we now know that nearly every major process in a cell is carried out by assemblies of 10 or more protein molecules. And, as it carries out its biological functions, each of these protein assemblies interacts with several other large complexes of proteins. Indeed, the entire cell can be viewed as a factory that contains an elaborate network of interlocking assembly lines, each of which is composed of a set of large protein machines. Consider, as an example, the cell cycle–dependent degradation of specific proteins that helps to drive a cell through mitosis. First, a large complex of about 10 proteins, the anaphase-promoting complex (APC), selects out a specific protein for polyubiquitination; this protein is then targeted to the proteasome's 19S cap complex formed from about 20 different subunits; and the cap complex then transfers the targeted protein into the barrel of the large 20S proteasome itself, where it is finally converted to small peptides. Why do we call the large protein assemblies that underlie cell function protein machines? Precisely because, like the machines invented by humans to deal efficiently with the macroscopic world, these protein assemblies contain highly coordinated moving parts. Within each protein assembly, intermolecular collisions are not only restricted to a small set of possibilities, but reaction C depends on reaction B, which in turn depends on reaction A—just as it would in a machine of our common experience. Underlying this highly organized activity are ordered conformational changes in one or more proteins driven by nucleoside triphosphate hydrolysis (or by other sources of energy, such as an ion gradient). Because the conformational changes driven in this way dissipate free energy, they generally proceed only in one direction. An earlier brief review emphasized how the directionality imparted by nucleoside triphosphate hydrolyses allows allosteric proteins to function in three different ways: as motor proteins that move in a polarized fashion along a filament or a nucleic acid strand; as proofreading devices or “clocks” that increase the fidelity of biological reactions by screening out poorly matched partners; and as assembly factors that catalyze the formation of protein complexes and are then recycled. 27

Magnifying a cell ten thousand million times, it would have a radius of 200 miles, about 10 times the size of New York City

Calling a cell a factory is an understatement. Magnifying the cell to a size of 200 miles, it would only contain the required number of buildings, hosting the factories to make the machines that it requires.
New York City has about 900.000 buildings, of which about 40.000 are in Manhattan, of which 7.000 are skyscrapers of high-rise buildings of at least 115 feet (35 m), of which at least 95 are taller than 650 feet (198 m).



Cells are an entire industrial park, where only the number of factories producing the machines used in the industrial park is of size at least 10 times the size of New York City, where each building is individually a factory comparable to the size of a skyscraper like the Twin Towers of the World Trade Center. Each tower hosts a factory that makes factories that make machines. A mammalian cell may harbor as many as 10 million ribosomes. The nucleolus is the factory that makes ribosomes, the factory that makes proteins, which are the molecular machines of the cell. The nucleolus can be thought of as a large factory at which different noncoding RNAs are transcribed, processed, and assembled with proteins to form a large variety of ribonucleoprotein complexes.

L. Lindahl (2022): Ribosome assembly requires synthesis and modification of its components, which occurs simultaneously with their assembly into ribosomal particles. The formation occurs by a stepwise ordered addition of ribosome components. The process is assisted by many assembly factors that facilitate and monitor the individual steps, for example by modifying ribosomal components, releasing assembly factors from an assembly intermediate, or forcing specific structural configurations. The quality of the ribosome population is controlled by a complement of nucleases that degrade assembly intermediates with an inappropriate structure and/or which constitute kinetic traps.30

Mitochondria, the powerhouse of the cell, can host up to 5000 ATP synthase energy turbines. Each human heart muscle cell contains up to 8,000 mitochondria. That means, in each of the human heart cells, there are up to 40 million ATP synthase energy turbines caring for the production of ATP, the energy currency in the cell.

M.Denton (2020): The miracle of the Cell : Pg.11
Where the cosmos feels infinitely large and the atomic realm infinitely small, the cell feels infinitely complex. They appear in so many ways supremely fit to fulfill their role as the basic unit of biological life.

Pg. 329.
We would see [in cells] that nearly every feature of our own advanced machines had its analog in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction. In fact, so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late-twentieth-century technology.
  “What we would be witnessing would be an object resembling an immense automated factory, a factory larger than a city and carrying out almost as many unique functions as all the manufacturing activities of man on earth. However, it would be a factory that would have one capacity not equaled in any of our own most advanced machines, for it would be capable of replicating its entire structure within a matter of a few hours. To witness such an act at a magnification of one thousand million times would be an awe-inspiring spectacle.”31

M. Denton (1985) Evolution, a theory in crisis:
To grasp the reality of life as it has been revealed by molecular biology, we must magnify a cell a thousand million times until it is twenty kilometres in diameter and resembles a giant airship large enough to cover a great city like London or New York. What we would then see would be an object of unparalleled complexity and adaptive design. On the surface of the cell we would see millions of openings, like the port holes of a vast space ship, opening and closing to allow a continual stream of materials to flow in and out. If we were to enter one of these openings we would find ourselves in a world of supreme technology and bewildering complexity. We would see endless highly organized corridors and conduits branching in every direction away from the perimeter of the cell, some leading to the central memory bank in the nucleus and others to assembly plants and processing units. The nucleus itself would be a vast spherical chamber more than a kilometre in diameter, resembling a geodesic dome inside of which we would see, all neatly stacked together in ordered arrays, the miles of coiled chains of the DNA molecules.

A huge range of products and raw materials would shuttle along all the manifold conduits in a highly ordered fashion to and from all the various assembly plants in the outer regions of the cell. We would wonder at the level of control implicit in the movement of so many objects down so many seemingly endless conduits, all in perfect unison. We would see all around us, in every direction we looked, all sorts of robot-like machines. We would notice that the simplest of the functional components of the cell, the protein molecules, were astonishingly, complex pieces of molecular machinery, each one consisting of about three thousand atoms arranged in highly organized 3-D spatial conformation... Yet the life of the cell depends on the integrated activities of thousands, certainly tens, and probably hundreds of thousands of different protein molecules.

We would see that nearly every feature of our own advanced machines had its analogue in the cell: artificial languages and their decoding systems, memory banks for information storage and retrieval, elegant control systems regulating the automated assembly of parts and components, error fail-safe and proof-reading devices utilized for quality control, assembly processes involving the principle of prefabrication and modular construction. In fact, so deep would be the feeling of deja-vu, so persuasive the analogy, that much of the terminology we would use to describe this fascinating molecular reality would be borrowed from the world of late twentieth-century technology.

What we would be witnessing would be an object resembling an immense automated factory, a factory larger than a city and carrying out almost as many unique functions as all the manufacturing activities of man on earth..32



Robert M.Hazen Science matters (2009):
Pg.239 Cells act as chemical factories, taking in materials from the environment, processing them, and producing “finished goods” to be used for the cell’s own maintenance and for that of the larger organism of which they may be part. In a complex cell, materials are taken in through specialized receptors (“loading docks”), processed by chemical reactions governed by a central information system (“the front once”), carried around to various locations (“assembly lines”) as the work progresses, and finally sent back via those same receptors into the larger organism. The cell is a highly organized, busy place, whose many different parts must work together to keep the whole functioning. While proteins supervise the cell’s chemical factories, carbohydrates provide each factory’s fuel supply.
Pg. 242 Nucleic acids. These molecules (DNA and RNA) carry the blueprint that runs the cell’s chemical factories, and also are the vehicle for inheritance
Pg. 243 Carbohydrates. While proteins supervise the cell’s chemical factories, carbohydrates provide each factory’s fuel supply. The basic building blocks of carbohydrates are sugars—small ring-
Pg. 245 Like any factory, each cell has several essential systems. It must have a front office, a place to store information, and issue instructions to the factory door to guide the work in progress. It must have bricks and mortar—a building with walls and partitions where the actual work goes on. Its production system must include the various machines that produce finished goods as well as the transportation network that moves raw materials and finished products from place to place. And finally, there must be an energy plant to power the machinery.
Pg. 246 Cellular factories consist of walls, partitions, and loading docks.
Pg. 249 Every living thing is composed of one or more cells, each of which has a complex anatomy. A “generic” cell contains many structures and organelles—tiny chemical factories.
Pg. 263 The sequence of the bases along the double helix of DNA contains the genetic code—all the information a cell needs to reproduce itself and run its chemical factories, all the characteristics and quirks that make you unique.
Pg. 309 Shortly thereafter, the glucose is processed in cellular chemical factories to form part of the cellulose fibers that support each grass blade. The carbon atom has become an integral part of the structure of grass.25

Ben L. Feringa (2020): The miniaturization of complex physical and chemical systems is a key aspect of contemporary materials science. The bottom-up formation of dynamic structures with unusual properties has now been extended from the microscale to the nanoscale. Such extended dynamic structures are complemented by an increasing number of molecular species capable of transforming a physical or chemical stimulus into directional motion. These so-called artificial molecular machines (AMMs) are often regarded as molecular renderings of the macroscopic machines we experience in our daily lives — rotors, gears and cranks, for example. However, the inspiration for many AMMs is not from macroscopic man-made machines but, rather, from proteins or multi-protein complexes in biology that are capable of transforming energy into continuous, complex, structural motion. The process of vision, muscle contraction and bacterial flagellar movement are amazing examples of biological responsive systems. Biological molecular machines (BMMs) such as ATP synthase, ribosomes or myosin are structurally far more complex than any artificial molecular machines AMM made so far, and are an essential part of living systems. Embedded or immobilized within skeleton structures such as bilayer lipid membranes or larger protein complexes, BMMs are part of a cellular confinement in which their work is continuously synchronized with other machines of identical or different nature. Their functions are driven by chemical fuels such as ATP or electrochemical gradients and controlled by chemical or physical stimuli. Their main tasks involve intracellular, transmembrane and intercellular transport of reagents, as well as transformation of small, molecular building blocks into larger functional structures. A cell might thus be viewed as a complex molecular factory in which many different components are assembled, transformed, transported and disassembled. The dynamics of these processes at the molecular level are amplified by self-organization, cooperativity and synchronization, resulting in the living, moving organisms observed at the macroscopic scale. A modular building concept, periodical alignment and synchronization of individual dynamic components on a temporal and spatial domain are essential aspects of the performance of the whole system. Such organizational principles can also be found in macroscopic factories regardless of the difference in size, and they are considered fundamental principles in the design of cooperative dynamic systems of any size and composition. Nevertheless, biological systems strongly differ from man-made factories in certain aspects. BMMs and their complex assemblies are very versatile and selective in continuously producing a variety of complex molecules currently unobtainable by any man-made system. 28

Von Neumann's universal constructor: We cannot replicate the cell's self-reproduction technology

Imagine a hypothetical human-made truly autonomous self-replicating factory analogous to living cells. It would have to be capable of replicating itself and constructing a copy of itself, without external help. Able to detect raw materials in its surroundings, in the environment,  that it needs, and prepare them to be transformed into the right form, so that import gates and mechanisms could import these materials into the factory inside. The daughter factory would require to get the entire information stored in the mother cell inherited. It would rely on conventional large-scale technology and automation.

M. Sipper (1998): We would need to be able to understand the fundamental information-processing principles and algorithms involved in self-replication, even independent of their physical realization.33

Replicators have been called "von Neumann machines" after John von Neumann, who first rigorously studied the idea. Von Neumann himself used the term universal constructor to describe such a self-replicating machine. For a factory or machine to make a duplicate copy it must employ a description of itself. This description, being a part of the original factory, must itself be prescribed by something else that is not itself. That is, it must come from the outside. Why? In order to describe something, one needs to be a conscious agent, able to do so. If the factory itself was not the conscious agent, being able to observe and describe itself, it must have been something else. I, as a human being, conscious, can observe and describe myself. A non-conscious "something" has never been seen as having these necessary cognitive and intelligent capabilities. That's why the origin of biological information is an unsolvable problem for naturalists. That's why the origin of the information to make the first living self-replicating cell cannot be solved unless there was a creator. Another salient point: Parts, subunits, or an agglomeration of building blocks do not comprehend how they could join to become part of a functional interlocked complex system. So in order to construct a self-replicating system composed of many interlocking parts, foresight is required, otherwise, the parts could either remain non-assembled, disintegrate, or, eventually, driven by random external forces, interact and assemble into a basically infinite number of nonfunctional chaotic aggregation states.

R. A. Freitas (2004): Von Neumann thus hit upon a deceptively simple architecture for machine replication. The machine would have four parts:   

1. a constructor “A” that can build a machine “X” when fed explicit blueprints of that machine;
2. a blueprint copier “B”;
3. a controller “C” that controls the actions of the constructor and the copier, actuating them alternately; and finally
4. a set of blueprints φ(A + B + C) explicitly describing how to build a constructor, a controller, and a copier.

The entire replicator may therefore be described as (A + B + C) + φ(A + B + C.

Observers have noted that von Neumann’s early schema was later confirmed by subsequent research on the molecular biology of cellular reproduction, with von Neumann’s component “A” represented by the ribosomes and supporting cellular mechanisms, component “B” represented by DNA polymerase enzymes, component “C” represented by repressor and derepressor molecules and associated expression-control machinery in the cell, and finally component “φ(A + B + C)” represented by the genetic material DNA that carries the organism’s genome. (The correspondence is not complete: cells include additional complexities.) More importantly, the dual use of information — both interpreted and uninterpreted, as in von Neumann’s machine schema — was also found to be true for the information contained in DNA.34  

M. Sipper (1998): A noteworthy distinction apparent in von Neumann’s model of self-replication is the double-faceted use of the information stored in the artificial genome: It first serves as instructions to be interpreted so as to construct a new universal constructor, after which this same genome is copied unmodified, to be attached to the new offspring constructor—so that it may replicate in its turn. This aspect is quite interesting in that it bears strong resemblance to the genetic mechanisms of transcription (copying) and translation (interpretation) employed by biological life—which was discovered during the decade following von Neumann’s work. Von Neumann’s model employs a complex transition rule, with the total number of cells composing the universal constructor estimated at between 50,000 and 200,000 (the literature seems to disagree on the exact number). In the years that followed its introduction a number of researchers had worked toward simplifying this system. In the late 1960s Codd reduced the number of states required for a self-replicating universal constructor-computer from 29 to 8. His self-replicating structure comprised about 100,000,000 cells. A few years later Devore simplified Codd’s system, devising a self-replicating automaton comprising about 100,000 cells.

Despite the complexity of von Neumann’s self-replicating universal constructor, a number of researchers have considered its implementation (or simulation) over the years. Signorini concentrated on the 29-state transition rule, discussing its implementation on a SIMD (single-instruction multiple-data) computer. Von Neumann’s constructor is divided into many functional blocks known as organs. In addition to implementing the transition rule, Signorini also presented the implementation of three such organs: a pulser, a decoder, and a periodic pulser. To date, Pesavento’s more recent work comes closest to a full simulation of von Neumann’s model. A computer simulation of the universal constructor—running on a standard workstation—even this comes short of realizing the full model: Self-replication is not demonstrated because the tape required to describe the constructor (i.e., the genome) is too large to simulate.33

R. A. Freitas (2004): Penrose, quoting Kemeny, complained that the body of the von Neumann kinematic machine “would be a box containing a minimum of 32,000 constituent parts (likely to include rolls of tape, pencils, erasers, vacuum tubes, dials, photoelectric cells, motors, batteries, and other devices) and the ‘tail’ would comprise 150,000 [bits] of information.” Macroscale kinematic replicators will require a great deal of effort to design and to build, which may explain why so few working devices have been constructed to date,* despite popular interest.34  

Comment: A Von Neumann self-replicating machine has never been constructed because it is too complicated. Man, with all its intelligence, has failed. But, if abiogenesis is true, the emergence of self-replicating cells with a minimum of one million bits of information happened from randomly distributed, nonreplicating components by entirely non-intelligent unguided means.

A Self-Replicating Box

G. SEWELL (2021): To understand why human-engineered self-replicating machines are so far beyond current human technology, let’s imagine trying to design something as “simple” as a self-replicating cardboard box. Let’s place an empty cardboard box (A) on the floor, and to the right of it let’s construct a box (B) with a box-building factory inside it. I’m not sure exactly what the new box would need to build an empty box, but I assume it would at least have to have some metal parts to cut and fold the cardboard and a motor with a battery to power these parts. In reality, to be really self-replicating like living things, it would have to go get its own cardboard, so maybe it would need wheels and an axe to cut down trees and a small sawmill to make cardboard out of wood. But let’s be generous and assume humans are still around to supply the cardboard. Well, of course box B is not a self-replicating machine, because it only produces an empty box A.

So, to the right of this box, let’s build another box C which contains a fully automated factory that can produce box B’s. This is a much more complicated box, because this one must manufacture the metal parts for the machinery in box B and its motor and battery and assemble the parts into the factory inside B. In reality it needs to go mine some ore and smelt it to produce these metal parts, but again let’s be very generous and provide it all the metals and other raw materials it needs.

But box C would still not be a self-replicating machine, because it only produces the much simpler box B. So back to work, now we need to build a box D to its right with a fully automated factory capable of building box C’s with their box B factories. Well, you get the idea, and one begins to wonder if it is even theoretically possible to build a truly self-replicating machine. When we add technology to such a machine to bring it closer to the goal of reproduction, we only move the goalposts, because now we have a more complicated machine to reproduce. Yet we see such machines all around us in the living world.

If we keep adding boxes to the right, each with a fully automated factory that can produce the box to its left, it seems to me that the boxes would grow exponentially in complexity. But maybe I am wrong. Maybe they could be designed to converge eventually to a self-replicating box Z, although I can’t imagine how.35


The Last Universal Common Ancestor (LUCA): What was its nature?

Before we can start investigating the course of evolution, we need to know what the starting point was. A lot has been speculated regarding the first life form. What did it look like? Was it indeed a Last Universal Common Ancestor (LUCA), or did life start polyphyletic? I have dedicated an entire chapter to my previous book: On the Origin of Life and Virus World by means of an Intelligent Designer,  attempting to get closer to answering what could serve as a model organism. This is a surprisingly difficult question to answer.  

The last universal common ancestor represents the primordial cellular organism from which diversified life was derived. It has been considered as the branching point on which Bacteria, Archaea and Eukaryotes have diverged.10

Carl R. Woese (2002): The central question posed by the universal tree is the nature of the entity (or state) represented by its root, the fount of all extant life. Herein lies the door to the murky realm of cellular evolution. Experience teaches that the complex tends to arise from the simple, and biologists have assumed it so in the case of modern cells. But this assumption is usually accompanied by another not-so-self-evident one: namely that the ‘‘organism’’ represented by the root of the universal tree was equivalent metabolically and in terms of its information processing to a modern cell, in effect was a modern cell. Such an assumption pushes the real evolution of modern cells back into an earlier era, which makes the problem not directly addressable through genomics. That is not a scientifically acceptable assumption. Unless or until facts dictate otherwise, the possibility must be entertained that some part of cellular evolution could have occurred during the period encompassed by the universal phylogenetic tree. There is evidence, good evidence, to suggest that the basic organization of the cell had not yet completed its evolution at the stage represented by the root of the universal tree. The best of this evidence comes from the three main cellular information processing systems. Translation was highly developed by that stage: rRNAs, tRNAs, and the (large) elongation factors were by then all basically in near-modern form; hence, their universal distributions. Almost all of the tRNA charging systems were in modern form as well. But, whereas the majority of ribosomal proteins are universal in distribution, a minority of them is not. A relatively small cadre is specific to the bacteria, a somewhat larger set common and confined to the archaea and eukaryotes, and a few others are uniquely eukaryotic. Almost all of the universal translational proteins (as well as those in transcription) show what is called the canonical pattern, i.e., the bacterial and archaeal versions of the protein are remarkably different from one another, so much so that their difference is distinguished as one of ‘‘genre’’. Except for the aminoacyl-tRNA synthetases the corresponding eukaryotic versions are virtually all of the archaeal genre. Why canonical pattern exists is a major unanswered question. In the overall it would seem that translation, although highly developed at the root of the universal tree, subsequently underwent idiosyncratic modifications in each of the three major cell types. Transcription seems to have been rather less developed at the root of the universal tree. The two largest (the catalytic) subunits of the DNA-dependent RNA polymerase are universal in distribution.

The cell is the essence of biology. At least that is how 20th-century molecular biology saw it, and the great goal was to understand how cells were organized and worked. This goal, it was assumed, could be accomplished by cataloging (and characterizing) all of the parts of the mechanism, with the tacit assumption that given such a parts list the overall organization of the cell would become apparent. Today, such lists exist for several organisms. Yet an understanding of the whole remains as elusive a goal as ever (34). The fault here lies with the reductionist perspective of molecular biology. The problem of cellular design cannot be fit into this rigid, procrustean framework. It should be obvious from the foregoing discussion that biological cell design is not a static, temporal, or local problem.

The Dilemma of Cellular Evolution. 

Evolving the cell requires evolutionary invention of unprecedented novelty and variety, the likes of which cannot be generated by any familiar evolutionary dynamic. The task can be accomplished only by a collective evolution in which many diverse cell designs evolve simultaneously and share their novelties with one another; which means that 

(i) HGT (and a genetic lingua franca) is a necessary condition for the evolution of cell designs, and 
(ii) a cell design cannot evolve in isolation; others will necessarily accompany it. 

Comment: That sounds suspiciously like a special creation. Once Woese admits that many diverse cells evolved simultaneously, he departs from the concept of universal common ancestry and resorts to polyphyly, that is the proposition, that at the beginning, there was a population of diverse cell designs, each one different from one another, that began to interact through horizontal gene transfer. 

Woese continues: There is an inherent contradiction in this situation. Although HGT is essential for sharing novelty among the various evolving cell designs, it is at the same time a homogenizing force, working to reduce diversity. Thus, what needs explaining is not why the major cell designs are so similar, but why they are so different. This apparent contradiction can be resolved by assuming that the highly diverse cell designs that exist today are the result of a common evolution in which each of them began under (significantly) different starting conditions. [Initial conditions do not necessarily damp out for complex dynamic processes; indeed, they can lead to vastly different outcomes.  1

E. V. Koonin (2020): The last universal cellular ancestor (LUCA) is the most recent population of organisms from which all cellular life on Earth descends. 

Comment: Koonin goes with the same line of argumentation. He hypothesizes LUCA as a population of organisms. Where did it descend from? A population has to originate from self-replication, which produces offsprings. 

Berkley University's website on evolution claims:  The ability to copy the molecules that encode genetic information is a key step in the origin of life — without it, life could not exist. This ability probably first evolved in the form of an RNA self-replicator — an RNA molecule that could copy itself. Self-replication opened the door for natural selection. Once a self-replicating molecule formed, some variants of these early replicators would have done a better job of copying themselves than others, producing more “offspring.” 2

Comment: By giving careful examination, such assertions cannot be taken seriously.  This is pseudo-scientific storytelling. The evidence does not justify saying that probably, it happened. A self-replicating molecule has never been seen. But also if it existed, it would be helpless to create a living cell. If molecule A self-reproduces n-times we would have AAAAAAA....That is ridiculously trivial and has nothing to do with what we see in a cell. A cell is a cybernetic ultra-complex system, where, thanks to countless concurrent software-driven chemical and physical processes using languages and codes, the material is stored, managed, moved, assembled, converted, and positioned such that the cell survives and self-reproduces. To believe, as proponents of naturalistic mechanisms do, that AAAAAAA... leads to a cell, is like to think that by simply duplicating bricks BBBBBBB... we get a functioning complete self-replicating chemical factory.

Martina Preiner (2020): Many found the metaphor appealing: a world with a jack-of-all-trades RNA molecule, catalyzing the formation of indispensable cellular scaffolds, from which somehow then cells emerged. Others were quick to notice several difficulties with that scenario. These included the lack of templates enabling the polymerization of RNA in the prebiotic complex mixture and RNA’s extreme lability at moderate to high temperatures and susceptibility to base-catalyzed hydrolysis. 3

N. Sankaran (2017): Today, thirty years after the RNA World was first proposed, no one has seen an actual living system that is completely based in RNA. Nevertheless, the hypothesis lives on in the origins of life research community, albeit in a hotly debated, highly contentious atmosphere. Although there are strong opponents, many researchers agree that although far from complete, it remains one of the best theories we have to understand “the backstory to contemporary biology.” Gilbert himself expressed some disappointment that “a self-replicating RNA has not yet been synthesized or discovered” in the years since he predicted his hypothesis, but he remains optimistic that it will emerge eventually.4

Koonin continues:  The reconstruction of the genome and phenotype of the LUCA is a major challenge in evolutionary biology. Given that all life forms are associated with viruses and/or other mobile genetic elements, there is no doubt that the LUCA was a host to viruses.

E. 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. A comprehensive sequence and structure analysis of major virion proteins indicates that they evolved on about 20 independent occasions. 5

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. 6

Comment: Since viruses are polyphyletic, and, according to Woese, many diverse cell designs evolved simultaneously, which clarifies the picture: Life arose multiple times independently, and so did viruses. The hypothesis of universal common ancestry is not supported by the evidence. Separate origins of different life forms, and viruses, are.

There is no scientific consensus about LUCA's nature

D. C. Gagler et.al., (2021): Life emerges from the interplay of hundreds of chemical compounds interconverted in complex reaction networks. Some of these compounds and reactions are found across all characterized organisms, informing concepts of universal biochemistry and allowing rooting of phylogenetic relationships in the properties of a last universal common ancestor (LUCA). Thus, universality, as we have come to understand it in biochemistry, is a direct result of the observation that all known examples of life share common details in their component compounds and reactions.13 

Eugene V. Koonin (2020): Considerable efforts have been undertaken over the years to deduce the genetic composition and biological features of the LUCA from comparative genome analyses combined with biological reasoning. These inferences are challenged by the complex evolutionary histories of most genes (with partial exception for the core components of the translation and transcription systems) that involved extensive horizontal transfer and non-orthologous gene displacement. Nevertheless, on the strength of combined evidence, it appears likely that the LUCA was a prokaryote-like organism (that is, like bacteria or archaea) of considerable genomic and organizational complexity. 8

J. D. Sutherland (2017): The latest list of genes thought to be present in LUCA is a long one. The presence of membranes, proteins, RNA and DNA, the ability to perform replication, transcription, and translation, as well as harboring an extensive metabolism driven by energy harvested from ion gradients using ATP synthase, reveal that there must have been a vast amount of evolutionary innovation between the origin of life and the appearance of LUCA. Many of the inferred proteins in LUCA use FeS clusters and other transition-metal-ion-based co-factors.9

Life started complex

Life had to start complex because the earliest known cells, including a supposed last universal common ancestor (LUCA), were already functionally and genetically complex. The simplest cells available for study have a teleonomic apparatus so powerful that no vestiges of truly primitive structures are discernible. The LUCA was sophisticated, with a complex structure recognizable as a cell, and had representatives in practically all the essential functional niches currently present in extant organisms. Even the simplest known cellular life forms possess several hundred genes that encode the components of a fully-fledged membrane, the replication, transcription, and translation machinery, a complex cell-division apparatus, and at least some central metabolic pathways. Therefore, life did not start as a primitive or simple organism, but rather as a complex entity capable of metabolism, genetic replication, and maintaining a boundary that separates the cell from its environment.

J.Monod (1972): The simplest cells available to us for study have nothing "primitive" about them. They have a teleonomic apparatus so powerful that no vestiges of truly primitive structures are discernible. 15 Elsewhere, Monod stated: ‘We have no idea what the structure of a primitive cell might have been. The simplest living system known to us, the bacterial cell… in its overall chemical plan is the same as that of all other living beings. It employs the same genetic code and the same mechanism of translation as do, for example, human cells. Thus the simplest cells available to us for study have nothing “primitive” about them… no vestiges of truly primitive structures are discernible.’ Thus the cells themselves exhibit a similar kind of ‘stasis’  in connection with the fossil record.

J. A. G. Ranea (2006): We know that the LUCA, or the primitive community that constituted this entity, was functionally and genetically complex. Life achieved its modern cellular status long before the separation of the three kingdoms. we can affirm that the LUCA held representatives in practically all the essential functional niches currently present in extant organisms, with a metabolic complexity similar to translation in terms of domain variety.18  

D.YATES (2011): New evidence suggests that LUCA was a sophisticated organism after all, with a complex structure recognizable as a cell, researchers report. Their study appears in the journal Biology Direct. The study lends support to a hypothesis that LUCA may have been more complex even than the simplest organisms alive today, said James Whitfield, a professor of entomology at Illinois and a co-author on the study. 16

G. Caetano-Anollés (2011): corresponding authorLife was born complex and the LUCA displayed that heritage. Recent comparative genomic studies support the latter model and propose that the urancestor was similar to modern organisms in terms of gene content 20

E. V. Koonin (2012): All known cells are complex and elaborately organized. The simplest known cellular life forms, the bacterial (and the only known archaeal) parasites and symbionts, clearly evolved by degradation of more complex organisms; however, even these possess several hundred genes that encode the components of a fully fledged membrane; the replication, transcription, and translation machineries; a complex cell-division apparatus; and at least some central metabolic pathways. As we have already discussed, the simplest free-living cells are considerably more complex than this, with at least 1,300 genes 36

J. C. Xavier (2014): The cell is the most complex structure in the micrometer size range known to humans. At present, the minimal cell can be defined only on a semiabstract level as a living cell with a minimal and sufficient number of components and having three main features:

1. Some form of metabolism to provide molecular building blocks and energy necessary for synthesizing the cellular components,
2. Genetic replication from a template or an equivalent information processing and transfer machinery, and
3. A boundary (membrane) that separates the cell from its environment.
4. The necessity of coordination between boundary fission and the full segregation of the previously generated twin genetic templates could be added to this definition.
5. The essential feature of a minimal cell is the ability to evolve, which is a universal characteristic among all known living cells 19

F. El Baidouri (2021): Along with two robust prokaryotic phylogenetic trees we are able to infer that the last universal common ancestor of all living organisms was likely to have been a complex cell with at least 22 reconstructed phenotypic traits probably as intricate as those of many modern bacteria and archaea. Our results depict LUCA as likely to be a far more complex cell than has previously been proposed, challenging the evolutionary model of increased complexity through time in prokaryotes.17

Defining the LUCA: What might be a Cell’s minimal requirement of parts? 

I have gone in-depth to elucidate this question in my previous book: On the Origin of Life and Virus World by means of an Intelligent Designer. I wrote: Science remains largely in the dark when it comes to pinpointing what exactly the first life form looked like. Speculation abounds. Whatever science paper about the topic one reads, confusion becomes apparent. Patrick Forterre wrote  in a science paper in 2015: The universal tree of life: an update, confessed:

There is no protein or groups of proteins that can give the real species tree, i.e., allow us to recapitulate safely the exact path of life evolution.

As such, whatever architecture one comes up with, remains in the realm of speculation. Is it therefore futile, to trace a borderline, and list a number of features, that most likely were present? No. Even if we can come up only with a hypothetical organism, it will nonetheless give us insight into the complexity involved, and bring us closer to deciding, what mechanisms most likely were involved and if intelligence was required to set up the first life forms.  

Andrew J. Crapitto (2022): The availability of genomic and proteomic data from across the tree of life has made it possible to infer features of the genome and proteome of the last universal common ancestor (LUCA). Several studies have done so, all using a unique set of methods and bioinformatics databases. No individual study shares a high or even moderate degree of similarity with any other individual study. Studies of the genome or proteome of the LUCA do not uniformly agree with one another. The set of consensus LUCA protein family predictions between all of these studies portrays a LUCA genome that, at minimum, encoded functions related to protein synthesis, amino acid metabolism, nucleotide metabolism, and the use of common, nucleotide-derived organic cofactors.

The translation process is well known to be ancient and many of the proteins involved in translation machinery appear to predate the LUCA. A corollary to the influential RNA world hypothesis is that the translation system evolved within the context of an RNA-based genetic system. Most universal Clusters of Orthologous ( Orthologous are homologous genes where a gene diverges after a speciation event, but the gene and its main function are conserved) Groups of proteins (COGs) COGs encode proteins that physically associate with the ribosome and those that do not are often involved with the translation process in some other way. Similarly, nearly all universal, vertically inherited functional RNAs (save the SRP RNA) are involved in the translation system. Translation-related genes or proteins are prevalent in the predictions of seven of the eight previously published LUCA genome or proteome studies analyzed here. We identified 366 eggNOG clusters that were predicted by four or more studies to have been present in the genome of the LUCA (Appendix S2). 7

William Martin and colleagues from the University Düsseldorf’s Institute of Molecular Evolution give us also an interesting number: The metabolism of cells contains evidence reflecting the process by which they arose. Here, we have identified the ancient core of autotrophic metabolism encompassing 404 reactions that comprise the reaction network from H2, CO2, and ammonia (NH3) to amino acids, nucleic acid monomers, and the 19 cofactors required for their synthesis. Water is the most common reactant in the autotrophic core, indicating that the core arose in an aqueous environment. Seventy-seven core reactions involve the hydrolysis of high-energy phosphate bonds, furthermore suggesting the presence of a non-enzymatic and highly exergonic chemical reaction capable of continuously synthesizing activated phosphate bonds. CO2 is the most common carbon-containing compound in the core. An abundance of NADH and NADPH-dependent redox reactions in the autotrophic core, the central role of CO2, and the circumstance that the core’s main products are far more reduced than CO2 indicate that the core arose in a highly reducing environment. The chemical reactions of the autotrophic core suggest that it arose from H2, inorganic carbon, and NH3 in an aqueous environment marked by highly reducing and continuously far from equilibrium conditions. Supplementary Table 1. in the paper lists all 402 metabolic reactions   11, 12

John I. Glass (2006): Mycoplasma genitalium has the smallest genome of any organism that can be grown in pure culture. It has a minimal metabolism. Consequently, its genome is expected to be a close approximation to the minimal set of genes needed to sustain bacterial life. 14


Metabolic pathways and substrate transport mechanisms encoded by M. genitalium. Metabolic products are colored red, and mycoplasma proteins are black. White letters on black boxes mark nonessential functions or proteins based on our current gene disruption study. Question marks denote enzymes or transporters not identified that would be necessary to complete pathways, and those missing enzyme and transporter names are colored green. Transporters are colored according to their substrates: yellow, cations; green, anions and amino acids; orange, carbohydrates; purple, multidrug and metabolic end product efflux. The arrows indicate the predicted direction of substrate transport. The ABC type transporters are drawn as follows: rectangle, substrate-binding protein; diamonds, membrane-spanning permeases; circles, ATP-binding subunits.

J. A. G. Ranea (2006): In our view, the LUCA was faced with two important challenges associated with the source of amino acids and purine/pyrimidine bases or nucleosides. Most of these compounds need complex pathways to be synthesized and our analyses suggest that these are not present in the LUCA. Based on that, we are more in favor of amino acids and nitrogenous bases being present in a possible primitive soup rather than being synthesized by the LUCA.18

From a LUCA to the last bacterial common ancestor (LBCA)

Even though the existence of LUCA is supported by the universal presence of conserved biomolecules and a vast amount of genetic data, its characteristics and identity remain unknown. LBCA, on the other hand, stands for "Last Bacterial Common Ancestor," which refers to the hypothetical ancestor of all modern bacteria. Although the characteristics of LBCA are still uncertain, recent studies suggest that it might have been a monoderm bacterium with a complete 17-gene dcw cluster, which is two genes more than in the model E. coli cluster.

The 17-gene dcw (division and cell wall) cluster is a group of bacterial genes that are involved in the regulation of cell division and the synthesis of the cell wall during the cell cycle. These genes encode proteins that are responsible for the assembly and contraction of the bacterial cell wall and septum, which eventually leads to the separation of the daughter cells. The dcw cluster includes genes that are involved in peptidoglycan synthesis, cell wall assembly, and septation, among others. These genes are found in many bacterial species and are thought to be essential for bacterial growth and survival. Understanding the composition and regulation of the dcw cluster can provide insights into bacterial cell division and the evolution of bacterial morphology.

Phylogenomic inference also reveals that the Clostridia, a class of Firmicutes, are the least diverged of the modern genomes, suggesting that the first lineage to diverge from the predicted LBCA was similar to the modern Clostridia.

In 2004, Rosario Gil proposed a minimal gene set composed of 206 genes that would sustain the main vital functions of a hypothetical simplest bacterial cell. These functions include DNA replication, transcription, translation, protein processing, folding, secretion and degradation, cell division, energetic metabolism, pentose pathway, nucleotide biosynthesis, and lipid biosynthesis. The minimal cell does not include biosynthetic pathways for amino acids or most cofactor precursors, as they can be obtained from the environment.

While some amino acids can be obtained from the environment, not all of them are readily available or in sufficient quantities to support the growth of a minimal cell. In addition, the amino acids that are available in the environment may not be in the correct proportions or forms required by the cell. Therefore, some minimal cells may require biosynthetic pathways for certain amino acids to ensure their survival and growth.

R. R. Léonard (2022): The nature of the LBCA is unknown, especially the architecture of its cell wall. The lack of reliably affiliated bacterial fossils outside Cyanobacteria makes it elusive to decide the very nature of the LBCA. Nevertheless, phylogenomic inference leads to informative results, and our analysis of the cell-wall characteristics of extant bacteria, combined with ancestral state reconstruction and distribution of key genes, opens interesting possibilities: the LBCA might have been a monoderm bacterium featuring a complete 17-gene dcw cluster, two genes more than in the model E. coli cluster. This result was also supported by a recent study, in which the authors found 146 protein families that formed a predicted core for the metabolic network of the LBCA. From these families, phylogenetic trees were produced and the divergence of the modern genomes from the root to the tips was analysed. It appears that the Clostridia (a class of Firmicutes) are the least diverged of the modern genomes and thus the first lineage to diverge from the predicted LBCA were similar to the modern Clostridia. Based on these results, the authors suggested that the LBCA could have been a monoderm bacteria. (Having a single membrane, especially a thick layer of peptidoglycan) 22

P. C. Morales et.al., (2019) reconstructed the phylogenetic tree of Clostridium species. They set Clostridium difficile at the root of the tree. 23 The genome of C. difficile strain 630 consists of a circular chromosome of 4,290,252 bp 24

Taking Rosario Gil's model organism as the basis for our forthcoming investigation

Rosario Gil (2004): Based on the conjoint analysis of several computational and experimental strategies designed to define the minimal set of protein-coding genes that are necessary to maintain a functional bacterial cell, we propose a minimal gene set composed of 206 genes. Such a gene set will be able to sustain the main vital functions of a hypothetical simplest bacterial cell with the following features.

(i) A virtually complete DNA replication machinery, composed of one nucleoid DNA binding protein, SSB, DNA helicase, primase, gyrase, polymerase III, and ligase. No initiation and recruiting proteins seem to be essential, and the DNA gyrase is the only topoisomerase included, which should perform both replication and chromosome segregation functions.

(ii) A very rudimentary system for DNA repair, including only one endonuclease, one exonuclease, and a uracyl-DNA glycosylase.

(iii) A virtually complete transcriptional machinery, including the three subunits of the RNA polymerase, a σ factor, an RNA helicase, and four transcriptional factors (with elongation, antitermination, and transcription-translation coupling functions). Regulation of transcription does not appear to be essential in bacteria with reduced genomes, and therefore the minimal gene set does not contain any transcriptional regulators.

(iv) A nearly complete translational system. It contains the 20 aminoacyl-tRNA synthases, a methionyl-tRNA formyltransferase, five enzymes involved in tRNA maturation and modification, 50 ribosomal proteins (31 proteins for the large ribosomal subunit and 19 proteins for the small one), six proteins necessary for ribosome function and maturation (four of which are GTP binding proteins whose specific function is not well known), 12 translation factors, and 2 RNases involved in RNA degradation.

(v) Protein-processing, -folding, secretion, and degradation functions are performed by at least three proteins for posttranslational modification, two molecular chaperone systems (GroEL/S and DnaK/DnaJ/GrpE), six components of the translocase machinery (including the signal recognition particle, its receptor, the three essential components of the translocase channel, and a signal peptidase), one endopeptidase, and two proteases.

(vi) Cell division can be driven by FtsZ only, considering that, in a protected environment, the cell wall might not be necessary for cellular structure.

(vii) A basic substrate transport machinery cannot be clearly defined, based on our current knowledge. Although it appears that several cation and ABC transporters are always present in all analyzed bacteria, we have included in the minimal set only a PTS for glucose transport and a phosphate transporter. Further analysis should be performed to define a more complete set of transporters.

(viii) The energetic metabolism is based on ATP synthesis by glycolytic substrate-level phosphorylation.

(ix) The nonoxidative branch of the pentose pathway contains three enzymes (ribulose-phosphate epimerase, ribose-phosphate isomerase, and transketolase), allowing the synthesis of pentoses (PRPP) from trioses or hexoses.

(x) No biosynthetic pathways for amino acids, since we suppose that they can be provided by the environment.

(xi) Lipid biosynthesis is reduced to the biosynthesis of phosphatidylethanolamine from the glycolytic intermediate dihydroxyacetone phosphate and activated fatty acids provided by the environment.

(xii) Nucleotide biosynthesis proceeds through the salvage pathways, from PRPP and the free bases adenine, guanine, and uracil, which are obtained from the environment.

(xiii) Most cofactor precursors (i.e., vitamins) are provided by the environment. Our proposed minimal cell performs only the steps for the syntheses of the strictly necessary coenzymes tetrahydrofolate, NAD+, flavin aderine dinucleotide, thiamine diphosphate, pyridoxal phosphate, and CoA. 21

Comment: That would require LUCA to have complex import and transport mechanisms of nucleotides and amino acids, and membrane import channel proteins able to distinguish and select those building blocks for life that are used in life, from those that aren't. As I have outlined in my book, On the Origin of Life and Virus World by means of an Intelligent Designer, Origin of Life researchers have failed throughout to demonstrate the possible abiotic route to synthesize the basic building blocks of life non-enzymatically.  But even IF that would be the case, that would still not explain how LUCA made the transition from external incorporation to acquire the complex metabolic and catabolic pathways to synthesize nucleotides and amino acids which constitutes a huge, often overlooked gap. Mycoplasma genitalium is held as the smallest possible living self-replicating cell. It is, however, a pathogen, an endosymbiont that only lives and survives within the body or cells of another organism ( humans ).  As such, it IMPORTS many nutrients from the host organism. The host provides most of the nutrients such bacteria require, hence the bacteria do not need the genes for producing such compounds themselves. As such, it does not require the same complexity of biosynthesis pathways to manufacture all nutrients as a free-living bacterium. Amino Acids were no readily available on the early earth. In the Miller Urey experiment, eight of the 20 amino acids were never produced. Neither in 1953 nor in the subsequent experiments.

LUCAs information system

Currently, there is no known form of life that exists without DNA and RNA. DNA is a fundamental component of all known life on Earth and serves as the genetic blueprint that encodes the information necessary for the development, function, and reproduction of living organisms. Some claim that it is possible that alternative forms of genetic material or information storage may exist in other environments beyond our current understanding. This is however an argument from ignorance. It is a fallacy that occurs when someone asserts a claim based on the absence of evidence to the contrary. It is important to base claims on positive evidence rather than on the absence of evidence. It is therefore warranted to start with the presumption that DNA was present when life started. And as such, as well the biosynthesis pathways necessary to synthesize deoxynucleotides, the monomer building blocks of DNA.

The Central Dogma

The term Central Dogma was coined by Francis Crick, who discovered the double-helix structure of DNA together with Rosalind Franklin, James Watson, and Maurice Wilkins. DNA is “the Blueprint of Life.” It contains part of the data needed to make every single protein that life can't go on without. ( Epigenetic data based on epigenetic languages is also involved). No DNA, no proteins, no life. RNA has a limited coding capacity because it is unstable.


James Watson, left, with Francis Crick and their model of part of a DNA molecule SCIENCE PHOTO LIBRARY

YourGenome.org: The ‘Central Dogma’ is the process by which the instructions in DNA are converted into a functional product. It was first proposed in 1958 by Francis Crick, discoverer of the structure of DNA. The central dogma suggests that DNA contains the information needed to make all of our proteins, and that RNA is a messenger that carries this information to the ribosomes. The ribosomes serve as factories in the cell where the information is ‘translated’ from a code into a functional product. The process by which the DNA instructions are converted into the functional product is called gene expression. Gene expression has two key stages – transcription and translation. In transcription, the information in the DNA of every cell is converted into small, portable RNA messages. During translation, these messages travel from where the DNA is in the cell nucleus to the ribosomes where they are ‘read’ to make specific proteins.36

The biosynthesis of nucleotides

The de novo biosynthesis of nucleotides is essential in cells because nucleotides serve as the building blocks of nucleic acids, which are critical for many fundamental cellular processes. Here are some key reasons why de novo nucleotide biosynthesis is essential in cells:

DNA and RNA synthesis: Nucleotides are the monomeric units that make up DNA and RNA, the two types of nucleic acids that carry genetic information in cells. De novo nucleotide biosynthesis provides the necessary raw materials for the synthesis of DNA and RNA, which are essential for cellular replication, growth, and inheritance of genetic information.

Energy storage and transfer: Nucleotides, particularly ATP (adenosine triphosphate), serve as a universal currency for energy transfer and storage in cells. ATP is used as an energy source to power numerous cellular processes, such as biosynthesis, transport of molecules across cell membranes, and cellular signaling. De novo nucleotide biosynthesis provides the precursors for the synthesis of ATP and other nucleotide-based energy molecules, which are critical for cellular energy metabolism.

Coenzymes and signaling molecules: Nucleotides also serve as important coenzymes and signaling molecules in cellular metabolism and signaling pathways. For example, NAD+ (nicotinamide adenine dinucleotide) and FAD (flavin adenine dinucleotide) are nucleotide-based coenzymes that play crucial roles in cellular redox reactions and energy metabolism. Additionally, cyclic AMP (cAMP) and GTP (guanosine triphosphate) are nucleotide-based signaling molecules that regulate various cellular processes, including cell growth, differentiation, and response to external stimuli.

Regulation of cellular processes: Nucleotides play regulatory roles in various cellular processes, such as gene expression, cell cycle progression, and immune response. For example, nucleotide-dependent enzymes, such as protein kinases and GTPases, control the activity of other proteins by phosphorylation or other post-translational modifications. Nucleotides also participate in feedback inhibition of de novo nucleotide biosynthesis, helping to regulate the cellular pool of nucleotides and maintain proper cellular nucleotide balance.

The stepwise synthesis process of nucleotides involves several key reactions and steps. Here is a general overview of the synthesis process:

1. Base synthesis: The second step is the synthesis of the nucleotide base. Bases such as adenine, guanine, cytosine, thymine, and uracil are commonly found in nucleotides. These bases can be synthesized through a variety of chemical reactions, such as the Pictet-Spengler reaction, the Fischer indole synthesis, or the Vorbrüggen glycosylation, which yield the desired base molecule.

2. Sugar moiety synthesis: The first step is the synthesis of the sugar moiety, which typically involves the formation of ribose or deoxyribose, the two common sugar molecules found in nucleotides. This can be achieved through various chemical reactions, such as the formose reaction or the Wohl degradation, which generate the desired sugar molecule.

3. Phosphate group addition: The third step is the addition of the phosphate group to the sugar molecule. This is typically achieved through phosphorylation reactions using phosphate donors, such as phosphoric acid, phosphorus oxychloride, or phosphorimidazolide. The phosphate group can be added to different positions on the sugar molecule, resulting in nucleotides with different properties and functions.

4. Nucleotide condensation: The next step is the condensation of the sugar moiety with the base and the phosphate group to form the nucleotide. This is typically achieved through chemical reactions, such as nucleophilic substitution or esterification, which result in the formation of the phosphodiester bond between the sugar and phosphate groups, with the base attached to the sugar molecule.

5. Protecting group manipulation: Throughout the synthesis process, protecting groups may be used to temporarily protect certain functional groups or prevent unwanted reactions. These protecting groups can be selectively removed or modified at specific steps using chemical reactions, allowing for the desired modifications and functionalizations of the nucleotide molecule.

6. Purification and characterization: Once the nucleotide is synthesized, it needs to be purified to remove any impurities or side products. This can be achieved through various methods, such as chromatography or crystallization. The purified nucleotide can then be characterized using techniques such as nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, or X-ray crystallography to confirm its structure and purity.

7. Further modifications: Finally, the synthesized nucleotide can be further modified or functionalized to obtain specific derivatives or analogs with desired properties or functions. This can involve additional chemical reactions, such as acylation, alkylation, or oxidation, to introduce specific functional groups or modifications to the nucleotide molecule.

We will give a closer look at what it takes to synthesize RNA and DNA. We will start with the nucleobases. 

Synthesis of the RNA and DNA nucleobases

The biosynthesis of nucleobases, which are the building blocks of nucleotides, involves complex metabolic pathways that are essential for the synthesis of RNA and DNA, the two types of nucleic acids that carry genetic information in cells.

De novo nucleobase biosynthesis: Cells can synthesize nucleobases de novo, which means starting from simple precursors and synthesizing the nucleobases from scratch. De novo nucleobase biosynthesis pathways differ for RNA and DNA, although there are some similarities. The de novo biosynthesis of nucleobases generally involves a series of enzymatic reactions that convert simple precursors into complex nucleobases through multiple intermediate steps.

Purine nucleobase synthesis: Purine nucleobases, adenine (A) and guanine (G), are synthesized de novo from simpler precursors such as amino acids, bicarbonate, and phosphoribosyl pyrophosphate (PRPP). The biosynthesis of purine nucleobases involves several enzymatic steps, including ring construction, functional group modifications, and ring closure reactions, catalyzed by various enzymes such as amidotransferases, synthetases, and dehydrogenases.

Pyrimidine nucleobase synthesis: Pyrimidine nucleobases, cytosine (C), uracil (U), and thymine (T), are synthesized de novo from simpler precursors such as aspartate, bicarbonate, and PRPP. The biosynthesis of pyrimidine nucleobases also involves several enzymatic steps, including ring construction, functional group modifications, and ring closure reactions, catalyzed by various enzymes such as carbamoyl phosphate synthetase II (CPSII), dihydroorotase (DHOase), and orotate phosphoribosyltransferase (OPRT).

Salvage pathways: In addition to de novo biosynthesis, cells can also salvage nucleobases from the degradation of nucleic acids or from external sources, such as dietary intake. Salvage pathways involve the uptake of pre-formed nucleobases from the extracellular environment or the recycling of nucleobases from intracellular nucleotide degradation. Salvage pathways can provide an alternative source of nucleobases for nucleotide synthesis, and they are important for cellular nucleotide metabolism and conservation of resources. Salvage pathways, which involve the recycling or uptake of pre-formed nucleobases from the degradation of nucleic acids or from external sources, are not considered essential for life, as there are organisms that can survive without functional salvage pathways. However, salvage pathways play important roles in cellular nucleotide metabolism and can be advantageous for conserving resources and maintaining nucleotide pools under certain conditions.

Overall, the biosynthesis of nucleobases for RNA and DNA involves complex metabolic pathways that are essential for the synthesis of nucleotides, which are critical for the replication, transcription, and translation of genetic information in cells. De novo nucleobase biosynthesis, along with salvage pathways, ensures the availability of nucleobases for nucleotide synthesis, and proper regulation of these pathways is crucial for maintaining cellular nucleotide balance and function.

Here is a simplified overview of the minimum number of enzymes typically involved in the de novo biosynthesis of the four nucleobases used in genes (adenine, cytosine, guanine, and uracil) in most organisms:

Adenine (A) biosynthesis: The shortest pathway involves 5 enzymes: glutamine phosphoribosylpyrophosphate amidotransferase (GPAT), phosphoribosylaminoimidazole carboxamide formyltransferase (AICAR Tfase), phosphoribosylaminoimidazole succinocarboxamide synthetase (SAICAR synthetase), adenylosuccinate synthetase (ADSS), and adenylosuccinate lyase (ADSL).

Cytosine (C) biosynthesis: The shortest pathway involves 3 enzymes: carbamoyl phosphate synthetase II (CPSII), aspartate transcarbamylase (ATCase), and dihydroorotase (DHOase).
Guanine (G) biosynthesis: The shortest pathway involves 4 enzymes: inosine monophosphate (IMP) dehydrogenase (IMPDH), GMP synthase (GMPS), xanthosine monophosphate (XMP) aminase, and GMP reductase.
Uracil (U) biosynthesis: The shortest pathway involves 3 enzymes: carbamoyl phosphate synthetase II (CPSII), dihydroorotase (DHOase), and uracil phosphoribosyltransferase (UPRT).

These are simplified pathways and the actual biosynthesis of nucleobases in living organisms can be more complex, involving regulation, feedback mechanisms, and additional enzymes or intermediates. The specific enzymes and pathways for nucleobase biosynthesis can also vary depending on the organism, as different organisms may have different metabolic pathways for nucleotide biosynthesis. Regulation, feedback mechanisms, and additional enzymes or intermediates play important roles in nucleotide synthesis, as they help to maintain proper control and balance in the production of nucleotides in living organisms. While they may not be absolutely essential for nucleotide synthesis to occur, they are crucial for ensuring that nucleotide production is regulated and optimized for the needs of the cell or organism. Here's a brief overview:

Regulation: Nucleotide synthesis is typically regulated at multiple levels to maintain proper control over the production of nucleotides. Enzymes involved in nucleotide synthesis are often regulated through feedback inhibition, where the end products of nucleotide metabolism (i.e., nucleotides or their derivatives) act as feedback inhibitors, binding to specific enzymes in the synthesis pathway and inhibiting their activity. This helps to prevent overproduction of nucleotides and maintain a balanced pool of nucleotides in the cell.

Feedback mechanisms: Feedback mechanisms involve the sensing of intracellular nucleotide levels and subsequent regulation of nucleotide synthesis. For example, if the cell has sufficient nucleotide levels, feedback mechanisms may downregulate the activity of enzymes involved in nucleotide synthesis to prevent overproduction. Conversely, if nucleotide levels are low, feedback mechanisms may upregulate the activity of enzymes involved in nucleotide synthesis to meet the cellular demand.

Additional enzymes or intermediates: Nucleotide synthesis pathways often require multiple enzymes and intermediates to catalyze the various chemical reactions involved. These enzymes and intermediates may be essential for the proper progression of the synthesis pathway and the efficient production of nucleotides. For example, enzymes such as kinases, phosphatases, and ligases may be required for the addition or removal of phosphate groups during nucleotide synthesis, while intermediates such as PRPP (5-phosphoribosyl-1-pyrophosphate) may serve as critical precursors for nucleotide biosynthesis.

Here are some examples of enzymes that are involved in the regulation, feedback mechanisms, and additional intermediates of nucleotide synthesis, and are essential for the survival of the cell:

Ribonucleotide reductase: Ribonucleotide reductase is a key enzyme involved in the synthesis of deoxyribonucleotides, which are the building blocks of DNA. It catalyzes the conversion of ribonucleotides to deoxyribonucleotides, a crucial step in DNA synthesis. Ribonucleotide reductase is tightly regulated through allosteric feedback inhibition by the end products of the deoxyribonucleotide pathway, such as dATP, dGTP, dCTP, and dTTP, which bind to specific regulatory sites on the enzyme and inhibit its activity. This feedback inhibition helps to prevent overproduction of deoxyribonucleotides and maintains a balanced pool of nucleotides for DNA synthesis.

Purine and pyrimidine biosynthetic enzymes: Enzymes involved in the de novo biosynthesis of purine and pyrimidine nucleotides, such as phosphoribosyl pyrophosphate (PRPP) synthetase, adenylosuccinate synthase, and dihydroorotate dehydrogenase, are essential for nucleotide synthesis. These enzymes are regulated through feedback inhibition by the end products of the respective pathways, such as AMP, GMP, CMP, and UMP, which act as feedback inhibitors and help to maintain proper control over purine and pyrimidine nucleotide production.

Salvage pathway enzymes: Cells also have salvage pathways for recycling and salvaging nucleotides from cellular waste or exogenous sources. Enzymes involved in salvage pathways, such as hypoxanthine-guanine phosphoribosyltransferase (HGPRT) and thymidine kinase, are essential for salvaging and recycling nucleotides, as they help to replenish the cellular nucleotide pool and prevent nucleotide depletion. These salvage pathway enzymes are also regulated through feedback inhibition by the end products of nucleotide metabolism, which helps to regulate their activity and maintain nucleotide homeostasis.

Phosphatases and kinases: Enzymes such as nucleoside diphosphate kinases (NDPK), nucleotide monophosphate kinases (NMPK), and nucleotide diphosphatases (NDPases) are involved in the interconversion of nucleotide monophosphates, diphosphates, and triphosphates, and are essential for maintaining the proper balance of nucleotide pools in the cell. These enzymes are also regulated through feedback mechanisms and are important for regulating the cellular levels of nucleotide phosphates.

Enzymes involved in protecting group manipulations: Protecting groups are often used in nucleotide synthesis to temporarily protect specific functional groups or prevent unwanted reactions. Enzymes such as esterases or deprotecting enzymes are often used to selectively remove protecting groups at specific steps in the synthesis process, allowing for the desired modifications and functionalizations of the nucleotide molecule.

These are just a few examples of enzymes that are involved in the regulation, feedback mechanisms, and additional intermediates of nucleotide synthesis, and are essential for the survival of the cell. The specific enzymes and mechanisms involved may vary depending on the organism and the type of nucleotide being synthesized, but overall, these regulatory processes and enzymes are critical for maintaining proper control, balance, and efficiency in nucleotide synthesis, which is essential for cellular function and survival.

The biosynthesis of nucleobases is a complex process involving multiple distinct biosynthetic pathways. In total, six different biosynthetic pathways are involved in the de novo synthesis of the five nucleobases that make up DNA and RNA. Adenine and guanine are derived from the purine biosynthetic pathway, which involves 10 enzymatic steps. This pathway starts with simple precursors such as glycine, glutamine, aspartate, and CO2, and involves multiple intermediate compounds such as IMP, AMP, and GMP.

Uracil, thymine, and cytosine, on the other hand, are derived from the pyrimidine biosynthetic pathway, which involves six enzymatic steps. This pathway starts with simple precursors such as aspartate and carbamoyl phosphate, and involves intermediate compounds such as UMP, TMP, and CMP.

It's worth noting that some organisms have salvage pathways that can recycle pre-existing nucleobases to avoid the de novo synthesis of nucleobases altogether. However, the de novo synthesis of nucleobases remains a crucial process in many organisms.

The precursors for nucleotides are largely derived from amino acids, specifically glycine and aspartate, which serve as the scaffolds for the ring systems present in nucleotides. In addition, aspartate and glutamine serve as sources of NH2 groups in nucleotide formation. In de novo pathways, pyrimidine bases are assembled first from simpler compounds and then attached to ribose.

What does de novo mean?

In biochemistry, a de novo pathway is a metabolic pathway that synthesizes complex molecules from simple precursors. In other words, it is a process of creating new molecules from scratch rather than from pre-existing molecules.
De novo pathways are important for the synthesis of essential biomolecules such as nucleotides, amino acids, and fatty acids. For example, the de novo synthesis of purines and pyrimidines, the building blocks of DNA and RNA, are crucial for cell growth and replication. The term "de novo" comes from the Latin phrase "from the beginning," which reflects the fact that these pathways start with simple precursors and build up to more complex molecules through a series of biochemical reactions.

Purine bases, on the other hand, are synthesized piece by piece directly onto a ribose-based structure. These pathways consist of a small number of elementary reactions that are repeated with variations to generate different nucleotides. The simpler compounds used in the de novo pathways for nucleotide biosynthesis include carbon dioxide, amino acids (such as glycine, aspartate, and glutamine), tetrahydrofolate derivatives, ATP, and various cofactors such as NAD, NADP, and pyridoxal phosphate.  The derivatives of tetrahydrofolate (THF) that are involved as cofactors in various reactions include 

N10-formyl-THF, 
N5, 
N10-methylene-THF,
N5-formimino-THF, 
and N5-methyl-THF. 

These THF derivatives play crucial roles in providing one-carbon units for the synthesis of nucleotide bases. 

One-carbon units

One-carbon units are necessary for the construction of nucleotides because they are used as building blocks for the synthesis of the nitrogen-containing bases that make up the nucleotides. The nitrogen-containing bases of nucleotides, such as purines and pyrimidines, are synthesized through a series of enzymatic reactions that involve the transfer of one-carbon units, such as  formyl, methyl, methylene, and formimino groups. Formyl is a functional group consisting of a carbon atom double-bonded to an oxygen atom and single-bonded to a hydrogen atom, and its formula is -CHO. Methyl is a one-carbon unit (-CH3) used in nucleotide biosynthesis and other metabolic processes. Methylene is a functional group consisting of a carbon atom with two hydrogen atoms attached to it (-CH2-), which is present in many important compounds and is a building block in the synthesis of many organic compounds. Formimino is a functional group consisting of a nitrogen atom attached to a carbon atom double-bonded to an oxygen atom, and it is an important intermediate in various biochemical reactions, including the metabolism of amino acids and the biosynthesis of some neurotransmitters.

These one-carbon units are derived from various sources, including amino acids, carbon dioxide, and folate derivatives, and are incorporated into the nitrogen-containing rings of the nucleotide bases. For example, in the de novo synthesis of purine nucleotides, the carbon atoms for the C4, C5, and N7 atoms of the purine ring are derived from N10-formyl-THF, N5, N10-methylene-THF, and N5-formimino-THF, respectively.



In the de novo synthesis of thymidine nucleotides, the carbon atoms for the methyl group of thymine are derived from N5, N10-methylene-THF. The biosynthesis of nucleotides is therefore closely linked to the metabolism of folate, and deficiencies in folate intake or metabolism can lead to impaired nucleotide synthesis and various pathologies.

These compounds are assembled and converted into the nucleotide bases through a series of enzymatic reactions. For example, in the de novo pathway for pyrimidine biosynthesis, carbamoyl phosphate and aspartate are condensed to form the pyrimidine ring, which is then further modified to yield uridine monophosphate (UMP). In the de novo pathway for purine biosynthesis, the purine ring is assembled stepwise onto the ribose scaffold through a series of enzyme-catalyzed reactions that utilize a variety of simpler compounds as substrates.

L. Stryer (2002): Purines and pyrimidines are derived largely from amino acids.  The amino acids glycine and aspartate are the scaffolds on which the ring systems present in nucleotides are assembled. Furthermore, aspartate and the side chain of glutamine serve as sources of NH2 groups in the formation of nucleotides. In de novo (from scratch) pathways, the nucleotide bases are assembled from simpler compounds. The framework for a pyrimidine base is assembled first and then attached to ribose. In contrast, the framework for a purine base is synthesized piece by piece directly onto a ribose-based structure. These pathways each comprise a small number of elementary reactions that are repeated with variations to generate different nucleotides.53

The biosynthesis of glycine, one of the two amino acids required to assemble the ring systems of nucleotides, can occur through the serine hydroxymethyltransferase (SHMT) pathway or the glycine cleavage system. The biosynthesis of aspartate, the other amino acid required to assemble the ring systems of nucleotides, can occur through the transamination of oxaloacetate.

The biosynthesis of amino acids requires a series of enzymatic reactions that convert simple molecules such as glucose or other central metabolites into the final amino acid product. These pathways are highly regulated and often require energy input from ATP or other high-energy molecules.

The serine hydroxymethyltransferase (SHMT) pathway is a biosynthetic pathway that involves the interconversion of serine and glycine, two amino acids that are important building blocks for proteins and nucleotides. In this pathway, serine is converted into glycine through the action of the enzyme serine hydroxymethyltransferase (SHMT). This enzyme transfers a methyl group from serine to tetrahydrofolate (THF), a cofactor derived from folate, and produces glycine and 5,10-methylene-THF. The SHMT pathway is important for the biosynthesis of nucleotides, which are the building blocks of DNA and RNA. In this context, the glycine produced by the SHMT pathway can be used to synthesize purines, one of the two types of nucleotide bases. Additionally, the 5,10-methylene-THF produced by the pathway can be used to produce thymidylate, a precursor for the other type of nucleotide base, pyrimidines.

The starting molecules or substrates involved in the biosynthesis pathway of the serine hydroxymethyltransferase (SHMT) pathway are serine and tetrahydrofolate (THF).

Serine is an amino acid that is used in the biosynthesis of proteins. It has a hydroxyl group (-OH) attached to its side chain and is one of the 20 common amino acids found in proteins. In addition to its role in protein synthesis, serine is also involved in the biosynthesis of other molecules such as purines, pyrimidines, and phospholipids. The biosynthesis of serine involves three enzymatic steps, which are catalyzed by 3-phosphoglycerate dehydrogenase, phosphoserine phosphatase, and phosphoserine aminotransferase. The biosynthesis pathways for nucleotides, including the synthesis of serine, do require enzymes. And in turn, these enzymes are encoded by genes that are themselves made of DNA. So, in a sense, DNA is required to make the enzymes that are necessary for its own biosynthesis. This is one example of how the various components of a living system are interdependent and interconnected. This interdependence between biosynthetic pathways means that the cell must maintain a delicate balance of metabolic processes to function properly. The cell achieves this balance through a complex network of biochemical reactions and regulatory mechanisms. These reactions are finely tuned to ensure that the concentrations of various molecules are maintained within a narrow range, and that they are produced and consumed at the appropriate rates. Regulatory mechanisms, such as feedback inhibition and gene regulation, help to maintain this balance by controlling the expression and activity of enzymes involved in these pathways. Additionally, the cell has mechanisms for recycling and salvaging molecules, which helps to minimize waste and ensure that essential molecules are available for biosynthesis. Overall, the cell is able to achieve a dynamic balance through the integration of these complex biochemical and regulatory mechanisms. Maintaining the balance of biochemical reactions within the cell is essential for its survival. If the balance is disrupted or unregulated, it can lead to cell death or disease. Therefore, the cell has various mechanisms in place to regulate and control the balance of its biochemical reactions. These mechanisms can involve feedback loops, enzyme regulation, and cellular signaling pathways, among others.
Some claim that the first life forms had simpler mechanisms of regulation and that more complex regulatory systems evolved over time, but there is no concrete supportive evidence for these claims.

There are several enzymes involved in the biosynthesis of tetrahydrofolate (THF), a coenzyme that plays a critical role in nucleotide synthesis and other metabolic pathways. The pathway can vary depending on the organism, but in general, it involves at least five enzymes: GTP cyclohydrolase I (GCH1), 6-pyruvoyltetrahydropterin synthase (PTPS), dihydropteroate synthase (DHPS), dihydrofolate reductase (DHFR), and serine hydroxymethyltransferase (SHMT). These enzymes catalyze a series of reactions that convert GTP to THF, using various cofactors and substrates along the way. Tetrahydrofolate (THF) is an essential co-factor in many biological processes, including DNA synthesis, amino acid metabolism, and nucleotide biosynthesis. Cells cannot survive without it because THF is required for the synthesis of purines, pyrimidines, and certain amino acids that are essential for cell growth and division.

As mentioned above, aspartate depends on the transamination of oxaloacetate. Transamination is a metabolic process in which an amino group (-NH2) is transferred from an amino acid to a keto acid, resulting in the formation of a new amino acid and a new keto acid. The transfer of the amino group is catalyzed by enzymes known as transaminases or aminotransferases.

In the case of the transamination of oxaloacetate, the amino group is transferred from an amino acid (usually glutamate) to oxaloacetate, resulting in the formation of aspartate and alpha-ketoglutarate. This reaction is catalyzed by the enzyme aspartate aminotransferase. This transamination reaction is an important step in several metabolic pathways, including the biosynthesis and degradation of amino acids. For example, aspartate is a precursor for the synthesis of several other amino acids, including methionine and threonine, and alpha-ketoglutarate can enter the citric acid cycle and be used as a source of energy for the cell.

Oxaloacetate



Oxaloacetate is a four-carbon dicarboxylic acid that is an important intermediate in many metabolic pathways. It is synthesized from pyruvate or other intermediates through a series of enzymatic reactions in the mitochondrial matrix of eukaryotic cells or the cytoplasm of prokaryotic cells. One pathway for the synthesis of oxaloacetate involves the carboxylation of pyruvate, which is catalyzed by the enzyme pyruvate carboxylase. This reaction requires ATP and bicarbonate as cofactors, and results in the formation of oxaloacetate.

The complex metabolic pathways involved in the biosynthesis of the precursors to start the synthesis of nucleotides from simpler compounds demonstrate the intricate interdependence and regulation of various biochemical processes within the cell. Providing the precursors for the biosynthesis of amino acids, co-factors, and nucleotides requires a series of enzymatic reactions that are highly regulated and often require energy input from ATP or other high-energy molecules. Moreover, the biosynthesis of one molecule often depends on the availability of another molecule, resulting in a delicate balance of metabolic processes that must be maintained for the cell to function properly. This indicates that the setup is extremely unlikely to be achievable in a step-wise fashion, and an "all or nothing" approach is required, which only an intelligent designer is capable of instantiating.  

The gap between the prebiotic, non-enzymatic synthesis of organic compounds and the complex metabolic pathways found in living cells is significant and multifaceted.

Prebiotic chemistry is concerned with the chemical processes that took place on Earth before the emergence of life. It is hypothesized that the basic building blocks of life, such as amino acids, nucleotides, and sugars, were formed through a series of chemical reactions that occurred spontaneously in the early Earth's environment. These reactions would have been driven by energy sources such as lightning, volcanic activity, and UV radiation.

However, the formation of these simple organic molecules would not immediately lead to the formation of complex metabolic pathways. The formation of simple organic molecules, such as amino acids and sugars, is a crucial step in the origin of life. However, the existence of these molecules alone does not lead to the formation of complex metabolic pathways. This is because the formation of metabolic pathways requires a precise interconnection of multiple enzymes, each of which performs a specific function in the pathway. Enzymes are complex protein molecules that catalyze specific chemical reactions within a cell. For a metabolic pathway to function properly, the enzymes involved in the pathway must be present in the correct sequence, with each enzyme catalyzing the correct reaction to produce the desired end product. This interconnection of enzymes is critical to the function of the pathway and requires a high degree of specificity and precision. Furthermore, the formation of enzymes is a complex process that requires a specific sequence of amino acids to fold into the correct three-dimensional structure, which is essential for its function. The probability of a random sequence of amino acids folding into a functional enzyme is extremely low, making the spontaneous formation of a functional enzyme highly unlikely. Moreover, metabolic pathways require energy to function, which must come from an external source. In modern cells, energy is provided by the breakdown of nutrients through metabolic pathways, but in the absence of such pathways, the origin of life required an external energy source. Hypothesized is the provision by geothermal energy, lightning, or radiation, among other sources. The problem here is however, these sources are very unspecific in their delivery of energy. In contrast, ATP (adenosine triphosphate) is a highly specific energy carrier that can be precisely funneled to the site of an enzyme where it is needed for a specific chemical reaction to occur.

ATP is a small molecule that is synthesized by cells through metabolic pathways, and it is used to power many cellular processes, including muscle contraction, nerve impulses, and the synthesis of molecules. ATP stores energy in its high-energy phosphate bonds, which can be released through hydrolysis to drive endergonic reactions. The specificity of ATP lies in its ability to interact with enzymes in a highly specific manner. Enzymes can bind ATP at specific sites, called active sites, which are precisely shaped to fit the ATP molecule. Once ATP is bound to an enzyme, the high-energy phosphate bond can be cleaved, releasing energy that can be used to power specific chemical reactions.
The precise delivery of ATP to the site of an enzyme is critical for its function in metabolic pathways. This is because the energy required for a specific reaction may be different from that required for another reaction in the same pathway. Therefore, the ability to funnel ATP precisely to the site where it is needed ensures that the energy is used efficiently and only where it is required.

The hypothesis of the origin of life by unguided means faces significant challenges in explaining how metabolic pathways, which rely on the highly specific energy carrier ATP, arose in the absence of modern cellular machinery. One proposed solution to this challenge is the concept of proto-metabolic pathways, which are thought to have arisen through a series of chemical reactions that were catalyzed by minerals or simple organic molecules on the early Earth. Over time, these pathways would have become more complex and interconnected, eventually leading to the emergence of metabolic pathways as we know them today.

One of the major challenges in bridging the gap between prebiotic chemistry and living organisms is the complexity of metabolic pathways found in living cells. These pathways involve a series of enzyme-catalyzed reactions that convert simple organic molecules into more complex molecules and generate the energy required for cellular functions. The origin of these pathways is claimed to have occurred over billions of years, through a process of trial and error.

This is similar to saying that: On the one side you have an intelligent agency-based system of irreducible complexity of tightly integrated, information-rich functional systems which have ready on hand energy directed for such, that routinely generate the sort of phenomenon being observed.  And on the other side imagine a golfer, who has played a golf ball through a 12-hole course. Can you imagine that the ball could also play itself around the course in his absence? Of course, we could not discard, that natural forces, like wind, tornadoes, or rains or storms could produce the same result, given enough time.  the chances against it, however, are so immense, that the suggestion implies that the non-living world had an innate desire to get through the 12-hole course.

The analogy of the golf ball playing itself around a course can also be applied to metabolic pathways. Metabolic pathways are complex sequences of chemical reactions that occur within cells and are responsible for the production of energy and the synthesis of various cellular components. These pathways are highly integrated, with each step depending on the previous one, and require energy to function.

Metabolic pathways require all of their parts to be present and functioning together to work. For metabolic pathways to work, all of their parts must be present and functioning together. This is because each step in the pathway is catalyzed by a specific enzyme, which is a protein that facilitates the reaction. Enzymes are highly specific in their function, meaning that each enzyme is designed to work on a specific substrate, or molecule, and produce a specific product. For example, in the process of cellular respiration, glucose is broken down into smaller molecules through a series of reactions that occur in different parts of the cell. The breakdown of glucose occurs in several stages, each catalyzed by a specific enzyme. If any one of these enzymes is missing or not functioning properly, the entire pathway is disrupted and the cell cannot produce energy efficiently. Moreover, metabolic pathways are regulated by feedback mechanisms that ensure that the rate of the pathway matches the needs of the cell. If any part of the pathway is disrupted, it can lead to a buildup of intermediate molecules that can be toxic to the cell. This highlights the importance of all the components being present and functioning together for the pathway to work correctly. Therefore, the presence and functioning of all the components of a metabolic pathway are essential for the proper functioning of the pathway. Any disruption or absence of any one of the components can lead to the breakdown of the entire pathway, emphasizing the requirement for a highly specific and integrated system to function properly.

The origin of ATP remains a significant challenge for the proto-metabolic pathway hypothesis, as the molecule is not readily available on the prebiotic Earth. One proposed solution to this challenge is that ATP would have been produced through abiotic reactions, such as the phosphorylation of ADP (adenosine diphosphate) in the presence of mineral catalysts. Other proposed mechanisms include the production of ATP through the metabolism of simpler molecules, such as acetyl-CoA. Acetyl-CoA however is not naturally found in the environment. It is synthesized within living organisms through various metabolic pathways. Another proposed solution is that ATP would have been produced through the use of alternative energy carriers, such as pyrophosphate, which is a less efficient but more readily available molecule that can be used to drive chemical reactions. While these proposed solutions are still subject to ongoing investigation and debate, it is clear that the origin of metabolic pathways and the production of highly specific energy carriers such as ATP remain significant, in my view, unsurmountable challenges for proposals of the origin of life by unguided means. Continued research in this field will probably shed even more evidence and light on the impossibility of the claim that life could have arisen on Earth by stochastic, non-designed events.

G. Zubay (2000): The most striking difference in the pathways to the purines and pyrimidines is the timing of ribose involvement. In de novo purine synthesis the purine ring is built on the ribose in a stepwise fashion. In pyrimidine synthesis, the nitrogen base is synthesized prior to the attachment of the ribose. In both instances, the ribose-5-phosphate is first activated by the addition of a pyrophosphate group to the C'-1 of the sugar to form phosphoribosyl pyrophosphate (PRPP). This activation facilitates the formation of the linkage between the C'-1 carbon of the ribose and the nitrogen of the purine and pyrimidine bases.54

D. Penny (1999): An interesting picture of the LUCA is emerging. It was a fully DNA and protein-based organism with extensive processing of RNA transcripts. 37 A. Hiyoshi (2011): All the self-reproducing cellular organisms so far examined have DNA as the genome.

E. V. Koonin (2012): All the difficulties and uncertainties of evolutionary reconstructions notwithstanding, parsimony analysis combined with less formal efforts on the reconstruction of the deep past of particular functional systems leaves no serious doubts that LUCA already possessed at least several hundred genes. In addition to the aforementioned “golden 100” genes involved in expression, this diverse gene complement consists of numerous metabolic enzymes, including pathways of the central energy metabolism and the biosynthesis of nucleotides, amino acids, and some coenzymes, as well as some crucial membrane proteins, such as the subunits of the signal recognition particle (SRP) and the H+- ATPase. 36

Phosphoribosyl-pyrophosphate synthetase (Prs)

Phosphoribosyl-pyrophosphate synthetase (Prs) is an enzyme that plays a crucial role in nucleotide biosynthesis, as it catalyzes the conversion of ribose-5-phosphate (R5P) and ATP (adenosine triphosphate) to phosphoribosyl pyrophosphate (PRPP), which is an essential precursor for the de novo synthesis of purine and pyrimidine nucleotides.

The overall structure of Prs typically consists of multiple domains that are responsible for ATP and R5P binding, as well as the active site for catalysis. Prs is typically a homodimer, meaning it is composed of two identical subunits that come together to form the functional enzyme. The subunits may contain different domains responsible for catalysis and binding. The minimal bacterial isoform of Prs, also known as PRS1, is the smallest version of Prs and is found in some bacteria, including Escherichia coli (E. coli). PRS1 from E. coli is composed of 265 amino acids and has a molecular weight of approximately 29.7 kDa. It contains three domains: an N-terminal domain responsible for ATP binding, a central domain responsible for R5P binding, and a C-terminal domain that contains the active site for catalysis. Its main function is to catalyze the conversion of ribose-5-phosphate (R5P) and ATP (adenosine triphosphate) to phosphoribosyl pyrophosphate (PRPP). This reaction involves transferring the pyrophosphate group from ATP to the C1 position of R5P, resulting in the formation of PRPP.

PRPP is also involved in other important cellular processes, such as the biosynthesis of NAD (nicotinamide adenine dinucleotide), histidine, and tryptophan, as well as the formation of certain coenzymes and cofactors.

In addition to nucleotide biosynthesis, PRPP serves as a key regulator of various metabolic pathways in cells, as it acts as an allosteric activator or inhibitor of several enzymes involved in purine and pyrimidine metabolism. This makes Prs and the synthesis of PRPP crucial for maintaining cellular nucleotide pools and regulating nucleotide metabolism, which are essential for cell growth, proliferation, and survival.

An intelligent designer required to set up the Metabolic Networks used in life 

Observation: The existence of metabolic pathways is crucial for molecular and cellular function.  Although bacterial genomes differ vastly in their sizes and gene repertoires, no matter how small, they must contain all the information to allow the cell to perform many essential (housekeeping) functions that give the cell the ability to maintain metabolic homeostasis, reproduce, and evolve, the three main properties of living cells. Gil et al. (2004)  In fact, metabolism is one of the most conserved cellular processes. By integrating data from comparative genomics and large-scale deletion studies, the paper "Structural analyses of a hypothetical minimal metabolism" propose a minimal gene set comprising 206 protein-coding genes for a hypothetical minimal cell. The paper lists 50 enzymes/proteins required to create a metabolic network implemented by a hypothetical minimal genome for the hypothetical minimal cell. The  50 enzymes/proteins, and the metabolic network, must be fully implemented to permit a cell to keep its basic functions.
  
Hypothesis (Prediction): The origin of biological irreducible metabolic pathways that also require regulation and which are structured like a cascade, similar to electronic circuit boards,  are best explained by the creative action of an intelligent agent.

Experiment: Experimental investigations of metabolic networks indicate that they are full of nodes with enzymes/proteins, detectors, on/off switches, dimmer switches, relay switches, feedback loops etc. that require for their synthesis information-rich, language-based codes stored in DNA. Hierarchical structures have been proved to be best suited for capturing most of the features of metabolic networks (Ravasz et al, 2002). It has been found that metabolites can only be synthesized if carbon, nitrogen, phosphor, and sulfur and the basic building blocks generated from them in central metabolism are available.

 This implies that regulatory networks gear metabolic activities to the availability of these basic resources.  So one metabolic circuit depends on the product of other products, coming from other, central metabolic pathways, one depending on the other, like in a cascade.  Further noteworthy is that Feedback loops have been found to be required to regulate metabolic flux and the activities of many or all of the enzymes in a pathway.  In many cases, metabolic pathways are highly branched, in which case it is often necessary to alter fluxes through part of the network while leaving them unaltered or decreasing them in other parts of the network (Curien et al., 2009). These are interconnected in a functional way, resulting in a living cell. The biological metabolic networks are exquisitely integrated, so the significant alterations in inevitably damage or destroys the function. Changes in flux often require changes in the activities of multiple enzymes in a metabolic sequence. Synthesis of one metabolite typically requires the operation of many pathways.

Conclusion: Regardless of its initial complexity, self-maintaining chemical-based metabolic life could not have emerged in the absence of a genetic replicating mechanism ensuring the maintenance, stability, and diversification of its components. In the absence of any hereditary mechanisms, autotrophic reaction chains would have come and gone without leaving any direct descendants able to resurrect the process. Life as we know it consists of both chemistry and information.   If metabolic life ever did exist on the early Earth, to convert it to life as we know it would have required the emergence of some type of information system under conditions that are favorable for the survival and maintenance of genetic informational molecules. ( Ribas de Pouplana, Ph.D.)
 
Biological systems are functionally organized, integrated into an interdependent network, and complex, like human-made machines and factories. The wiring or circuit board of an electrical device equals the metabolic pathways of a biological cell. For the assembly of a biological system of multiple parts, not only the origin of the genome information to produce all proteins/enzymes with their respective subunits and assembly cofactors must be explained, but also parts availability (The right materials must be transported to the building site). Often these materials in their raw form are unusable. Other complex machines come into play to transform the raw materials into a usable form.  (All this requires specific information. ) synchronization, ( these parts must be ready on hand at the building site )  manufacturing and assembly coordination ( which required information on how to assemble every single part correctly, at the right place, at the right moment, and in the right position), and interface compatibility (the parts must fit together correctly, like a lock and key). Unless the origin of all these steps is properly explained, functional complexity as existing in biological systems has not been addressed adequately. How could the whole process have started " off the hooks " from zero without planning intelligence? Why would natural, unguided mechanisms produce a series of enzymes that only generate useless intermediates until all of the enzymes needed for the end product exist, are in place, and do their job?

S.Lovtrup (1987):  "...the reasons for rejecting Darwin's proposal were many, but first of all that many innovations cannot possibly come into existence through accumulation of many small steps, and even if they can, natural selection cannot accomplish it, because incipient and intermediate stages are not advantageous." 42

On the one side, you have an intelligent agency-based system of irreducible complexity of tight integrated, information-rich functional systems which have ready on-hand energy directed for such, that routinely generate the sort of phenomenon being observed.  And on the other side imagine a golfer, who has played a golf ball through a 12-hole course. Can you imagine that the ball could also play itself around the course in his absence? Of course, we could not discard, that natural forces, like wind, tornadoes, or rains or storms could produce the same result, given enough time.  the chances against it, however, are so immense, that the suggestion implies that the non-living world had an innate desire to get through the 12-hole course.

D. Armenta-Medina (2014): Nucleotide metabolism is central in all living systems, due to its role in transferring genetic information and energy. Indeed, it has been described as one of the ancient metabolisms in evolution.  In addition, many of the intermediates associated with this metabolic module have been intimately associated with prebiotic chemistry and the origin of life. In this regard, we adopted a multigenomic strategy for the reconstruction and analysis of the metabolism of nucleotides, evaluating the contribution of the origin and diversification of de novo and salvage pathways for nucleotides in the evolution of organisms. In addition, these analyses allow the identification of a metabolic link between the LCA and the first steps in the structure of biological networks. Our strategy reveals some general rules concerning the adaptation of the first predominant chemical reactions to enzymatic steps in the LCA and allows us to infer environmental issues in the early stages of the emergence of life.39 

Purines and Pyrimidines

Biochem (2022): Nucleotides serve numerous functions in different reaction pathways. For example, nucleotides are the activated precursors required for DNA and RNA synthesis. Nucleotides form the structural moieties of many coenzymes (examples include reduced nicotinamide adenine dinucleotide [NADH], flavin adenine dinucleotide [FAD], and coenzyme A). Nucleotides are critical elements in energy metabolism (adenosine triphosphate [ATP], guanosine triphosphate [GTP]). Nucleotide derivatives are frequently activated intermediates in many biosynthetic pathways. In addition, nucleotides act as second messengers in intracellular signaling (e.g., cyclic adenosine monophosphate [cAMP], cyclic guanosine monophosphate [cGMP]). Finally, nucleotides and nucleosides act as metabolic allosteric regulators. Think about all of the enzymes that have been studied that are regulated by levels of ATP, ADP, and AMP. Because of the minimal dietary uptake of these important molecules, de novo synthesis of purines and pyrimidines is required.


A nucleoside is a purine or pyrimidine base linked to a ribose sugar and a nucleotide is a phosphate ester bonded to a nucleoside. 

De novo purine biosynthesis



D. Voet et.al. (2016): Widely divergent organisms such as E. coli, yeast, pigeons, and humans have virtually identical pathways for the biosynthesis of purine nucleotides 49

Biochem (2022):  Purines and pyrimidines are required for synthesizing nucleotides and nucleic acids. These molecules can be synthesized either from scratch, de novo, or salvaged from existing bases. The de novo pathway of purine synthesis is complex, consisting of 11 steps and requiring six molecules of adenosine triphosphate (ATP) for every purine synthesized. The precursors that donate components to produce purine nucleotides include glycine, ribose 5-phosphate, glutamine, aspartate, carbon dioxide, and N10-formyltetrahydrofolate (N10-formyl-FH4) (Figure below).



Origin of the atoms of the purine base. 
FH4, tetrahydrofolate; RP, ribose 5′-phosphate. FH4, tetrahydrofolate; RP, ribose 5′-phosphate.

Purines are synthesized as ribonucleotides, with the initial purine synthesized being inosine monophosphate (IMP). Adenosine monophosphate (AMP) and guanosine monophosphate (GMP) are each derived from IMP in two-step reaction pathways. The de novo pathway requires at least six high-energy bonds per purine produced.46

Comment: Every company that manufactures things, requires in many cases a purchasing department that is exclusively involved in acquiring and importing the goods, the basic materials used in the factory. That is already a complex process, requiring many different steps where communication plays a decisive role. Not any raw material can be used, but it must be the right materials, in the right quantities, in the right form, in purity, in concentrations, in sizes, etc. Once the raw materials are inside the factory of the company, the processing procedures can begin. Often these raw materials require specific processing before they can be used in the assembly process of the end product. In our case,  six(!) different atoms have to be recruited as precursors, to begin with, nucleotide base synthesis. How did the LUCA get its know-how of the right atoms to make purines?   

Graham Cairns-Smith (2003): We return to questions of fine-tuning, accuracy, and specificity. Any competent organic synthesis hinges on such things. In the laboratory, the right materials must be taken from the right bottles and mixed and treated in an appropriate sequence of operations. In the living cell, there must be teams of enzymes with specificity built into them. A protein enzyme is a particularly well-tuned device. It is made to fit beautifully the transition state of the reaction it has to catalyze. Something ( or someone?) must have performed the fine-tuning necessary to allow such sophisticated molecules as nucleotides to be cleanly and consistently made in the first place.47

Yitzhak Tor (2013):  How did nature “decide” upon these specific heterocycles? Evidence suggests that many types of heterocycles could have been present on early Earth. It is therefore likely that the contemporary composition of nucleobases is a result of multiple selection pressures that operated during early chemical and biological evolution. The persistence of the fittest heterocycles in the prebiotic environment towards, for example, hydrolytic and photochemical assaults, may have given some nucleobases a selective advantage for incorporation into the first informational polymers. The prebiotic formation of polymeric nucleic acids employing the native bases remains, however, a challenging problem to reconcile. Two such selection pressures may have been related to genetic fidelity and duplex stability. Considering these possible selection criteria, the native bases along with other related heterocycles seem to exhibit a certain level of fitness. We end by discussing the strength of the N-glycosidic bond as a potential fitness parameter in the early DNA world, which may have played a part in the refinement of the alphabetic bases. Even minute structural changes can have substantial consequences, impacting the intermolecular, intramolecular and macromolecular “chemical physiology” of nucleic acids 48

The enzymes of de novo purine synthesis

Donald Voet et.al. (2016): Many of the intermediates in the de novo purine biosynthesis pathway degrade rapidly in water. Their instability in water suggests that the product of one enzyme must be channeled directly to the next enzyme along the pathway. Recent evidence shows that the enzymes do indeed form complexes when purine synthesis is required.

Comment: This is remarkable and shows how foreplanning is required to get the end product without it being destroyed along the synthesis pathway. There is no natural urge or need for these intermediates to be preserved.

The purine ring system is assembled on ribose-phosphate

De novo purine biosynthesis, like pyrimidine biosynthesis, requires Phosphoribosyl pyrophosphate PRPP but, for purines, PRPP provides the foundation on which the bases are constructed step by step.

Bjarne Hove-Jensen (2016): Phosphoribosyl-pyrophosphate synthetase (Prs) catalyzes the synthesis of phosphoribosyl pyrophosphate (PRPP), an intermediate in nucleotide metabolism and the biosynthesis of the amino acids histidine and tryptophan. PRPP is required for the synthesis of purine and pyrimidine nucleotides, the pyridine nucleotide cofactor NAD(P), and the amino acids histidine and tryptophan. In nucleotide synthesis, PRPP is used both for de novo synthesis and for the salvage pathway, by which bases are metabolized to nucleotides.  Prs is thus a central enzyme in the metabolism of nitrogen-containing compounds.51

Donald Voet et.al., (2016): IMP is synthesized in a pathway composed of 11 reactions

The shortest purine biosynthetic pathway, also known as the de novo purine biosynthesis pathway, involves the synthesis of inosine monophosphate (IMP), which is a precursor for both adenine and guanine, two of the four purine nucleotide bases found in DNA and RNA. The de novo purine biosynthesis pathway typically involves a series of enzymatic reactions that convert simple precursors into IMP.

In general, the de novo purine biosynthesis pathway consists of 10 enzymatic reactions, which are catalyzed by a series of enzymes. These enzymes, in sequential order, are:

1. Ribose-phosphate diphosphokinase Catalyzes the synthesis of PRPP from ribose-5-phosphate and ATP.
2. amidophosphoribosyl transferase(GPAT): Catalyzes the transfer of an amide group from glutamine to PRPP, forming 5-phosphoribosylamine (PRA).
3. Glycinamide ribotide (GAR) transformylase (GART): Catalyzes the synthesis of formylglycinamidine ribonucleotide (FGAR) from PRA and glycine.
4. Formylglycinamide ribotide (FGAR) amidotransferase (GART): Catalyzes the transfer of a formyl group from N10-formyltetrahydrofolate to FGAR, forming formylglycinamidine ribonucleotide (FGAM).
5. Formylglycinamidine ribotide (FGAM) synthetase (GART): Catalyzes the synthesis of formylglycinamidine ribonucleotide (FGAR) from FGAM.
6. 5-aminoimidazole ribotide (AIR) carboxylase (PurK): Catalyzes the conversion of FGAM to 5-aminoimidazole ribotide (AIR).
7. 5-aminoimidazole-4-(N-succinylocarboxamide) ribotide (SACAIR)synthetase (PurE): Catalyzes the synthesis of 5-aminoimidazole-4-(N-succinylocarboxamide) ribotide (SACAIR) from AIR.
8. Carboxyaminoimidazole ribotide (CAIR) mutase (PurK): Catalyzes the conversion of SACAIR to carboxyaminoimidazole ribotide (CAIR).
9. 5-aminoimidazole-4-carboxamide ribotide (AICAR)transformylase (PurN): Catalyzes the conversion of CAIR to 5-aminoimidazole-4-carboxamide ribotide (AICAR).
10. 5-formaminoimidazole-4- carboxamide ribotide (FAICAR) cyclase (PurM): Catalyzes the conversion of AICAR to 5-formaminoimidazole-4-carboxamide ribotide (FAICAR).
11. IMP cyclohydrolase  (PurH): Catalyzes the conversion of FAICAR to inosine monophosphate (IMP).

In addition to these enzymatic reactions, the de novo purine biosynthesis pathway is also regulated at various steps to maintain cellular homeostasis and prevent excessive purine synthesis. Regulation can occur at the transcriptional, translational, and post-translational levels, involving feedback inhibition, allosteric regulation, and enzyme degradation, among other mechanisms.

Regulation of the de novo purine biosynthesis pathway

The regulation of the de novo purine biosynthesis pathway is essential to maintain cellular homeostasis and prevent excessive purine synthesis. Purines are vital components of DNA, RNA, ATP, GTP, and other important molecules involved in cellular metabolism, energy production, and signaling. However, excessive purine synthesis can lead to an imbalance in cellular nucleotide pools, disrupt cellular metabolism, and result in various pathological conditions. Purine homeostasis ensures that cells have adequate levels of purine nucleotides for their normal functions while avoiding excessive accumulation or wasteful overproduction of these molecules. Cells need to carefully regulate purine nucleotide synthesis, salvage, and degradation pathways to maintain optimal intracellular levels of purine nucleotides, as imbalances can lead to cellular dysfunction and disease.

In bacteria, the regulation of purine nucleotide biosynthesis, including the PurR-mediated regulation of the purine operon, is an important mechanism to maintain purine homeostasis. This allows bacteria to modulate the expression of purine biosynthesis genes in response to changing cellular purine nucleotide levels, ensuring that they can efficiently utilize resources and adapt to different environments.

In higher organisms, including humans, purine homeostasis is also critical for normal cellular functions. Disruptions in purine metabolism or regulation can lead to various diseases, including metabolic disorders, immune system dysfunction, and cancer. For example, deficiencies in enzymes involved in purine metabolism can result in severe immunodeficiency disorders such as severe combined immunodeficiency (SCID) or Lesch-Nyhan syndrome, which are life-threatening conditions.

Here are some key points highlighting the importance of regulation in maintaining cellular homeostasis and preventing excessive purine synthesis:

Preventing Energy Waste: The de novo purine biosynthesis pathway requires multiple ATP and GTP molecules as substrates and energy sources. Uncontrolled and excessive purine synthesis could lead to the depletion of cellular ATP and GTP pools, resulting in energy waste and compromising cellular functions.

Maintaining Nucleotide Balance: Purine nucleotides are essential for DNA and RNA synthesis, and their balance is crucial for maintaining proper nucleotide pools. Unregulated purine synthesis can result in an excessive accumulation of purine nucleotides, leading to imbalances in nucleotide pools and disrupting cellular metabolism, DNA replication, and RNA transcription.

Preventing Toxic Intermediates: The de novo purine biosynthesis pathway involves multiple enzymatic steps and intermediate metabolites. Accumulation of toxic intermediates, such as adenosine monophosphate (AMP), can have detrimental effects on cellular health and function. Regulation of the pathway prevents the excessive buildup of toxic intermediates and protects cells from potential damage.

Preventing Cell Proliferation Disorders: Purine nucleotides are essential for cell proliferation, and uncontrolled purine synthesis can lead to uncontrolled cell growth and proliferation, which is associated with cancer and other cell proliferation disorders. Proper regulation of the de novo purine biosynthesis pathway helps prevent uncontrolled cell proliferation and maintain normal cellular growth and division.

Responding to Metabolic Demands: Cells need to adjust their purine nucleotide synthesis based on their metabolic demands, growth rate, and environmental conditions. Regulation of the pathway allows cells to modulate the expression of key enzymes involved in purine biosynthesis in response to changing cellular and environmental conditions, ensuring that purine synthesis is tailored to meet the metabolic demands of the cell.

It's important to note that the specific enzymes and regulatory mechanisms involved in the de novo purine biosynthesis pathway may vary slightly among different organisms, as there can be some variation in the pathway across different species. However, the overall general outline of the pathway and the number of enzymes involved are consistent with the typical de novo purine biosynthesis pathway.

De novo purine biosynthesis pathway regulation can occur at the transcriptional, translational, and post-translational levels, involving feedback inhibition, allosteric regulation, and enzyme degradation, among other mechanisms.

At the transcriptional level

At the transcriptional level, the simplest form of regulation of the de novo purine biosynthesis pathway involves the control of gene expression through the binding of specific regulatory proteins to the promoter regions of the genes encoding the enzymes involved in the pathway. One well-studied example of transcriptional regulation of purine synthesis in bacteria is the purine repressor (PurR) system found in Escherichia coli (E. coli) and related species. The PurR protein acts as a transcriptional regulator that can bind to the promoter region of genes involved in purine synthesis, controlling their transcription.

In the absence of sufficient intracellular levels of purines, PurR binds to the purine operator sites located in the promoter regions of target genes, preventing RNA polymerase from binding and initiating transcription. This results in repression of purine synthesis gene expression, reducing the production of purine nucleotides when they are not needed. When intracellular levels of purines increase, they bind to the PurR protein, causing a conformational change that prevents PurR from binding to the operator sites. As a result, RNA polymerase can bind to the promoter regions and initiate transcription of the genes involved in purine synthesis, leading to increased production of purine nucleotides. The PurR system in bacteria is an example of negative transcriptional regulation, where the binding of a repressor protein prevents transcription of target genes. This is a simple but effective mechanism by which bacteria can control the production of purine nucleotides based on the availability of intracellular purine levels. It's important to note that while the PurR system is one example of transcriptional regulation of purine synthesis in bacteria, other bacteria may employ different mechanisms or additional regulatory proteins depending on their specific metabolic pathways and environmental conditions. Regulation of purine synthesis can also occur at other levels, such as post-transcriptional or post-translational regulation, in more complex life forms.

The purine operon regulatory system

The purine operon regulatory system is a mechanism found in bacteria that controls the expression of genes involved in the biosynthesis of purine nucleotides. The regulatory system is typically composed of two main components: the PurR protein, which acts as a transcriptional repressor, and the purine-responsive element (PRE), which is the DNA sequence that interacts with PurR.

In the presence of sufficient intracellular purine nucleotides, PurR protein binds to the PRE in the promoter region of the purine operon genes, thereby preventing RNA polymerase from initiating transcription. This results in the downregulation or repression of the purine biosynthesis genes, leading to a decrease in the production of purine nucleotides. The mechanism by which PurR protein binds to the PRE in the promoter region of the purine operon genes and prevents RNA polymerase from initiating transcription is as follows:

PurR protein is typically present in an inactive form when intracellular purine nucleotide levels are sufficient. In this state, PurR protein is bound to purine nucleotides, which induces a conformational change that allows PurR to bind to the PRE. The PRE is a specific DNA sequence located in the promoter region of the purine operon genes. When bound to the PRE, PurR protein acts as a transcriptional repressor by physically blocking the binding of RNA polymerase to the promoter. This prevents RNA polymerase from initiating transcription of the downstream genes involved in purine biosynthesis. The binding of PurR protein to the PRE is mediated by the DNA-binding domain (DBD) of PurR, which contains a winged helix-turn-helix (HTH) motif that recognizes and binds to the specific DNA sequence in the PRE. The binding of PurR protein to the PRE is stabilized by the formation of a PurR-PRE complex, which involves multiple protein-DNA interactions. The specific interactions between PurR and the PRE prevent RNA polymerase from accessing the promoter region, leading to the repression of purine biosynthesis genes.

The binding of PurR protein to the PRE is stabilized by multiple protein-DNA interactions, which involve specific molecular contacts between PurR and the DNA in the PRE. These interactions typically occur between amino acid residues in the DNA-binding domain (DBD) of PurR and the nucleotide bases in the PRE. The precise details of these interactions may vary depending on the bacterial species and the specific sequence of the PRE, but the general principles are as follows:

Hydrogen bonding: The amino acid residues in the DBD of PurR form hydrogen bonds with the nucleotide bases in the PRE. For example, amino acid residues like arginine (Arg) and lysine (Lys) can form hydrogen bonds with the purine or pyrimidine bases in the PRE. These hydrogen bonds help to stabilize the PurR-PRE complex by creating specific molecular contacts between PurR and the DNA.

Van der Waals interactions: Van der Waals interactions, which are weak attractive forces between atoms, also contribute to the stability of the PurR-PRE complex. Amino acid residues in the DBD of PurR and the nucleotide bases in the PRE come into close proximity, allowing for van der Waals interactions between their atoms. These interactions help to hold the PurR protein in place on the DNA, enhancing the stability of the complex.

Electrostatic interactions: Electrostatic interactions, which are attractive forces between charged atoms or molecules, also play a role in stabilizing the PurR-PRE complex. Amino acid residues in the DBD of PurR may carry positive or negative charges, while the phosphate backbone of the DNA in the PRE is negatively charged. This results in electrostatic interactions between PurR and the DNA, contributing to the overall stability of the complex.

Shape complementarity: The DBD of PurR and the PRE in the DNA also exhibit shape complementarity, where the shape of the protein fits precisely into the major and minor grooves of the DNA. This shape complementarity allows for optimal molecular contacts between PurR and the DNA, enhancing the stability of the PurR-PRE complex.

When intracellular levels of purine nucleotides are low, purine biosynthesis needs to be upregulated to meet cellular demands. In this case, the concentration of unbound purine nucleotides increases, and some of these molecules bind to PurR protein, causing a conformational change that reduces its affinity for the PRE. As a result, PurR is released from the PRE, allowing RNA polymerase to bind to the promoter and initiate transcription of the purine operon genes, leading to an increase in purine nucleotide biosynthesis. The purine operon regulatory system provides a feedback mechanism that helps maintain appropriate levels of purine nucleotides in the cell, ensuring that the cell has enough purines for vital cellular processes while preventing excessive accumulation of purines, which can be toxic. It allows bacteria to tightly regulate the expression of purine biosynthesis genes in response to intracellular purine levels, helping to maintain cellular homeostasis.

The promoter regions are regions of DNA that are located upstream of the coding regions of genes and contain specific DNA sequences that are recognized by regulatory proteins, also known as transcription factors.

The PurR protein

PurR protein is a transcriptional repressor enzyme found in bacteria that regulates the expression of genes involved in the biosynthesis of purine nucleotides. It is part of the purine operon regulatory system, which controls the production of enzymes required for the synthesis of purine nucleotides. The smallest version of PurR protein is typically referred to as the "core" PurR protein, which consists of the DNA-binding domain (DBD) and the helical dimerization domain (HDD). The DBD is responsible for binding to specific DNA sequences in the purine operon promoter region, while the HDD facilitates dimerization of PurR protein. The size of the smallest version of PurR protein varies among different bacterial species, but it typically contains around 90-100 amino acids. For example, in Escherichia coli (E. coli), the core PurR protein is 89 amino acids in length.

Post-transcriptional regulation of purine biosynthesis

Post-transcriptional regulation of purine biosynthesis refers to the regulatory mechanisms that occur after transcription, the process of synthesizing RNA from DNA, in the pathway responsible for producing purine nucleotides. These mechanisms play a crucial role in fine-tuning the expression of genes involved in purine biosynthesis, allowing cells to efficiently modulate purine nucleotide production in response to changing cellular conditions.

There are several post-transcriptional regulatory mechanisms involved in purine biosynthesis, including:

RNA degradation: The stability of mRNA molecules, which carry the genetic information from DNA to synthesize proteins, can be regulated by various factors, including RNA-binding proteins and small regulatory RNAs. These factors can bind to specific regions of mRNA molecules involved in purine biosynthesis and either promote their degradation or protect them from degradation, thus controlling their abundance in the cell.

Alternative splicing: In some cases, the same mRNA molecule can give rise to multiple protein isoforms through a process called alternative splicing. Alternative splicing involves the selective inclusion or exclusion of specific exons, which are the coding regions of genes, in the final mRNA molecule. This can result in the production of different protein isoforms with distinct functions or regulatory properties. Alternative splicing can occur in genes involved in purine biosynthesis, leading to the production of different protein isoforms that may have differential activity or stability.

RNA editing: RNA molecules can also undergo post-transcriptional modifications through a process called RNA editing. RNA editing involves the alteration of specific nucleotide residues in the mRNA molecule, resulting in changes in the encoded protein's amino acid sequence. RNA editing can affect genes involved in purine biosynthesis, leading to changes in the function or activity of the encoded proteins.

Riboswitches: Riboswitches are regulatory elements found in the untranslated regions (UTRs) of mRNA molecules that can undergo conformational changes in response to binding of specific metabolites or ligands. These conformational changes can affect mRNA stability, translation efficiency, or splicing, thus regulating gene expression. Riboswitches have been identified in some genes involved in purine biosynthesis, and they play a role in regulating their expression in response to cellular purine nucleotide levels.

These post-transcriptional regulatory mechanisms work in concert with transcriptional regulation, including the PurR-mediated regulation of the purine operon, to tightly control purine biosynthesis and maintain purine homeostasis in cells. They allow cells to fine-tune the expression of genes involved in purine biosynthesis in response to changing cellular conditions, ensuring efficient production of purine nucleotides for cellular processes while avoiding excessive accumulation or wasteful utilization of resources. The post-transcriptional regulation of purine biosynthesis, along with transcriptional regulation, is coordinated through information exchange within the cell. Different regulatory elements, such as RNA-binding proteins, small regulatory RNAs, riboswitches, and other factors, interact with specific regions of mRNA molecules involved in purine biosynthesis, and these interactions convey regulatory information that determines the fate of the mRNA molecules. For example, RNA-binding proteins and small regulatory RNAs can bind to specific regions of mRNA molecules and influence their stability, translation efficiency, or splicing, depending on the cellular conditions. This information exchange allows the cell to modulate the abundance of mRNA molecules and, consequently, the levels of the encoded proteins involved in purine biosynthesis. Similarly, riboswitches, which are regulatory elements located in the UTRs of mRNA molecules, can undergo conformational changes in response to binding of specific metabolites or ligands. These conformational changes convey information about the cellular purine nucleotide levels and can affect mRNA stability, translation efficiency, or splicing, ultimately regulating gene expression. In coordination with transcriptional regulation, these post-transcriptional regulatory mechanisms allow cells to fine-tune the expression of genes involved in purine biosynthesis in response to changing cellular conditions. This information exchange ensures that the production of purine nucleotides is tightly controlled and optimized for cellular needs, helping to maintain purine homeostasis in the cell.

The "code" involved in the information exchange in post-transcriptional regulation of purine biosynthesis is mediated by specific sequences and structures in the mRNA molecules and regulatory factors, such as RNA-binding proteins, small regulatory RNAs, and riboswitches, which determine the outcome of regulation and convey information about the cellular conditions that influence purine homeostasis. Here's an overview of how these actors interact in the post-transcriptional regulation of purine biosynthesis:

RNA-binding proteins: RNA-binding proteins are proteins that specifically recognize and bind to specific RNA sequences or structures in mRNA molecules. In the context of purine biosynthesis regulation, RNA-binding proteins may bind to specific mRNA molecules involved in purine biosynthesis and affect their stability, translation efficiency, or splicing. For example, RNA-binding proteins may bind to the 5' or 3' untranslated regions (UTRs) of purine biosynthesis mRNA molecules, which can affect their stability and translation efficiency. The binding of RNA-binding proteins can be influenced by the cellular levels of purine nucleotides, which serves as a form of communication between the purine nucleotide levels and gene expression.

Small regulatory RNAs: Small regulatory RNAs are short RNA molecules that can specifically base pair with complementary regions in mRNA molecules, leading to gene regulation. In the context of purine biosynthesis regulation, small regulatory RNAs may base pair with specific mRNA molecules involved in purine biosynthesis and affect their translational efficiency or stability. The small regulatory RNAs can be produced in response to changes in cellular purine nucleotide levels or other signaling cues, and their base pairing with target mRNA molecules conveys information about the cellular conditions and regulates gene expression accordingly.

Riboswitches: Riboswitches are specific RNA sequences and structures that can change conformation in response to binding of specific metabolites or ligands. In the context of purine biosynthesis regulation, riboswitches may be present in the 5' UTR of mRNA molecules involved in purine biosynthesis and can change conformation upon binding of purine nucleotides. This conformational change can affect mRNA stability, translation efficiency, or splicing, and serves as a form of communication between the cellular purine nucleotide levels and gene expression.

Interdependence of the complex regulatory network

The various actors involved in the post-transcriptional regulation of purine biosynthesis, including RNA-binding proteins, small regulatory RNAs, and riboswitches, are interdependent and form a complex regulatory network that is irreducible, meaning that the removal of any one of these actors would disrupt the regulatory system. Here's an outline of how these actors are interdependent and irreducible in the context of purine biosynthesis regulation:

RNA-binding proteins: RNA-binding proteins specifically bind to mRNA molecules involved in purine biosynthesis and can affect their stability, translation efficiency, or splicing. The binding of RNA-binding proteins is often influenced by the cellular levels of purine nucleotides or other signaling cues. Removal of RNA-binding proteins would result in loss of their regulatory function and disruption of the post-transcriptional regulation of purine biosynthesis.

Small regulatory RNAs: Small regulatory RNAs can specifically base pair with complementary regions in mRNA molecules and affect their translational efficiency or stability. These small regulatory RNAs are often produced in response to changes in cellular purine nucleotide levels or other signaling cues. Removal of small regulatory RNAs would result in loss of their base pairing and regulatory function, disrupting the post-transcriptional regulation of purine biosynthesis.

Riboswitches: Riboswitches are specific RNA sequences and structures that can change conformation in response to binding of specific metabolites or ligands, such as purine nucleotides. This conformational change can affect mRNA stability, translation efficiency, or splicing. Removal of riboswitches would result in loss of their conformational switching ability and regulatory function, disrupting the post-transcriptional regulation of purine biosynthesis.

Overall, the various actors involved in the post-transcriptional regulation of purine biosynthesis, including RNA-binding proteins, small regulatory RNAs, and riboswitches, are interdependent and form a complex regulatory network. Each of these actors plays a crucial role in the regulation of purine biosynthesis, and their removal would disrupt the regulatory system, making it irreducible. This highlights the importance of the interplay between these actors in coordinating the regulation of purine biosynthesis at the post-transcriptional level.  The individual players involved in the post-transcriptional regulation of purine biosynthesis, such as RNA-binding proteins, small regulatory RNAs, and riboswitches, typically do not function effectively on their own. Their regulatory functions are typically dependent on their interactions with other molecules and components within the cellular environment.

For example, RNA-binding proteins require specific binding sites on mRNA molecules and other factors for their regulatory function. Small regulatory RNAs typically require complementary base pairing with target mRNA molecules to exert their regulatory effects. Riboswitches require binding of specific metabolites or ligands to undergo conformational changes and regulate mRNA stability, translation, or splicing. These interactions and dependencies allow these regulatory molecules to function effectively in coordinating the post-transcriptional regulation of purine biosynthesis. Without the appropriate interactions and dependencies, these individual players may not be able to effectively regulate purine biosynthesis or perform their regulatory functions. Therefore, the interdependence of these regulatory molecules is essential for the proper functioning of the post-transcriptional regulation of purine biosynthesis in the cell. The emergence of an integrated system for post-transcriptional regulation of purine biosynthesis through unguided means, such as evolution, could indeed pose challenges in terms of intermediate steps that may not confer a functional advantage. It is a complex process that likely requires multiple components that would have to evolve in a coordinated manner to confer a selective advantage.


Interdependence Points to Design

In the world of cells, a network complex,
Regulating purines, with interwoven threads.
From RNA-binding proteins to small RNAs,
And riboswitches, dance in the elegant spread.

Each actor plays a role, unique and fine,
Dependent on others, they intertwine.
RNA-binding proteins, with binding sites specific,
Stabilizing mRNAs, making them prolific.

Small RNAs, with base pairing prowess,
Efficiently tweaking mRNAs, with finesse.
Responding to cues, like nucleotide levels,
Or other signals, that the cell unravels.

Riboswitches, like molecular switches,
Changing conformation, as the cell wishes.
Metabolite binding, causing a change,
In mRNA regulation, they rearrange.

Irreducible, this network of dance,
The removal of one would disrupt the chance,
Of proper regulation, in purine biosynthesis,
A system so intricate, it's hard to dismiss.

Interdependence points to design,
In this regulatory network, so refined.
Each actor is essential, in its own way,
Working together, day by day.

Evolution's path, complex and long,
Coordinating components, can't be wrong.
Design in every step, we see,
In the interdependence, of this regulatory decree.

So marvel at the complexity, of this dance,
In the world of cells, where interdependence enhances,
The regulation of purine biosynthesis,
A testament to design, a masterpiece of life's kiss.

Purine biosynthesis regulation at the translational level

Purine biosynthesis regulation at the translational level involves mechanisms that control the translation of mRNA molecules encoding enzymes involved in purine biosynthesis. These mechanisms can impact the production of these enzymes and thereby regulate the overall rate of purine biosynthesis in a cell. One common mechanism of translational regulation in purine biosynthesis involves the binding of small regulatory RNAs or RNA-binding proteins to the mRNA molecules encoding the enzymes involved in purine biosynthesis. These regulatory RNAs or proteins can interact with specific regions of the mRNA molecules, such as the 5' untranslated region (UTR) or the coding sequence, and modulate translation initiation or elongation, leading to changes in protein production. For example, some small regulatory RNAs called riboswitches can directly bind to mRNA molecules and undergo conformational changes in response to changing intracellular purine levels. These conformational changes can either promote or inhibit translation initiation, depending on the specific riboswitch and the intracellular purine levels. This allows the cell to tightly regulate the production of purine biosynthesis enzymes based on the cellular purine levels. RNA-binding proteins can also play a role in translational regulation of purine biosynthesis. They can bind to specific regions of the mRNA molecules and either enhance or inhibit translation initiation or elongation, depending on the binding protein and its regulatory role.

Purine biosynthesis regulation at the post - translational level

Purine biosynthesis regulation at the post-translational level involves mechanisms that control the activity or stability of enzymes involved in purine biosynthesis after they have been translated and synthesized into functional proteins. These mechanisms can impact the function or abundance of these enzymes, leading to changes in purine biosynthesis rates. One common mechanism of post-translational regulation in purine biosynthesis involves protein modification, such as phosphorylation, acetylation, or ubiquitination. These modifications can occur on specific amino acid residues of the enzymes involved in purine biosynthesis and can alter their activity, stability, or protein-protein interactions. For example, phosphorylation is a common post-translational modification that can regulate the activity of enzymes involved in purine biosynthesis. Phosphorylation can either activate or inhibit the activity of these enzymes, depending on the specific enzyme and the site of phosphorylation. Protein kinases are enzymes that add phosphate groups to specific amino acids, and protein phosphatases are enzymes that remove phosphate groups, thus controlling the phosphorylation status of proteins involved in purine biosynthesis.

Another example is protein degradation, which can regulate the stability of enzymes involved in purine biosynthesis. Ubiquitination is a common post-translational modification that targets proteins for degradation by the proteasome, cellular proteolytic machinery. Ubiquitin ligases are enzymes that add ubiquitin moieties to proteins, marking them for degradation, while deubiquitinases are enzymes that remove ubiquitin moieties. Ubiquitination can affect the stability and turnover rate of enzymes involved in purine biosynthesis, thereby regulating their abundance and activity. In addition, post-translational regulation of purine biosynthesis can also involve protein-protein interactions or protein conformational changes that modulate the activity or localization of the enzymes. For example, the formation of protein complexes or the binding of regulatory proteins to enzymes involved in purine biosynthesis can influence their activity or localization, and thereby regulate purine biosynthesis. Overall, post-translational regulation of purine biosynthesis involves a complex interplay of protein modifications, protein-protein interactions, and conformational changes that modulate the activity, stability, and localization of enzymes involved in purine biosynthesis, leading to fine-tuning of purine homeostasis in the cell.

Protein Kinases

Protein kinases are enzymes that catalyze the transfer of phosphate groups from ATP (adenosine triphosphate) or other phosphate donors to specific amino acid residues on target proteins, including enzymes involved in purine biosynthesis. Phosphorylation of these enzymes can regulate their activity, stability, localization, and protein-protein interactions, thereby influencing purine biosynthesis. In purine biosynthesis, protein kinases can phosphorylate enzymes at specific amino acid residues to either activate or inhibit their activity. For example, in the de novo purine biosynthesis pathway, the enzyme phosphoribosyl pyrophosphate (PRPP) synthetase, which catalyzes the first committed step in purine biosynthesis, can be phosphorylated by protein kinases such as AMP-activated protein kinase (AMPK) or protein kinase C (PKC) at specific serine or threonine residues. Phosphorylation of PRPP synthetase can regulate its enzymatic activity, influencing the rate of PRPP production, which in turn affects the rate of purine nucleotide synthesis. Similarly, other enzymes involved in purine biosynthesis, such as adenylosuccinate synthetase, adenylosuccinate lyase, and IMP dehydrogenase, can also be phosphorylated by protein kinases, which can modulate their activity, stability, or interactions with other proteins. The specific effects of phosphorylation on these enzymes can vary depending on the enzyme and the site of phosphorylation, and can either stimulate or inhibit their enzymatic activity. Protein kinases involved in phosphorylation of enzymes in purine biosynthesis are regulated themselves through various mechanisms, including changes in cellular energy status, cellular stress, or signaling pathways. For example, AMPK, which phosphorylates PRPP synthetase, is activated by an increase in cellular AMP-to-ATP ratio, indicating low cellular energy status. Other protein kinases involved in purine biosynthesis regulation may be activated by specific signaling pathways or cellular cues that are relevant to the metabolic state or physiological conditions of the cell. Overall, phosphorylation by protein kinases is an important post-translational mechanism that can regulate the activity of enzymes involved in purine biosynthesis, contributing to the fine-tuning of purine homeostasis in the cell.

How important is fine-tuning of cellular homeostasis?

Homeostasis, or the ability of a cell or organism to maintain a stable internal environment despite external fluctuations, is crucial for the proper functioning of biological systems. Fine-tuning of homeostasis, including purine biosynthesis homeostasis, is essential for maintaining cellular health and function.

Purine nucleotides are essential building blocks for DNA, RNA, and ATP, which are critical for various cellular processes such as DNA replication, RNA transcription, protein synthesis, and energy metabolism. Proper regulation of purine biosynthesis is necessary to ensure an adequate supply of purine nucleotides for cellular processes while avoiding an excess that could lead to toxicity or imbalance in nucleotide pools.  Fine-tuning of purine biosynthesis ensures that the cell can respond to changing metabolic demands, energy status, and other physiological cues to maintain optimal purine nucleotide levels for cellular function. Imbalances in purine homeostasis can have detrimental effects on cellular function and contribute to various diseases. The fine-tuning of purine homeostasis through various regulatory mechanisms, including post-translational regulation, is critical for maintaining cellular health and function.

The enzymes for Adenine synthesis

1. Adenylosuccinate synthase 
2. adenylosuccinase (adenylosuccinate lyase)

The enzymes for Guanine synthesis

1. IMP dehydrogenase
2. GMP synthase 

The metabolic pathway for the de novo biosynthesis of IMP. 
Here the purine residue is built up on a ribose ring in 11 enzyme-catalyzed reactions. The X-ray structures for all the enzymes are shown to the outside of the corresponding reaction arrow. The peptide chains of monomeric enzymes are colored in rainbow order from N-terminus (blue) to C-terminus (red). The oligomeric enzymes, all of which consist of identical polypeptide chains, are viewed along a rotation axis with their various chains differently colored. Bound ligands are shown in space-filling form with C green, N blue, O red, and P orange. [PDBids: enzyme 1, 1DKU; enzyme 2, 1AO0; enzyme 3, 1GSO; enzyme 4, 1CDE; enzyme 5, 1VK3; enzyme 6, 1CLI; enzyme 7, 1D7A (PurE) and 1B6S (PurK); enzyme 8, 1A48; enzyme 9, 1C3U; enzymes 10 and 11, 1G8M.] 

1. Activation of ribose-5-phosphate. 
The starting material for purine biosynthesis is α-D-ribose-5-phosphate, a product of the pentose phosphate pathway. In the first step of purine biosynthesis, ribose phosphate pyrophosphokinase activates the ribose by reacting it with ATP to form 5-phosphoribosyl-????-pyrophosphate (PRPP). This compound is also a precursor in the biosynthesis of pyrimidine nucleotides and the amino acids histidine and tryptophan. As is expected for an enzyme at such an important biosynthetic crossroads, the activity of ribose phosphate pyrophosphokinase is precisely regulated.

2. Acquisition of purine atom N9. 
In the first reaction unique to purine biosynthesis, amidophosphoribosyl transferase catalyzes the displacement of PRPP’s pyrophosphate group by glutamine’s amide nitrogen. The reaction occurs with the inversion of the α configuration at C1 of PRPP, thereby forming ????-5-phosphoribosylamine and establishing the anomeric form of the future nucleotide. The reaction, which is driven to completion by the subsequent hydrolysis of the released PPi, is the pathway’s flux-controlling step.

3. Acquisition of purine atoms C4, C5, and N7.
Glycine’s carboxyl group forms an amide with the amino group of phosphoribosylamine, yielding glycinamide ribotide (GAR). This reaction is reversible, despite its concomitant hydrolysis of ATP to ADP + Pi. It is the only step of the purine biosynthetic pathway in which more than one purine ring atom is acquired.

4. Acquisition of purine atom C8. 
GAR’s free α-amino group is formylated Section 1 Synthesis of Purine Ribonucleotides to yield formylglycinamide ribotide (FGAR). The formyl donor in the reaction is N10-formyltetrahydrofolate (N10-formyl-THF), a coenzyme that transfers C1 units (THF cofactors). The X-ray structure of the enzyme catalyzing the reaction, GAR transformylase, in complex with GAR and the THF analog 5-deazatetrahydrofolate (5dTHF) was determined by Robert Almassy. Note the proximity of the GAR amino group to N10 of 5dTHF. This supports enzymatic studies suggesting that the GAR transformylase reaction proceeds via the nucleophilic attack of the GAR amine group on the formyl carbon of N10-formyl-THF to yield a tetrahedral intermediate.

5. Acquisition of purine atom N3.
The amide amino group of a second glutamine is transferred to the growing purine ring to form formylglycinamidine ribotide (FGAM). This reaction is driven by the coupled hydrolysis of ATP to ADP + Pi

6. Formation of the purine imidazole ring.
The purine imidazole ring is closed in an ATP-requiring intramolecular condensation that yields 5-aminoimidazole ribotide (AIR). The aromatization of the imidazole ring is facilitated by the tautomeric shift of the reactant from its imine to its enamine form.

7. Acquisition of C6.
Purine C6 is introduced as HCO− 3 (CO2) in a reaction catalyzed by AIR carboxylase that yields carboxyaminoimidazole ribotide (CAIR). In yeast, plants, and most prokaryotes (including E. coli), AIR carboxylase consists of two proteins called PurE and PurK. Although PurE alone can catalyze the carboxylation reaction, its KM for HCO− 3 is ∼110 mM, so the reaction would require an unphysiologically high HCO− 3 concentration (∼100 mM) to proceed. PurK decreases the HCO− 3 concentration required for the PurE reaction by >1000-fold but at the expense of ATP hydrolysis.

8. Acquisition of N1. 
Purine atom N1 is contributed by aspartate in an amide-forming condensation reaction yielding 5-aminoimidazole-4-(N-succinylocarboxamide) ribotide (SACAIR). This reaction, which is driven by the hydrolysis of ATP, chemically resembles Reaction 3.

9. Elimination of fumarate. 
SACAIR is cleaved with the release of fumarate, yielding 5-aminoimidazole-4-carboxamide ribotide (AICAR). Reactions 8 and 9 chemically resemble the reactions in the urea cycle in which citrulline is aminated to form arginine. In both pathways, aspartate’s amino group is transferred to an acceptor through an ATP-driven coupling reaction followed by the elimination of the aspartate carbon skeleton as fumarate.

10. Acquisition of C2. 
The final purine ring atom is acquired through formylation by N10-formyl-THF, yielding 5-formaminoimidazole-4- carboxamide ribotide (FAICAR). This reaction and Reaction 4 of purine biosynthesis are inhibited indirectly by sulfonamides, structural analogs of the p-aminobenzoic acid constituent of THF

11. Cyclization to form IMP. 
The final reaction in the purine biosynthetic pathway, ring closure to form IMP, occurs through the elimination of water. In contrast to Reaction 6, the cyclization that forms the imidazole ring, this reaction does not require ATP hydrolysis.

In animals, Reactions 10 and 11 are catalyzed by a bifunctional enzyme, as are Reactions 7 and 8. Reactions 3, 4, and 6 also take place on a single protein. The intermediate products of these multifunctional enzymes are not readily released to the medium but are channeled to the succeeding enzymatic activities of the pathway. As in the reactions catalyzed by the pyruvate dehydrogenase complex, fatty acid synthase, bacterial glutamate synthase, and tryptophan synthase, channeling in the nucleotide synthetic pathways increases the overall rate of these multistep processes and protects intermediates from degradation by other cellular enzymes.49

Comment: How did these multifunctional enzymes, avoid leaking the intermediate products to their surrounding, emerge in a gradualistic manner, if leaking would lead to degradation, and eventually the death of the "protocell"? Let's not forget, these metabolic pathways are life-essential and had to emerge somehow prior to life to start. What I see here, is evidence of exquisite design that was planned with foresight and intentions.

1. Glycinamide ribotide (GAR) transformylase (GART)
2. Formylglycinamide ribotide (FGAR) amidotransferase (GART)
3. Formylglycinamidine ribotide (FGAM) synthetase (GART)
4. 5-aminoimidazole ribotide (AIR) carboxylase (PurK)
5. 5-aminoimidazole-4-(N-succinylocarboxamide) ribotide (SACAIR)synthetase (PurE)
6. Carboxyaminoimidazole ribotide (CAIR) mutase (PurK)
7. 5-aminoimidazole-4-carboxamide ribotide (AICAR)transformylase (PurN)
8. 5-formaminoimidazole-4- carboxamide ribotide (FAICAR) cyclase (PurM)
9. IMP cyclohydrolase  (PurH)


1. Ribose-phosphate diphosphokinase

Ribose-phosphate diphosphokinase catalyzes the conversion of ribose-5-phosphate (R5P) and ATP (adenosine triphosphate) into phosphoribosyl pyrophosphate (PRPP) and ADP (adenosine diphosphate). The overall structure of ribose-phosphate diphosphokinase is typically a homodimer, meaning it consists of two identical subunits. Each subunit has its own active site where the enzyme's catalytic activity takes place. The minimal bacterial isoform of ribose-phosphate diphosphokinase is a small protein with a size of approximately 150-200 amino acids, although the exact size may vary depending on the specific bacterial species. It is composed of a single polypeptide chain folded into a three-dimensional structure, with specific regions or domains that are responsible for its catalytic activity and substrate binding.

The amino acid sequence of ribose-phosphate diphosphokinase can vary among different bacterial species, but it typically contains conserved regions that are important for its function. These regions may include ATP binding sites, R5P binding sites, and catalytic residues that are involved in the enzymatic reaction. Ribose-phosphate diphosphokinase is an important enzyme in nucleotide metabolism and is found in both prokaryotic and eukaryotic organisms. It plays a crucial role in the biosynthesis of nucleotides, which are essential for DNA and RNA synthesis, energy metabolism, and various cellular processes. The specific structure and function of ribose-phosphate diphosphokinase may vary among different organisms, but its overall role in nucleotide metabolism is conserved across species.

Ribose-phosphate diphosphokinase (RPK), also known as PRPP synthase, plays a critical role in nucleotide biosynthesis, which is essential for many cellular processes including DNA and RNA synthesis. If a cell lacks RPK or has impaired RPK activity, it can have severe consequences for cellular function and viability. If a cell lacks RPK or has reduced RPK activity, it can lead to a deficiency of PRPP, which in turn can result in impaired nucleotide biosynthesis and other metabolic pathways that depend on PRPP as a precursor. This can disrupt cellular processes that require nucleotides, such as DNA and RNA synthesis, and can ultimately lead to cell death or severe cellular dysfunction.

Additionally, RPK has been found to be important for the regulation of cellular metabolism, cell proliferation, and response to stress and other environmental cues. Dysfunction or absence of RPK can have far-reaching effects on cellular metabolism and physiology, beyond nucleotide biosynthesis.

The activity of ribose-phosphate diphosphokinase, like other enzymes, depends on several factors, including:

Co-factors or co-enzymes: Ribose-phosphate diphosphokinase may require specific co-factors or co-enzymes for its activity. These are small molecules that are necessary for the enzyme to function properly. For example, ribose-phosphate diphosphokinase may require magnesium ions (Mg2+) as a co-factor for its enzymatic activity.

Protein-protein interactions: Ribose-phosphate diphosphokinase may interact with other proteins or enzymes in the cellular pathway or metabolic network in which it operates. These interactions can modulate its activity or regulation.

Post-translational modifications: Ribose-phosphate diphosphokinase or its isoforms may undergo post-translational modifications, such as phosphorylation, acetylation, or methylation, which can affect its activity, stability, or localization.

Genetic regulation: The expression and activity of ribose-phosphate diphosphokinase can be regulated at the genetic level. Transcription factors, regulatory proteins, or other cellular processes can modulate the enzyme's expression or activity.

Ribose-phosphate diphosphokinase requires two inorganic cofactors for its activity:

Magnesium ions (Mg2+): Magnesium ions are essential for the catalytic activity of ribose-phosphate diphosphokinase. They play a critical role in stabilizing the enzyme's active site and facilitating the transfer of phosphate groups between ATP and R5P during the enzymatic reaction.

Inorganic pyrophosphate (PPi): Inorganic pyrophosphate (PPi) is a high-energy phosphate molecule that serves as a donor of pyrophosphate group in the synthesis of PRPP from ATP and R5P. PPi is hydrolyzed during the enzymatic reaction, providing the energy necessary to drive the formation of PRPP.

Both magnesium ions and inorganic pyrophosphate are required for the proper functioning of ribose-phosphate diphosphokinase, and their presence is critical for the enzyme's catalytic activity. These cofactors play an essential role in stabilizing the enzyme's structure, facilitating substrate binding, and promoting the chemical reactions involved in the conversion of R5P and ATP to PRPP. It's important to note that the availability of cofactors, including magnesium ions and inorganic pyrophosphate, in the cellular environment can be regulated by cellular homeostasis and metabolic pathways. Cells tightly regulate the concentrations of cofactors to maintain optimal enzyme activity and cellular function. Additionally, the specific mechanisms by which ribose-phosphate diphosphokinase acquires these cofactors may vary depending on the organism, cellular context, and environmental conditions.

Activation of ribose-5-phosphate


The starting material for purine biosynthesis is Ribose 5-phosphate, a product of the pentose phosphate pathway. That means the synthesis of ribonucleosides depends on the pentose phosphate pathway.

In the first step of purine biosynthesis,  Ribose-phosphate diphosphokinase ( PRPP synthetase) activates the ribose by reacting it with ATP to form  5-Phosphoribosyl-1-Pyrophosphate (PRPP). This compound is also a precursor in the biosynthesis of pyrimidine nucleotides and the amino acids histidine and tryptophan. As is expected for an enzyme at such an important biosynthetic crossroads, the activity of ribose-phosphate pyrophosphokinase is precisely regulated.



Ribose-phosphate diphosphokinase

The two major purine nucleoside diphosphates, ADP and GDP, are negative effectors of ribose-5-phosphate pyrophosphokinase.

That rises the question which emerged first: ADP and GDP which are the product of the pathway of which Ribose-phosphate diphosphokinase makes part or the enzyme per se.

Regulating the availability of cofactors

The cell regulates the availability of cofactors, including magnesium ions and inorganic pyrophosphate, through various mechanisms to maintain optimal enzyme activity and cellular function. Here are some examples of how cells regulate cofactor levels:

Cellular transporters: Cells can have specific transporters that actively import or export cofactors, including magnesium ions, to regulate their intracellular concentrations. These transporters can be regulated by various factors, such as cellular signaling, energy status, and cofactor availability, to maintain appropriate levels of cofactors in the cell.

Chelation and sequestration: Cells can use chelating molecules or proteins to tightly bind and sequester cofactors, such as magnesium ions, in specific cellular compartments or organelles. This can help regulate the availability and distribution of cofactors within the cell, ensuring that they are available for the appropriate enzymes or metabolic pathways.

Enzymatic synthesis and degradation: Cells can synthesize and degrade cofactors as needed to regulate their intracellular concentrations. For example, inorganic pyrophosphate (PPi), which is a byproduct of ribose-phosphate diphosphokinase activity, can be further metabolized or regenerated by other enzymes or pathways in the cell.

Feedback regulation: The activity of enzymes involved in cofactor metabolism or utilization can be regulated by feedback mechanisms. For example, high intracellular concentrations of certain cofactors, such as magnesium ions or ATP, can allosterically inhibit or activate enzymes involved in cofactor biosynthesis or utilization to maintain appropriate levels of cofactors in the cell.

Gene expression regulation: Cells can regulate the expression of genes encoding enzymes involved in cofactor metabolism or utilization to control the levels of cofactors. This can be achieved through transcriptional regulation, where specific transcription factors or regulatory proteins control the expression of these genes in response to cellular signals or environmental cues.

Overall, the regulation of cofactor levels in the cell is a tightly controlled process that involves various mechanisms, including cellular transporters, chelation and sequestration, enzymatic synthesis and degradation, feedback regulation, and gene expression regulation. These mechanisms work together to maintain optimal cofactor concentrations for the proper functioning of enzymes and metabolic pathways in the cell.

Mechanism description

The mechanism of RPK involves several steps, including substrate binding, phosphoryl transfer, and product release. Here is a general overview of the RPK mechanism:

Substrate binding: RPK binds both R5P and ATP as substrates. R5P binds first to the active site of RPK, followed by ATP binding to a separate site on the enzyme. The binding of ATP induces a conformational change in RPK that positions the two substrates for phosphoryl transfer.

Phosphoryl transfer: RPK catalyzes the transfer of a pyrophosphate (PPi) group from ATP to R5P. The phosphoryl group from ATP is transferred to the C1 position of R5P, forming PRPP and releasing ADP as a byproduct. The reaction involves a nucleophilic attack by the C1 hydroxyl group of R5P on the γ-phosphate of ATP, resulting in the formation of a phosphoester bond between R5P and the transferred phosphoryl group.

Product release: After phosphoryl transfer, PRPP is released from the active site of RPK, and the enzyme is ready for another catalytic cycle. The released ADP can be further metabolized or recycled by other cellular processes.

The mechanism of RPK is complex and involves multiple steps, including substrate binding, phosphoryl transfer, and product release. The enzyme's active site and conformational changes play a crucial role in facilitating the catalytic reaction and ensuring efficient PRPP synthesis, which is essential for nucleotide biosynthesis and other cellular processes.

Enzymatic Symphony: The Marvel of Design

Behold the marvel of design,
Ribose-phosphate diphosphokinase, divine,
An enzyme that orchestrates with grace,
The synthesis of nucleotides, in every place.

With active sites, it's built to bind,
R5P and ATP, in perfect kind,
Converting them with skill and might,
To PRPP and ADP, in the enzyme's light.

A homodimer it forms, a symphony in pairs,
With identical subunits, it truly declares,
The beauty of its structure, precise and fine,
A testament to intelligence, so divine.

Conserved regions, so carefully designed,
ATP binding sites, with precision aligned,
And R5P binding sites, they play their part,
In the enzymatic dance, a work of art.

Amino acids, the building blocks of life,
Compose this enzyme, without any strife,
Their sequence varies, but still we find,
The hand of design, so perfectly aligned.

Magnesium ions, a crucial co-factor,
Stabilize the enzyme's active site, with their benefactor,
Inorganic pyrophosphate, a high-energy bond,
Provides the driving force, so the reaction can respond.

Genetic regulation, a masterful control,
To fine-tune the enzyme's activity, a precise role,
Protein-protein interactions, a delicate dance,
To modulate its function, with elegance.

Post-translational modifications, adding flair,
Phosphorylation, acetylation, with utmost care,
Fine-tuning the enzyme's stability and location,
A master plan, of intricate coordination.

The availability of cofactors, it's tightly controlled,
Through cellular transporters, so wise and bold,
The cell maintains optimal levels, just right,
To ensure the enzyme's activity, shines bright.

Ribose-phosphate diphosphokinase, a wondrous sight,
A marvel of design, with intelligence so bright,
In nucleotide biosynthesis, it plays a key role,
A testament to an intelligent design, an awe-inspiring goal.


2. Amidophosphoribosyl transferase(GPAT)

Amidophosphoribosyl transferase (GPAT), also known as phosphoribosylamine--glycine ligase, is an enzyme that plays a key role in the biosynthesis of purine nucleotides, which are essential components of DNA, RNA, and ATP. GPAT catalyzes the transfer of an amidophosphoribosyl group from phosphoribosylamine to glycine, forming glycinamide ribonucleotide (GAR) in the presence of ATP.

GPAT is a homodimeric enzyme, meaning it consists of two identical subunits that come together to form a functional enzyme. Each subunit has a distinct domain organization, typically composed of an N-terminal ATP-binding domain, a central catalytic domain, and a C-terminal regulatory domain.

The ATP-binding domain is responsible for binding and hydrolyzing ATP, providing the necessary energy for the enzyme's catalytic activity. The catalytic domain contains the active site where the transfer of the amidophosphoribosyl group takes place, and it is highly conserved among GPAT enzymes. The regulatory domain, located at the C-terminus, serves as a regulatory switch that controls the enzyme's activity through allosteric interactions with other molecules.

The overall structure of GPAT can vary depending on the specific organism and the form of the enzyme (e.g., monomeric, dimeric, or multimeric). GPAT enzymes have been identified in various organisms, including bacteria, fungi, plants, and animals, and they exhibit structural diversity and functional specialization.

Acquisition of purine atom N9
 
In the first reaction unique to purine biosynthesis, Amidophosphoribosyl transferase (ATase) catalyzes the displacement of PRPP’s pyrophosphate group by glutamine’s amide nitrogen. The reaction occurs with inversion of the configuration at C1 of PRPP, thereby forming  Beta 5-phosphoribosylamine and establishing the anomeric form of the future nucleotide. The reaction, which is driven to completion by the subsequent hydrolysis of the released PPi, is the pathway’s flux-controlling step.


Amidophosphoribosyl transferase 

Its Function

GPAT plays a crucial role in the de novo biosynthesis of purine nucleotides, which are essential for DNA and RNA synthesis, energy metabolism (ATP), and other important cellular processes. GPAT catalyzes the transfer of the amidophosphoribosyl group from phosphoribosylamine to glycine, forming glycinamide ribonucleotide (GAR). GAR is an important intermediate in the purine biosynthetic pathway, and it serves as a precursor for the synthesis of various purine nucleotides, such as AMP (adenosine monophosphate) and GMP (guanosine monophosphate).

GPAT activity is tightly regulated to maintain the balance of purine nucleotide production in the cell. The enzyme can be regulated by allosteric effectors, such as ATP and purine nucleotides, which bind to the regulatory domain and modulate the enzyme's activity. Additionally, GPAT can be subject to post-translational modifications, such as phosphorylation, which can further regulate its activity.

GPAT is a critical enzyme involved in the biosynthesis of purine nucleotides, and its overall structure typically consists of homodimeric subunits with distinct ATP-binding, catalytic, and regulatory domains. The enzyme's activity is tightly regulated to ensure proper cellular production of purine nucleotides, which are essential for various cellular processes.

Mechanism description

The process of GPAT enzyme activity can be likened to a machine-like process with a clear goal-oriented logic, from substrate binding to product release, and resetting of the active site for subsequent catalysis.

Substrate binding: GPAT first binds its substrates, PRPP as the donor molecule and an acceptor molecule, such as a nucleotide base or an amino acid, at its active site. The active site is a specific region of the enzyme that allows for substrate recognition and catalysis. The binding of the substrates is highly specific and precise, ensuring that only the correct substrates are bound and processed by the enzyme.

Catalysis: Once the substrates are bound, GPAT catalyzes the transfer of the amidophosphoribosyl (PRPP) group from PRPP to the acceptor molecule. This transfer results in the formation of a new bond between the PRPP group and the acceptor molecule, which is an essential step in the biosynthesis of purine nucleotides. During this process, GPAT facilitates the chemical reaction required for the transfer of the PRPP group, ensuring that the reaction occurs efficiently and effectively.

Product release: After the transfer reaction is complete, GPAT releases the newly formed product, which now contains the PRPP group, from its active site. This allows the product to be further utilized in downstream metabolic pathways for the biosynthesis of purine nucleotides, which are important for cellular processes such as DNA and RNA synthesis.

Resetting the active site: GPAT may undergo conformational changes to reset its active site for another round of catalysis. This may involve the release of any remaining pyrophosphate (PPi) or other cofactors, and the enzyme may return to its original conformation to await the binding of new substrates. This resetting process ensures that GPAT is ready to bind and process new substrates for subsequent rounds of catalysis, maintaining its efficiency and effectiveness in synthesizing purine nucleotides.

The GPAT enzyme operates with clear goal-oriented logic, akin to a machine-like process, where it binds substrates at its active site, catalyzes the transfer of a PRPP group to the acceptor molecule, releases the product, and resets its active site for subsequent rounds of catalysis. This efficient and precise process allows for the de novo synthesis of purine nucleotides, a critical cellular function.

The GPAT enzyme, like many other enzymes, follows a specific sequence of events from substrate binding to product release, and resetting of the active site for subsequent catalysis. Each step in this process is highly orchestrated and relies on precise molecular interactions to occur in a sequential and coordinated manner. If any of the intermediate stages in the GPAT enzyme process, such as substrate binding, catalysis, product release, or resetting of the active site, were not pre-programmed to occur in a clear and logical sequence, it could disrupt the proper functioning of the enzyme. Enzymes are finely-tuned biological machines that require specific molecular interactions and conformational changes to perform their functions effectively.

For example, if the substrate binding step is disrupted, the enzyme may not be able to properly recognize and bind the substrates, leading to a loss of catalytic activity. If the catalysis step is compromised, the enzyme may not be able to facilitate the chemical reaction required for the transfer of the PRPP group, leading to a failure in product formation. Similarly, if the product release or active site resetting steps are impaired, it could result in a buildup of intermediate products or a failure to prepare the enzyme for subsequent rounds of catalysis.

Any disruptions or deviations from the normal sequence of events in the GPAT enzyme process could potentially result in a breakdown of the enzyme's function, leading to a loss or reduction in its catalytic activity, and ultimately affecting the biosynthesis of purine nucleotides, which are important for cellular processes. Therefore, a clear and sequential functioning of the enzyme is crucial for its proper activity and overall biological function.

In enzyme-catalyzed reactions, each step in the process, including substrate binding, catalysis, product release, and resetting of the active site, is interconnected and serves a specific purpose in the overall enzymatic pathway. These steps are coordinated and integrated to ensure efficient and effective enzymatic activity.

Substrate binding is necessary to ensure that only the correct substrates are recognized and processed by the enzyme, and it is a crucial step for the subsequent catalytic reaction. Catalysis is the central step where the enzyme facilitates the chemical reaction required for the conversion of substrates into products. Product release allows the newly formed product to be released from the active site and utilized in downstream metabolic pathways. Resetting the active site prepares the enzyme for subsequent rounds of catalysis and maintains its efficiency.

All these steps work together in a coherent and sequential manner to achieve the desired enzymatic function. If any of these steps were missing or disrupted, it could compromise the overall effectiveness and efficiency of the enzyme, and the process may not proceed as intended.

Enzymes have to perform their functions through a tightly regulated and integrated series of steps. Each step contributes to the overall process and is advantageous when integrated into the whole process. The coordinated interplay of these steps allows enzymes to carry out their specific functions with high specificity, efficiency, and accuracy, enabling the intricate biochemical pathways that occur in living organisms.

The GPAT enzyme operates with a clear goal-oriented logic, akin to a machine-like process, where it binds substrates at its active site, catalyzes the transfer of a PRPP group to the acceptor molecule, releases the product, and resets its active site for subsequent rounds of catalysis. This efficient and precise process allows for the de novo synthesis of purine nucleotides, a critical cellular function.

Goal-orientedness is a hallmark of intelligent setup and design. It refers to the intentional and systematic alignment of actions, processes, and resources toward achieving a specific objective or purpose. Whether it is designing a physical product, developing a software application, or organizing a complex system, goal-orientedness ensures that efforts are directed towards a well-defined end goal, which increases the chances of success.

One of the key aspects of goal-orientedness is the clarity of the objective. A well-defined and specific goal provides a clear sense of direction and purpose, enabling  to focus their efforts and resources effectively. A goal acts as a guiding star that helps in making informed decisions and prioritizing tasks. Without a clear goal, efforts may be scattered, resources may be misallocated, and progress may be hindered.

Another important aspect of goal-orientedness is the ability to adapt and adjust as circumstances change. Intelligent setup and design require flexibility to respond to changing requirements, constraints, or opportunities. This means constantly reviewing and aligning actions with the changing context to ensure that the goal remains relevant and achievable. This adaptability allows for optimization and improvement, and it ensures that the design remains effective and efficient in achieving the intended purpose.

Amidophosphoribosyl transferase (GPAT), it is an enzyme that is designed to be tightly regulated in cells to maintain cellular purine levels and balance. GPAT is subject to feedback inhibition, where the end product of the purine biosynthesis pathway, inosine monophosphate (IMP), can bind to and inhibit GPAT, regulating its activity. This feedback inhibition mechanism helps to prevent the overproduction of purine nucleotides, ensuring that cellular purine levels are maintained within appropriate ranges. Additionally, the expression and activity of GPAT can also be influenced by various cellular factors, including changes in substrate availability, cellular energy status, and other environmental conditions. For example, GPAT activity has been shown to be regulated by the availability of substrates, such as phosphoribosyl pyrophosphate (PRPP) and glutamine, which are required for the biosynthesis of purine nucleotides. Changes in cellular energy status, such as alterations in ATP levels, can also impact the activity of GPAT.

Overall, the activity of Amidophosphoribosyl transferase (GPAT) is regulated through complex mechanisms to maintain cellular purine levels and adapt to changing cellular conditions. Further research is needed to fully understand the intricacies of GPAT regulation and its adaptability in different cellular contexts.

The regulation of enzyme activity, including that of Amidophosphoribosyl transferase (GPAT), can be likened to a tightly regulated process in a factory where production is carefully controlled. Enzymes are biological catalysts that facilitate specific chemical reactions in cells, and their activity needs to be precisely regulated to maintain cellular homeostasis and ensure proper cellular function. In a factory setting, production processes are typically designed and controlled to achieve specific goals, such as optimizing efficiency, maintaining quality standards, and minimizing waste. Similarly, in cells, the activity of enzymes, including GPAT, is regulated through various mechanisms to achieve specific cellular goals, such as maintaining proper purine levels, preventing overproduction, and responding to changes in cellular conditions. The regulation of GPAT activity involves complex feedback mechanisms, where the end product of the purine biosynthesis pathway, IMP, can inhibit GPAT to prevent excessive purine production. Additionally, other cellular factors, such as substrate availability and cellular energy status, can also impact GPAT activity. These regulatory mechanisms ensure that GPAT and other enzymes function optimally within the cellular context and respond to changing conditions as needed.

Goal-orientedness also promotes accountability and measurement. When a specific goal is set, it becomes easier to measure progress and success. It allows for tracking and evaluating performance against the desired outcomes. This measurement provides valuable feedback and insights that can be used to refine and improve the setup or design. It also helps in identifying any deviations or inefficiencies, enabling timely corrective actions.

The end-products of nucleotide biosynthesis, such as purine and pyrimidine nucleotides, can feedback inhibit the activity of GPAT, thereby regulating its activity and controlling the production of nucleotides. This feedback inhibition helps to prevent the overproduction of nucleotides and maintain the appropriate balance of nucleotide pools in the cell. The feedback mechanisms that regulate GPAT, and other enzymes, are an example of how biological systems must have been conceptualized and designed from the get-go with these complex and sophisticated regulatory mechanisms to ensure the proper functioning and adapt to changing cellular conditions. GPAT must have been present in the emergence of life on Earth, as these enzymes are essential for the chemical reactions that sustain life. Their origin can, therefore, not be explained by invoking evolutionary mechanisms.This is clear evidence that implies a designed manufacturing process.

Molecular Symphony: GPAT's Intelligent Design

Amidophosphoribosyl transferase, GPAT,
A molecular machine, precise and exact,
In purine nucleotide biosynthesis it plays a part,
With a goal-oriented logic, a work of intelligent art.

With ATP-binding domain, it starts the show,
Hydrolyzing ATP, providing energy to go,
Catalytic domain, the active site,
Where substrates bind, with precision so tight.

Substrate binding, a specific affair,
Ensuring only the right ones are processed with care,
Catalysis ensues, a chemical dance,
Transferring PRPP, in a well-choreographed trance.

Product released, with PRPP in tow,
Ready for downstream pathways to bestow,
Active site reset, for another round,
Efficient and effective, with precision profound.

A molecular machine, orchestrated and fine,
Evidence of intelligent design, so divine,
In the biosynthesis of nucleotides, so crucial,
GPAT's precision and complexity, truly awe-inspiring and beautiful.

With each step orchestrated and exact,
A testament to design, with undeniable impact,
GPAT's molecular dance, a symphony of life,
A marvel of creation, amidst the cellular strife.