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

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


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Evolution: Where Do Complex Organisms Come From?

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Where Do Complex Organisms Come From?

https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from

How do biological multicellular complexity and a spatially organized body plan emerge?
https://reasonandscience.catsboard.com/t2990-how-does-biological-multicellular-complexity-and-a-spatially-organized-body-plan-emerge

The architecture of multicellular organisms arises from a complex interplay of at least 47 key developmental processes, 33 genetic codes, and over 223 epigenetic, manufacturing, and regulatory codes. These elements are coordinated through hundreds of signaling networks, embodying functional integration and systemic complexity. This holistic ensemble, showcasing emergent properties and synergy, hints at a level of organization often observed to require an intelligent agent for setup.

Key Developmental Processes Shaping Organismal Form and Function
https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from

The different genetic codes
https://reasonandscience.catsboard.com/t2277-the-different-genetic-codes

The various codes in the cell
https://reasonandscience.catsboard.com/t2213-the-various-codes-in-the-cell

Overview  on Various Signaling Pathways
https://reasonandscience.catsboard.com/t2351-the-essential-signaling-pathways-for-animal-development#10693

The mechanisms behind the complexity of organisms, anatomical features, and the diversity of life is pre-programmed and complex information encoded in multiple genetic codes—at least 33 known variations—as well as in over 223 epigenetic, manufacturing, and regulatory codes. These codes are necessary for complex communication networks that operate at a structural level, functioning in a coordinated and interconnected manner. This pre-set programming is essential for guiding growth and development, adapting to nutritional needs and environmental changes, regulating reproduction, maintaining homeostasis, managing metabolism, orchestrating defense mechanisms, and controlling cell lifecycle events.  Such sophisticated, information-driven systems, given their integrated complexity, require an intelligent designer to establish them. This perspective challenges the idea that undirected, gradual evolutionary processes can fully account for such complexity, especially considering that if all necessary components are not simultaneously present, individual parts would lack function and thus could not be favored by natural selection.

1. Genetic and epigenetic information ( at least 33 variations of genetic codes, and over 230 manufacturing, signaling, and operational codes 4) and hundreds, (in prokaryotes probably thousands) of signaling networks direct the making of complex multicellular organisms, biodiversity, form, and architecture. Furthermore, there is growing evidence, that life is based on polyphyly, not monophyly. There are over 50 lines of evidence, that refute universal common descent. 
2. Biological information is programmed in many cases through digital semiotic language ( syntax, semantics, and pragmatics) to get a functional outcome. Each protein, metabolic pathway, organelle, or system, each biomechanical structure and motion works based on principles that provide a specific function.
3. Information is not physical, it is conceptual, and is simply beyond the sphere of influence of any undirected physical process. To suggest that a physical process can create semiotic code is like suggesting that a rainbow can write poetry, or a blueprint,  is never going to happen! Programming instructional assembly information and getting a specific functional outcome as we see in biology is always prescriptive, the result of a mind with intention, goals, and foresight, able to instantiate a distant specific goal.
4. Therefore, the origin of complex organismal architecture and biodiversity is best explained as the result of intelligent design, a deliberate creative intellectual process, rather than unguided evolution.  

Premise 1. Life is embroidered with a profound amalgamation of genetic and epigenetic codes. With at least 33 distinct genetic variations and over 230 intertwined manufacturing, signaling, and operational codes, together with hundreds, and in prokaryotes probably thousands of intricate signaling networks, these codes collectively choreograph the exquisite dance of multicellular organisms, sculpting the vast biodiversity, nuanced form, and majestic architecture we observe.
Premise 2. This monumental wealth of information isn't random. It's meticulously orchestrated, often resembling the digital semiotic languages characterized by syntax, semantics, and pragmatics. Every protein, each metabolic trajectory, and every biomechanical construct operates with precision, abiding by principles finely tuned for specific functions.
Premise 3.  While the foundations of life are tangible, the essence of information transcends the physical. It's conceptual, operating in realms beyond the reach of spontaneous and aimless physical phenomena. Arguing that such processes can birth semiotic codes is akin to believing a rainbow might pen a sonnet or winds could draft architectural wonders. The directive, purposeful nature inherent in biological programming suggests intention, foresight, and specific goals.
Conclusion: The staggering complexity and deliberate design seen in organismal architecture and biodiversity beckon consideration beyond mere chance. It suggests that these wonders are not just products of random evolution but the handiwork of a deliberate and intelligent design.

Instructional assembly information encoded in 33 genetic, and at least 230 epigenetic codes and languages, and hundreds of signaling networks operating on a structural level in an integrated interlocked fashion are the mechanisms explaining the organismal architecture, development, operation, and adaptation, directing/dictating the make and control of complex molecular physiological integrated structures and their development - the making of irreducible complex molecular machines, robotic molecular production lines, protein-protein interactions, metabolic signaling and transcription-regulatory networks, chemical cell factories, and multicellular organisms and organizations. There is a high degree of internal order that governs the cell’s molecular, and extracellular organization.

Having that information at hand, we can ask:

Do evolutionary, non-intelligent mechanisms explain adequately the observations? In my opinion, the answer is no. All historical, observational, testable, and repeatable examples have demonstrated that instantiating information and operational functionality dictated by prescribed information come from intelligent sources. Etiology, the science of causes, in regards to the origin of biocomplexity, the hypothesis that natural, unguided random or evolutionary mechanisms, natural selection, genetic drift, and flow, were responsible, have led to dead ends, to the constatation that these causes produce too limited results that do not explain biological form. Only an intelligent agency with intent and foresight can in principle, conceptualize and instantiate hardware and software, that directs the making of integrated operational systems with specific functions that work in an integrated manner.  Finely orchestrated order and fine-tuning, instructions that convey and create purposeful function, are all positive evidence of a mind at work as opposed to blind, randomness operating in stochastic chaos. What we find is a gold nugget of truth...a mind is more than likely behind biological form and variation...therefore it is rational and reasonable to believe in an intelligent designer.

Observation:
The integrated complexity and specificity of biological systems based on a large number of genetic and epigenetic codes, complex signaling networks, and the precise orchestration of cellular and organismal functions, closely mirror the complexity of human-engineered systems. These biological systems involve not only a vast array of components but also highly detailed instructions for assembling proteins, regulating cellular activities, and ensuring survival and reproduction. Such a level of complexity and integration is typically associated with the output of intelligent design in human contexts, where complex systems are deliberately planned and executed to achieve specific goals.

Hypothesis:
If the biological structures and systems observed in nature exhibit a level of complexity, specificity, information, multilevel interdependent communications systems, and purposefulness akin to those produced by intelligent human designers, it suggests that such natural systems  be the result of intelligent design. This hypothesis posits that the information and systems seen in biology are not solely the result of undirected evolutionary processes but  indicate the involvement of a guiding intelligence.

Experiment:
The existence of complex information systems in biology, such as the genetic and epigenetic codes, the optimized nature of the genetic code, and the elaborate signaling networks that govern cellular and organismal functions has been unraveled. Characteristics that indicate design, such as irreducible complexity, where systems are composed of several well-matched, interacting parts that contribute to the basic function, and the system ceases to function if any one of the parts is removed, have been found. Also, specified and integrated complexity, where systems exhibit a complexity that is highly unlikely to have occurred by evolutionary mechanisms also conforms to an independently given pattern or set of rules.

Conclusion:
The presence of complex information systems in biology, characterized by a multitude of interdependent codes, highly efficient and error-correcting processes, and elaborate networks for regulation and communication, challenges the explanatory power of unguided evolutionary mechanisms alone. The resemblance of these biological systems to human-engineered systems, known to result from intelligent design, suggests the plausible inference that a similar type of intelligence may underlie the origin of complex biological systems. This argument does not necessarily identify the nature of the designing intelligence but posits that the best explanation for the observed complexity and specificity in biological systems is an intelligent cause, rather than undirected natural evolutionary processes.

Evolution: Where Do Complex Organisms Come From? Sem_t207

Paul C. W. Davies: The algorithmic origins of life 2013 Feb 6
The algorithm for building an organism is not only stored in a linear digital sequence (tape), but also in the current state of the entire system (e.g. epigenetic factors such as the level of gene expression, post-translational modifications of proteins, methylation patterns, chromatin architecture, nucleosome distribution, cellular phenotype and environmental context). The algorithm itself is therefore highly delocalized, distributed inextricably throughout the very physical system whose dynamics it encodes.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3565706/

Gerd B. Müller: Why an extended evolutionary synthesis is necessary 18 August 2017
These examples of conceptual change in various domains of evolutionary biology represent only a condensed segment of the advances made since the inception of the MS theory some 80 years ago. Relatively minor attention has been paid to the fact that many of these concepts, which are in full use today, sometimes contradict or expand central tenets of the MS theory. Given proper attention, these conceptual expansions force us to consider what they mean for our present understanding of evolution. Obviously, several of the cornerstones of the traditional evolutionary framework need to be revised and new components incorporated into a common theoretical structure.
Although today's organismal systems biology is mostly rooted in biophysics and biological function, its endeavors are profoundly integrative, aiming at multiscale and multilevel explanations of organismal properties and their evolution. Instead of chance variation in DNA composition, evolving developmental interactions account for the specificities of phenotypic construction.
https://royalsocietypublishing.org/doi/10.1098/rsfs.2017.0015

Laland, Uller, et al (2014) state In our view, this ‘gene-centric’ focus fails to capture the full gamut of processes that direct evolution. Missing pieces include how physical development influences the generation of variation (developmental bias); how the environment directly shapes organisms’ traits (plasticity); how organisms modify environments (niche construction); and how organisms transmit more than genes across generations (extra-genetic inheritance). 

How do biological multicellular complexity and a spatially organized body plan emerge?
https://reasonandscience.catsboard.com/t2990-how-does-biological-multicellular-complexity-and-a-spatially-organized-body-plan-emerge

The findings show a clear Lamarckian epigenetic contribution to gene network evolution and the classic Darwinian interpretation of evolution alone cannot explain our observations. “The findings support the idea that both genetic and epigenetic mechanisms need to be combined in a ‘grand unified theory of evolution,’”
https://news.yale.edu/2020/10/27/yeast-study-yields-insights-longstanding-evolution-debate

Macroevolution has also been defined by Professor Jerry Coyne as “large changes in body form or the evolution of one type of plant or animal from another type”

MICHAEL J. BEHE Experimental Support for the Design Inference DECEMBER 27, 1987
In order to say that some function is understood, every relevant step in the process must be elucidated. The relevant steps in biological processes occur ultimately at the molecular level, so a satisfactory explanation of a biological phenomenon such as sight, or digestion, or immunity, must include a molecular explanation. It is no longer sufficient, now that the black box of vision has been opened, for an ‘evolutionary explanation’ of that power to invoke only the anatomical structures of whole eyes, as Darwin did in the 19th century and as most popularizers of evolution continue to do today. Anatomy is, quite simply, irrelevant. So is the fossil record. It does not matter whether or not the fossil record is consistent with evolutionary theory, any more than it mattered in physics that Newton’s theory was consistent with everyday experience. The fossil record has nothing to tell us about, say, whether or how the interactions of 11-cis-retinal with rhodopsin, transducin, and phosphodiesterase could have developed step-by-step. Neither do the patterns of biogeography matter, or of population genetics, or the explanations that evolutionary theory has given for rudimentary organs or species abundance.
https://www.discovery.org/a/54/

To understand novelty in evolution, we need to understand organisms down to their individual building blocks, down to the workings of their deepest components, for these are what undergo change.
Dr. Marc W. Kirschner: The Plausibility of Life: Resolving Darwin's Dilemma 2005

For a complete understanding of biological processes that define the intricate development of body architecture with striking precision, the orchestration of organismal development, cell and tissue shape, organization, and body form, it is necessary to understand as many integrative elements of biological systems as possible. Complex pattern formation involves numerous highly intricate biomolecular mechanisms that lead to the superb formation of tissue structures. That includes providing information that gives mechanical cues directing intra and extracellular shape changes and movements on the level of individual cells, but also tissue substratum as a whole. Answering the questions about how cells, tissues, and organisms masterfully develop and form, precedes the question IF evolutionary claims are compelling answers, explaining IF the evolutionary changes permit a purely blind primary macroevolutionary transition zone, morphogenesis of an entire organism moving and morph from one species to another on a first-degree speciation level, where novel features arise, like wings, eyes, ears, legs, arms, and so forth. The fact and truth are, that science is still far and away from having a complete answer to that question. But what we do know, permits to make informed conclusions. 

Biodiversity and complex organismal architecture is explained by trillions of bits. Incredible amounts of data far beyond our imagination. Instructions, complex codified specifications, INFORMATION. Algorithms masterfully encoded in various genetic and sophisticated epigenetic languages and communication channels and networks. Neurotransmitters, through nanotubes between cells,  communication through vesicles and amazingly, even light photons. Genes, but as well and especially various striking epigenetic signaling and bioelectric codes through various signaling networks provide cues to molecules and macromolecule complexes, and ingenious scaffold networks interpret and react in a variety of ways upon decoding and data processing of those instructions. Since signaling pathways work in an extraordinarily precise, in a synergetic integrated manner with the transcriptional regulatory network and complex short and long-range cross-talk between cells, these crucial instructions, crucial for advanced life forms, could not be the result of a random gradual increase of information. These superb information networks only operate and work in an integrated fashion, and had to be "born", and fully set up right from the beginning. Conveying codes, a system of rules to convert information, such as letters and words, into another form, and translation ciphers of one language to another are always sourced back to intelligent set-up. What we see in biochemistry is incredibly complex instructional codified information being stored through the genetic code ( codons) in a masterful information-storage molecule  (DNA), encoded & transcribed ( RNA polymerase), sent (mRNA), and decoded & translated ( Ribosome), as well as epigenetic codes and languages, and several signaling pathways. The morphogenesis of organismal structure and shape is classified into two groups: The various instructional codes and languages using molecules that provide complex instructional cues of action based on information through signaling and secondly by force-generating molecules that are precisely directed through those signals, which are responsible for fantastic cell morphogenesis. Blueprints, instructional information, and master plans, which permit the striking autonomous self-organization and control of complex machines ( molecular machines) and exquisite factory parks ( cells) upon these are both always tracked back to an intelligent source which made both for purposeful, specific goals.   That brings us unambiguously to intelligent design. To the origin by an intelligent designer.

What are the REAL mechanisms of biodiversity, replacing macroevolution?
https://www.youtube.com/watch?v=_IGrzrk6iBEre=youtu.be

Why Darwin's theory of evolution does not explain biodiversity
https://reasonandscience.catsboard.com/t2623-why-darwins-theory-of-evolution-does-not-explain-biodiversity

1. Biological sciences have come to discover in the last decades that major morphological innovation, development and body form are based on at least 47 different, but integrative mechanisms.
2. These varied mechanisms orchestrate gene expression, generate Cell types and patterns, perform various tasks essential to cell structure and development, are responsible for important tasks of organismal development, affect gene transcription, switch protein-coding genes on or off,  determine the shape of the body, regulate genes, provide critical structural information and spatial coordinates for embryological development,  influence the form of a developing organism and the arrangement of different cell types during embryological development, organize the axes, and act as chemical messengers for development
3. Neo-Darwinism and Modern Synthesis have proposed traditionally a gene-centric view, a scientific metabiological proposal going back to Darwin's " On the Origin of species ", where first natural selection was proposed as the mechanism of biodiversity, and later,  gene variation defining how bodies are built and organized. Not even recently proposed alternatives, like the third way, neutral theory, inclusive fitness theory, Saltationism, Saltatory ontogeny, mutationism, Genetic drift, or combined theories, do full justice by taking into account all organizational physiological hierarchy and complexity which empirical science has come to discover.
4. Only a holistic view, namely structuralism and systems biology, takes into account all influences that form cell form and size, body development, and growth, providing adequate descriptions of the scientific evidence.

1. Genetic and epigenetic information directs the making of complex multicellular organisms, biodiversity, form, and architecture
2. This information is preprogrammed and prescribed to get a purposeful outcome. Each protein, metabolic pathway, organelle or system, each biomechanical structure and motion works based on principles that provide a specific function.
3.  Preprogramming and prescribing a specific outcome is always the result of intention with foresight, able to instantiate a distant specific goal.
4. Foresight comes always from an intelligent agent. Therefore, biodiversity is the result of intelligent design, rather than unguided evolution. 

They are apt to communicate, crosstalk, signal, regulate, govern, control, recruit, interpret, recognize, orchestrate, elaborate strategies, guide and so forth. All codes, blueprints, and languages are inventions by intelligence. Therefore, the genetic and epigenetic codes and signaling networks and the instructions to build cells and complex biological organisms were most likely created by an intelligent agency.

Biological cells and organisms are characterized by Irreducible complexity and hierarchical top-down systems interdependence, which is understood as irreducible functional systems complexity. And such is specified by genetic and epigenetic informational codes and signals used to set up and create front-loaded instructional blueprints, which direct how bodies are built, but also how life can self-correct, adapt to the environment and evolve. It is perfectly comparable to how a blueprint instructs to make machines and factories, and industries. Such things come undoubtedly from preexisting intelligence.

To understand the major trends in animal diversity and if the various kinds of morphology are due to evolution, we must first understand how animal form is generated. As science has unraveled, the make of body form, phenotype, and organismal architecture is due to several genetic and principally, epigenetic interlocked and interconnected mechanisms. The modern, extended evolutionary synthesis does not take into consideration all relevant factors. Structuralism proposes that complex structure emerges holistically from the dynamic interaction of all parts of an organism. It denies that biological complexity can be reduced to natural selection, gene drift and gene flow, and argues that pattern formation is driven principally by multilevel processes that involve various functional units, working in an interdependent manner, pre-programmed to respond to ecological and environmental cues and conditions, food resource availability, and development programs.  Various genetic and epigenetic Codes, an integrated understanding of the structural and functional aspects of epigenetics and several signalling pathways, nuclear architecture during differentiation, chromatin organization, morphogenetic fields, amongst many other mechanisms.

The Gene regulation network
Epigenetics refers to heritable changes in gene expression that occur without alteration in DNA sequence. These changes may be induced spontaneously, induced by environmental factors or as a consequence of specific mutations. There are two primary and interconnected epigenetic mechanisms: DNA methylation and covalent modification of histones. 42 . In addition, it has become apparent that non-coding RNA is also intimately involved in this process. The different mechanisms that control epigenetic changes do not stand alone, and there are a clear interconnection and interdependency between:
 
Genes involved in Cell-Cell communication and transcriptional control are especially important for animal development
What are the genes that animals share with one another but not with other kingdoms of life? These would be expected to include genes required specifically for animal development but not needed for unicellular existence. Comparison of animal genomes with the genome of budding yeast—a unicellular eukaryote— suggests that three classes of genes are especially important for multicellular organization.

The first class includes genes that encode proteins used for cell–cell adhesion and cell signaling; hundreds of human genes encode signal proteins, cell-surface receptors, cell adhesion proteins, or ion channels that are either not present in yeast or present in much smaller numbers.

The second class includes genes encoding proteins that regulate transcription and chromatin structure: more than 1000 human genes encode transcription regulators, but only about 250 yeast genes do so. The development of animals is dominated by cell–cell interactions and by differential gene expression.

The third class of noncoding RNAs has a more uncertain status: it includes genes that encode microRNAs (miRNAs); there are at least 500 of these in humans. Along with the regulatory proteins, they play a significant part in controlling gene expression during animal development, but the full extent of their importance is still unclear.

Chromatin dance in the nucleus through extensile motors
Transcription and gene regulation Genome topology has emerged as a key player in all genome functions. Although a contribution of local genome looping in transcription has long been appreciated, recent observations have revealed the importance of long-range interactions, and genome-wide studies have uncovered the universal nature of such regulatory genome topology interactions in gene regulation. Several types of chromosomal interactions, either in the form of loops between sequences on the same chromosomes or interchromosomal interactions, have emerged as key mechanisms in gene regulation.
The nature of genome topology is very precise, and so its regulatory functions in gene expression and genome maintenance. The emerging picture is one of extensive self-enforcing feedback between activity and spatial organization of the genome, suggestive of a self-organizing and self-perpetuating system that uses epigenetic dynamics to regulate genome function in response to regulatory cues and to propagate cell-fate memory

Post-transcriptional modifications (PTMs) of histones affect gene transcription
According to the histone code hypothesis, the pattern of histone modification is recognized by proteins much like a language or code. One pattern of histone modification may attract proteins that inhibit transcription. Alternatively, a different combination of histone modifications may attract proteins, such as ATP-dependent chromatin-remodeling complexes, that promote gene transcription. In this way, the histone code plays a key role in accessing the information within the genomes of eukaryotic species. Post-translational modifications (PTMs) of histones provide a fine-tuned mechanism for regulating chromatin structure and dynamics.  In addition to combinatorial PTMs that function together both synergistically and antagonistically, there is now an appreciation for PTM asymmetry within individual nucleosomes, novel types of PTMs with unique functions, nucleosomes bearing histone variants, and nuclear compartmentalization events that are all contributing to the final output of chromatin organization and function

The DNA methylation code and language
One of the best known epigenetic mechanisms is DNA methylation in which a small molecule (a methyl group) is added to the DNA macromolecule at particular locations. Like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on. This DNA methylation is accomplished via the action of a protein machine that adds the methyl group at precisely the right location in the DNA strand. Methylation of DNA occurs at certain target sites along the DNA sequence where specific short DNA sequences appear. These sequences are found by special proteins as they move along the DNA. The special proteins search for these sequences and add a methyl group to the adenine base that appears within the sequence. The protein binds to the DNA, twists the helix so the adenine base rotates into a precisely shaped pocket in the protein, and the protein then facilitates the transfer of the methyl group from a short donor molecule for example to adenine.

Homeobox and Hox Genes
This family of related genes determines the shape of the body. It subdivides the embryo along the head-to-tail axis into fields of cells that eventually become limbs and other structures.  Starting as a fertilized egg with a homogeneous appearance, an embryo made of skin, muscles, nerves and other tissues gradually arises through the division of cells. Long before most cells in the emerging body begin to specialize, however, a plan that designates major regions of the body-the head, the trunk, the tail and so on is established. This plan helps seemingly identical combinations of tissues arrange themselves into distinctly different anatomical structures, such as arms and legs. Individual genes mediate some of the developmental decisions involved in establishing the embryonic body plan.

" Junk DNA "
MicroRNAs--"Once Dismissed as Junk"--Confirmed To Have Important Gene Regulatory Function In 2008 Scientific American noted that microRNAs were "once dismissed as junk" and said the following:
Tiny snippets of the genome known as microRNA were long thought to be genomic refuse because they were transcribed from so-called "junk DNA," sections of the genome that do not carry information for making proteins responsible for various cellular functions. Evidence has been building since 1993, however, that microRNA is anything but genetic bric-a-brac. Quite the contrary, scientists say that it actually plays a crucial role in switching protein-coding genes on or off and regulating the amount of protein those genes produce.

Transposons and Retrotransposons
striking evidence has accumulated indicating that some proviral sequences and HERV proteins might even serve the needs of the host and are therefore under positive selection. The remarkable progress in the analysis of host genomes has brought to light the significant impact of HERVs and other retroelements on genetic variation, genome evolution, and gene regulation.

Centrosomes
Centrosomes play a central role in development: a frog egg can be induced to develop into a frog merely by injecting a sperm centrosome—no sperm DNA is needed. Another non-genetic factor involved in development is the membrane pattern of the egg cell. 

Cytoskeletal arrays 
The precise arrangement of microtubules in the cytoskeleton constitutes a form of critical structural information. neither the tubulin subunits nor the genes that produce them account for the differences in the shape of the microtubule arrays that distinguish different kinds of embryos and developmental pathways. Instead, the structure of the microtubule array itself is, once again, determined by the location and arrangement of its subunits, not the properties of the subunits themselves. Jonathan Wells explains it this way: “What matters in [embryological] development is the shape and location of microtubule arrays, and the shape and location of a microtubule array is not determined by its units.” Directed transport involves the cytoskeleton, but it also depends on spatially localized targets in the membrane that are in place before transport occurs. Developmental biologists have shown that these membrane patterns play a crucial role in the embryological development of fruit flies.

Signaling between cells orients the mitotic spindle
In multicellular animals, cell communication sometimes serves to orient the direction in which cells divide. Control of division orientation has been proposed to be critical for partitioning developmental determinants and for maintaining epithelial architecture. Surprisingly, there are few cases where we understand the mechanisms by which external cues, transmitted by intercellular signalling, specify the division orientation of animal cells. One would predict that cytosolic molecules or complexes exist that are capable of interpreting extrinsic cues, translating the positions of these cues into forces on microtubules of the mitotic spindle. In recent years, a key intracellular complex has been identified that is required for pulling forces on mitotic spindles in Drosophila, C. elegans and vertebrate systems. One member of this complex, a protein with tetratricopeptide repeat (TPR) and GoLoco (Gα-binding) domains, has been found localized in positions that coincide with the positions of spindle-orienting extracellular cues. Do TPR-GoLoco proteins function as conserved, spatially-regulated mediators of spindle orientation by intercellular signalling? Here, we review the relevant evidence among cases from diverse animal systems where this protein complex has been found to localize to specific cell-cell contacts and to be involved in orienting mitotic spindles.

Membrane targets
Preexisting membrane targets, already positioned on the inside surface of the egg cell, determine where these molecules will attach and how they will function. These membrane targets provide crucial information—spatial coordinates—for embryological development.

Ion Channels and Electromagnetic Fields
Experiments have shown that electromagnetic fields have “morphogenetic” effects—in other words, effects that influence the form of a developing organism. In particular, some experiments have shown that the targeted disturbance of these electric fields disrupts normal development in ways that suggest the fields are controlling morphogenesis.2 Artificially applied electric fields can induce and guide cell migration. There is also evidence that direct current can affect gene expression, meaning internally generated electric fields can provide spatial coordinates that guide embryogenesis.3 Although the ion channels that generate the fields consist of proteins that may be encoded by DNA (just as microtubules consist of subunits encoded by DNA), their pattern in the membrane is not. Thus, in addition to the information in DNA that encodes morphogenetic proteins, the spatial arrangement and distribution of these ion channels influence the development of the animal.

The Sugar Code
These sequence-specific information-rich structures influence the arrangement of different cell types during embryological development. Thus, some cell biologists now refer to the arrangements of sugar molecules as the “sugar code” and compare these sequences to the digitally encoded information stored in DNA. As biochemist Hans-Joachim Gabius notes, sugars provide a system with “high-density coding” that is “essential to allow cells to communicate efficiently and swiftly through complex surface interactions.” According to Gabius, “These [sugar] molecules surpass amino acids and nucleotides by far in information-storing capacity.” So the precisely arranged sugar molecules on the surface of cells clearly represent another source of information independent of that stored in DNA base sequences.  These cascades are, along with the cell event itself, associated with the “coding information” on a cell surface, or, using another terminology, are realized due to an instruction for the cell from the morphogenetic field of an organism. The concrete signal transduction pathways connecting the "coding information" on a cell surface and the expression of the given sets of genes need to be elucidated. 

Above and beyond: epigenetic information 
genes alone do not determine the three-dimensional form and structure of an animal.  Developmental biologists, in particular, are now discovering more and more ways that crucial information for building body plans is imparted by the form and structure of embryonic cells, including information from both the unfertilized and fertilized egg. DNA helps direct protein synthesis. Parts of the DNA molecule also help to regulate the timing and expression of genetic information and the synthesis of various proteins within cells. Yet once proteins are synthesized, they must be arranged into higher-level systems of proteins and structures. The three-dimensional structure or spatial architecture of embryonic cells plays important roles in determining body-plan formation during embryogenesis. Developmental biologists have identified several sources of epigenetic information in these cells.

Stephen C. Meyer, Darwin's doubt: Neo darwinism and the challenge of epigenetic information 
These different sources of epigenetic information in embryonic cells pose an enormous challenge to the sufficiency of the neo-Darwinian mechanism. According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy—within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn’t wholly responsible for the way an embryo develops— for body-plan morphogenesis—then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand. Even in a best-case scenario—one that ignores the immense improbability of generating new genes by mutation and selection—mutations in DNA sequence would merely produce new genetic information. But building a new body plan requires more than just genetic information. It requires both genetic and epigenetic information—information by definition that is not stored in DNA and thus cannot be generated by mutations to the DNA. It follows that the mechanism of natural selection acting on random mutations in DNA cannot by itself generate novel body plans, such as those that first arose in the Cambrian explosion.

" Junk DNA "
MicroRNAs--"Once Dismissed as Junk"--Confirmed To Have Important Gene Regulatory Function

In 2008 Scientific American noted that microRNAs were "once dismissed as junk" and said the following:
Tiny snippets of the genome known as microRNA were long thought to be genomic refuse because they were transcribed from so-called "junk DNA," sections of the genome that do not carry information for making proteins responsible for various cellular functions. Evidence has been building since 1993, however, that microRNA is anything but genetic bric-a-brac. Quite the contrary, scientists say that it actually plays a crucial role in switching protein-coding genes on or off and regulating the amount of protein those genes produce.

Transposons and Retrotransposons
striking evidence has accumulated indicating that some proviral sequences and HERV proteins might even serve the needs of the host and are therefore under positive selection. The remarkable progress in the analysis of host genomes has brought to light the significant impact of HERVs and other retroelements on genetic variation, genome evolution, and gene regulation.

Morphogen Gradients and Pattern Formation 
Compartment boundaries are the sources of morphogens. Morphogens are signaling molecules that are produced from a localized source forming long-range concentration gradients that pattern a field of cells

Principal Meanings of Evolution in Biology Textbooks

What is fact :
1. Change over time; history of nature; any sequence of events in nature
2. Changes in the frequencies of alleles in the gene pool of a population
3. Limited common descent: the idea that particular groups of organisms have descended from
a common ancestor.
4. The mechanisms responsible for the change required to produce limited descent with modification; chiefly natural selection acting on random variations or mutations

What is not fact: 
5. Universal common descent: the idea that all organisms have descended from a single common ancestor.
6. Blind watchmaker thesis: the idea that all organisms have descended from common ancestors through unguided, unintelligent, purposeless, material processes such as natural
selection acting on random variations or mutations; the idea that the Darwinian mechanism of natural selection acting on random variation, and other similarly naturalistic mechanisms, completely suffice to explain the origin of novel biological forms and the appearance of design in complex organisms.

1. Neo-Darwinism and the Modern Synthesis propose a gene-centric view, a scientific metabiological proposal going back to Darwin's landmark book " On the origin of species " in 1859, where first natural selection was proposed as the mechanism of biodiversity, and later,  gene variation defining how bodies are built and organized.

2. Science researchers have discovered, that robust networks of interactions and biological function, major morphological innovation, development and body form are based on integrative mechanisms, the interplay of genes with the gene regulatory network, Transposons and Retrotransposons, so-called Junk DNA, splicing, and over a dozen epigenetic codes, Membrane targets and patterns, Cytoskeletal arrays, Centrosomes, Ion channels, Sugar molecules on the exterior of cells (the sugar code), that are not specified by nuclear DNA - that is, inheritance is not defined through DNA sequences alone.

3. Science is coming to recognize, that none of the recently proposed alternatives, like the third way, Saltationism, Saltatory ontogeny, mutationism, Genetic drift, or combined theories, do full justice by taking into account all organizational biophysiological hierarchy and complexity which empirical science has come to discover. As such, only a holistic view, namely structuralism,  takes into consideration all influences that form cell form and size, body development and growth, doing justice to the scientific evidence.

4. Scrutinizing which causes ultimately respond for the complexity discovered in life is only satisfying, once the epistemologically flawed foundation of methodological naturalism is taken out of the box, and replaced by a new paradigm, where all possible mechanisms and causal influences are permitted to be scrutinized, investigated, and scientifically tested, including the interaction and creative force of an external intelligent, mental agency outside the known physical world, which through its transcendent power creates, forms and builds all physiobiological lifeforms in all its astounding diversity.

If the mechanisms as proposed by the modern extended evolutionary synthesis are insufficient, then it has to be figured out what OTHER mechanisms define body architecture, grow, differentiation, phenotype, and body form, and THEN it can be evaluated, how the origin of these mechanisms are best explained. As it comes out, the BIG contributor to explain life and its complexity is INFORMATION. Instructional, complex, specified, codified information that acts like a blueprint ( genes ), but also information that is PRE-PROGRAMMED and stored in epigenetic cell features on a structural level, which is pre-instructed to respond to environmental cues, development, and nutrition demands, and they are apt to communicate, crosstalk, signal, regulate, govern, control, recruit, interpret, recognize, orchestrate, elaborate strategies, guide and so forth.

1. Cells use sophisticated information transmission and amplification systems (signalling pathways), information interpretation, combination and selection ( the Gene regulatory network ) encoding and transcription ( DNA & RNA polymerase machines ) transmission (mRNA), and decoding ( Ribosome ) systems.
2. Setup of information transmission systems, aka.  transmission, amplification, interpretation, combination, selection, encoding, transmission, and decoding are always a deliberate act of intelligence
3. The existence of the genetic information transmission system is best explained by the implementation of an intelligent designer.

Meyer, Darwins doubt, page 212:
According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy—within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn’t wholly responsible for the way an embryo develops— for body-plan morphogenesis—then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand.




Evolution: Where Do Complex Organisms Come From? Macroe10

https://reasonandscience.catsboard.com/t2316-where-do-complex-organisms-come-from

1. http://www.jodkowski.pl/ke/Meanings2000.pdf
2.https://reasonandscience.catsboard.com/t1390-macroevolution#1982
3. https://royalsocietypublishing.org/doi/10.1098/rsif.2020.0154
4. Prinz, R. (2023). Biological Codes: A Field Guide for Code Hunters. Biological Theory.



Last edited by Otangelo on Thu Mar 21, 2024 8:33 am; edited 197 times in total

https://reasonandscience.catsboard.com

2Evolution: Where Do Complex Organisms Come From? Empty DEVELOPMENTAL GENE REGULATORY NETWORKS Sun Mar 06, 2016 8:22 am

Otangelo


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Even in a best-case scenario—one that ignores the immense improbability of generating new genes by mutation and selection—mutations in DNA sequence would merely produce new genetic information. But building a new body plan requires more than just genetic information. It requires both genetic and epigenetic information—information by definition that is not stored in DNA and thus cannot be generated by mutations to the DNA. It follows that the mechanism of natural selection acting on random mutations in DNA cannot by itself generate novel body plans.

Intelligent agents have foresight. Such agents can determine or select functional goals before they are physically instantiated. They can devise or select material means to accomplish those ends from among an array of possibilities. They can then actualize those goals in accord with a preconceived design plan or set of functional requirements. Rational agents can constrain combinatorial space with distant information-rich outcomes in mind. (Darwin’s Doubt, pp. 362-363)

Intelligent agents sometimes produce material entities through a series of gradual modifications (as when a sculptor shapes a sculpture over time). Nevertheless, intelligent agents also have the capacity to introduce complex technological systems into the world fully formed. Often such systems bear no resemblance to earlier technological systems — their invention occurs without a material connection to earlier, more rudimentary technologies. When the radio was first invented, it was unlike anything that had come before, even other forms of communication technology. For this reason, although intelligent agents need not generate novel structures abruptly, they can do so. Thus, invoking the activity of a mind provides a causally adequate explanation for the pattern of abrupt appearance in the Cambrian fossil record. (pp. 373, 375)

“Top-down” causation begins with a basic architecture, blueprint, or plan and then proceeds to assemble parts in accord with it. The blueprint stands causally prior to the assembly and arrangement of the parts. But where could such a blueprint come from? One possibility involves a mental mode of causation. Intelligent agents often conceive of plans prior to their material instantiation — that is, the preconceived design of a blueprint often precedes the assembly of parts in accord with it. An observer touring the parts section of a General Motors plant will see no direct evidence of a prior blueprint for GM’s new models, but will perceive the basic design plan immediately upon observing the finished product at the end of the assembly line. Designed systems, whether automobiles, airplanes, or computers, invariably manifest a design plan that preceded their first material instantiation. But the parts do not generate the whole. Rather, an idea of the whole directed the assembly of the parts. (pp. 371-372)

Integrated circuits in electronics are systems of individually functional components such as transistors, resistors, and capacitors that are connected together to perform an overarching function. … [I]n our experience, complex integrated circuits — and the functional integration of parts in complex systems generally — are known to be produced by intelligent agents — specifically, by engineers. Moreover, intelligence is the only known cause of such effects. Since developing animals employ a form of integrated circuitry, and certainly one manifesting a tightly and functionally integrated system of parts and subsystems, and since intelligence is the only known cause of these features, the necessary presence of these features would seem to indicate that intelligent agency played a role in their origin. (p. 364)

Intelligent agents, due to their rationality and consciousness, have demonstrated the power to produce specified or functional information in the form of linear sequence-specific arrangements of characters. Digital and alphabetic forms of information routinely arise from intelligent agents. A computer user who traces the information on a screen back to its source invariably comes to a mind — a software engineer or programmer. The information in a book or inscription ultimately derives from a writer or scribe. Our experience-based knowledge of information flow confirms that systems with large amounts of specified or functional information invariably originate from an intelligent source. The generation of functional information is “habitually associated with conscious activity.” Our uniform experience confirms this obvious truth. (p. 360)




Rational agents can arrange both matter and symbols with distant goals in mind. They also routinely solve problems of combinatorial inflation. In using language, the human mind routinely “finds” or generates highly improbable linguistic sequences to convey an intended or preconceived idea. In the process of thought, functional objectives precede and constrain the selection of words, sounds, and symbols to generate functional (and meaningful) sequences from a vast ensemble of meaningless alternative possible combinations of sound or symbol. Similarly, the construction of complex technological objects and products, such as bridges, circuit boards, engines, and software, results from the application of goal-directed constraints. Indeed, in all functionally integrated complex systems where the cause is known by experience or observation, designing engineers or other intelligent agents applied constraints on the possible arrangements of matter to limit possibilities in order to produce improbable forms, sequences, or structures. Rational agents have repeatedly demonstrated the capacity to constrain possible outcomes to actualize improbable but initially unrealized future functions. Repeated experience affirms that intelligent agents (minds) uniquely possess such causal powers. (p. 362)

The highly specified, tightly integrated, hierarchical arrangements of molecular components and systems within animal body plans also suggest intelligent design. This is, again, because of our experience with the features and systems that intelligent agents — and only intelligent agents — produce. Indeed, based on our experience, we know that intelligent human agents have the capacity to generate complex and functionally specified arrangements of matter — that is, to generate specified complexity or specified information. Further, human agents often design information-rich hierarchies, in which both individual modules and the arrangement of those modules exhibit complexity and specificity. Individual transistors, resistors, and capacitors in an integrated circuit exhibit considerable complexity and specificity of design. Yet at a higher level of organization, the specific arrangement and connection of these components within an integrated circuit requires additional information and reflects further design.

Conscious and rational agents have, as part of their powers of purposive intelligence, the capacity to design information-rich parts and to organize those parts into functional information-rich systems and hierarchies. (p. 366)


Where Do Complex Organisms Come From?
https://reasonandscience.catsboard.com/t2316-where-do-complex-organisms-come-from

Here I outline in red, each of the 17 mechanisms, and quote science papers which affirm the relevance of the mechanism to explain organismal development, architecture, and complexity, and as such, science falsifies darwins gene-centric view, that mutations, natural selection, gene flow and drift explain biodiversity and organismal complexity:

1. The Gene regulation network orchestrates gene expression
2. Various signalling pathways generate Cell types and patterns
3. At least 23 Epigenetic Codes are multidimensional and perform various tasks essential to cell structure and development
4. Cell-Cell communication in various forms, especially important for animal development
5. Chromatin dance in the nucleus through extensile motors affect transcription and gene regulation
6. Post-transcriptional modifications (PTMs) of histones affect gene transcription
7. The DNA methylation code is like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on.
8. Homeobox and Hox genes determine the shape of the body.
9. Noncoding DNA  ( Junk DNA ) is transcribed into functional non-coding RNA molecules and switches protein-coding genes on or off.
10.  Transposons and Retrotransposons regulate genes
11. Centrosomeplay a central role in development
12. The precise arrangement of Cytoskeletal arrays provides critical structural information.
13. Membrane targets provide crucial information—spatial coordinates—for embryological development.
14. Ion Channels and Electromagnetic Fields influence the form of a developing organism
15. The Sugar Code forms information-rich structures which influence the arrangement of different cell types during embryological development.
16. Egg-polarity genes encode macromolecules deposited in the egg to organize the axes
17. Hormones  are special chemical messengers for development



1. The Gene regulation network orchestrates gene expression

EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY
Eric H. Davidson 2011 Feb 12
The neo-Darwinism ‘erroneously assumes that change in protein coding sequence is the basic cause of change in developmental program; and it erroneously assumes that evolutionary change in body plan morphology occurs by a continuous process. All of these assumptions are basically counterfactual.’
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751/

2. Various signalling pathways generate Cell types and patterns

- Hedgehog (Hh)
The Hedgehog (Hh) pathway plays a central role in the development of most tissues and organs in mammals.
https://www.sciencedirect.com/science/article/pii/S0929664615000340  

- Wingless related (Wnt)
Almost 40 years of basic research in different model systems have painted a picture of a signalling cascade that is absolutely essential for the development of all multicellular animals, and for the growth and maintenance of various adult tissues.
http://dev.biologists.org/content/145/12/dev165902  


- Transforming growth factor-β (TGF-β)
The TGF-beta family of cytokines are ubiquitous, multifunctional and essential to survival. They play important roles in growth and development, inflammation and repair and host immunity.
https://www.ncbi.nlm.nih.gov/pubmed/9611771

- Receptor tyrosine kinase (RTK)
Receptor tyrosine kinases (RTKs) are essential components of signaling transduction that mediate cell-to-cell communication.
https://www.sinobiological.com/receptor-tyrosine-kinase-rtk-signaling-transduction.html

- Notch
Notch signaling is evolutionarily conserved and operates in many cell types and at various stages during development. Notch signaling must therefore be able to generate appropriate signaling outputs in a variety of cellular contexts. This need for versatility in Notch signaling is in apparent contrast to the simple molecular design of the core pathway.
http://dev.biologists.org/content/138/17/3593

- Janus kinase (JAK)/signal transducer  
The Janus kinase (JAK)/signal transducer and activator of transcription (STAT) pathway is crucial for transducing signals from a variety of metabolically relevant hormones and cytokines including growth hormone, leptin, erythropoietin, IL4, IL6 and IFNγ.
https://www.cell.com/trends/endocrinology-metabolism/pdf/S1043-2760(17)30150-9.pdf

- Activators of transcription (STAT) protein kinases
Cytokines play a critical role in the normal development and function of the immune system. On the other hand, many rheumatologic diseases are characterized by poorly controlled responses to or dysregulated production of these mediators. Over the past decade tremendous strides have been made in clarifying how cytokines transmit signals via pathways using the Janus kinase (Jak) protein tyrosine kinases and the Signal transducer and activator of transcription (Stat) proteins.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC129988/

- Nuclear hormone pathways
Thyroid hormones control various aspects of gut development and homeostasis. The best-known example is in gastrointestinal tract remodeling during amphibian metamorphosis. It is well documented that these hormones act via the TR nuclear receptors, which are hormone-modulated transcription factors. Several studies have shown that thyroid hormones regulate the expression of several genes in the Notch signaling pathway, indicating a possible means by which they participate in the control of gut physiology.
http://dev.biologists.org/content/142/16/2764

- Bone morphogenetic proteins (BMP)
Bone Morphogenetic Proteins (BMPs) are a group of signaling molecules that belongs to the Transforming Growth Factor-β (TGF-β) superfamily of proteins. Initially discovered for their ability to induce bone formation, BMPs are now known to play crucial roles in all organ systems.
https://www.ncbi.nlm.nih.gov/pubmed/25401122


- Epidermal growth factor receptors (EGFR)
EGFR signaling is crucial for the development of several organs including skin (reviewed in Ref. 116). EGFR signaling is especially crucial to keratinocyte migration and proliferation during wound healing.
https://www.sciencedirect.com/topics/medicine-and-dentistry/epidermal-growth-factor-receptor

- Fibroblast growth factors (FGF)
Fibroblast growth factors (FGFs) are a family of structurally related polypeptides that are essential for embryonic development and that function postnatally as homoeostatic factors, in the response to injury, in the regulation of electrical excitability of cells and as hormones that regulate metabolism.
https://academic.oup.com/jb/article/149/2/121/837258

- DNA methylation
An appropriate DNA methylation is critical in development. Indeed, a precise temporal and spatial pattern of early gene expression is mandatory for a normal embryogenesis.
https://www.ncbi.nlm.nih.gov/pubmed/23877618

- Histone modification and incorporation of histone variants
Variants have a crucial role in chromosome segregation, transcriptional regulation, DNA repair, and other processes.
https://www.researchgate.net/publication/270654681_Histone_Variants_and_Epigenetics

- Chromatin remodelling in Eukaryotic Cells
Chromatin remodelling is an important mechanism of regulating eukaryotic gene expression, which makes tightly condensed DNA
https://www.news-medical.net/life-sciences/Chromatin-Remodeling-Mechanisms-and-Importance.aspx

- Non-coding RNA-mediated epigenetic regulation
Epigenetic related ncRNAs include miRNA, siRNA, piRNA and lncRNA. In general, ncRNAs function to regulate gene expression at the transcriptional and post-transcriptional level.
https://www.whatisepigenetics.com/non-coding-rna/

3. Epigenetic Codes perform various tasks essential to cell structure and development

Epigenetic Codes:
Genetic & Epigenetic Codes:
1.  The 31 Genetic Codes 
2.  The Acoustic codes
3.  The Adhesion Code
4.  The Apoptosis Code
5.  The Bioelectric Code
6.  The Biophoton Code
7.  The Calcium Code
8.  The Chaperone Code
9.  The Chromatin Code
10. The Circular motif ( ribosome) Code
11. The Cytoskeleton Code
12. The Coactivator/corepressor/epigenetic Code
13. The Code of human language
14. The compartment Code
15. The Hidden Code within the Genetic Code
16. The DNA methylation Code
17. The Differentiation Code
18. The Domain substrate specificity Code of Nonribosomal peptide synthetases (NRPS)
19. The Error correcting Code
20. The Genomic Code
21. The Genomic regulatory Code
22. The Glycomic Code
23. The Histone Code
24. The HOX Code
25. The immune response code, or language
26. The Lamin Code
27. The Metabolic Code
28. The Myelin Code
29. The Neuronal spike-rate Code
30. The Non-ribosomal Code
31. The Nucleosome Code
32. The Nuclear signalling Code
33. The Olfactory Code
34. The Operon Code
35. The Phosphorylation Code
36. The Post-translational modification Code for transcription factors
37. The RNA Code
38. The Ribosomal Code
39. The Riboswitch Code
40. The Splicing Codes
41. The Signal transduction Code
42. The Signal Integration Codes
43. The Sugar Code
44. The Synaptic Adhesive Code
45. The Talin Code
46. The Transcription factor Code
47. The Transcriptional cis-regulatory Code
48. The Tubulin Code
49. The Ubiquitin Code


https://reasonandscience.catsboard.com/t2213-the-various-codes-in-the-cell

4. Cell-Cell communication in various forms, especially important for animal development

Genes involved in Cell-Cell communication and transcriptional control are especially important for animal development
What are the genes that animals share with one another but not with other kingdoms of life? These would be expected to include genes required specifically for animal development but not needed for unicellular existence. Comparison of animal genomes with the genome of budding yeast—a unicellular eukaryote— suggests that three classes of genes are especially important for multicellular organization.

The first class includes genes that encode proteins used for cell-cell adhesion and cell signalling; hundreds of human genes encode signal proteins, cell-surface receptors, cell adhesion proteins, or ion channels that are either not present in yeast or present in much smaller numbers.

The second class includes genes encoding proteins that regulate transcription and chromatin structure: more than 1000 human genes encode transcription regulators, but only about 250 yeast genes do so. The development of animals is dominated by cell-cell interactions and by differential gene expression.

The third class of noncoding RNAs has a more uncertain status: it includes genes that encode microRNAs (miRNAs); there are at least 500 of these in humans. Along with the regulatory proteins, they play a significant part in controlling gene expression during animal development, but the full extent of their importance is still unclear.
Molecular Biology of the Cell, 5th Ed, 2008: page 1308

5. Chromatin dance in the nucleus through extensile motors affect transcription and gene regulation

Transcription and gene regulation Genome topology has emerged as a key player in all genome functions. Although a contribution of local genome looping in transcription has long been appreciated, recent observations have revealed the importance of long-range interactions, and genome-wide studies have uncovered the universal nature of such regulatory genome topology interactions in gene regulation. Several types of chromosomal interactions, either in the form of loops between sequences on the same chromosomes or interchromosomal interactions, have emerged as key mechanisms in gene regulationThe nature of genome topology is very precise, and so its regulatory functions in gene expression and genome maintenance. The emerging picture is one of extensive self-enforcing feedback between activity and spatial organization of the genome, suggestive of a self-organizing and self-perpetuating system that uses epigenetic dynamics to regulate genome function in response to regulatory cues and to propagate cell-fate memory
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837811/

6. Post-transcriptional modifications (PTMs) of histones affect gene transcription

According to the histone code hypothesis, the pattern of histone modification is recognized by proteins much like a language or code. One pattern of histone modification may attract proteins that inhibit transcription. Alternatively, a different combination of histone modifications may attract proteins, such as ATP-dependent chromatin-remodeling complexes, that promote gene transcription. In this way, the histone code plays a key role in accessing the information within the genomes of eukaryotic species. Post-translational modifications (PTMs) of histones provide a fine-tuned mechanism for regulating chromatin structure and dynamics.  In addition to combinatorial PTMs that function together both synergistically and antagonistically, there is now an appreciation for PTM asymmetry within individual nucleosomes, novel types of PTMs with unique functions, nucleosomes bearing histone variants, and nuclear compartmentalization events that are all contributing to the final output of chromatin organization and function
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4099259/

7. The DNA methylation code is like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on.

DNA methylation has several uses in the vertebrate cell. A very important role is to work in conjunction with other gene expression control mechanisms to establish a particularly efficient form of gene repression. This combination of mechanisms ensures that unneeded eukaryotic genes can be repressed to very high degrees. For example, the rate at which a vertebrate gene is transcribed can vary 10^6-fold between one tissue and another. The unexpressed vertebrate genes are much less “leaky” in terms of transcription than bacterial genes, in which the largest known differences in transcription rates between expressed and unexpressed gene states are about 1000-fold. DNA methylation helps to repress transcription in several ways. The methyl groups on methylated cytosines lie in the major groove of DNA and interfere directly with the binding of proteins (transcription regulators as well as the general transcription factors) required for transcription initiation. In addition, the cell contains a repertoire of proteins that bind specifically to methylated DNA.The best characterized of these associate with histone modifying enzymes, leading to a repressive chromatin state where chromatin structure and DNA methylation act synergistically.  One reflection of the importance of DNA methylation to humans is the widespread involvement of “incorrect” DNA methylation patterns in cancer progression
Molecular Biology of the Cell, 5th Ed, 2008: Cell, page 467

8. Homeobox and Hox genes determine the shape of the body

This family of related genes determines the shape of the body. It subdivides the embryo along the head-to-tail axis into fields of cells that eventually become limbs and other structures.  Starting as a fertilized egg with a homogeneous appearance, an embryo made of skin, muscles, nerves and other tissues gradually arises through the division of cells. Long before most cells in the emerging body begin to specialize, however, a plan that designates major regions of the body-the head, the trunk, the tail and so on is established. This plan helps seemingly identical combinations of tissues arrange themselves into distinctly different anatomical structures, such as arms and legs. Individual genes mediate some of the developmental decisions involved in establishing the embryonic body plan.
https://www.jstor.org/stable/pdf/24996862.pdf?seq=1#page_scan_tab_contents

9. Noncoding DNA  ( Junk DNA ) is transcribed into functional non-coding RNA molecules and switches protein-coding genes on or off.

Fundamental importance in the regulation of mammalian gene expression programs, from transcriptional initiation, termination and stability, through recruitment of the exon-junction complex to the recruitment of chromatin remodelers through the spliceosome. Eukaryotic cells use a variety of strategies to control their transcriptional output that employ a large number of regulatory factors that, in turn, must be tightly regulated. Introns, as genetic entities or RNA segments ( previously held as junk ), facilitate or participate in this amazing regulation feat by sheltering information for small regulatory RNAs allowing for concerted expression of multiple molecules in a given context, influencing where and when a messenger RNA is spliced and translated, preventing or attenuating translation off context or, on the contrary, diversifying the type and function of the molecules produced depending on the internal and external environment.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394429/


10.  Transposons and Retrotransposons regulate genes

Striking evidence has accumulated indicating that some proviral sequences and HERV proteins might even serve the needs of the host and are therefore under positive selection. The remarkable progress in the analysis of host genomes has brought to light the significant impact of HERVs and other retroelements on genetic variation, genome evolution, and gene regulation.
Despite often being classified as selfish or junk DNA, transposable elements (TEs) are a group of abundant genetic sequences that have a significant impact on mammalian development and genome regulation.
http://dev.biologists.org/content/143/22/4101

11. Centrosomes play a central role in development

Centrosome integrity is critically important for successful fertilization and embryo development. In humans, the sperm contributes the dominant centrosomal material containing centrioles and centrosomal components onto which oocyte centrosomal proteins assemble after sperm incorporation to form the sperm aster that is essential for uniting sperm and oocyte pronuclei.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734160/

12. The precise arrangement of Cytoskeletal arrays provides critical structural information.

The three major cytoskeletal filaments are responsible for different aspects of the cell’s spatial organization and mechanical properties. Actin filaments determine the shape of the cell’s surface and are necessary for whole-cell locomotion; they also drive the pinching of one cell into two. Microtubules determine the positions of membrane-enclosed organelles, direct intracellular transport, and form the mitotic spindle that segregates chromosomes during cell division. Intermediate filaments provide mechanical strength. All of these cytoskeletal filaments interact with hundreds of accessory proteins that regulate and link the filaments to other cell components, as well as to each other. The accessory proteins are essential for the controlled assembly of the cytoskeletal filaments in particular locations, and they include the motor proteins, remarkable molecular machines that convert the energy of ATP hydrolysis into mechanical force that can either move organelles along the filaments or move the filaments themselves.
Molecular Biology of the Cell By Bruce Alberts 6th. ed. page 889

13. Membrane targets provide crucial information—spatial coordinates—for embryological development.

Preexisting membrane targets, already positioned on the inside surface of the egg cell, determine where these molecules will attach and how they will function. These membrane targets provide crucial information—spatial coordinates—for embryological development.


14. Ion Channels and Electromagnetic Fields influence the form of a developing organism

Experiments have shown that electromagnetic fields have “morphogenetic” effects—in other words, effects that influence the form of a developing organism. In particular, some experiments have shown that the targeted disturbance of these electric fields disrupts normal development in ways that suggest the fields are controlling morphogenesis. Artificially applied electric fields can induce and guide cell migration. There is also evidence that direct current can affect gene expression, meaning internally generated electric fields can provide spatial coordinates that guide embryogenesis. Although the ion channels that generate the fields consist of proteins that may be encoded by DNA (just as microtubules consist of subunits encoded by DNA), their pattern in the membrane is not. Thus, in addition to the information in DNA that encodes morphogenetic proteins, the spatial arrangement and distribution of these ion channels influence the development of the animal.

https://pure.tue.nl/ws/files/10243383/20151217_CO_Vanegas.pdf

15. The Sugar Code forms information-rich structures which influence the arrangement of different cell types during embryological development.

These sequence-specific information-rich structures influence the arrangement of different cell types during embryological development. Thus, some cell biologists now refer to the arrangements of sugar molecules as the “sugar code” and compare these sequences to the digitally encoded information stored in DNA. As biochemist Hans-Joachim Gabius notes, sugars provide a system with “high-density coding” that is “essential to allow cells to communicate efficiently and swiftly through complex surface interactions.” According to Gabius, “These [sugar] molecules surpass amino acids and nucleotides by far in information-storing capacity.” So the precisely arranged sugar molecules on the surface of cells clearly represent another source of information independent of that stored in DNA base sequences.  These cascades are, along with the cell event itself, associated with the “coding information” on a cell surface, or, using another terminology, are realized due to an instruction for the cell from the morphogenetic field of an organism. The concrete signal transduction pathways connecting the "coding information" on a cell surface and the expression of the given sets of genes need to be elucidated. 
https://www.ncbi.nlm.nih.gov/pubmed/15174156

16. Egg-polarity genes encode macromolecules deposited in the egg to organize the axes

- Splicing Code: Jon Lieff, M.D. about the 
As important as the DNA code is, the alternative RNA splicing is equally, or more, important. In fact, recent research shows that alternative splicing may be the critical source of evolutionary changes differentiating primates and humans from other creatures such as worms and flies with a similar number of genes.
http://jonlieffmd.com/blog/alternative-rna-splicing-in-evolution

17. Hormones  are special chemical messengers for development

The endocrine system provides an electrochemical connection from the hypothalamus of the brain to all the organs that control the body metabolism, growth and development, and reproduction.
https://en.wikibooks.org/wiki/Human_Physiology/The_endocrine_system


Following list, each of the 17 mechanisms, and quote of science papers which affirm the relevance of the mechanism to explain organismal development and architecture

https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from#6645

Following are the list of peer-reviewed scientific papers that demonstrate the REAL mechanisms that replace Darwin's gene-centric theory of mutations, natural selection, gene drift & flow to explain organismal architecture and complexity. I outline each of the 17 mechanisms and quote science papers which affirm the relevance of the mechanism:

Evidence points to preprogrammed specifying - instructional complex INFORMATION ( blueprints ) encoded in various genetic and epigenetic languages and signalling communication networks as the true mechanisms responsible for major morphological architecture and innovation & adaptation, development and body form:

EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751/

Hedgehog (Hh)
https://www.sciencedirect.com/science/article/pii/S0929664615000340  

Wingless related (Wnt)
http://dev.biologists.org/content/145/12/dev165902  

Transforming growth factor-β (TGF-β)
https://www.ncbi.nlm.nih.gov/pubmed/9611771

Receptor tyrosine kinase (RTK)
https://www.sinobiological.com/receptor-tyrosine-kinase-rtk-signaling-transduction.html

Notch
http://dev.biologists.org/content/138/17/3593


Janus kinase (JAK)/signal transducer  
https://www.cell.com/trends/endocrinology-metabolism/pdf/S1043-2760(17)30150-9.pdf

Activators of transcription (STAT) protein kinases
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC129988/

Nuclear hormone pathways
http://dev.biologists.org/content/142/16/2764

Bone morphogenetic proteins (BMP)
https://www.ncbi.nlm.nih.gov/pubmed/25401122


Epidermal growth factor receptors (EGFR)
https://www.sciencedirect.com/topics/medicine-and-dentistry/epidermal-growth-factor-receptor

Fibroblast growth factors (FGF)
https://academic.oup.com/jb/article/149/2/121/837258

DNA methylation
https://www.ncbi.nlm.nih.gov/pubmed/23877618

Histone modification and incorporation of histone variants
https://www.researchgate.net/publication/270654681_Histone_Variants_and_Epigenetics


Chromatin remodelling in Eukaryotic Cells
https://www.news-medical.net/life-sciences/Chromatin-Remodeling-Mechanisms-and-Importance.aspx

Non-coding RNA-mediated epigenetic regulation
https://www.whatisepigenetics.com/non-coding-rna/

3. Epigenetic Codes perform various tasks essential to cell structure and development
Genetic & Epigenetic Codes:
1.  The 31 Genetic Codes 
2.  The Acoustic codes
3.  The Adhesion Code
4.  The Apoptosis Code
5.  The Bioelectric Code
6.  The Biophoton Code
7.  The Calcium Code
8.  The Chaperone Code
9.  The Chromatin Code
10. The Circular motif ( ribosome) Code
11. The Cytoskeleton Code
12. The Coactivator/corepressor/epigenetic Code
13. The Code of human language
14. The compartment Code
15. The Hidden Code within the Genetic Code
16. The DNA methylation Code
17. The Differentiation Code
18. The Domain substrate specificity Code of Nonribosomal peptide synthetases (NRPS)
19. The Error correcting Code
20. The Genomic Code
21. The Genomic regulatory Code
22. The Glycomic Code
23. The Histone Code
24. The HOX Code
25. The immune response code, or language
26. The Lamin Code
27. The Metabolic Code
28. The Myelin Code
29. The Neuronal spike-rate Code
30. The Non-ribosomal Code
31. The Nucleosome Code
32. The Nuclear signalling Code
33. The Olfactory Code
34. The Operon Code
35. The Phosphorylation Code
36. The Post-translational modification Code for transcription factors
37. The RNA Code
38. The Ribosomal Code
39. The Riboswitch Code
40. The Splicing Codes
41. The Signal transduction Code
42. The Signal Integration Codes
43. The Sugar Code
44. The Synaptic Adhesive Code
45. The Talin Code
46. The Transcription factor Code
47. The Transcriptional cis-regulatory Code
48. The Tubulin Code
49. The Ubiquitin Code


4. Cell-Cell communication in various forms, especially important for animal development
Molecular Biology of the Cell, 5th Ed, 2008: page 1308

5. Chromatin dance in the nucleus through extensile motors affect transcription and gene regulation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837811/

6. Post-transcriptional modifications (PTMs) of histones affect gene transcription
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4099259/

7. The DNA methylation code is like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on.
Molecular Biology of the Cell, 5th Ed, 2008: Cell, page 467

8. Homeobox and Hox genes determine the shape of the body
https://www.jstor.org/stable/pdf/24996862.pdf?seq=1#page_scan_tab_contents

9. Noncoding DNA  ( Junk DNA ) is transcribed into functional non-coding RNA molecules and switches protein-coding genes on or off.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394429/

10.  Transposons and Retrotransposons regulate genes
http://dev.biologists.org/content/143/22/4101

11. Centrosomes play a central role in development
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734160/

12. The precise arrangement of Cytoskeletal arrays provides critical structural information.
Molecular Biology of the Cell By Bruce Alberts 6th. ed. page 889

13. Membrane targets provide crucial information—spatial coordinates—for embryological development.

14. Ion Channels and Electromagnetic Fields influence the form of a developing organism
https://pure.tue.nl/ws/files/10243383/20151217_CO_Vanegas.pdf

15. The Sugar Code forms information-rich structures which influence the arrangement of different cell types during embryological development.
https://www.ncbi.nlm.nih.gov/pubmed/15174156

16. Egg-polarity genes encode macromolecules deposited in the egg to organize the axesSplicing Code: Jon Lieff, M.D. 
http://jonlieffmd.com/blog/alternative-rna-splicing-in-evolution

17. Hormones  are special chemical messengers for development
https://en.wikibooks.org/wiki/Human_Physiology/The_endocrine_system

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751/
https://www.sciencedirect.com/science/article/pii/S0929664615000340 
http://dev.biologists.org/content/145/12/dev165902 
https://www.ncbi.nlm.nih.gov/pubmed/9611771
https://www.sinobiological.com/receptor-tyrosine-kinase-rtk-signaling-transduction.html
http://dev.biologists.org/content/138/17/3593
https://www.cell.com/trends/endocrinology-metabolism/pdf/S1043-2760(17)30150-9.pdf
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC129988/
http://dev.biologists.org/content/142/16/2764
https://www.ncbi.nlm.nih.gov/pubmed/25401122
https://www.sciencedirect.com/topics/medicine-and-dentistry/epidermal-growth-factor-receptor
https://academic.oup.com/jb/article/149/2/121/837258
https://www.ncbi.nlm.nih.gov/pubmed/23877618
https://www.researchgate.net/publication/270654681_Histone_Variants_and_Epigenetics
https://www.news-medical.net/life-sciences/Chromatin-Remodeling-Mechanisms-and-Importance.aspx
https://www.whatisepigenetics.com/non-coding-rna/
Molecular Biology of the Cell, 5th Ed, 2008: page 1308
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837811/
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4099259/
Molecular Biology of the Cell, 5th Ed, 2008: Cell, page 467
https://www.jstor.org/stable/pdf/24996862.pdf?seq=1#page_scan_tab_contents
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394429/
http://dev.biologists.org/content/143/22/4101
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734160/
Molecular Biology of the Cell By Bruce Alberts 6th. ed. page 889
https://pure.tue.nl/ws/files/10243383/20151217_CO_Vanegas.pdf
https://www.ncbi.nlm.nih.gov/pubmed/15174156
http://jonlieffmd.com/blog/alternative-rna-splicing-in-evolution
https://en.wikibooks.org/wiki/Human_Physiology/The_endocrine_system



Last edited by Otangelo on Wed Aug 30, 2023 4:31 am; edited 17 times in total

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Stephen C Meyer , Darwin's doubt pg.268:
THE HIERARCHICAL ORGANIZATION OF GENETIC AND EPIGENETIC  INFORMATION
In addition to the information stored in individual genes and the information present in the integrated  networks of genes and proteins in dGRNs, animal forms exemplify hierarchical arrangements or layers of information-rich molecules, systems, and structures. For example, developing embryos require epigenetic information in the form of specifically arranged
 
(a) membrane targets and patterns, 
(b) cytoskeletal arrays, 
(c) ion channels, and 
(d) sugar molecules on the exterior of cells (the sugar code).

 
Much of this epigenetic information resides in the structure of the maternal egg and is inherited directly from membrane to membrane independently of DNA.  This three-dimensional structural information interacts with other information-rich molecules and systems of molecules to ensure the proper development of an animal. In particular, epigenetic information influences the proper positioning and thus the function of regulatory proteins (including  DNA-binding proteins), messenger RNAs, and various membrane components. Epigenetic information also influences the function of developmental gene regulatory networks. Thus, information at a higher structural level in the maternal egg helps to determine the function of both whole networks of genes and proteins (dGRNs) and individual molecules (gene products) at a lower level within a developing animal. Genetic information is necessary to specify the arrangement of amino acids in a protein or bases in an RNA molecule. Similarly, dGRNs are necessary to specify the location and/or function of many gene products. And, in a similar way, epigenetic information is necessary to specify the location and determine the function of lower-level molecules and systems of molecules, including the dGRNs themselves.  Furthermore, the role of epigenetic information provides just one of many examples of the hierarchical arrangement (or layering) of information-rich structures, systems, and molecules within animals. Indeed, at every level of the biological hierarchy, organisms require specified and highly improbable (information-rich) arrangements of lower-level constituents in order to maintain their form and function. Genes require specified arrangements of nucleotide bases; proteins require specified arrangements of amino acids; cell structures and cell types require specified arrangements of proteins or systems of proteins; tissues and organs require specific arrangements of specific cell types; and body plans require specialized arrangements of tissues and organs. Animal forms contain information-rich lower-level components (such as proteins and genes). But they also contain information-rich arrangements of those components (such as the arrangement of genes and gene products in dGRNs or proteins in cytoskeletal arrays or membrane targets). Finally, animals also exhibit information-rich arrangements of higher-level systems and structures (such as the arrangements of specific cell types, tissues, and organs that form specific body plans).
 
The highly specified, tightly integrated, hierarchical arrangements of molecular components and systems within animal body plans also suggest intelligent design. This is, again, because of our experience with the features and systems that intelligent agents—and only intelligent agents— produce. Indeed, based on our experience, we know that intelligent human agents have the capacity to generate complex and functionally specified arrangements of matter—that is, to generate specified complexity or specified information. Further, human agents often design information-rich hierarchies, in which both individual modules and the arrangement of those modules exhibit complexity and specificity—specified information. Individual transistors, resistors, and capacitors in an integrated circuit exhibit considerable complexity and specificity of design. Yet at a higher level of organization, the specific arrangement and connection of these components within an integrated circuit requires additional information and reflects further design (see Fig.below).
 
Evolution: Where Do Complex Organisms Come From? Inform11
 
Figure 14.2.

Conscious and rational agents have, as part of their powers of purposive intelligence, the capacity to design information-rich parts and to organize those parts into functional information-rich systems and hierarchies. We know of no other causal entity or process that has this capacity. Clearly, we have good reason to doubt that mutation and selection, self-organizational processes, or any of the other undirected processes cited by other materialistic evolutionary theories, can do so. Thus, based upon our present experience of the causal powers of various entities and a careful assessment of the efficacy of various evolutionary mechanisms, we can infer intelligent design as the best explanation for the origin of the hierarchically organized layers of information needed to build the animal forms that arose in the Cambrian period.
 
There is another remarkable aspect of the hierarchical organization of information in animal forms.  Many of the same genes and proteins play very different roles, depending upon the larger organismal  and informational context in which they find themselves in different animal groups. For example, the  same gene (Pax-6 or its homolog, called eyeless), helps to regulate the development of the eyes of fruit flies (arthropods) and those of squid and mice (cephalopods and vertebrates, respectively). Yet arthropod eyes exemplify a completely different structure from vertebrate or cephalopod eyes. The fruit fly possesses a compound eye with hundreds of separate lenses (ommatidia), whereas both mice and squid employ a camera-type eye with a single lens and retinal surface. In addition, although the eyes of squid and mice resemble each other optically (single lens, large internal chamber, single retinal surface), they focus differently. They undergo completely different patterns of development and utilize different internal structures and nerve connections to the visual centers of the brain. Yet the Pax-6 gene and its homologs play a key role in regulating the construction of all three of these different adult sensory structures. Moreover, evolutionary and developmental biologists have found that this pattern of "same genes, different anatomy" recurs throughout the bilaterian phyla, for features  as fundamental as appendages, segmentation, the gut, heart, and sense organs
 
Evolution: Where Do Complex Organisms Come From? Gene_e11
 
This pattern contradicts the expectations of textbook evolutionary theory. Neo-Darwinism predicts that disparate adult structures should be produced by different genes. This prediction follows directly from the neo-Darwinian assumption that all evolutionary (including anatomical) transformations begin with mutations in DNA sequences—mutations that are fixed in populations by natural selection, genetic drift, or other evolutionary processes. The arrow of causality flows one way from genes (DNA) to development to adult anatomy. Thus, if biologists observe different animal forms, it follows that they should expect that different genes will specify those forms during animal development. Given the profound differences between the fruit-fly compound eye and the vertebrate camera eye, neo-Darwinian theory would not predict that the "same" genes would be involved in building different eyes in arthropods and chordates.

DEVELOPMENTAL GENE REGULATORY NETWORKS

Darwins doubt, page 199

Another line of research in developmental biology has revealed a related challenge to the creative power of the neo-Darwinian mechanism. Developmental biologists have discovered that many gene products (proteins and RNAs) needed for the development of specific animal body plans transmit signals that influence the way individual cells develop and differentiate themselves. Additionally, these signals affect how cells are organized and interact with each other during embryological development. These signaling molecules influence each other to form circuits or networks of coordinated interaction, much like integrated circuits on a circuitboard. For example, exactly when a signaling molecule gets transmitted often depends upon when a signal from another molecule is received, which in turn affects the transmission of still others—all of which are coordinated and integrated to perform specific time-critical functions. The coordination and integration of these signaling molecules in cells ensures the proper differentiation and organization of distinct cell types during the development of an animal body plan. Consequently, just as mutating an individual regulatory gene early in the development of an animal will inevitably shut down development, so too will mutations or alterations in the whole network of interacting signaling molecules destroy a developing embryo. No biologist has explored the regulatory logic of animal development more deeply than Eric Davidson, at the California Institute of Technology. Early in his career, collaborating with molecular biologist Roy Britten, Davidson formulated a theory of “gene regulation for higher cells.”1 By “higher cells” Davidson and Britten meant the differentiated, or specialized, cells found in any animal after the earliest stages of embryological development. Davidson observed that the cells of an individual animal, no matter how varied in form or function, “generally contain identical genomes.” During the life cycle of an organism, the genomes of these specialized cells express only a small fraction of their DNA at any given time and produce different RNAs as a result. These facts strongly suggest that some animal-wide system of genetic control functions to turn specific genes on and off as needed throughout the life of the organism—and that such a system functions during the development of an animal from egg to adult as different cell types are being constructed.

When they proposed their theory in 1969, Britten and Davidson acknowledged that “little is known. . . of the molecular mechanisms by which gene expression is controlled in differentiated cells.” Nevertheless, they deduced that such a system must be at work. Given:

(1) that tens or hundreds of specialized cell types arise during the development of animals, and
(2) that each cell contains the same genome, they reasoned
(3) that some control system must determine which genes are expressed in different cells at different times to ensure the differentiation of different cell types from each other—some system-wide regulatory logic must oversee and coordinate the expression of the genome.

Davidson has dedicated his career to discovering and describing the mechanisms by which these systems of gene regulation and control work during embryological development. During the last two decades, research in genomics has revealed that nonprotein-coding regions of the genome control and regulate the timing of the expression of the protein-coding regions of the genome. Davidson has shown that the nonprotein-coding regions of DNA that regulate and control gene expression and the protein-coding regions of the genome together function as circuits. These circuits, which Davidson calls “developmental gene regulatory networks” (or dGRNs) control the embryological development of animals.

Evolution: Where Do Complex Organisms Come From? Gene_r10

On arriving at Caltech in 1971, Davidson chose the purple sea urchin, Strongylocentrotus purpuratus, as his experimental model system. The biology of S. purpuratus makes it an attractive laboratory subject: the species occurs abundantly along the Pacific coast, produces enormous quantities of easily fertilized eggs in the lab, and lives for many years. Davidson and his coworkers pioneered the technology and experimental protocols required to dissect the sea urchin’s genetic regulatory system. The remarkable complexity of what they found needs to be depicted visually. Figure 13.4a shows the urchin embryo as it appears six hours after development has begun (top left of diagram). This is the 16-cell stage, meaning that four rounds of cell division have already occurred (1 → 2 → 4 → 8 → 16). As development proceeds in the next four stages, both the number of cells and the degree of cellular specialization increases, until, at 55 hours, elements of the urchin skeleton come into focus. Figure 13.4b shows, corresponding to these drawings of embryo development, a schematic diagram with the major classes of genes (for cell and tissue types) represented as boxes, linked by control arrows. Last, Figure 13.4c shows what Davidson calls “the genetic circuitry” that turns on the specific biomineralization genes that produce the structural proteins needed to build the urchin skeleton. 2

This last diagram represents a developmental gene regulatory network (or dGRN), an integrated network of protein and RNA-signaling molecules responsible for the differentiation and arrangement of the specialized cells that establish the rigid skeleton of the sea urchin. Notice that, to express the biomineralization genes that produce structural proteins that make the skeleton, genes far upstream, activated many hours earlier in development, must first play their role. This process does not happen fortuitously in the sea urchin but via highly regulated and precise control systems, as it does in all animals. Indeed, even one of the simplest animals, the worm C. elegans, possessing just over 1,000 cells as an adult, is constructed during development by dGRNs of remarkable precision and complexity. In all animals, the various dGRNs direct what Davidson describes as the embryo’s “progressive increase in complexity”—an increase, he writes, that can be measured in “informational terms.” Davidson notes that, once established, the complexity of the dGRNs as integrated circuits makes them stubbornly resistant to mutational change—a point he has stressed in nearly every publication on the topic over the past fifteen years. “In the sea urchin embryo,” he points out, “disarming any one of
these subcircuits produces some abnormality in expression.” Developmental gene regulatory networks resist mutational change because they are organized hierarchically. This means that some developmental gene regulatory networks control other gene regulatory networks, while some influence only the individual genes and proteins under their control. At the center of this regulatory hierarchy are the regulatory networks that specify the axis and global form of the animal body plan during development. These dGRNs cannot vary without causing catastrophic effects to the organism. Indeed, there are no examples of these deeply entrenched, functionally critical circuits varying at all. At the periphery of the hierarchy are gene regulatory networks that specify the arrangements for smaller-scale features that can sometimes vary. Yet, to produce a new body plan requires altering the axis and global form of the animal. This requires mutating the very circuits that do not vary without catastrophic effects. As Davidson emphasizes, mutations affecting the dGRNs that regulate body-plan development lead to “catastrophic loss of the body part or loss of viability altogether.”3  He explains in more detail:

There is always an observable consequence if a dGRN subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.

ENGINEERING CONSTRAINTS


Davidson’s findings present a profound challenge to the adequacy of the neo-Darwinian mechanism. Building a new animal body plan requires not just new genes and proteins, but new dGRNs. But to build a new dGRN from a preexisting dGRN by mutation and selection necessarily requires altering the preexisting developmental gene regulatory network. (the very kind of change that  cannot arise without multiple coordinated mutations). In any case, Davidson’s work has also shown that such alterations inevitably have catastrophic consequences. Davidson’s work highlights a profound contradiction between the neo-Darwinian account of how
new animal body plans are built and one of the most basic principles of engineering—the principle of constraints. Engineers have long understood that the more functionally integrated a system is, the more difficult it is to change any part of it without damaging or destroying the system as a whole. Davidson’s work confirms that this principle applies to developing organisms in spades. The system of gene regulation that controls animal-body-plan development is exquisitely integrated, so that significant alterations in these gene regulatory networks inevitably damage or destroy the developing animal.

As Davidson explains, “Interference with expression of any [multiply linked dGRNs] by mutation or experimental manipulation has severe effects on the phase of development that they initiate. This accentuates the selective conservation of the whole subcircuit, on pain of developmental catastrophe” (Davidson and Erwin, “An Integrated View of Precambrian Eumetazoan Evolution”

But given this, how could a new animal body plan, and the new dGRNs necessary to produce it, ever evolve gradually via mutation and selection from a preexisting body plan and set of dGRNs? Davidson makes clear that no one really knows: “contrary to classical evolution theory, the processes that drive the small changes observed as species diverge cannot be taken as models for the evolution of the body plans of animals.” He elaborates:

Neo-Darwinian evolution . . . assumes that all process works the same way, so that evolution of enzymes or flower colors can be used as current proxies for study of evolution of the body plan. It erroneously assumes that change in protein-coding sequence is the basic cause of change in developmental program; and it erroneously assumes that evolutionary change in body-plan morphology occurs by a continuous process. All of these assumptions are basically counterfactual. This cannot be surprising, since the neo-Darwinian synthesis from which these ideas stem was a premolecular biology concoction focused on population genetics and . . . natural history, neither of which have any direct mechanistic import for the genomic regulatory systems that drive embryonic development of the body plan.

NOW AND THEN

Eric Davidson’s work, like that of Nüsslein-Volhard and Wieschaus, highlights a difficulty of obvious relevance to the Cambrian explosion. Typically, paleontologists understand the Cambrian explosion as the geologically sudden appearance of new forms of animal life. Building these forms requires new developmental programs—including both new early-acting regulatory genes and new developmental gene regulatory networks. Yet if neither early-acting regulatory genes nor dGRNs can be altered by mutation without destroying existing developmental programs (and thus animal form), then mutating these entities will leave natural selection with nothing favorable to select and the evolution of animal form will, at that point, terminate. Darwin’s doubt about the Cambrian explosion centered on the problem of missing fossil intermediates. Not only have those forms not been found, but the Cambrian explosion itself illustrates a profound engineering problem that fossil evidence does not address—the problem of building a new form of animal life by gradually transforming one tightly integrated system of genetic components and their products into another. 

Although evidence is all around us of a deep geological past, and of multifarious genealogical relationships among ourselves and the organisms we currently share the planet with, scientists still have only sketchy ideas about how complex living forms arose in the course of evolution. As James Shapiro described in a recent Huffington Post blog entry, there has been good progress in understanding how complex cells arose from simpler ones by cell mergers, or "symbiogenesis." But even "simple" cells are quite complex, and the origins of cellular life (aka "chemical evolution"; read more here), are far from settled.

What about the complex bodies and organs of animals and plants? This is what primarily concerned the nineteenth century naturalists Alfred Russel Wallace and Charles Darwin (neither of whom knew anything about the internal intricacies of cells, including the nature of their genes), as they pondered the transformations of life throughout its history. Their solution was "natural selection," the acquisition of new forms and functions in populations of organisms by small increments, over long times, with each gradual change being subject to the sieve of "adaptation." Was each heritable variation better suited to some pre-existing task? If so, its exemplars increased and multiplied. If not, their kind faded away.

While it may be an adequate scenario for the refinement of some already-existing characters -- the beaks of finches, color intensity of moths -- the "microevolutionary" process envisioned by Darwin and his successors does not account in any plausible way for "macroevolutionary" patterns such as the differences between oysters and grasshoppers, fish and birds. In fact, adaptationist gradualism, though still popular in some scientific circles, is increasingly questioned and found wanting by evolutionary biologists working in an expanded set of disciplines.

By incorporating embryonic development and its underlying physico-genetic processes into evolutionary theory, investigators are learning that abrupt alterations in body plan and other aspects of organismal form can occur in response to environmental change or gene mutation in ways that affect multiple members of a population and exhibit consistent patterns of inheritance. Furthermore, there is increasing emphasis on the resourcefulness of organisms and their ability to construct their own niches. Having a "phenotype" (the outward manifestation of biological identity), very different from that of one's progenitors is no longer considered disqualifying for survival.

Although the writings of Wallace and Darwin's predecessor Jean-Baptiste Lamarck anticipated some current ideas about the morphologically prolific processes of embryo generation ("Le pouvoir de la vie") and the active strivings of organisms for survival in their environmental settings ("L'influence des circonstances"), Darwin's less speculative approach encouraged readier acceptance of his ideas by other scientists and the educated public. (The playwright George Bernard Shaw, in the preface to Back to Methuselah, put it more sharply as "Why Darwin converted the crowd.") By specifying that the variations in organismal form and function sorted out by natural selection were entirely incremental, Darwin's theory could side-step any questions about how the altered forms actually arose. It also created an incentive to deny the relevance of the more profound changes (Darwin called them "sports") that were well known to arise in natural populations. This may have been the best that could be done circa 1850, but its retention in the so-called modern evolutionary synthesis a century later was a scandalous legacy of the banishment of developmental biology (embryology) from the synthesis, and the indifferent attitude of biological education regarding the physical sciences.

The physical science of Darwin's time, which provided a backdrop to his thinking, was dominated by Newton's concept that material bodies only change course in proportion to external forces that act on them. It also included the often more pertinent notion (e.g., for the molding of pliable materials) from Aristotle of matter changing position or shape only to the extent that it continues to be pushed. These ideas, however, did not pretend to account for the sudden reorganizational changes (freezing, melting, phase separation, compositional change) seen in complex chemically and mechanically active materials. We now recognize that the tissues of a developing embryo are indeed such non-Newtonian, non-Aristotelian materials. By the end of Darwin's life new physical theories were being put forward to explain abrupt and large-scale changes in such materials, and by extension, the character and transformations of organisms and their organs.

Here is a partial list of late nineteenth and early twentieth-century physical concepts that have proved relevant to developmental processes (with the phenomenon they explain, at least partly, in parentheses): dynamical systems (ability of cells having the same genome to switch between different "types"), phase separation of liquids (capacity of embryonic tissues to form several non-mixing layers), chemical oscillations (propensity of embryonic tissues to organize into tandem segments), "Turing-type" reaction-diffusion systems (the formation in tissues of regularly spaced structures like feather and hair buds, pigment stripes, or the bones of the limb skeleton). All or most of these processes (termed "mesoscale," being most relevant to objects the size and texture of cell clusters), along with several others, are harnessed and mobilized by the secreted products of specific genes during embryogenesis in every one of the animal phyla (e.g., arthropods, mollusks, nematodes, chordates and so forth).

What can the existence and action of such protean generative processes tell us about the origin of organismal complexity? First, let's look at some of the expectations of the natural selection-based modern synthesis: (i) the largest differences within given categories of multicellular organisms, the animals or plants, for example, should have appeared gradually, only after exceptionally long periods of evolution; (ii) the extensive genetic changes required to generate such large differences over such vast times would have virtually erased any similarity between the sets of genes coordinating development in the different types of organism; and (iii) evolution of body types and organs should continue indefinitely. Since genetic mutation never ceases, novel organismal forms should constantly be appearing.


All these predictions of the standard model have proved to be incorrect. The actual state of affairs however, are expected outcomes of the "physico-genetic" picture outlined above. Briefly, we now know that complex multicellular organisms appeared rapidly (on a geological time scale, i.e., two episodes of no more than 10-20 million years each), employing for developmental patterning not newly evolved genes, but genes that had evolved for entirely different functions in single-celled ancestors. Generation of novel complex forms was able to happen so rapidly because the genetic ingredients were already at hand, but in addition because the mesoscale physical processes described above also did not require an incremental sequence of steps to come into existence. Everything was in place for an organismal "big bang" once simple multicellular clusters had appeared.

Unlike the presumption of the standard model, however, the physico-genetic scenario for the origination of complex multicellular forms is not open-ended and limitless. As with any material organizational process (think waves and eddies in liquid water), the relevant physics can only elicit those structural motifs inherent to the material in question. Thus we should not expect to see, and indeed don't, the "endless forms" that Darwin invoked in The Origin of Species.

With a 19th century notion of incremental material transformations no longer relevant to comprehending the range of organismal variation that has appeared throughout the history of life on Earth, the other pillar of the standard model can be discarded along with it. Specifically, if, as affirmed by niche construction theory, phenotypically novel animals or plants can invent new modes of existence in novel settings, rather than succumbing to a struggle for survival in the niches of their origin, there is no need for cycles of selection for marginal adaptive advantage to be the default explanation for macroevolutionary change.

Additional reading

Newman, S.A. (2012). Physico-genetic determinants in the evolution of development. Science 338, 217-219.

Müller, G.B. (2007). Evo-devo: extending the evolutionary synthesis. Nature Reviews Genetic 8, 943-949.

Forgacs, G., and Newman, S.A. (2005). Biological physics of the developing embryo (Cambridge, Cambridge Univ. Press).

Odling-Smee, F.J., Laland, K.N., and Feldman, M.W. (2003). Niche construction: the neglected process in evolution (Princeton, N.J., Princeton University Press).
Follow Stuart A. Newman on Twitter: www.twitter.com/sanewman1

1) http://www.huffingtonpost.com/stuart-a-newman/complex-organisms_b_2240232.html
1) https://embryo.asu.edu/pages/gene-regulation-higher-cells-theory-1969-roy-j-britten-and-eric-h-davidson
2) http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2329687/
3) http://www.sciencedirect.com/science/article/pii/S0012160611000911?np=y
4) https://arxiv.org/ftp/arxiv/papers/1205/1205.1158.pdf

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Otangelo


Admin

Before we can understand what influences biological change, we need to know what influences biological development, cell structure, size, and form, and biological body architecture.

Every time, a proponent of evolution argues that a proponent of intelligent design does not know how evolution works, asking following will elucidate if the questioner himself actually meets the demand.

Which of the 23 items below does NOT define Cell and body form, size and shape, and organism development? If you cannot point it out, you demonstrate lack of knowledge to argue about if Darwins Theory is true,  and confirmed, or not:

Genetic:
1.DNA Code sequence

Epigenetic ( beyond or outside the genetic information ) :
1. Membrane targets and patterns
2. Cytoskeletal arrays
3. Centrosomes
4. Ion channels, and their location in the cell membrane
5. Sugar molecules on the exterior of cells (the sugar or glycan code)
6. Gene regulatory networks
7. Splicing Code
8. Metabolic Code
9. Signal Transduction Codes
10. Signal Integration Codes
11. Histone Code
12. Tubulin Code
13. Glycomic Code
14. Calcium Code
15. RNA Code
16. MicroRNAs
17. Transposons and Retrotransposons
18. DNA dinucleotide methylation
19. DNA CpG island methylation
20. Histone methylation
21. Chromatin remodeling
22. DNA coiling
23. microRNA regulation

The answer :
ALL of above 23 mentioned items ( and many more which science will discover ) do influence cell shape, body form, and development. There is just ONE item which is genetic, namely the genetic DNA sequence, which upon Mutation, migration (gene flow), genetic drift, and natural selection has influence in a VERY limited range.

I think, we, Creationists / ID-proponentists, have made it into a hobby, to point out why Darwins Theory is false. Above points it out in a nutshell, why. You can save this list on your laptop, and use it, every time when an atheist wishes to educate you on evolution.

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Otangelo


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Replacing Darwins Theory of Evolution

Pinpointing what REALLY defines body architecture, the orchestration of organism development, cell shape and body form, and exposing the correct explanation of biochemical mechanisms of biodiversity is the holy grail of biological sciences

Preprogrammed codified information and signalling replaces Darwin's theory and its various subsequent adaptations, extensions, and new proposals like the modern extended synthesis. Some have also proposed a " third way ". Darwins Theory of Evolution to explain biodiversity can be replaced with

" Biochemical systems programming and signalling"

Following list is the result of years of my investigation. It is for sure not complete, ( there must be more mechanisms ), but I do not know of anyone else that has exposed a more complete framework. The only book I came across ( and has been part of my education ) Is Stephen C. Meyers: Darwin's doubt.

Where Do Complex Organisms Come From?
https://reasonandscience.catsboard.com/t2316-where-do-complex-organisms-come-from

- The Gene regulation network orchestrates gene expression
- Various signalling pathways generate Cell type and patterns
- Epigenetic Codes are multidimensional and perform various tasks essential to cell structure and development
- Cell-Cell communication in various forms, especially important for animal development
- Chromatin dance in the nucleus through extensile motors affect transcription and gene regulation
- Post-transcriptional modifications (PTMs) of histones affect gene transcription
- The DNA methylation code and language which, like a barcode or marker, the methyl group indicates which genes in the DNA are to be turned on.
- Homeobox and Hox genes determine the shape of the body.
- " Junk DNA "has a crucial role in switching the right protein-coding genes on or off
- Gene regulation through Transposons and Retrotransposons
- The precise arrangement of Cytoskeletal arrays
- Membrane targets which provide crucial information—spatial coordinates—for embryological development.
- Ion Channels and Electromagnetic Fields that influence the form of a developing organism
- The Sugar Code forms sequence-specific information-rich structures which influence the arrangement of different cell types during embryological development.
- Egg-polarity genes encode macromolecules deposited in the egg to organize the axes
- hormones

Almost everybody knows the main tenets of evolutionary biology and how it supposedly works: mutations by natural selection. And a few better informed know that it englobes genetic drift and gene flow. But nobody has empirical evidence that these mentioned mechanisms are in fact responsible to explain biodiversity. It is believed to be true, despite never been observed. The claim is that it takes long periods of time, therefore it is justified to claim that this IS the mechanism, despite not observed. Not true. Lenski's experiment with e.coli bacteria over decades and myriads of generations has never demonstrated bacterias to become something new.

The claim that science is still working on it is also false. Science has upon what I have researched a pretty good understanding on a holistic level, the true mechanisms are known, but not expressly mentioned because of the evolutionary underpinning and obsolete philosophical framework, where everything has to be pressed into evolutionary thinking. When put on the table, point by point, what defines body form, and analysed in a systemic approach, it becomes clear, that dozens of different mechanisms are in play.

But the BIG hero on the block which permeates all processes is preprogrammed information transmission and processing on a systemic level, stored in DNA, but principally epigenetic information and SIGNALLING in a myriad of forms and varieties. Information which is NOT stored in DNA, but epigenetic information systems, like the glycan Code on the cell surface which is more complex and permits far more information exchange and processing than DNA. Other at least 22 epigenetic codes are also involved in all kind of cellular processes, from defining WHEN certain biochemical processes have to occur, exactly how many cell divisions have to take place ( if the Cells in the human body would divide just ONE time more then necessary, we would look worse than Frankenstein ) Sex determination in mammals is determined by hormones, which are also signalling molecules. Adaptation to the environment depends on the transmission of signals to the chromosome, which instructs them what proteins have to be expressed to best adapt to the environmental conditions. The Cell cycle is entirely controlled with high precision by checkpoints which depend on getting the right signals to know when to permit the next stage to take place, and so on.

Signalling, pre-programmed information, and Code systems that permit send and transmit codified information and receivers that recognize and decode it correctly, and execute the right biochemical tasks to sustain life, that permit development of multicellular organisms in an orderly, orchestrated, precise fashion, and permit the organism to adapt to the environment upon received information through signalling, is undeniable evidence of a superintelligent mind, which did set it all up. Life was with extreme certainty, designed.

Evolution: Where Do Complex Organisms Come From? Worldv10

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Otangelo


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Dembski and J.Wells: The design of life, general notes, page 16:

What Besides DNA Controls Development? If DNA does not control development, what does? Actually, there is good evidence for the involvement of at least two other factors in the developing egg: the cytoskeleton and the membrane. Every animal cell contains a network of microscopic fibers called a cytoskeleton. These fibers include microtubules, which are known to be involved in patterning embryos. For example, one of the gene products involved in head-to-rear patterning of fruit fly embryos is delivered to its proper location by microtubules; if the microtubules are experimentally disrupted, the gene product doesn’t reach its proper destination and the embryo is grossly deformed. Microtubules consist of many identical protein subunits, and each subunit is produced according to a template in the organism’s DNA. What matters in development is the organization of microtubule arrays, and the organization of a microtubule array is not determined by its subunits any more than the layout of a house is determined by its bricks. Instead, microtubule arrays are formed by organelles called centrosomes, which are inherited independently of an organism’s DNA. Centrosomes play a central role in development: a frog egg can be induced to develop into a frog merely by injecting a sperm centrosome—no sperm DNA is needed. Another non-genetic factor involved in development is the membrane pattern of the egg cell. 

Cell membranes are not merely featureless bags, but highly complex structures. For example, a membrane contains specialized channels that pump molecules in and out of the cell, enabling it to control its interactions with the external environment. An egg cell membrane also contains “targets” which ensure that molecules synthesized in the nucleus reach their proper destinations in the embryo. The gene product, which is involved in head-to-rear patterning of fruit fly embryos and which depends on microtubules to deliver it to its proper location, also needs a target molecule to keep it in place after it arrives. The target is already there, embedded in the membrane. Experiments with single-celled animals show that membrane patterns are determined by pre-existing membranes, not by DNA. Like microtubule subunits, the proteins embedded in a membrane are produced according to templates in the organism’s DNA; but like the form and location of microtubule arrays, the patterns of those embedded proteins are inherited independently of the organism’s DNA. So the control exercised by microtubule arrays and membrane patterns over embryonic development is not encoded in DNA sequences. This does not mean that we now understand developmental programs. Far from it! But it is quite clear that they cannot be reduced to genetic programs, written in the language of DNA sequences. It would be more accurate to say that a developmental program is written into the structure of the entire fertilized egg—including its DNA, microtubule arrays, and membrane patterns—in a language of which we are still largely ignorant.

EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY 1
Never in the modern history of evolutionary bioscience have such essentially different ideas about how to understand evolution of the animal body plan been simultaneously current. The first is the classic neo-Darwinian concept that evolution of animal morphology occurs by means of small continuous changes in primary protein sequence which in general require homozygosity to effect phenotype. The second paradigm holds that evolution at all levels can be illuminated by detailed analysis of cis-regulatory changes in genes that are direct targets of sequence level selection, in that they control variation of immediate adaptive significance. An entirely different way of thinking is that the evolution of animal body plans is a system level property of the developmental gene regulatory networks (dGRNs) which control ontogeny of the body plan.


http://reasonandscience.heavenforum.org/t2318-gene-regulatory-networks-controlling-body-plan-development#4804

In the years since, Wells has developed a powerful argument against the adequacy of the neo-Darwinian mechanism as an explanation for the origin of animal body plans. His argument turns on the importance of epigenetic information to animal development. To see why epigenetic information poses an additional challenge to neo-Darwinism and what exactly biologists mean by “epigenetic” information, let’s examine the relationship between biological form and biological information.
Stephen C Meyer , Darwin's doubt pg.11:

FORM AND INFORMATION
 Biologists typically define “form” as a distinctive shape and arrangement of body parts. Organismal forms exist in three spatial dimensions and arise in time—in the case of animals during development from embryo to adult. Animal form arises as material constituents are constrained to establish specific arrangements with an identifiable three-dimensional shape or “topography”—one that we would recognize as the body plan of a particular type of animal. A particular “form,” therefore, represents a highly specific arrangement of material components among a much larger set of possible arrangements. Understanding form in this way suggests a connection to the notion of information in its most theoretically general sense.  Shannon’s mathematical theory of information equated the amount of information transmitted with the amount of uncertainty reduced or eliminated in a series of symbols or characters. Information, in Shannon’s theory, is thus imparted as some options, or possible arrangements, are excluded and others are actualized. The greater the number of arrangements excluded, the greater the amount of information conveyed. Constraining a set of possible material arrangements, by whatever means, involves excluding some options and actualizing others. Such a process generates information in the most general sense of Shannon’s theory. It follows that the constraints that produce biological form also impart information, even if this information is notencoded in digital form.
 
DNA contains not only Shannon information but also functional or specified information. The arrangements of nucleotides in DNA or of amino acids in a protein are highly improbable and thus contain large amounts of Shannon information. But the function of DNA and proteins depends upon extremely specific arrangements of bases and amino acids. Similarly, animal body plans represent, not only highly improbable, but also highly specific
arrangements of matter. Organismal form and function depend upon the precise arrangement of various constituents as they arise during, or contribute to, embryological development. Thus, the specific arrangement of the other building blocks of biological form—cells, clusters of similar cell types, dGRNs, tissues, and organs—also represent a kind of specified or functional information. I noted that the ease with which Shannon’s information theory applies to molecular biology has sometimes led to confusion about the kind of information contained in DNA and proteins. It may have also created confusion about the places that specified information might reside in organisms. Perhaps because the information-carrying capacity of the gene can be so easily measured, biologists have often treated DNA, RNA, and proteins as the sole repositories of biological information. Neo-Darwinists have assumed that genes possess all the information necessary to specify the form of an animal. They have also assumed that mutations in genes will suffice to generate the new information necessary to build a new form of animal life. Yet if biologists understand organismal form as resulting from constraints on the possible arrangements of matter at many levels in the biological hierarchy—from genes and proteins, to cell types and tissues, to organs and body plans —then biological organisms may well exhibit many levels of information-rich structure. Discoveries in developmental biology have confirmed this possibility.


ABOVE AND BEYOND: EPIGENETIC INFORMATION
 In 2003, MIT Press published a groundbreaking collection of scientific essays titled Origination of Organismal Form: Beyond the Gene in Developmental and Evolutionary Biology, edited by two distinguished developmental and evolutionary biologists, Gerd Müller, of the University of Vienna, and Stuart Newman, of New York Medical College. In their volume, Müller and Newman included a number of scientific articles describing recent discoveries in genetics and developmental biology—discoveries suggesting that genes alone do not determine the three-dimensional form and structure of an animal. Instead, many of the scientists in their volume reported that so-called epigenetic information—information stored in cell structures, but not in DNA sequences—plays a crucial role. The Greek prefix epi means “above” or “beyond,” so epigenetics refers to a source of information that lies beyond the genes. As Müller and Newman explain in their introduction, “Detailed information at the level of the gene does not serve to explain form.” Instead, as Newman explains, “epigenetic” or “contextual information” plays a crucial role in the formation of animal “body assemblies” during embryological development. Müller and Newman not only highlighted the importance of epigenetic information to the formation of body plans during development; they also argued that it must have played a similarly important role in the origin and evolution of animal body plans in the first place. They concluded that recent discoveries about the role of epigenetic information in animal development pose a formidable challenge to the standard neo-Darwinian account of the origin of these body plans—perhaps the most formidable of all. In the introductory essay to their volume, Müller and Newman list a number of “open questions” in evolutionary biology, including the question of the origin of Cambrian-era animal body plans and the origin of organismal form generally, the latter being the central topic of their book. They note that though “the neo-Darwinian paradigm still represents the central explanatory framework of evolution,” it has “no theory of the generative.” In their view, neo-Darwinism “completely avoids [the question of] the origination of phenotypic traits and of organismal form.” As they and others in their volume maintain, neo-Darwinism lacks an explanation for the origin of organismal form precisely because it cannot explain the origin of epigenetic information. I first learned about the problem of epigenetic information and the Spemann and Mangold experiment while driving to a private meeting of Darwin-doubting scientists on the central coast of California in 1993. In the car with me was Jonathan Wells , who was then finishing a Ph.D. in developmental biology at the University of California at Berkeley. Like some others in his field, Wells had come to reject the (exclusively) “gene-centric” view of animal development and to recognize the importance of nongenetic sources of information. By that time, I had studied many questions and challenges to standard evolutionary theories arising out of molecular biology. But epigenetics was new to me. On our drive, I asked Wells why developmental biology was so important to evolutionary theory and to assessing neo-Darwinism. I’ll never forget his reply. “Because” he said, “that’s where the whole theory is going to unravel.”


BEYOND GENES
 Many biologists no longer believe that DNA directs virtually everything happening within the cell. Developmental biologists, in particular, are now discovering more and more ways that crucial information for building body plans is imparted by the form and structure of embryonic cells, including information from both the unfertilized and fertilized egg.Biologists now refer to these sources of information as “epigenetic.”10 Spemann and Mangold’s experiment is only one of many to suggest that something beyond DNA may be influencing the development of animal body plans. Since the 1980s, developmental and cell biologists such as Brian Goodwin, Wallace Arthur, Stuart Newman, Fred Nijhout, and Harold Franklin have discovered or analyzed many sources of epigenetic information. Even molecular biologists such as Sidney Brenner, who pioneered the idea that genetic programs direct animal development, now insist that the information needed to code for complex biological systems vastly outstrips the information in DNA. DNA helps direct protein synthesis. Parts of the DNA molecule also help to regulate the timing and expression of genetic information and the synthesis of various proteins within cells. Yet once proteins are synthesized, they must be arranged into higher-level systems of proteins and structures. Genes and proteins are made from simple building blocks—nucleotide bases and amino acids, respectively—arranged in specific ways. Similarly, distinctive cell types are made of, among other things, systems of specialized proteins. Organs are made of specialized arrangements of cell types and tissues. And body plans comprise specific arrangements of specialized organs. Yet the properties of individual proteins do not fully determine the organization of these higher-level structures and patterns. Other sources of information must help arrange individual proteins into systems of proteins, systems of proteins into distinctive cell types, cell types into tissues, and different tissues into organs. And different organs and tissues must be arranged to form body plans.
 
The hierarchical layering or arrangement of different sources of information. Note that the information necessary to build the lower-level electronic components does not determine the arrangement of those components on the circuit board or the arrangement of the circuit board and the other parts necessary to make a computer. That requires additional informational inputs. Two analogies may help clarify the point. At a construction site, builders will make use of many materials: lumber, wires, nails, drywall, piping, and windows. Yet building materials do not determine the floor plan of the house or the arrangement of houses in a neighborhood. Similarly, electronic circuits are composed of many components, such as resistors, capacitors, and transistors. But such lower-level components do not determine their own arrangement in an integrated circuit (see Fig. 14.2). In a similar way, DNA does not by itself direct how individual proteins are assembled into these larger systems or structures—cell types, tissues, organs, and body plans—during animal development.

Harold, “From Morphogenes to Morphogenesis,” 2774; Moss, What Genes Can’t Do. Of course, many proteins bind chemically with each other to form complexes and structures within cells. Nevertheless, these “self-organizational” properties do not fully account for higher levels of organization in cells, organs, or body plans. Or, as Moss has explained “Neither DNA nor any other aperiodic crystal constitutes a unique repository of heritable stability in the cell; in addition, the chemistry of the solid state does not constitute either a unique or even an ontologically or causally privileged basis for explaining the existence and continuity of order in the living world . . .” Moss, What Genes Can’t Do, 76.

Instead, the three-dimensional structure or spatial architecture of embryonic cells plays important roles in determining body-plan formation during embryogenesis. Developmental biologists have identified several sources of epigenetic information in these cells.
 
CYTOSKELETAL ARRAYS
Eukaryotic cells have internal skeletons to give them shape and stability. These “cytoskeletons” are made of several different kinds of filaments including those called the “microtubules.” The structure and location of the microtubules in the cytoskeleton influence the patterning and development of embryos. Microtubule “arrays” within embryonic cells help to distribute essential proteins used during development to specific locations in these cells. Once delivered, these proteins perform functions critical to development, but they can only do so if they are delivered to their correct locations with the help of preexisting, precisely structured microtubule or cytoskeletal arrays (see Figures below).

Thus, the precise arrangement of microtubules in the cytoskeleton constitutes a form of critical structural information. These microtubule arrays are made of proteins called tubulin, which are gene products. Nevertheless, like bricks that can be used to assemble many different structures, the tubulin proteins in the cell’s microtubules are identical to one another. Thus, neither the tubulin subunits, nor the genes that produce them, account for the differences in the shape of the microtubule arrays that distinguish different kinds of embryos and developmental pathways. Instead, the structure of the microtubule array itself is, once again, determined by the location and arrangement of its subunits, not the properties of the subunits themselves. Jonathan Wells explains it this way: “What matters in [embryological] development is the shape and location of microtubule arrays, and the shape and location of a microtubule array is not determined by its units.” For this reason, as University of Colorado cell biologist Franklin Harold notes, it is impossible to predict the structure of the cytoskeleton of the cell from the characteristics of the protein constituents that form that structure.

Another cell structure influences the arrangement of the microtubule arrays and thus the precise structures they form and the functions they perform. In an animal cell, that structure is called the centrosome (literally, “central body”), a microscopic organelle that sits next to the nucleus between cell divisions in an undividing cell. Emanating from the centrosome is the microtubule array that gives a cell its three-dimensional shape and provides internal tracks for the directed transport of organelles and essential molecules to and from the nucleus. During cell division the centrosome duplicates itself. The two centrosomes form the poles of the cell-division apparatus, and each daughter cell inherits one of the centrosomes; yet the centrosome contains no DNA. Though centrosomes are made of proteins—gene products—the centrosome structure is not determined by genes alone.
Another important source of epigenetic information resides in the two-dimensional patterns of proteins in cell membranes. When messenger RNAs are transcribed, their protein products must be transported to the proper locations in embryonic cells in order to function properly. Directed transport involves the cytoskeleton, but it also depends on spatially localized targets in the membrane that are in place before transport occurs. Developmental biologists have shown that these membrane patterns play a crucial role in the embryological development of fruit flies.

Membrane Targets
For example, early embryo development in the fruit fly Drosophila melanogaster requires the regulatory molecules Bicoid and Nanos (among others). The former is required for anterior (head) development, and the latter is required for posterior (tail) development. In the early stages of embryological development, nurse cells pump Bicoid and Nanos RNAs into the egg. (Nurse cells provide the cell that will become the egg—known as the oocyte—and the embryo with maternally encoded messenger RNAs and proteins.) Cytoskeletal arrays then transport these RNAs through the oocyte, where they become attached to specified targets on the inner surface of the egg. Once in their proper place—but only then—Bicoid and Nanos play critical roles in organizing the head-to-tail axis of the developing fruit fly. They do this by forming two gradients (or differential concentrations), one with Bicoid protein most concentrated at the anterior end and another with Nanos protein most concentrated at the posterior end. Insofar as both of these molecules are RNAs—that is, gene products—genetic information plays an important role in this process. Even so, the information contained in the bicoid and nanos genes does not by itself ensure the proper function of the RNAs and proteins for which the genes code. Instead, preexisting membrane targets, already positioned on the inside surface of the egg cell, determine where these molecules will attach and how they will function. These membrane targets provide crucial information—spatial coordinates—for embryological development.

Ion Channels and Electromagnetic Fields
Membrane patterns can also provide epigenetic information by the precise arrangement of ion channels—openings in the cell wall through which charged electrical particles pass in both directions. For example, one type of channel uses a pump powered by the energy-rich molecule ATP to transport three sodium ions out of the cell for every two potassium ions that enter the cell. Since both ions have a charge of plus one (Na+, K+), the net difference sets up an electromagnetic field across the cell membrane. 1 Experiments have shown that electromagnetic fields have “morphogenetic” effects—in other words, effects that influence the form of a developing organism. In particular, some experiments have shown that the targeted disturbance of these electric fields disrupts normal development in ways that suggest the fields are controlling morphogenesis.2 Artificially applied electric fields can induce and guide cell migration. There is also evidence that direct current can affect gene expression, meaning internally generated electric fields can provide spatial coordinates that guide embryogenesis.3 Although the ion channels that generate the fields consist of proteins that may be encoded by DNA (just as microtubules consist of subunits encoded by DNA), their pattern in the membrane is not. Thus, in addition to the information in DNA that encodes morphogenetic proteins, the spatial arrangement and distribution of these ion channels influences the development of the animal.

The Sugar Code
Biologists know of an additional source of epigenetic information stored in the arrangement of sugar molecules on the exterior surface of the cell membrane. Sugars can be attached to the lipid molecules that make up the membrane itself (in which case they are called “glycolipids”), or they can be attached to the proteins embedded in the membrane (in which case they are called “glycoproteins”). Since simple sugars can be combined in many more ways than amino acids, which make up proteins, the resulting cell surface patterns can be enormously complex. As biologist Ronald Schnaar explains, “Each [sugar] building block can assume several different positions. It is as if an A could serve as four different letters, depending on whether it was standing upright, turned upside down, or laid on either of its sides. In fact, seven simple sugars can be rearranged to form hundreds of thousands of unique words, most of which have no more than five letters.” These sequence-specific information-rich structures influence the arrangement of different cell types during embryological development. Thus, some cell biologists now refer to the arrangements of sugar molecules as the “sugar code” and compare these sequences to the digitally encoded information stored in DNA. As biochemist Hans-Joachim Gabius notes, sugars provide a system with “high-density coding” that is “essential to allow cells to communicate efficiently and swiftly through complex surface interactions.” According to Gabius, “These [sugar] molecules surpass amino acids and nucleotides by far in information-storing capacity.” So the precisely arranged sugar molecules on the surface of cells clearly represent another source of information independent of that stored in DNA base sequences.


First, we suggest that the geometry of the organism and its parts is coded by a molecular code located on the cell surfaces in such a way that, with each cell, there can be associated a corresponding matrix, containing this code. As a particular model, we propose coding by several types of oligosaccharide residues of glycoconjugates. 1 
1. During embryogenesis, each cell undergoes cell divisions, growth, movements (shifts) and expression of specific molecules according to a determinate plan, invariant for each living species. 
2. This determinate plan for development of an organism can be considered as a tree of cell events from the initial state of the first cell (zygote) to a final predetermined state of an organism, where under cell event we understand “developmental events”, such as cell divisions, cell growth (death), cell differentiation and cell shifts. 
3. This determinate plan is coded by a set of specific biological markers, which, most likely, may exist and be transmitted as a set of cell membrane markers. Our main assumption is that such a code may be provided by a pattern of short oligosaccharide residues of glycoproteins (glycoconjugates) on a cell surface, changing in time and space. It is possible that some other cell surface markers, e.g. specific proteins, may play this coding role; however, short oligosaccharide residues of glycoconjugates have several specific features which make them the most plausible substances for such coding.
4. The general laws for cell events (cell motion laws), namely, the dependence of cell events on coded and positional biological information, have to be the same for all living species, leading to different forms and shapes resulting from different sets of species-specific molecular parameters. Our main goal is to describe these cell motion laws. 
5. Cell motion laws can be mathematically formulated using the notion of a morphogenetic field.  It is important to note that, in the framework of our model, the cascades of specific molecular events that correlate with pattern formation (e.g. differential gene expression, directed protein traffic, etc.) appear not to be the reason for a cell event. Rather, these cascades are, along with the cell event itself, associated with the “coding information” on a cell surface, or, using another terminology, are realized due to an instruction for the cell from the morphogenetic field of an organism. The concrete signal transduction pathways connecting the "coding information" on a cell surface and the expression of the given sets of genes need to be elucidated. 

NEO-DARWINISM AND THE CHALLENGE OF EPIGENETIC INFORMATION
These different sources of epigenetic information in embryonic cells pose an enormous challenge to the sufficiency of the neo-Darwinian mechanism. According to neo-Darwinism, new information, form, and structure arise from natural selection acting on random mutations arising at a very low level within the biological hierarchy—within the genetic text. Yet both body-plan formation during embryological development and major morphological innovation during the history of life depend upon a specificity of arrangement at a much higher level of the organizational hierarchy, a level that DNA alone does not determine. If DNA isn’t wholly responsible for the way an embryo develops— for body-plan morphogenesis—then DNA sequences can mutate indefinitely and still not produce a new body plan, regardless of the amount of time and the number of mutational trials available to the evolutionary process. Genetic mutations are simply the wrong tool for the job at hand. Even in a best-case scenario—one that ignores the immense improbability of generating new genes by mutation and selection—mutations in DNA sequence would merely produce new genetic information. But building a new body plan requires more than just genetic information. It requires both genetic and epigenetic information—information by definition that is not stored in DNA and thus cannot be generated by mutations to the DNA. It follows that the mechanism of natural selection acting on random mutations in DNA cannot by itself generate novel body plans, such as those that first arose in the Cambrian explosion.

GENE-CENTRIC RESPONSES
Many of the biological structures that impart important three-dimensional spatial information—such as cytoskeletal arrays and membrane ion channels—are made of proteins. For this reason, some biologists have insisted that the genetic information in DNA that codes for these proteins does account for the spatial information in these various structures after all. In each case, however, this exclusively “gene-centric” view of the location of biological information—and the origin of biological form—has proven inadequate. First, in at least the case of the sugar molecules on the cell surface, gene products play no direct role. Genetic information produces proteins and RNA molecules, not sugars and carbohydrates. Of course, important glycoproteins and glycolipids (sugar-protein and sugar-fat composite molecules) are modified as the result of biosynthetic pathways involving networks of proteins. Nevertheless, the genetic information that generates the proteins in these pathways only determines the function and structure of the individual proteins; it does not specify the coordinated interaction between the proteins in the pathways that result in the modification of sugars. More important, the location of specific sugar molecules on the exterior surface of embryonic cells plays a critical role in the function that these sugar molecules play in intercellular communication and arrangement. Yet their location is not determined by the genes that code for the proteins to which these sugar molecules might be attached. Instead, research suggests that protein patterns in the cell membrane are transmitted directly from parent membrane to daughter membrane during cell division rather than as a result of gene expression in each new generation of cells. Since the sugar molecules on the exterior of the cell membrane are attached to proteins and lipids, it follows that their position and arrangement probably result from membrane-to-membrane transmission as well. Consider next the membrane targets that play a crucial role in embryological development by attracting morphogenetic molecules to specific places on the inner surface of the cell. These membrane targets consist largely of proteins, most of which are mainly specified by DNA. Even so, many “intrinsically disordered” proteins fold differently depending on the surrounding cellular context. This context thus provides epigenetic information. Further, many membrane targets include more than one protein, and these multiprotein structures do not automatically self-organize to form properly structured targets. Finally, it is not only the molecular structure of these membrane targets, but also their specific location and distribution that determines their function. Yet the location of these targets on the inner surface of the cell is not determined by the gene products out of which they are made any more than, for example, the locations of the bridges across the River Seine in Paris are determined by the properties of the stones out of which they are made.Similarly, the sodium-potassium ion pumps in cell membranes are indeed made of proteins. Nevertheless, it is, again, the location and distribution of those channels and pumps in the cell membrane that establish the contours of the electromagnetic field that, in turn, influence embryological development. The protein constituents of these channels do not determine where the ion channels are located. Like membrane targets and ion channels, microtubules are also made of many protein subunits, themselves undeniably the products of genetic information. In the case of microtubule arrays, defenders of the gene-centric view do not claim that individual tubulin proteins determine the structure of these arrays. Nevertheless, some have suggested that other proteins, or suites of proteins, acting in concert could determine such higher-level form. For example, some biologists have noted that so-called helper proteins—which are gene products—called “microtubule associated proteins” (MAPs) help to assemble the tubulin subunits in the microtubule arrays. Yet MAPs, and indeed many other necessary proteins, are only part of the story. The locations of specified target sites on the interior of the cell membrane also help to determine the shape of the cytoskeleton. And, as noted, the gene products out of which these targets are made do not determine the location of these targets. Similarly, the position and structure of the centrosome—the microtubuleorganizing center—also influences the structure of the cytoskeleton. Although centrosomes are made of proteins, the proteins that form these structures do not entirely determine their location and form. As Mark McNiven, a molecular biologist at the Mayo Clinic, and cell biologist Keith Porter, formerly of the University of Colorado, have shown, centrosome structure and membrane patterns as a whole convey three-dimensional structural information that helps determine the structure of the cytoskeleton and the location of its subunits. Moreover, as several other biologists have shown, the centrioles that compose the centrosomes replicate independently of DNA replication: daughter centrioles receive their form from the overall structure of the mother centriole, not from the individual gene products that constitute them. Additional evidence of this kind comes from ciliates, large single-celled eukaryotic organisms. Biologists have shown that microsurgery on the cell membranes of ciliates can produce heritable changes in membrane patterns without altering the DNA. This suggests that membrane patterns (as opposed to membrane constituents) are impressed directly on daughter cells. In both cases—in membrane patterns and centrosomes—form is transmitted from parent three-dimensional structures to daughter three-dimensional structures directly. It is not entirely contained in DNA sequences or the proteins for which these sequences code. Instead, in each new generation, the form and structure of the cell arises as the result of both gene products and the preexisting three-dimensional structure and organization inherent in cells, cell membranes, and cyto-skeletons. Many cellular structures are built from proteins, but proteins find their way to correct locations in part because of preexisting three-dimensional patterns and organization inherent in cellular structures. Neither structural proteins nor the genes that code for them can alone determine the three-dimensional shape and structure of the entities they build. Gene products provide necessary, but not sufficient, conditions for the development of three-dimensional structure within cells, organs, and body plans. If this is so, then natural selection acting on genetic variation and mutations alone cannot produce the new forms that arise in the history of life.

EPIGENETIC MUTATIONS
When I explain this in public talks, I can count on getting the same question. Someone in the audience will ask whether mutations could alter the structures in which epigenetic information resides. The questioner wonders if changes in epigenetic information could supply the variation and innovation that natural selection needs to generate new form, in much the same way that neo-Darwinists envision genetic mutations doing so. It’s a reasonable thing to ask, but it turns out that mutating epigenetic information doesn’t offer a realistic way of generating new forms of life. First, the structures in which epigenetic information inheres—cytoskeletal arrays and membrane patterns, for example—are much larger than individual nucleotide bases or even stretches of DNA. For this reason, these structures are not vulnerable to alteration by many of the typical sources of mutation that affect genes such as radiation and chemical agent. Second, to the extent that cell structures can be altered, these alterations are overwhelmingly likely to have harmful or catastrophic consequences. The original Spemann and Mangold experiment did, of course, involve forcibly altering an important repository of epigenetic information in a developing embryo. Yet the resulting embryo, though interesting and illustrative of the importance of epigenetic information, did not stand a chance of surviving in the wild, let alone reproducing. Altering the cell structures in which epigenetic information inheres will likely result in embryo death or sterile offspring—for much the same reason that mutating regulatory genes or developmental gene regulatory networks also produces evolutionary dead ends. The epigenetic information provided by various cell structures is critical to body-plan development, and many aspects of embryological development depend upon the precise three-dimensional placement and location of these informationrich cell structures. For example, the specific function of morphogenetic proteins, the regulatory proteins produced by master regulatory (Hox) genes, and developmental gene regulatory networks (dGRNs) all depend upon the location of specific, information-rich, and preexisting cell structures. For this reason, altering these cell structures will in all likelihood damage something else crucial during the developmental trajectory of the organism. Too many different entities involved in development depend for their proper function upon epigenetic information for such changes to have a beneficial or even neutral effect.

DARWIN’S GROWING ANOMALY
With the publication of On the Origin of Species in 1859, Darwin advanced, first and foremost, an explanation for the origin of biological form. At the time, he acknowledged that the pattern of appearance of the Cambrian animals did not conform to his gradualist picture of the history of life. Thus, he regarded the Cambrian explosion as primarily a problem of incompleteness in the fossil record.
 Yet clearly a more fundamental problem now afflicts the whole edifice of modern neo-Darwinian theory. The neo-Darwinian mechanism does not account for either the origin of the genetic or the epigenetic information necessary to produce new forms of life. Consequently, the problems posed to the theory by the Cambrian explosion remain unsolved. But further, the central problem that Darwin set out to answer in 1859, namely the origin of animal form in general, remains unanswered—as Müller and Newman in particular have noted. Contemporary critics of neo-Darwinism acknowledge, of course, that preexisting forms of life can diversify under the twin influences of natural selection and genetic mutation. Known microevolutionary processes can account for small changes in the coloring of peppered moths, the acquisition of antibiotic resistance in different strains of bacteria, and cyclical variations in the size of Galápagos finch beaks. Nevertheless, many biologists now argue that neo-Darwinian theory does not provide an adequate explanation for the origin of new body plans or events such as the Cambrian explosion. For example, evolutionary biologist Keith Stewart Thomson, formerly of Yale University, has expressed doubt that large-scale morphological changes could accumulate by minor changes at the genetic level.38 Geneticist George Miklos, of the Australian National University, has argued that neo-Darwinism fails to provide a mechanism that can produce large-scale innovations in form and structure. Biologists Scott Gilbert, John Opitz, and Rudolf Raff have attempted to develop a new theory of evolution to supplement classical neo-Darwinism, which, they argue, cannot adequately explain large-scale macroevolutionary change. As they note:

Starting in the 1970s, many biologists began questioning its [neo-Darwinism’s] adequacy in explaining evolution. Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian. Microevolution looks at adaptations that concern the survival of the fittest, not the arrival of the fittest. As Goodwin (1995) points out, “the origin of species—Darwin’s problem—remains unsolved.” Gilbert and his colleagues have tried to solve the problem of the origin of form by invoking mutations in genes called Hox genes, which regulate the expression of other genes involved in animal development. Notwithstanding, many leading biologists and paleontologists—Gerry Webster and Brian Goodwin, Günter Theissen, Marc Kirschner, and John Gerhart, Jeffrey Schwartz, Douglas Erwin, Eric Davidson, Eugene Koonin, Simon Conway Morris, Robert Carroll, Gunter Wagner, Heinz-Albert Becker and Wolf-Eckhart Lönnig, Stuart Newman and Gerd Müller, Stuart Kauffman, Peter Stadler, Heinz Saedler, James Valentine, Giuseppe Sermonti, James Shapiro and Michael Lynch, to name several—have raised questions about the adequacy of the standard neo-Darwinian mechanism, and/or the problem of evolutionary novelty in particular. 

The perspective of Eugene Koonin, a biologist at the National Center for Biotechnology Information at the National Institutes of Health, provides just one good example of this skepticism. Koonin, “The Origin at 150,” He argues: 
“The edifice of the modern synthesis has crumbled, apparently, beyond repair . . . The summary of the state of affairs on the 150th anniversary of the Origin is somewhat shocking. In the postgenomic era, all major tenets of the modern synthesis have been, if not outright overturned, replaced by a new and incomparably more complex vision of the key aspects of evolution. So, not to mince words, the modern synthesis is gone. What comes next? The answer suggested by the Darwinian discourse of 2009 is a postmodern state, not so far a postmodern synthesis. Above all, such a state is characterized by the pluralism of processes and patterns in evolution that defies any straightforward generalization.”


Evolution: Where Do Complex Organisms Come From? Kinesi10

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Among the key empirical insights are that phenotypic variation often involves changes in the gene regulatory machinery that alters the timing, location, amount or type of gene product. This modification of pre-existing developmental processes can bring about coordinated changes in suites of characters, effectively enabling diversification through the differential coupling and decoupling of phenotypic modules


1. https://royalsocietypublishing.org/doi/full/10.1098/rspb.2015.1019

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Where Do Complex Organisms Come From?

Pinpointing what REALLY defines body architecture, the orchestration of organism development, cell shape and body form and the mechanisms of adaptation and secondary speciation, and exposing the correct explanation of biochemical mechanisms of biodiversity is the holy grail of biological sciences. Preprogrammed codified information and signalling replaces Darwin's theory and its various subsequent adaptations, extensions, and new proposals like the modern extended synthesis or the so-called " third way ". The true mechanism is " Biochemical systems programming and signalling", and special creation of species and/or kinds by an intelligent powerful creator. Long periods of time and gradual, evolutionary development is not possible, face the fact that cells and organisms work like gigantic interlocked machines and factory complexes, where in any case, if one tiny part is missing, nothing goes. Natural selection would not select for components of a complex system that would be useful only in the completion of that much larger system. No glycine amino acids, no pyrimidines, no DNA - no life. No Watson Crick base pair fine-tuning, no DNA - no life. No ribosomal mechanism for amino acid amide bondage, no proteins, no life. No nitrogenase enzymes to fix nitrogen in an energy demanding, triple bond breaking process, no ammonia, required to make amino acids - no nitrogen cycle - no advanced life. No chlorophylls, no absorption of light to start photosynthesis, no starch and glucose - cells will have no food supply to sustain complex organisms - no advanced life on earth. No rubisco, no fix of CO2, no hydrocarbons - no advanced life. No counterion in retinal, and rhodopsin could not receive visible light - and there would be no vision on earth by any organism.

1. Biological sciences have come to discover in the last decades that major morphological innovation, development and body form are based on at least 16 different, but integrative mechanisms, the interplay of genes with the gene regulatory network, Trans and Retrotransposons, so-called Junk DNA, gene splicing and recombination, and at least two dozen epigenetic informational code systems, some, like the glycan ( sugar) code, far more complex than the genetic code, on the membrane - exterior side of cells, Post-transcriptional modifications (PTMs) of histones, hormones, Ion Channels and Electromagnetic Fields that are not specified by nuclear DNA, Membrane targets and patterns, Cytoskeletal arrays, Centrosomes, and inheritance by cell memory which is not defined through DNA sequences alone.

2. These varied mechanisms orchestrate gene expression, generate Cell types and patterns, perform various tasks essential to cell structure and development, are responsible for important tasks of organismal development, affect gene transcription, switch protein-coding genes on or off,  determine the shape of the body, regulate genes, provide critical structural information and spatial coordinates for embryological development,  influence the form of a developing organism and the arrangement of different cell types during embryological development, organize the axes, and act as chemical messengers for development

3. Neo-Darwinism and the Modern Synthesis have proposed traditionally a gene-centric view, a scientific metabiological proposal going back to Darwin's " On the origin of species ", where first natural selection was proposed as the mechanism of biodiversity, and later,  gene variation defining how bodies are built and organized. Not even recently proposed alternatives, like the third way, neutral theory, inclusive fitness theory, Saltationism, Saltatory ontogeny, mutationism, Genetic drift, or combined theories, do full justice by taking into account all organizational physiological hierarchy and complexity which empirical science has come to discover.

4. Only a holistic view, namely structuralism and systems biology, take into account all influences that form cell form and size, body development and growth, providing adequate descriptions of the scientific evidence. The BIG ( umbrella ) contributor to explain organismal complexity is preprogrammed instructional complex INFORMATION encoded in various languages and communication through signalling through various signalling networks  that act  on a structural level, which are pre-instructed to respond to environmental cues, development, and nutrition demands, and they are apt to communicate, crosstalk, signal, regulate, govern, control, recruit, interpret, recognize, orchestrate, elaborate strategies, guide and so forth. All codes, blueprints, and languages are inventions by intelligence. Therefore, the genetic and epigenetic codes and signalling networks and the instructions to build cells and complex biological organisms were most likely created by an intelligent agency.


Biological cells and organisms are characterized by Irreducible complexity and hierarchical top-down systems interdependence, which is understood as irreducible functional systems complexity. And such is specified by genetic and epigenetic informational codes and signals, used to set up and create front-loaded instructional blueprints, which direct how bodies are built, but also how life can self-correct, adapt to the environment and evolve. It is perfectly comparable to how a blueprint instructs to make machines and factories, and industries. Such things come undoubtedly from preexisting intelligence.

To understand the major trends in animal diversity and if the various kinds of morphology are due to evolution, we must first understand how animal form is generated. As science has unravelled, the make of body form, phenotype, and organismal architecture is due to several genetic and principally, epigenetic interlocked and interconnected mechanisms. The modern, extended evolutionary synthesis does not take into consideration all relevant factors. Structuralism proposes that complex structure emerges holistically from the dynamic interaction of all parts of an organism. It denies that biological complexity can be reduced to natural selection, gene drift and gene flow, and argues that pattern formation is driven principally by multilevel processes that involve various functional units, working in an interdependent manner, pre-programmed to respond to ecological and environmental cues and conditions, food resource availability, and development programs.  Various genetic and epigenetic Codes, an integrated understanding of the structural and functional aspects of epigenetics and several signalling pathways, nuclear architecture during differentiation, chromatin organisation, morphogenetic fields, amongst many other mechanisms.

1. The Gene regulation network orchestrates gene expression
2. Various signalling pathways generate Cell types and patterns
3. At least 23 Epigenetic Codes are multidimensional and perform various tasks essential to cell structure and development
4. Cell-Cell communication in various forms, especially important for animal development
5. Chromatin dance in the nucleus through extensile motors affect transcription and gene regulation
6. Post-transcriptional modifications (PTMs) of histones affect gene transcription
7. The DNA methylation code is like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on.
8. Homeobox and Hox genes determine the shape of the body.
9. Noncoding DNA  ( Junk DNA ) is transcribed into functional non-coding RNA molecules and switches protein-coding genes on or off.
10.  Transposons and Retrotransposons regulate genes
11. Centrosomeplay a central role in development
12. The precise arrangement of Cytoskeletal arrays provides critical structural information.
13. Membrane targets provide crucial information—spatial coordinates—for embryological development.
14. Ion Channels and Electromagnetic Fields influence the form of a developing organism
15. The Sugar Code forms information-rich structures which influence the arrangement of different cell types during embryological development.
16. Egg-polarity genes encode macromolecules deposited in the egg to organize the axes
17. Hormones  are special chemical messengers for development

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If not macroevolution, what explains organismal form and biodiversity?

Evolution: Where Do Complex Organisms Come From? 0011

Bauplan is a German term used in biology which was first introduced by Joseph Henry Woodger in 1945 and means ground plan or structural plan. 

Evolution: Where Do Complex Organisms Come From? 015
Joseph Henry Woodger ( 1894 –  1981) was a British theoretical biologist and philosopher of biology

Woodger's attempts to make biological sciences more rigorous and empirical was significantly influential to the philosophy of biology in the twentieth century. Karl Popper, the prominent philosopher of science, claimed: "Woodger... influenced and stimulated the evolution of the philosophy of science in Britain and in the United States as hardly anybody else".

Before we can ask about the mechanisms and the origin and maintenance of body plans, we need to ask what mechanisms are currently responsible for the development and organismal architecture, form, and cell shape. Once these questions are elucidated, we can go a step further and ask questions about the origins of body plans and their structure. 

1. http://sci-hub.tw/https://link.springer.com/article/10.1007/s12052-012-0424-z

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If 99,999999999% of all biologists, biochemists, chemists, cytologists, evolutionary biologists, geneticists, development biologists say, that evolution by mutations and natural selection, drift and gene flow explains organismal complexity and variety, and that common ancestry is true, and that it is a fact, it still does not mean, it is a fact.

It takes just one scientist to falsify a consense view, and claims made by the majority of scientists.

It took just one scientist, Louis Pasteur, to demonstrate that life can only come from life. Sait 150 years ago, it is still true today.

But today, there is not just one. There are thousands of scientists, as well Nobel prize winners in physiology and medicine, even decades ago, that have actually looked into the science, and have come to the conclusion that the evolutionary claim is simply not true.

So why are there so many diverging opinions ?

I think most biologists do specialize in one discipline or another, and rarely grasp the whole picture. There is a reason, that there are millions of science papers related to evolution, biology, and biochemistry out there.

The Cell city is composed of millions of molecular machines, each demonstrating a unique set of architecture and function. Whole metabolic and signalling pathways, more complex than the internet covering the whole earth. Dozens of epigenetic languages, one, the glycan code by far more complex than the genetic Code. We don't know and do not fully understand what the junk part of DNA does. Science has not even started to unravel the language used in signalling....

It would take the effort of millions of scientists, all work together as a team, with a common goal, to do a project like ENCODE , and still getting just a superficial grasp of the whole picture of the Cell city and on a even far more complex, on organismal level.

The ignorance gives room to various opinions, depending also on bias and preference.

But science has come a long way along. I think, even with the superficial and still small knowledge we have, compared to the complexity unravelled in the molecular world, some important, and paradigm shifting conclusions can be made, with affirmative certainty.

Far more than genetic information is required to make complex organisms and body form.

Where Do Complex Organisms Come From?

https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from

Based on evidence seen in biochemistry on a molecular level, we can now say affirmatively and conclusively, that Darwins theory of evolution by natural selection in regards of first degree macroevolutionary level has been falsified.

The real mechanisms that explain biodiversity and complex organismal architecture is preprogrammed instructional complex INFORMATION encoded in various genetic and epigenetic languages and communication by various signalling codes through various signalling networks

That brings us to the origin by an intelligent designer.

1) phenotypic variation in a population, 2) differential reproductive success as a consequence of that variation, and 3) inheritance of said variation.

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Nobody has probably influenced natural sciences, and in special biology, more than Charles Darwin. His landmark book, On the origin of species, published in 1859, did not only influence how in the coming 160 years biologists did attempt to explain organismal complexity and biodiversity but, in special through the promotion of Darwins bulldog, Thomas Henry Huxley, the scientific framework of philosophical materialism was implemented in scientific circles, by the so-called X Club, late in the 19th century, and has persisted until today. Every scientific explanation had to be explained by natural means, no supernatural causes permitted. Before that, the most prolific fathers of science, from Isaac Newton to Maxwell, Boyle etc.,  and inventers of the greatest scientific discoveries were theists, mostly Christians, and they had no restriction nor any problem to acknowledge God as the creator and power behind the existence and creation of the physical world, and life. While never fully undisputed, Darwin's theory has come more and more under attack, in special amongst religious circles, which ever since have seen Darwin's theory as an attack on the biblical Genesis account, to which the theory stands in harsh opposition and contradicts it.

There is a consensus amongst biologists and professional scientists that the theory of evolution is true. And this is an argument brought forward numerous times when the issue is debated today. Nonetheless, the evidence does not prove the theory to be true beyond any reasonable doubt. In fact, several lines of evidence, and investigations in various fields of science, like palaeontology, biochemistry, biology, development biology, cytology etc. do not confirm the theory. In the current debate, opponents have mainly focussed on disproving the theory by demonstrating why the proposed mechanisms, in special mutations and natural selection, but also genetic drift, do not suffice to explain the extraordinary complexity seen in biology. That is the negative side. What about the positive side? What does actually replace evolution? What are the real mechanisms that explain organismal form and complexity?  Successive adaptations of the theory have done shy attempts to expand it and incorporate new recent findings. Alternative proposals have been made in recent years, like the third way.

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What mechanisms replace Darwins Theory of evolution?

Evolution: Where Do Complex Organisms Come From? 0011



Evolution: Where Do Complex Organisms Come From? 1215
Natural selection, genetic drift, and gene flow are the claimed mechanisms that cause changes in allele frequencies over time, resulting in evolution and diversity of all the living on the planet and organismal complexity. 

Evolution: Where Do Complex Organisms Come From? 12310
Over time, this explanation has come more and more under attack, not only by traditional opposers as creationists but as well by professional scientists.  

Evolution: Where Do Complex Organisms Come From? 115

First, we need to make an important distinction between micro and macroevolution.  Microevolution can be thought of as horizontal change, while macroevolution would involve vertical beneficial change in complexity.

Evolution: Where Do Complex Organisms Come From? 1234511
It is a common assertion, even held today by the majority of biologists, that microevolution leads to macroevolution. The article in Nature magazine, for example, claims in its conclusion remarks:

Evolution: Where Do Complex Organisms Come From? 12345611

Evolution: Where Do Complex Organisms Come From? 123411
Let's clarify: Organisms can and do adapt to their environment, which is often described as microevolution, but would be better described as adaptation. It is life essential and had to be fully set up when life began. Natural selection on a limited scale is a fact, but even in regards of adaptation or microevolution, not the main driving mechanism that explains it.  

Evolution: Where Do Complex Organisms Come From? 12345612
The points in question are that all life forms began with a common ancestor and then diverged in all life forms seen today, by means of evolutionary mechanisms, which include mutation and natural selection, genetic drift and gene flow.


But is that claim true ? And if not true, what mechanisms replaces it?

I will not focus on why evolution by mutations and natural selection does not suffice, but what replaces it.

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In order for a new limb to evolve, lets say arms, not only would have there to be new information of where to locate the new limb in the body to be functional, ( hox genes ) and develop in the right sequence and order, but also, at the same time, each of the seven mentioned items below would have to develop together :

1. Muscular system - essential for movement of the body, maintains posture and circulates blood throughout the body.
2. Skeletal system - is the internal framework of the body.
3. Nervous system - is the part that coordinates its actions by transmitting signals to and from different parts of its body.
4. Endocrine System- hormones are signalling molecules that target distant organs to regulate physiology and behaviour.
5. Circulatory system - is an organ system that permits blood to circulate and transport nutrients (such as amino acids and electrolytes), oxygen, carbon dioxide, hormones, and blood cells to and from the cells in the body.
6. Integumentary system - comprises the skin and its appendages acting to protect the body from various kinds of damage, such as loss of water or damages from outside
7. Lymphatic System It is part of the vascular system and an important part of the immune system, comprising a large network of lymphatic vessels that carry a clear fluid called lymph directionally towards the heart.

by evolution, or design ?

Nos novos dedos, o que evoluiu primeiro ? Muscular system Skeletal system Nervous system Endocrine System Circulatory system Integumentary system Lymphatic System ?



Last edited by Otangelo on Sat Dec 19, 2020 7:42 pm; edited 1 time in total

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Darwin's undisclosed fact has finally been revealed through decades of scientific inquiry and investigation, 150 years after evolution was popularized: The origin of life, biodiversity, and organismal complexity is not best explained by warm little ponds, turning goo into living cells, and biodiversity requires far more than unguided mutations, natural selection, genetic drift, and gene flow. Preprogrammed instructional complex INFORMATION encoded in various genetic and epigenetic codes based on symbols, languages, and communication by various signaling codes through various signaling networks. That brings us to the origin through an intelligent designer.

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Where Do Complex Organisms Come From?

https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from

How does biological multicellular complexity and a spatially organized body plan emerge?
https://reasonandscience.catsboard.com/t2990-how-does-biological-multicellular-complexity-and-a-spatially-organized-body-plan-emerge



What are the REAL mechanisms of biodiversity, replacing macroevolution?
https://www.youtube.com/watch?v=_IGrzrk6iBEre=youtu.be

1. Biological sciences have come to discover in the last decades that major morphological innovation, development and body form are based on at least 16 different, but integrative mechanisms, the interplay of genes with the gene regulatory network, Trans and Retrotransposons, so-called Junk DNA, gene splicing and recombination, and at least two dozen epigenetic informational code systems, some, like the glycan ( sugar) code, far more complex than the genetic code, on the membrane - exterior side of cells, Post-transcriptional modifications (PTMs) of histones, hormones, Ion Channels and Electromagnetic Fields that are not specified by nuclear DNA, Membrane targets and patterns, Cytoskeletal arrays, Centrosomes, and inheritance by cell memory which is not defined through DNA sequences alone.

2. These varied mechanisms orchestrate gene expression, generate Cell types and patterns, perform various tasks essential to cell structure and development, are responsible for important tasks of organismal development, affect gene transcription, switch protein-coding genes on or off,  determine the shape of the body, regulate genes, provide critical structural information and spatial coordinates for embryological development,  influence the form of a developing organism and the arrangement of different cell types during embryological development, organize the axes, and act as chemical messengers for development

3. Neo-Darwinism and the Modern Synthesis have proposed traditionally a gene-centric view, a scientific metabiological proposal going back to Darwin's " On the origin of species ", where first natural selection was proposed as the mechanism of biodiversity, and later,  gene variation defining how bodies are built and organized. Not even recently proposed alternatives, like the third way, neutral theory, inclusive fitness theory, Saltationism, Saltatory ontogeny, mutationism, Genetic drift, or combined theories, do full justice by taking into account all organizational physiological hierarchy and complexity which empirical science has come to discover.

4. Only a holistic view, namely structuralism and systems biology, take into account all influences that form cell form and size, body development and growth, providing adequate descriptions of the scientific evidence.

The BIG ( umbrella ) contributor to explain organismal complexity and biodiversity which falsifies and replaces unguided evolutionary mechanisms is preprogrammed prescribed instructional complex information encoded through various codes and biosemiotics. Besides the universal genetic code, there are ( at least ) 31 variations of genetic codes, and 30 epigenetic codes.  Complex communication networks use signalling  that act on a structural level in an integrated interlocked fashion, which are pre-programmed do direct growth and development, respond to nutrition demands, environmental cues, control reproduction, homeostasis, metabolism, defense systems, and cell death. 

1. Pre-programming and prescription of instructional complex codified information to get an intended purposeful outcome requires foresight.
2. Foresight comes always from an intelligent agent. 
3. Therefore, biodiversity is the result rather of divine intelligent design, than unguided evolution.   

1. The Gene regulation network orchestrates gene expression

EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3135751/

2. Various signalling pathways generate Cell types and patterns

- Hedgehog (Hh) 

Erica Yao, Pao Tien Chuang, Hedgehog signalling: From basic research to clinical applications
https://www.sciencedirect.com/science/article/pii/S0929664615000340  

- Wingless related (Wnt)

Katrin E. Wiese, Roel Nusse, Renée van Amerongen, Wnt signalling: conquering complexity
http://dev.biologists.org/content/145/12/dev165902  

- Transforming growth factor-β (TGF-β)

D A Clark, R Coker Transforming growth factor-beta (TGF-beta)
https://www.ncbi.nlm.nih.gov/pubmed/9611771

- Receptor tyrosine kinase (RTK)

Receptor Tyrosine Kinase (RTK) Signaling Transduction
https://www.sinobiological.com/receptor-tyrosine-kinase-rtk-signaling-transduction.html

- Notch

Emma R. Andersson, Rickard Sandberg, Urban Lendahl Notch signalling: simplicity in design, versatility in function 
http://dev.biologists.org/content/138/17/3593

- Janus kinase (JAK)/signal transducer  

David W. Dodington Harsh R. Desai Minna Woo    JAK/STAT – Emerging Players in Metabolism
https://www.cell.com/trends/endocrinology-metabolism/pdf/S1043-2760(17)30150-9.pdf

- Activators of transcription (STAT) protein kinases

Robert A Ortmann,1 Tammy Cheng,1 Roberta Visconti,1 David M Frucht ,1 and John J O'Shea1    Janus kinases and signal transducers and activators of transcription: their roles in cytokine signaling, development and immunoregulation
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC129988/

- Nuclear hormone pathways

Maria Sirakov, Amina Boussouar, Elsa Kress, Carla Frau, Imtiaz Nisar Lone, Julien Nadjar, Dimitar Angelov, Michelina Plateroti   The thyroid hormone nuclear receptor TRα1 controls the Notch signaling pathway and cell fate in murine intestine
http://dev.biologists.org/content/142/16/2764

- Bone morphogenetic proteins (BMP)

Richard N Wang 1, Jordan Green 1, Zhongliang Wang    Bone Morphogenetic Protein (BMP) signaling in development and human diseases
https://www.ncbi.nlm.nih.gov/pubmed/25401122

- Epidermal growth factor receptors (EGFR)

https://www.sciencedirect.com/topics/medicine-and-dentistry/epidermal-growth-factor-receptor

- Fibroblast growth factors (FGF)

Nobuyuki Itoh, David M. Ornitz    Fibroblast growth factors: from molecular evolution to roles in development, metabolism and disease
https://academic.oup.com/jb/article/149/2/121/837258

- DNA methylation
https://www.ncbi.nlm.nih.gov/pubmed/23877618

- Histone modification and incorporation of histone variants
https://www.researchgate.net/publication/270654681_Histone_Variants_and_Epigenetics

- Chromatin remodelling in Eukaryotic Cells
https://www.news-medical.net/life-sciences/Chromatin-Remodeling-Mechanisms-and-Importance.aspx

- Non-coding RNA-mediated epigenetic regulation

3. Epigenetic Codes perform various tasks essential to cell structure and development

1.  The 31 Genetic Codes 
2.  The Adhesion Code
3.  The Apoptosis Code
4.  The Bioelectric Code
5.  The Biophoton Code
6.  The Calcium Code
7.  The Chaperone Code
8.  The Chromatin Code
9.  The Circular motif ( ribosome) Code
10.  The Coactivator/corepressor/epigenetic Code
11. The Code of human language
12. The Hidden Code within the Genetic Code
13. The DNA methylation Code
14. The Differentiation Code
15. The Domain substrate specificity Code of Nonribosomal peptide synthetases (NRPS)
16. The Error correcting Code
17. The Genomic regulatory Code
18. The Glycomic Code
19. The Histone Code
20. The HOX Code
21. The Lamin Code
22. The Metabolic Code
23. The Myelin Code
24. The Neuronal spike-rate Code
25. The Non-ribosomal Code
26. The Nucleosome Code
27. The Olfactory Code
28. The Operon Code
29. The Phosphorylation Code
30. The Post-translational modification Code for transcription factors
31. The RNA Code
32. The Ribosomal Code
33. The Riboswitch Code
34. The Splicing Codes
35. The Signal Transduction Codes
36. The Signal transduction Code
37. The Signal Integration Codes
38. The Sugar Code
39. The Synaptic Adhesive Code
40. The Transcription factor Code
41. The Transcriptional cis-regulatory Code
42. The Tubulin Code
43. The Ubiquitin Code

4. Cell-Cell communication in various forms, especially important for animal development
Genes involved in Cell-Cell communication and transcriptional control are especially important for animal development
Molecular Biology of the Cell, 5th Ed, 2008: page 1308

5. Chromatin dance in the nucleus through extensile motors affect transcription and gene regulation
Transcription and gene regulation Genome topology has emerged as a key player in all genome functions. 
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5837811/

6. Post-transcriptional modifications (PTMs) of histones affect gene transcription
Post-translational modifications (PTMs) of histones provide a fine-tuned mechanism for regulating chromatin structure and dynamics.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4099259/

7. The DNA methylation code is like a barcode or marker, the methyl group indicates, for instance, which genes in the DNA are to be turned on.
DNA methylation has several uses in the vertebrate cell. A very important role is to work in conjunction with other gene expression control mechanisms to establish a particularly efficient form of gene repression. 
Molecular Biology of the Cell, 5th Ed, 2008: Cell, page 467

8. Homeobox and Hox genes determine the shape of the body
https://www.jstor.org/stable/pdf/24996862.pdf?seq=1#page_scan_tab_contents

9. Noncoding DNA  ( Junk DNA ) is transcribed into functional non-coding RNA molecules and switches protein-coding genes on or off.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4394429/

10. Transposons and Retrotransposons regulate genes
http://dev.biologists.org/content/143/22/4101

11. Centrosomeplay a central role in development
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2734160/

12. The precise arrangement of Cytoskeletal arrays provides critical structural information.
The three major cytoskeletal filaments are responsible for different aspects of the cell’s spatial organization and mechanical properties
Molecular Biology of the Cell By Bruce Alberts 6th. ed. page 889

13. Membrane targets provide crucial information—spatial coordinates—for embryological development.
Preexisting membrane targets, already positioned on the inside surface of the egg cell, determine where these molecules will attach and how they will function. These membrane targets provide crucial information—spatial coordinates—for embryological development.

14. Ion Channels and Electromagnetic Fields influence the form of a developing organism
https://pure.tue.nl/ws/files/10243383/20151217_CO_Vanegas.pdf

15. The Sugar Code forms information-rich structures which influence the arrangement of different cell types during embryological development. 
https://www.ncbi.nlm.nih.gov/pubmed/15174156

16. Egg-polarity genes encode macromolecules deposited in the egg to organize the axes
http://jonlieffmd.com/blog/alternative-rna-splicing-in-evolution

17. Hormones  are special chemical messengers for development
https://en.wikibooks.org/wiki/Human_Physiology/The_endocrine_system



Last edited by Otangelo on Wed Jan 13, 2021 5:24 pm; edited 5 times in total

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How is this genetic code translated into the vast array of cellular behaviors that unfold during the course of embryonic development, as the zygote slowly morphs into a new organism? Many of these cellular processes are driven by secreted or membrane-bound signaling molecules. Elucidating how the genetic code is translated into instructions or signals during embryogenesis, how signals are generated at the correct time and place and at the appropriate level, and finally, how these instructions are interpreted and put into action, are some of the central questions of developmental biology. Our understanding of the causes of congenital malformations and disease has improved substantially with the rapid advances in our knowledge of signaling pathways and their regulation during development.

Cells in the developing embryo are in constant communication with their neighbors, and the molecules they use to send and receive signals are essential for normal embryogenesis. Several intracellular signaling pathways have been identified, some of which are activated in response to secreted growth factors. In cases where the secreted factors form a concentration gradient and cell fate is specified as a function of growth factor concentration, these molecules are referred to as morphogens. Examples include the 

sonic hedgehog (SHH), 
wingless (WNT), 
retinoic acid (RA), 
bone morphogenetic protein (BMP), 
fibroblast growth factor (FGF) 

pathways. In addition to determining cell fate, these pathways also control proliferation and survival. Planar cell polarity (PCP) pathways, on the other hand, are used by cells to interpret their orientation within the plane of a tissue and control cell shape and polarity. The Notch signaling pathway is used by adjacent cells to communicate and control binary cell fate decisions and the formation of precise tissue patterns and boundaries. In this article, I will first provide a detailed overview of a few selected pathways. Then, I will refer to specific examples to show how a single signaling pathway may be used repeatedly for several purposes during embryogenesis, how small differences in signal strength is interpreted by cells, how signaling pathways are regulated and integrated with each other and finally, how morphogenesis and cell fate may be controlled.


1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3367549/

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Morphogenesis of eukaryotic cells, structure, and shape

https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from#7825

The morphogenesis of eukaryotic cells, structure, and shape is due to at least 38 different mechanisms. They are classified into two groups: The molecules that provide complex instructional cues of action based on information through signaling and force-generating molecules that are directed through those signals, which are responsible for cell morphogenesis. On a grand scheme, there are four weblike networks, which form the scaffolds that give form to the cells:  Spectrins, Actins, Microtubules, and the Extracellular Matrix.  These scaffold networks are dynamic, not static, and can change sizes and forms, polymerize, and depolymerize according to the informational cues received.

Following activities are performed by at least 36 different signaling molecules & mechanisms: 8 signal 4 orient 5 activate  2 direct 3 promote 2 regulate 1 guide 3 organize 1 inform 1 coordinate 1 specify 1 modulate 1 providing position cues 2 mediate 1 provoke change.

The molecules, acting upon the instructional signals received,  form patterns, force change, stretch, change and induce cell shape, position, orient,  move, provoke ingress, express,  align, deform, accumulate molecules, invaginate, extend, form a web, concentrate, hold together, support mechanically, stiffen, promote stability, form geometry, polarity, division-plane positioning, phosphorylate, dephosphorylate, force transmission, physical coupling, form gradients, deform, pull forces, promote cell rounding, transduce, specify cell-fate, extend, provide structural links, form aspect ratio, and size, form filament ends, etc.

Information is required to specify the molecules and proteins that are the actors in this grand scheme ( the workers in the factory ). And molecules that provide instructional information ( the engineers ) are required to direct the actors to perform their actions in an orchestrated manner. In cells, there are dozens of different engineers (signaling molecules ), which direct the factory workers ( molecule actors ) in their job. In an engineer's department, the individual engineers must elaborate their instruction plans in harmony as a team and orchestrate the plan of action, and instructions provided to the factory workers.

But while in human enterprises, in all steps, human intelligence is involved in a plan of action to achieve a specific goal, in cells, everything is pre-programmed and occurs without intelligent intervention. Cells are 100% autonomous factories with a director department, which also operates in a fully pre-programmed manner. But cell factories are not static. They work in a dynamic network together with neighbour and even distant cell factories in a joint venture to form tissues, organs, body members, and a bodies made of trillions of cells, all working together in a coordinated fashion. They adapt and react to the environment, food and energy supply, and a large variety of conditions.

In order for an organism to change from one species to another, the change must start at the smallest unit, which is the cell. The signaling molecules, and the language they operate upon, is not only stored in genes but in over 20 different epigenetic signaling codes. Any of those, if not working properly, can cause disease. This is a demonstration that the gene-centric view is false. It is based on a naive understanding of how biological systems work, going back to Darwins time. Today we know better.

The real mechanisms that explain biodiversity and complex organismal architecture is preprogrammed instructional complex INFORMATION encoded in various genetic and epigenetic languages and communication by various signaling codes through various signaling networks.

With that, we have elucidated just ONE of at least 17 different points that have to be specified in the formation of cells in a multicellular organism:

Explaining organismal form depends on explaining how organs, tissues, and cells form and gain shape. On the lowest level of the hierarchy, the formation of cells in a multicellular organism depends on the specification of: 

1. Morphogenesis of various eukaryotic cells, structures, and shapes
2. Cell fate determination and differentiation ( phenotype, or what cell type each one will become )
3. Cell growth and size
4. Development and cell division counting: cells need to be programmed  to stop self-replicating after the right number of cell divisions
5. Mechanisms of pattern formation
6. Hox genes
7. Position and place in the body. This is crucial. Limbs like legs, fins, eyes, etc. must all be placed at the right place.
8. What communication it requires to communicate with other cells, and the setup of the communication channels
9. What specific sensory and stimuli functions are required and do cells have to acquire in regard to its environment and surroundings?
10. What specific new regulatory functions do cells have to acquire
11. When will the development program of the organism express the genes to grow the new cells during development?
12. Change regulation in the composition of the cell membrane and/or secreted products.
13. Specification of the cell-cell adhesion proteins and which ones will be used in each cell to adhere to the neighbor cells ( there are 4 classes )
14. Apoptosis: programming of the time period the cell keeps alive in the body, and when is it time to self-destruct and be replaced by newly produced cells of the same kind
15. Set up each cells specific nutrition demands
16. Cell shape changes
17. Cell proliferation which  is the process that results in an increase of the number of cells, and is defined by the balance between cell divisions and cell loss through cell death or differentiation.

By design, or non-design?
 
More:
https://reasonandscience.catsboard.com/t2990-how-does-biological-multicellular-complexity-and-a-spatially-organized-body-plan-emerge

Actomyosin mediates apical constriction which drives a wide range of morphogenetic processes.
Actin filaments, actin crosslinkers, and myosin motors form an intracellular-contractile network which provokes changes in cell shape.
Actin filaments in animal cells are organized into several types of arrays: dendritic networks, bundles, and weblike (gel-like) networks which permit the formation of different cell structures. The Arp 2/3 complex and formins contribute to these formations.
Arp2/3 complex is an essential organizer of treadmilling actin filament arrays.
Biochemical signaling directs the graded distribution of a morphogen across a tissue, which permits cells to interpret their position to make fate choices. The morphogen concentration, therefore, provides positional coordinates along the embryonic axis.
Centrosomes provide precise cell division positioning rules
Chemical signaling cascades bridge the plasma membrane and the nucleus. Focal adhesion proteins such as zyxin and paxillin shuttle between the cytoplasm and nucleus to modulate transcriptional activity.
Conserved geometrical features provided by cleavage patterns. The geometry of these patterns may specify developmental axes, germ layers, and cell fates. 
Cortical force generators interact with spindle microtubules and are activated by cortical cues
Diverse sets of signaling pathways perform spatial-temporal coordination, regulation and control of actomyosin networks, co-responsible for morphogenesis, and cell shape change to get proper size and shape
Dynein force generators are employed to orient cell division axes at a specific angle. They work at the cell cortex and the cytoplasm. 
Ezrin, radixin, and moesin proteins (ERM) help organize membrane domains through their ability to interact with transmembrane proteins and the underlying cytoskeleton. In so doing, they not only provide structural links to strengthen the cell cortex, but also regulate the activities of signal transduction pathways. 
Extracellular matrix ECM stiffness directs differentiation or self-renewal of embryonic or somatic stem cells, and the ECM viscosity can also influence cell-fate specification. [/size
Filamins function as signaling scaffolds by connecting and coordinating a wide variety of cellular processes with the actin cytoskeleton. 
Ga/LGN/NuMA complex binds to dynein, which then generates microtubule pulling forces toward the cell cortex
Gelsolin proteins break an actin filament into many smaller filaments, thereby generating a large number of new filament ends.
Intracellular modules  such as the cytoskeleton inform and provide global and local cell geometry features, such as aspect ratio, size, or membrane curvature
Key regulator Rac activates the WAVE complex through coincident signals.
Lamellipodia permit the extension of sheetlike membrane projections that help cells to crawl across solid surfaces which is important for migration during early embryonic development.
Lamin A is a nuclear lamina component. In stiff tissue, tension from the ECM transmitted via the cytoskeleton to the nucleus can enhance lamin A transcription and stability of lamin A/C, leading to activation of Yap, serum response factor (SRF) and retinoic acid signaling pathways. 
Mechanosensing and transduction employed by cells sense forces and mechanical cues, and subsequently, control cell differentiation and morphogenesis.  How genetic cascades link cell-fate specification to tissue morphogenesis remains unclear.
Moesin also increases cortical stiffness to promote cell rounding during mitosis.  ERM proteins are thought to bind to and organize the cortical actin cytoskeleton in a variety of contexts, thereby affecting the shape and stiffness of the membrane as well as the localization and activity of signaling molecules.
Morphogen-mediated chemical signaling induces cell shape, cell geometry, deformation,  pulling forces of the extracellular matrix (ECM), and in the end, the architectural form of tissue. 
Physical mechanotransduction relies on direct force transmission from the cell surface to the nucleus through physical coupling between the nuclear membrane and the extracellular space by cytoskeletal components.
Protein gradients that are mostly independent of DNA or any cytoskeletal structure
RhoGEFs of the small GTPase Rho1 activates ROCK,  formin and formin-related proteins, such as Daam proteins, and they direct and regulate Myosin II motor protein phosphorylation and dephosphorylation
Signaling provides spatial information,  guiding cellular geometry, conveys polarity, cell morphogenesis, and division-plane positioning.
Spectrins are proteins that form a web. Spectrin is a long, flexible protein made out of four elongated polypeptide chains.  In the red blood cell, spectrin is concentrated just beneath the plasma membrane, where it forms a two-dimensional weblike network held together by short actin filaments whose precise lengths are tightly regulated by capping proteins at each end. The resulting network creates a strong, yet flexible cell cortex that provides mechanical support for the overlying plasma membrane, allowing the red blood cell to spring back to its original shape after squeezing through a capillary. Close relatives of spectrin are found in the cortex of most other vertebrate cell types, where they also help to shape and stiffen the surface membrane. A particularly striking example of spectrin’s role in promoting mechanical stability is the long, thin axon of neurons
Static and pulsed mechanical deformations of mesodermal cells have been shown to promote Folded gastrulation (Fog) signaling and apical myosin II accumulation, which is required for mesoderm invagination prior to germband extension.
The mitotic spindle directs spatial cues for cytokinesis (  the physical process of cell division ). Septum ingression is pre-specified from the position of the nucleus, and the spindle usually aligns orthogonal to the septum. 
The nucleus acts as a mechanosensor, whereby changes in nuclear shape can evoke transcriptional changes by locally altering the spatial accessibility of chromatin to transcriptional regulators. The physical links between the cytoskeleton and nuclear membrane proteins allow the entire cell to function as a single mechanically coupled system.
The dynamic orientation of nuclei and spindles, which are moved and oriented from the forces exerted by microtubules (MTs) and associated motors such as dynein. 
Tissue-scale mechanical signals can confer positional information and control gene expression and fate at the cellular level, thereby allowing cells to coordinate embryonic patterning.
Twist, a transcription factor, and activation of Rho signaling direct ratcheting which is critical for the generation of tissue‐level tension and changes in tissue shape. That is provided by βH‐spectrin which forms a network of filaments which co‐localize with Medio‐apical actomyosin fibers
Upstream developmental cues,  downstream force generators that orient cell division and cue-dependent spatial control of the force generators generate diversity in division axis orientation

Yap/Taz signaling, where mechanical tension arising from physical stretching of cells or increased stiffness of the extracellular matrix (ECM) activates F-actin remodeling and Yap/Taz nuclear localization.[/size]

Evolution: Where Do Complex Organisms Come From? Cell_f10

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Origin of complex organismal form: by blind evolutionary tinkering, or foreknowledge and divine intelligence?
Multicellular organisms do not use as a source of information only genetic, but mainly, and in special, epigenetic information. There is the information on a top-level, managing, controlling, operating, and orchestrating the interaction of various sources of information that work together in a synergistic multilayered integrated fashion. Cues from the environment, nutrition demands, and development programs ( evo-devo) are the input. This information is synergistically interpreted, computed, and processed, informing the gene regulatory network how to orchestrate gene expression.

Transcription factor molecules receive their signals, and bind to special DNA sequences and the output is controlling gene expression by turning genes on and off. To put it another way, this layer of management decides which proteins actually get made, and when, and in which cells. The next layer of management modifies these newly minted proteins as needed, making any final tweaks necessary for the proteins to start work. Another layer organizes the voyage of the newly synthesized proteins which are tagged so cell signaling proteins know how to transport them to their end destination, using an internal GPS system, taxi carriers, and molecular highways where these taxi proteins walk carrying their load. And a further layer of management provides additional supervision if needed after the proteins are ready to begin work.

Just in one single human cell, there are about 2,3 billion proteins in operation. That illustrates the complexity of the gene regulatory network, orchestrating the expression of the right proteins in each of the over 200 different cell types in the human body. Each cell type has an individually tailored proteome consisting of specific proteins amongst over 90000 different protein types for specific functions. Each cell type requires its own protein machines, and messages are constantly going back and forth between the neighboring and even distant cells to help coordinate it all.

Encoding the information in the genome to make the protein machinery however is just a tiny fraction, about 2% of the genome. The large majority of the genetic information, 98%, which up until recently was called junk, is employed to produce the products that regulate and orchestrate gene expression, like microRNAs, transcription factors, etc. That part is called the regulatory genome.  

This amazingly intricate network involves a huge number of correct interconnections and nodes — along with a lot of looping and branching — just like an algorithm in an enormously complex computer program. Imagine the precise orchestration of turning on and off each of the 20,000 genes in each of the 37 trillion cells in the human body. Each handles the process independently, but the intracellular communication amongst these trillions of cells gives rise to a functional whole.  

That requires unimaginably sophisticated prescribed instructional complex information that directs the whole enterprise and operation.  Who sits at the top, making sure that everything is going according to plan? Someone can claim that evolutionary unguided mechanisms are an adequate explanation. But Davidson writes:

The overall control principle is that the embryonic process is finely divided into precise little “jobs” to be done, and each is assigned to a specific subcircuit or wiring feature in the upper-level dGRN. No subcircuit functions are redundant with another, and that is why there is always an observable consequence if a dGRN subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.

The human body contains no central authority to manage gene expression across all the cells. Instead, it all works as an emergent system.  It is the result of all the individual players and parts that in a joint venture contribute to the final organismal form.  It’s a bit like an ant colony, which functions as a coherent whole, even though no central authority — not even the queen of the colony — micro-manages the tasks performed by the individual ants.

Primary speciation resulting in macroevolutionary change requires altering the entire body plan. And that depends on changing the entire organismal architecture and information on the organismal and systems level. That cannot be done by tinkering here and there. It requires more than that.  There is no way to write the code for all the organismal organization and operation unless one has foreknowledge of the organismal architecture in the end, and one can't know this unless one sees "the big picture" of the final form, it becomes very clear that believing it could "evolve" without deliberate planning, foreknowledge, etc. stretches plausibility, reason, and logic, to say the least.






Epigenetic Mechanisms Contribute to Evolutionary Adaptation of Gene Network Activity under Environmental Selection
https://www.sciencedirect.com/science/article/pii/S221112472031295X

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The Origin of Biological Information and the Higher Taxonomic Categories

Muller and Newman (2003:3-10) distinguish two distinct issues, namely:
(1) the causes of form generation in the individual organism during embryological development and
(2) the causes responsible for the production of novel organismal forms in the first place during the history of life.

We know more about the causes of ontogenesis, due to advances in molecular biology, molecular genetics and developmental biology, than we do about the causes of phylogenesis — the ultimate origination of new biological forms during the remote past.

Muller and Newman insist that population genetics, and thus evolutionary biology, has not identified a specifically causal explanation for the origin of true morphological novelty during the history of life. Central to their concern is what they see as the inadequacy of the variation of genetic traits as a source of new form and structure. In their view, the “genocentricity” and “incrementalism” of the neo-Darwinian mechanism has meant that an adequate source of new form and structure has yet to be identified by theoretical biologists. Instead, Muller and Newman see the need to identify epigenetic sources of morphological innovation during the evolution of life.

Thomson (1992:107) expressed doubt that large-scale morphological changes could accumulate via minor phenotypic changes at the population genetic level. Miklos (1993:29) argued that neo-Darwinism fails to provide a mechanism that can produce large-scale innovations in form and complexity. Gilbert et al. (1996) attempted to develop a new theory of evolutionary mechanisms to supplement classical neo-Darwinism, which, they argued, could not adequately explain macroevolution. As they put it in a memorable summary of the situation: “starting in the 1970s, many biologists began questioning its (neo-Darwinism’s) adequacy in explaining evolution. Genetics might be adequate for explaining microevolution, but microevolutionary changes in gene frequency were not seen as able to turn a reptile into a mammal or to convert a fish into an amphibian.

https://intelligentdesign.org/articles/the-origin-of-biological-information-and-the-higher-taxonomic-categories/

1. Genetische und epigenetische Informationen (mindestens 33 Variationen genetischer Codes und 45 epigenetische Codes) steuern die Entstehung komplexer vielzelliger Organismen, Biodiversität, Form und Architektur
2. Diese Informationen werden durch digitale semiotische Sprache (Syntax, Semantik und Pragmatik) programmiert, um ein funktionierendes ergebnis zu erzielen. Jedes Protein, jeder Stoffwechselweg, jedes Organell oder System, jede biomechanische Struktur und Bewegung basiert auf Prinzipien, die eine bestimmte Funktion erfüllen.
3. Informationen sind nicht physisch, sondern konzeptionell und liegen außerhalb des einflussbereichs eines ungeleiteten physischen Prozesses. Zu behaupten, dass ein physikalischer Prozess semiotische kodifizierung erzeugen kann, ist so, als würde man behaupten, dass ein Regenbogen Gedichte oder einen Blauplan schreiben kann. Wird nie passieren! Das Programmieren von Montageanleitungen und das Erzielen eines spezifischen funktionellen Ergebnisses, wie wir es in der Biologie sehen, ist immer etwas das vorgeschrieben werden muss, das Ergebnis eines Geistes mit Absicht, Zielen und Voraussicht, der in der Lage ist, ein entferntes spezifisches Ziel zu verwirklichen.
4. Daher lässt sich der Ursprung komplexer organismischer Architektur und Biodiversität am besten als Ergebnis eines intelligenten Designers, eines bewussten kreativen intellektuellen Prozesses, und nicht als ungelenkte Evolution erklären.

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The BIG ( umbrella ) contributor to explain organismal, or phenotypic complexity, anatomical architecture,  and biodiversity  is

pre-programmed, prescribed,  specified, complex, instructional assembly information

encoded through 33 genetic codes, and 45 epigenetic languages.
Preinstantiated complex biological communication networks use signaling that act on a structural level in an integrated interlocked fashion, which is pre-programmed do direct growth and development, adaptation, and respond to nutrition demands, environmental cues, control reproduction, homeostasis, metabolism, defense systems, and cell death.

Evolution is an idea, 160 years old, that should have been put to the grave a long time ago.

The effect is the path to the source. What we see in biology, is specified information directing the making of irreducible and interdependent machines, and factories.

That leads us to a powerful creator. A super intellect, architect, engineer, and designer. An agent with mental capacities, brilliance, creativity and sense of beauty.

Michael Levin (2022): Competency of the Developmental Layer Alters Evolutionary Dynamics in an Artificial Embryogeny Model of Morphogenesis

It is currently impossible to guess the anatomy of an organism by examining its genome — overall symmetry type, number and kinds of organs, size, regenerative capacity, etc. can only be estimated if one compares a genome to that of another organism for which all of these things are already known.”

https://arxiv.org/ftp/arxiv/papers/2207/2207.14729.pdf

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Biocomplexity and diversity: Due to evolution, or design? 

The best weapon against inferences based on deceptive thought is first having solid facts. There is the evidence ( what is, what we observe in nature), and we have to make the best out of it, giving the best interpretation of how it came to be. ( The philosophical circle around science). If the evidence or the premise is not clear, it is also more difficult to draw a solid conclusion. When we are talking about the origin of biodiversity and biocomplexity, what has to be understood, first, is: How complex organisms are built, what mechanisms are involved, and what mechanisms are involved in organismal development. Only then, we can ask, if intelligent or non-intelligent causes best explain the origin of these mechanisms. Science has still very incomplete pictures of how complex biological systems are since we are talking about the most complex structures in the universe, and the enormous diversity, of millions, if not trillions of different organisms (bacteria). Despite that, we know already a lot. When science is unraveling new layers of complexity, the more, science dealing with origins has to change its narrative as well and adapt to it. That is well expressed here:

Gerd B. Müller: Why an extended evolutionary synthesis is necessary 18 August 2017
These examples of conceptual change in various domains of evolutionary biology represent only a condensed segment of the advances made since the inception of the MS theory some 80 years ago. Relatively minor attention has been paid to the fact that many of these concepts, which are in full use today, sometimes contradict or expand central tenets of the MS theory. Given proper attention, these conceptual expansions force us to consider what they mean for our present understanding of evolution. Obviously, several of the cornerstones of the traditional evolutionary framework need to be revised and new components incorporated into a common theoretical structure.
Although today's organismal systems biology is mostly rooted in biophysics and biological function, its endeavors are profoundly integrative, aiming at multiscale and multilevel explanations of organismal properties and their evolution.

As an evolutionary biologist, he concludes:
Instead of chance variation in DNA composition, evolving developmental interactions account for the specificities of phenotypic construction.
https://royalsocietypublishing.org/doi/10.1098/rsfs.2017.0015

I disagree with the last sentence. In personal emails with Müller, he demonstrated the same attitude as Bill Martin. He thinks that intelligence should have no foot into the door to explain biocomplexity, a position held a priory, based on a philosophical commitment to naturalism. But his observation is spot on. The explanatory toolbox might deserve to be expanded or changed,  in accordance with new discoveries of biocomplexity. The problem is, that there is no boundary, where the paradigm shifts from non-intelligent ( evolutionary) mechanisms to intelligence, and so, no matter, what new discoveries are done, they are always incorporated into the evolutionary narrative. But a case-adequate conclusion can only be achieved if

1. The philosophical barrier is removed, and it is understood, that when it comes to historical sciences, ALL possible causes/mechanisms should be put on the table, and
2. a clear picture is drawn of what distinguishes artifacts made by intelligence, and not.

Another barrier is that historically, ID proponents have just focussed on pointing out why evolutionary mechanisms are inadequate to explain biocomplexity. While the points made are certainly valid, and even acknowledged by non-ID proponents, like Dennis Noble ( proposing a third way), rarely have ID proponents pointed out why a gene-centric view is inadequate. That is because one has to have a deep understanding on a systems level of how biological systems work.  Not many do have this knowledge. It requires an understanding of a broad field and expertise from various fields, coming from biophysicists and chemists, biologists, bioengineers, bioinformatics, genetic experts, evolutionary biologists, and even paleontologists.

Instructional assembly information encoded in 33 genetic, and at least 49 epigenetic codes and languages, and at least 5 signaling networks operating on a structural level in an integrated interlocked fashion are the mechanisms explaining organismal architecture, development, operation, and adaptation, directing/dictating the make and control of complex molecular physiological integrated structures and their development - the making of irreducible complex molecular machines, robotic molecular production lines, protein-protein interactions, metabolic signaling and transcription-regulatory networks, chemical cell factories, and multicellular organisms and organizations. There is a high degree of internal order that governs the cell’s molecular, and extracellular organization.

Having that information at hand, we can ask:

Do evolutionary, non-intelligent mechanisms explain adequately the observations? In my opinion, the answer is no. All historical, observational, testable, and repeatable examples have demonstrated that instantiating information and operational functionality dictated by prescribed information comes from intelligent sources. Etiology, the science of causes, in regards to the origin of biocomplexity, the hypothesis that natural, unguided random or evolutionary mechanisms, natural selection, genetic drift, and flow, were responsible, have led to dead ends, to the constatation that these causes produce too limited results that do not explain biological form. Only an intelligent agency with intent and foresight can in principle, conceptualize and instantiate hardware and software, that directs the making of integrated operational systems with specific functions that work in an integrated manner.  Finely orchestrated order and fine-tuning, instructions that convey and create purposeful function, are all positive evidence of a mind at work as opposed to blind, randomness operating in stochastic chaos. What we find is a gold nugget of truth...a mind is more than likely behind biological form and variation...therefore it is rational and reasonable to believe in an intelligent designer.

Historical sciences, and methodological naturalism
https://reasonandscience.catsboard.com/t1692-historical-sciences-and-methodological-naturalism

How to recognize the signature of (past) intelligent action
https://reasonandscience.catsboard.com/t2805-how-to-recognize-the-signature-of-past-intelligent-action

Why Darwin's theory of evolution does not explain biodiversity
https://reasonandscience.catsboard.com/t2623-why-darwins-theory-of-evolution-does-not-explain-biodiversity

Where Do Complex Organisms Come From?
https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from

https://reasonandscience.catsboard.com

Otangelo


Admin

Gerd B. Müller: Why an extended evolutionary synthesis is necessary 18 August 2017

https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from#9492

A century ago, it was noted in the domain of physics that ‘concepts that have proven useful in ordering things easily achieve such an authority over us that we forget their earthly origins and accept them as unalterable givens. Thus, they come to be stamped as “necessities of thought”, “a priori givens”, etc. The path of scientific advance is often made impassable for a long time through such errors. Evolutionary biology finds itself in a similar situation today. A well-established paradigm that has its roots in a major theoretical integration that took place approximately eight decades ago, traditionally labelled the modern synthesis (MS) or Synthetic Theory, still dominates evolutionary thought today. In the meantime, the biological sciences have progressed extensively. The material basis of inheritance has been unravelled and entire new fields of research have arisen, such as molecular genetics, evolutionary developmental biology and systems biology. In addition, new evolutionarily relevant factors have been described, including non-genetic inheritance, developmental bias, niche construction, genomic evolution and others. 

Comment: Observe the uncalled use of the word evolution in the last sentence. Science has unraveled new mechanisms in biology that influence inheritance, development, and how genes operate. Müller presupposes that these things are relevant and related to evolution, without providing evidence for this conclusion.  

Clearly, our understanding of evolution has significantly expanded, and it would be surprising if these empirical and conceptual advances had no theoretical consequences, so that in the midst of a substantial growth of knowledge, the central theory uniting the different fields of biology remained unaltered.

In fact, our theoretical understanding of biological evolution has not remained unaltered. Slight modifications and adjustments to the received theory are recognized even in the most traditional quarters. But in the past decade, without much notice by general audiences, a more wide-ranging debate has arisen from different areas of biology as well as from history and philosophy of science, about whether and in which ways evolutionary theory is affected, challenged or changed by the advances in biology and other fields. As usual in such cases, more conservative perspectives and more progressive ones are in conflict with each other, with differences ranging from minor to intense. A rising number of publications argue for a major revision or even a replacement of the standard theory of evolution [2–14], indicating that this cannot be dismissed as a minority view but rather is a widespread feeling among scientists and philosophers alike. In the present essay, I will concentrate on the arguments and debates triggered by one particular alternative to the standard theory that has become known under the term extended evolutionary synthesis (EES). This proposal for an integration of revised and additional components of evolutionary theory into a coherent explanatory framework, as recently elaborated by Laland et al. [15], has caught on as one of the crystallizing points in the ongoing debate. No claim is made that this approach represents the only way of addressing theory revision in biology.

The theory of evolution is the fundamental conceptual framework of biology all scientific explanations of living phenomena must be consistent with. 

Comment: Here, Müller clearly puts the cart in front of the horse. He presupposes that evolution must be true, and the driving force explaining biocomplexity, diversity, and development, rather than first weighting in all new evidence, the new phenomena's provided through scientific advances, and then eventually concluding that evolution explains the origin of the issues/phenomena in question. That is not how science should be done, and philosophical inferences are drawn. Evolution is not a holy cow that should not be sacrificed, no matter what. The proposition has to be tested and refuted if the evidence does lead elsewhere.

As it does not describe a universal law regarding a single natural phenomenon, such as gravity, but rather the principles of organismal change over time, based on the highly complex inputs and interactions of a multiplicity of different factors, evolutionary theory cannot be expected to remain static but is subject to change in the light of new empirical evidence. This is a normal process of scientific advancement and not a heretical undertaking as it is sometimes perceived to be. Explanations of organismal diversity have changed significantly during pre- and post-Darwinian periods, and it should not come as a surprise that fresh stimuli arise from the new methodologies and the expanded scope of modern biological research. Indeed, a growing number of challenges to the classical model of evolution have emerged over the past few years, such as from evolutionary developmental biology [16], epigenetics [17], physiology [18], genomics [19], ecology [20], plasticity research [21], population genetics [22], regulatory evolution [23], network approaches [14], novelty research [24], behavioural biology [12], microbiology [7] and systems biology [25], further supported by arguments from the cultural [26] and social sciences [27], as well as by philosophical treatments [28–31]. None of these contentions are unscientific,

all rest firmly on evolutionary principles and all are backed by substantial empirical evidence.

Comment: What does that mean? What evidence is that?

Sometimes these challenges are met with dogmatic hostility, decrying any criticism of the traditional theoretical edifice as fatuous [32], but more often the defenders of the traditional conception argue that ‘all is well’ with current evolutionary theory, which they see as having ‘co-evolved’ together with the methodological and empirical advances that already receive their due in current evolutionary biology [33]. But the repeatedly emphasized fact that innovative evolutionary mechanisms have been mentioned in certain earlier or more recent writings does not mean that the formal structure of evolutionary theory has been adjusted to them. To the contrary, the discrepancies between the current usage of evolutionary concepts and the predictions derived from the classical model have grown. Hence, it will be useful to characterize some of the differences that exist between the MS theory and proposed alternatives.

A problem agenda
When attempting to define the issues at stake in the current debate, it is necessary to keep in sight what it is that should be explained by a theory of evolution. Evolutionary biology, as practised today, does not represent a single coherent approach but includes sets of different topics and research programmes. For instance, one may be interested in the patterns of phylogenetic relatedness and the processes of species formation. Here, the emphasis is on reconstructing relationships among organisms and unravelling the principles of the separation and diversification of higher taxonomical clades, as pursued by the field of phylogenetics. 

Comment:  Major Evolutionary Analysis Tool Discredited September 2, 2022
The most common analytical method within population genetics is deeply flawed, according to a new study from Lund University in Sweden. This may have led to incorrect results and misconceptions about ethnicity and genetic relationships. The method has been used in hundreds of thousands of studies, affecting results within medical genetics and even commercial ancestry tests. The study is published in Scientific Reports.
https://crev.info/2022/09/major-evolutionary-analysis-tool-discredited/

Refuting phylogenetic relationships
Phylogenetic methods are philosophically grounded, and so can be philosophically biased in ways that limit explanatory power. None of these possible group (the proximity of N. equitans and of the Methanopyrales, of the Archaea and the Cyanobacteria, the possible groupings of Methanobacteriales/Methanoccocales and Thermosplasmatales, of Spirochaetes and the Actinobacteria and of the Proteobacteria and the firmicutes) should be taken as proven by this approach. Instead all of them should be tested further under the advice of biologists working with the organisms, with other markers or characters, and eventually be falsified.
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1574289/

Another approach examines genetic and phenotypic variation in populations in order to derive rules of variational change over time, a perspective most elaborately pursued by population genetics and quantitative genetics. Still another approach is the study of the origin of complex organismal features, such as morphological, physiological or behavioural traits, in order to explain the evolution of the processes that generate these features and how—in turn—these processes influence the course of evolution, as investigated by evolutionary developmental biology (evo-devo), systems biology, or the behavioural sciences.

Comment:  Marta Linde‑Medina On the problem of biological form 5 May 2020
At present, the problem of biological form remains unsolved. Another relevant finding has been the high degree of conservation of developmental genes across taxa. Developmental genes include those encoding transcription factors as well as genes encoding signalling molecules, both of which are involved in gene regulation during embryogenesis. Gene regulation provided an answer to some puzzling results, for example, why species as morphologically diferent as humans and mice nonetheless share 99% of their protein-coding sequences. 
https://sci-hub.ren/10.1007/s12064-020-00317-3

Finally, one may study evolution with a view to the origins of mind, language, society and culture, as well as their feedback on biological evolution, as conducted by the fields of cognitive biology, linguistics, anthropology and certain domains of the social sciences.

Comment: The Hard Problem of Consciousness
Consciousness presents a hard problem for science, or perhaps it marks the limits of what science can explain.
https://iep.utm.edu/hard-con/

John C. Eccles: “Since materialist solutions fail to account for our experienced uniqueness, I am constrained to attribute the uniqueness of the Self or Soul to a supernatural spiritual creation.”(Eccles 1989).

Idealism, dualism, or materialism? The Mind is Not The Brain
https://reasonandscience.catsboard.com/t1662-dualism-the-mind-is-not-the-brain


The vastly different explananda and the progress made in each of these fields must be kept in mind when we examine the tenets of the present theory of evolution. While documenting numerous empirical and theoretical advances, at the level of core assumption most current textbooks on evolution, whether explicitly or implicitly, still offer a theoretical framework that is largely based on the MS of the 1930s and 1940s. Even though it never constituted an encompassing formal synthesis [34], this movement had brought together the basic neo-Darwinian principles of variation, inheritance, differential reproduction and natural selection with Mendelian, experimental and population genetics, as well as with concepts and data addressing the patterns of evolution stemming from the fields of palaeontology, botany and systematics. The formalized core of the MS theory was—and still is—population genetics [35], a mathematical account of gene frequency dynamics in populations of organisms. The empirical basis and key concern of the population genetic approach is the measurement of trait variability in populations, and its intended explananda are adaptive variation, speciation and calculations of fitness. The flurry of fitness landscapes based on ever more nuanced algorithms is indicative of this received approach.

Even though claims have been made that classical evolutionary biology has continuously incorporated aspects from new conceptual domains [33,36], the majority of tenets and explanations that appear in characterizations of the current theory are still derived from the MS account and its population genetic principles [37]. In a condensed form, these tenets are as follows:

(i) all evolutionary explanation requires the study of populations of organisms;
(ii) populations contain genetic variation that arises randomly from mutation and recombination;
iii) populations evolve by changes in gene frequency brought about by natural selection, gene flow and drift;
(iv) genetic variants generate slight phenotypic effects and the resulting phenotypic variation is gradual and continuous;
(v) genetic inheritance alone accounts for the transmission of selectable variation;
(vi) new species arise by a prevention of gene flow between populations that evolve differently;
(vii) the phenotypic differences that distinguish higher taxa result from the incremental accumulation of genetic variation;
(viii) natural selection represents the only directional factor in evolution. For a more extensive description of tenets see Futuyma [37].

Comment:  Patricia J. Wittkopp: Cis-regulatory elements: molecular mechanisms and evolutionary processes underlying divergence 06 December 2011
Cis-regulatory elements (CREs) have essential roles in development, and their divergence is a common cause of evolutionary change. Over 40 years ago, mutations affecting the regulation of gene expression were predicted to be a common source of evolutionary change1–3. Since this time, and most rapidly during the past 5 to 10 years, empirical evidence has accumulated showing this prediction to be true.
https://www.nature.com/articles/nrg3095

Wittkopp assumes a prior, without demonstrating, that evolution can cause necessary changes to transition from one body plan & architecture to another by evolutionary changes of the gene regulatory network. But that is refuted by Davidson. He writes:

No subcircuit functions are redundant with another, and that is why there is always an observable consequence if a dGRN subcircuit is interrupted. Since these consequences are always catastrophically bad, flexibility is minimal, and since the subcircuits are all interconnected, the whole network partakes of the quality that there is only one way for things to work. And indeed the embryos of each species develop in only one way.

This challenges the view, that evolutionary changes could in a gradual manner account for the origin of the gene regulatory network.

Sean B.Carroll: From DNA to Diversity: Molecular Genetics and the Evolution of Animal Design, page 28:
How genes are turned on and off in different cells over the course of animal development is an exquisitely orchestrated regulatory program. Two classes of gene products with the most global effects on development are of special interest: families of proteins called transcription factors that regulate the expression of many other genes during development, and members of signaling pathways that mediate short- and long-range interactions between cells.

Michael Lynch: The evolution of genetic networks  by non-adaptive processes 2007
Although numerous investigators assume that the global features of genetic networks are moulded by natural selection, there has been no formal demonstration of the adaptive origin of any genetic network. The mechanisms by which genetic networks become established evolutionarily are far from clear. Many physicists, engineers and computer scientists, and some cell and developmental biologists, are convinced that biological networks exhibit properties that could only be products of natural selection; however, the matter has rarely been examined in the context of well-established evolutionary principles. Five popular concepts in biology today — redundancy, robustness, modularity, complexity and evolvability — invoke a vision of the cell as an electronic circuit, designed by and for adaptation. Terms like plug-ins, nucleation kernels, input and output switches, capacitance and hard wiring abound. Alon states that it is “…wondrous that the solutions found by evolution have much in common with good engineering.”  The physical mechanisms that give rise to genome architectural features are logically distinct from the adaptive processes that utilize such features as evolutionary resources. Contrary to some suggestions, there is no evidence that genetic pathways emerge de novo in response to a selective challenge. 

Rather, pathway evolution probably proceeds by a gradual augmentation, making use of mutational variation arising independently at different loci, as occurs in nearly all other evolutionary processes. 

Comment: Observe, how Lynch resorts to guesswork and ad-hoc claims to make a claim, rather than substantiated and demonstrated evidence.

Qualitative observations suggest that the complexity of regulatory and protein-interaction networks increases from prokaryotes to unicellular eukaryotes to multicellular eukaryotes, with simple autoregulatory loops being more common and multicomponent loops being less common in microbes, although the existing data are known to be subject to numerous potential biases

Comment: This following sentence reinforces the observation that Lynch has nothing else to rely on his conclusions than guesswork.

The conclusion that convergent evolution of network architectures in distantly related microbes provides compelling evidence for ‘optimal design’ will also be shown to be questionable.

Concluding remarks
Contrary to widespread belief, there is no compelling empirical or theoretical evidence that complexity, modularity, redundancy or other features of genetic pathways are promoted by natural selection. For example, despite the continued fascination with the putative adaptive basis of redundancy, this is not the first time that the difficulties of maintaining redundancy by natural selection have been pointed out. 
 In summary, a mechanistic understanding of network evolution is unlikely to be achieved without specific reference to the ubiquitous non-adaptive forces of evolution that operate at the levels of DNA (mutation and recombination) and populations (random genetic drift). A growing body of evidence supports the idea that many aspects of complexity at the genomic, molecular and cellular levels in multicellular species are likely to owe their origins to these non-adaptive forces, representing little more than passive outcomes of the unique population genetic environments that are presented by such lineages. Genomic features that are consistent with such evolution include the preservation of duplicate genes, the evolution of modular gene architecture, the establishment of introns and untranslated regions, and, now, the evolution of network architecture and redundant regulation. Although demonstrating the feasibility of such neutral evolution is not equivalent to verifying it as the only determinant of genomic architecture, the common view that natural selection alone is responsible for the evolution of organismal complexity seems to be not only unnecessary, but misleading. The failure to recognize this fact breeds a false sense of security in our understanding of evolutionary processes.

Comment: Right in the beginning, at the introduction of the paper, Lynch claims: This Analysis shows that many of the  qualitative features of known transcriptional networks can arise readily through the  non-adaptive processes of genetic drift, mutation and recombination. What he has done, however, is not showing anything, but demonstrating the feasibility of such neutral evolution, which is equivalent to an ad-hoc story, or an unwarranted hypothesis, that is far from being demonstrated.

U. ALON: Biological Networks: The Tinkerer as an Engineer 26 Sep 2003
The cell can be viewed as an overlay of at least three types of networks, which describes protein-protein, protein-DNA, and protein-metabolite interactions. Second, biological systems viewed as networks can readily be compared with engineering systems, which are traditionally described by networks such as flow charts and blueprints. Remarkably, when such a comparison is made, biological networks are seen to share structural principles with engineered networks. Here are three of the most important shared principles, modularity, robustness to component tolerances, and use of recurring circuit elements.

François Jacob pictured evolution as a tinkerer, not an engineer. Engineers and tinkerers arrive at their solutions by very different routes. Rather than planning structures in advance and drawing up blueprints (as an engineer would), evolution as a tinkerer works with odds and ends, assembling interactions until they are good enough to work. It is therefore wondrous that the solutions found by evolution have much in common with good engineering design. 
 http://science.sciencemag.org/content/301/5641/1866.full

Comment: Maybe it's not that wondrous if we consider that the solutions in question might be explained by the conscious actions of a powerful engineer, or an intelligent designer ?!!

The first principle, modularity
is an oft-mentioned property of biological networks. For example, proteins are known to work in slightly overlapping, coregulated groups such as pathways and complexes. Engineered systems also use modules, such as subroutines in software (13) and replaceable parts in machines. The following working definition of a module is proposed based on comparison with engineering: A module in a network is a set of nodes that have strong interactions and a common function. A module has defined input nodes and output nodes that control the interactions with the rest of the network. A module also has internal nodes that do not significantly interact with nodes outside the module. Modules in engineering, and presumably also in biology, have special features that make them easily embedded in almost any system. For example, output nodes should have “low impedance,” so that adding on additional downstream clients should not drain the output to existing clients

The second common feature of engineering and biological networks is robustness to component tolerances.
In both engineering and biology, the design must work under all plausible insults and interferences that come with the inherent properties of the components and the environment. Thus, Escherichia coli needs to be robust with respect to temperature changes over a few tens of degrees, and no circuit in the cell should depend on having precisely 100 copies of protein X and not 103. This point has been made decades ago for developmental systems

The third feature common to engineering and biological networks is the use of recurring circuit elements. 
An electronic device, for example, can include thousands of occurrences of circuit elements such as operational amplifiers and memory registers. Biology displays the same principle, using key wiring patterns again and again throughout a network. Metabolic networks use regulatory circuits such as feedback inhibition in many different pathways

Preprogrammed decision-making of the gene regulatory network 
1. Cells continuously process a multitude of input signals to make decisions about their appropriate responses that lead to changes in gene expression, enzymatic activity, rewiring of their signaling networks, migration, growth, or division, as well as programmed cell death as the output information. In a computing device, the input information is mathematically processed into a digital signal. This signal is a code representation of the physical cues and assumes a sequence of discrete values. For instance, in the case of a binary code, the basic unit of information is denoted as a series of “0” and “1” digits. The binary digits indicate the two states of the logic circuit. A threshold is implemented to define the input and output range that can be categorized under each logic set. If the value is either lower or higher than the threshold, the state of the circuit is defined as either “0” or “1”, respectively. Digital circuits make extensive use of logic elements that are interconnected to create logic gates, capable of executing Boolean logic functions including NOT, OR, AND, and all their possible combinations
2. Molecular and biomolecular logic gates and their networks process chemical input signals similar to human-made computers. The similarities in the processing of information by biological systems and human-designed devices are broadly recognized by many researchers.
3. Decision-making is either a) something performed directly by intelligence, or b) programmed by intelligence to be performed by machines, like computers. It has never been observed, that unguided, evolutionary mechanisms could produce a decision-making machine with the purpose to generate specific outcomes further ahead. Foresight is a quality exclusively performed by intelligence.  If the analogy of two phenomena be very close and striking, while, at the same time, the cause of one is very obvious, it becomes scarcely possible to refuse to admit the action of an analogous cause in the other, though not so obvious in itself. A metaphor (“A biological cell is like a production system”) demonstrates that similar behaviors are driven by similar causal mechanisms.
4. Therefore, the decision-making process observed in the cell is most probably the result of divine superintelligent design.

Gerd B. Müller: As can be noted from the listed principles, current evolutionary theory is predominantly oriented towards a genetic explanation of variation, and, except for some minor semantic modifications, this has not changed over the past seven or eight decades. Whatever lip service is paid to taking into account other factors than those traditionally accepted, we find that the theory, as presented in extant writings, concentrates on a limited set of evolutionary explananda, excluding the majority of those mentioned among the explanatory goals above. The theory performs well with regard to the issues it concentrates on, providing testable and abundantly confirmed predictions on the dynamics of genetic variation in evolving populations, on the gradual variation and adaptation of phenotypic traits, and on certain genetic features of speciation. If the explanation would stop here, no controversy would exist. But it has become habitual in evolutionary biology to take population genetics as the privileged type of explanation of all evolutionary phenomena, thereby negating the fact that, on the one hand, not all of its predictions can be confirmed under all circumstances, and, on the other hand, a wealth of evolutionary phenomena remains excluded. For instance, the theory largely avoids the question of how the complex organizations of organismal structure, physiology, development or behaviour—whose variation it describes—actually arise in evolution, and it also provides no adequate means for including factors that are not part of the population genetic framework, such as developmental, systems theoretical, ecological or cultural influences.

Criticisms of the shortcomings of the MS framework have a long history. One of them concerns the profoundly gradualist conception the MS has inherited from the Darwinian account of evolution. Darwin saw slight, incremental and accumulating variation as the essential prerequisite without which ‘my theory would absolutely break down.’  a position already characterized by Huxley in 1901  as an ‘unnecessary difficulty.’ Subsequently, the perceived necessity of a slow and continuous flux of variation seemed to have been supported by innumerable studies that demonstrate corresponding behaviours of character variation in natural populations or under artificial selection regimes. The notion of slight successive variation was further reinforced by the molecular conception of genetic variation. When mutation of individual genes or even smaller entities of DNA is taken as the predominant source of variation, it seemed inevitable that phenotypic modifications should be small, because larger changes were deemed to be disruptive and unlikely to produce adaptive outcomes. The supposed randomness of genetic variation further contributed to this view. Today, all of these cherished opinions have to be revised, not least in the light of genomics, which evokes a distinctly non-gradualist picture.

Natural selection, the cornerstone of the MS theory so intimately linked to both gradualism and adaptationism, has itself been the subject of a fair share of critical debate. In this case, it is not so much the principle itself that is contested, but the uniqueness of the causal agency that has been ascribed to it. Are all features of biological organisms necessarily the result of natural selection, and is it the only factor in the evolutionary process that provides directionality to organismal change? Numerous authors have challenged the pervasiveness of natural selection as a unique ‘force’ of evolution, whereas others have questioned whether the individual is the sole and appropriate ‘target’ of selection or whether other levels of selection at supra- and infra-individual levels also need to be included in selectionist scenarios. Again we are confronted with a classical criticism that stood at the centre of multiple debates in the past, but the issue is as unresolved as ever.

Finally, it is apparent that nearly all of the relevant predictions that derive from the MS theory are based on genetic principles and gene determinist convictions. Although the long-held belief that genes are the unique determinants of biological form in development and evolution has been challenged by an extensive number of commentators, the genetic program idea underlying MS theory has remained unaltered. This is also true with regard to the mechanisms of transgenerational inheritance. The proposition of uniquely genetic inheritance has been falsified multiple times, but the gene-centric position remains constitutive of the MS. The contemporary version of this position, gene regulatory network evolution, really represents only an extension of the ‘gene-determines-phenotype’ view.

Comment: Not only genes, and the gene regulatory network are in play to orchestrate the making of complex organismal architecture and form, and its development and adaptation to the environment, but 17 mechanisms, that operate in an integrated fashion together. In order to warrant that one species can evolve into another, and one body plan into a different, eventually more complex one (macroevolution),  the origin of all at least 17 mechanisms have to be taken into consideration, and their origins explained.

The limitations of the MS theory are not only highlighted by the criticisms directed against several of its traditional tenets but also by the failure to address some of the most important phenomena of organismal evolution. The question, for instance, of how complex phenotypic organizations arise in evolution is sidestepped by the population theoretical account, as is the reciprocal influence of these features of higher levels of organization on the evolutionary process. Indeed, the MS theory lacks a theory of organization that can account for the characteristic features of phenotypic evolution, such as novelty, modularity, homology, homoplasy or the origin of lineage-defining body plans. As will be shown below, evo-devo, niche construction, systems biology and other areas harbour the capacity to address at least certain aspects of these topics where the classical theory fails.

All the extensive discussions, led over decades, seem not to have altered the preponderant stance to hold on to the classical prerequisites of gradualism, adaptationism, selectionism and gene-centrism. 

Evolutionary developmental biology
A suite of new concepts emerges from evo-devo, a field of research that arose in the early 1980s from a discontent with the exclusion of developmental biology from evolutionary theory. The subsequent rise of new molecular methodologies for a comparative analysis of gene regulation resulted in a huge increase of our understanding of how the processes of development evolve. In its theoretical domain, the evo-devo approach starts from the premise that the genotype–phenotype relation is not merely a statistical correlation, but that the rules of developmental processes govern phenotypic outcomes while relying on additional inputs not coming from the genome. It is abundantly clear that development is not a linear reading out of a code or program but a systemic process of feedback interactions between genetic and non-genetic templates, cells and tissues that mobilizes physical and autonomous properties at different scales and depends on local as well as global environments. Hence, development is a systems relation in which no component is informationally privileged. A number of evolutionary concepts result from the evo-devo study of these relations, three of which shall be mentioned here.

Comment: This substantiates and backs up the view that in order to explain biocomplexity, the gene-centric view has to be abandoned, and replaced with the attempt to explain the origin of systems interactions, genetics + epigenetic information, and signaling networks, that operate in an integrated fashion together. 

Regulation is essential in biology
1. Regulation is ubiquitous in biology, and a fundamental property of living systems. Keeping a stable internal cellular environment requires constant adjustments as conditions change inside and outside the cell. The adjusting of systems within a cell is called homeostatic regulation. Because the internal and external environments of a cell are constantly changing, adjustments must be made continuously to stay at or near the set point (the normal level or range). Regulation of biological processes occurs when any process is modulated in its frequency, rate or extent. Biological processes are regulated by many means; examples include the control of gene expression, protein modification or interaction with a protein or substrate molecule. While Gene expression in prokaryotes is regulated primarily at the transcriptional level, in eukaryotic cells, it is regulated at many levels (epigenetic, transcriptional, post-transcriptional, translational, and post-translational). Metabolism or intracellular signaling also requires regulation. Gene regulation is a dynamical process composed of a number of steps, for example the binding of Transcription Factors to DNA, recruitment of transcription machinery and the production of the messenger RNA, post-transcriptional regulation, splicing and transport of mRNA, translation, maturation and possible localization of proteins. 
2. Regulation requires a distinctive architecture of functional relationships, and specifically the action of a dedicated subsystem whose activity is dynamically decoupled from that of the constitutive regime. Regulate means control or maintain the rate or speed of (a machine or process) so that it operates properly. Regulation is the management of complex systems according to a set of rules and trends. It is a rule or directive made and maintained by an authority. Regulating is always either a) a preprogrammed action by an intelligent agency, or b) an action where an intelligent agent is directly actively involved. 
3. Setting rules, giving directives for specific purposes or functions is always the result of a mental action. It is logical to conclude that biological regulation requires intelligent set up.

The research approach of evo-devo permits addressing the processes responsible for the evolution of phenotypic organization, a topic thoroughly avoided by the synthesis theory. The issue cannot be reduced to the evolution of gene regulation, because, on the one hand, highly conserved developmental control genes, e.g. homeotic genes, can exhibit non-homologous expression domains in embryos of closely related phylogenetic lineages, and on the other hand, homologous structures can be specified by non-homologous genes, a characteristic of the genotype–phenotype relation described by developmental systems drift. Evo-devo-based concepts of structural organization emphasize the integrative stability provided by shared developmental pathways and the modularity of developmental processes. Morphological templates that result from the mobilization of physical forces are seen to represent basic organizing themes in animals  and plants  that become integrated through a hierarchization of regulatory networks and fixated as patterns of phenotypic construction. Increasingly elaborate gene regulatory systems serve to reproduce morphological templates, and the close mapping between genotype and morphological phenotype may not represent the cause but a consequence of evolution. Hence, evo-devo mechanisms of phenotypic organization could not only be responsible for higher-level complexity but could also affect further organismal evolution, a claim that is supported by experiment and modelling.

Within an embryo, several processes play out at the cellular and tissue level to create an organism. These processes include cell proliferation, differentiation, and cellular movement
1. Cell fate determination depends on various kinds of codified information, communication and feedback systems, signaling, and bar-code marking.  These information systems prescribe, drive, direct, operate, control, and induce reacting to stimuli, provide patterning cues, regulation, determine and permit the making of decisions based on memory, control transcription, remodel chromatin structure and state, control cell-cell interactions, differential gene expression, regulate which genes are transcribed in a cell ( which genes are turned on and off ), influence the arrangement of different cell types during embryological development, give cues to cleavage patterns, create asymmetry from homogeneity, induce concentration gradients, cell positioning, and many more. 
2. These are not simply chemical reactions, but actions directed by prescribed, instructional complex information input.  This orchestration depends on a network of logic interactions programmed into the DNA sequence, epigenetic information, and signaling networks that amount essentially to a hardwired biological computational device. Animal forms depend on tightly integrated networks of genes, proteins, and other molecules to regulate their development.
3. Neither proponents of "evo-devo," nor proponents of other proposed materialistic theories of evolution, have identified a mutational mechanism capable of generating anything even remotely resembling a complex integrated circuit. In our experience, the functional integration of parts in complex systems generally—are known to be produced by intelligent agents—specifically, by engineers. Intelligence is the only known cause of such effects. Developing animals employ a form of integrated circuitry, and certainly one manifesting a tightly and functionally integrated system of parts and subsystems, and intelligence is the only known cause of these features. Once established, the complexity of integrated circuits and signaling networks makes them stubbornly resistant to mutational change. Disarming any one of these hierarchically structured systems produces some abnormality in expression.


One of the necessary mechanisms of multicellular complexity: the Gene regulatory network: By evolution, or design?
https://reasonandscience.catsboard.com/t2884-the-real-mechanisms-of-organismal-complexity-the-gene-regulatory-network

Gene Regulatory Networks Controlling Body Plan Development
https://reasonandscience.catsboard.com/t2318-gene-regulatory-networks-controlling-body-plan-development

Control of Gene Expression and gene regulatory networks point to intelligent design
https://reasonandscience.catsboard.com/t2194-control-of-gene-expression-and-gene-regulatory-networks-point-to-intelligent-design

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Otangelo


Admin

What is the best way to challenge/refute evolutionary claims?

Over the years, I have participated in many ID/evolution debates, in written form, or video, in special on Facebook. One of the common tactics adopted by ID proponents is to poke holes in evolutionary storytelling, presenting evidence that falsifies the theory. 
Certainly a successful approach. The evidence is plenty.  Another entirely different way of refutation is to demonstrate what replaces evolution. And doing that is a much harder task. The first time I did find answers to that question was in Steve Meyers: Darwin's doubt. I took that as a starting point to dig deeper in an attempt to find more answers. And I did. There are many different mechanisms involved in constructing complex organismal forms and body architecture. One reason it is rarely brought up as an argument is, that it is an exceedingly difficult question to answer, involves unraveling and describing a very complex biological state of affairs and requires knowledge of systems biology, and various other fields in biology, in special development and evolutionary biology. Hard to find those that have knowledge in that broader sense. In special, when most scientists specialize often to investigate one specific issue with open questions, some invest a lifetime in just one single protein, like topoisomerase, or the ribosome. 
 As I understand it, before one can ask about how things came to be, one needs to understand how biological systems work and develop. Only then do we have a tool to ask the question of the origins. What adds difficulty, is that there is not one way, but many different ways of how organisms develop from an embryo/zygote to an adult. Studying and understanding just the development of one organism takes a lot. 

Evolutionary biologists are confessing today their ignorance of the question of the origins. For example:

M. Linde‑Medina On the problem of biological form 5 May 2020
At present, the problem of biological form remains unsolved. Another relevant finding has been the high degree of conservation of developmental genes across taxa. Developmental genes include those encoding transcription factors as well as genes encoding signaling molecules, both of which are involved in gene regulation during embryogenesis. Gene regulation provided an answer to some puzzling results, for example, why species as morphologically different as humans and mice nonetheless share 99% of their protein-coding sequences. 
https://sci-hub.ren/10.1007/s12064-020-00317-3

A remarkable admission, when many with high confidence claim to know, arguing that biologists regard evolution as a settled fact. But isn't that in reality just the successful result of indoctrination of 160 years of evolution, and that supposedly nothing makes sense in biology except in the light of evolution? Today, more and more scientists in the field are starting to recognize that the construction of body form & architecture depends on mechanisms that science is far from having fully explored and unraveled. I have listed almost 50 epigenetic codes and languages ( Even Marcelo Barbieri, a specialist in biosemiotics, didn't know that there are that many), and in most of them, it is a mystery for science where and how the information is stored. Answering how things came to be, depends on knowing how things are made, develop, operate, controlled, adapt,  and work. Some are recognizing this and trying to incorporate these recently unraveled mechanisms into an expanded evolutionary framework. 

Gerd B. Müller: Why an extended evolutionary synthesis is necessary 18 August 2017
These examples of conceptual change in various domains of evolutionary biology represent only a condensed segment of the advances made since the inception of the MS theory some 80 years ago. Relatively minor attention has been paid to the fact that many of these concepts, which are in full use today, sometimes contradict or expand central tenets of the MS theory. Given proper attention, these conceptual expansions force us to consider what they mean for our present understanding of evolution. Obviously, several of the cornerstones of the traditional evolutionary framework need to be revised and new components incorporated into a common theoretical structure.
Although today's organismal systems biology is mostly rooted in biophysics and biological function, its endeavors are profoundly integrative, aiming at multiscale and multilevel explanations of organismal properties and their evolution. Instead of chance variation in DNA composition, evolving developmental interactions account for the specificities of phenotypic construction.
https://royalsocietypublishing.org/doi/10.1098/rsfs.2017.0015

One can always bend, stretch, evolve, change the theory of evolution, incorporate new mechanisms, and claim that evolution did it. The challenge is: Where and when is the threshold reached, where is it justified to draw a line, and where it is unreasonable to resort to natural selection, drift, and shift, and replace evolution with intelligent design? I think the two already-known and well-established ID tenets do that just fine and demonstrate why it is a superior hypothesis. The fact is that the instantiation of languages, codes, and information requires a mind, and so does the making of irreducibly complex integrated machines and factories based on information transmission systems that are the link between the cell's hardware and software, and the cellular machinery that is made, operated and controlled upon it.  The more the number of different software/hardware on genetic and epigenetic levels is unraveled, that operates on an intra and extracellular (systems) level, there it is evidence that unguided, non-intelligent natural mechanisms are inadequate, and do not suffice to explain the phenomena in question, and ID becomes a better, more case-adequate explanation. We are already deep in this territory. 

Making a wider audience aware of this takes time. Maybe generations. But that is the fight. Someone once said that this fight started in the early nineties, we are in the mid of the fight, and it will take another twenty years or so to get the message out, and have it acknowledged by a wider number of people.   


Why Darwins theory of evolution does not explain biodiversity
https://reasonandscience.catsboard.com/t2623-why-darwins-theory-of-evolution-does-not-explain-biodiversity

The various codes in the cell
https://reasonandscience.catsboard.com/t2213-the-various-codes-in-the-cell

Where Do Complex Organisms Come From?
https://reasonandscience.catsboard.com/t2316-evolution-where-do-complex-organisms-come-from

How do biological multicellular complexity and a spatially organized body plan emerge?
https://reasonandscience.catsboard.com/t2990-how-does-biological-multicellular-complexity-and-a-spatially-organized-body-plan-emerge

Falsification of evolution is impossible
https://reasonandscience.catsboard.com/t1713-the-theory-of-evolution-cannot-be-falsified

https://reasonandscience.catsboard.com

Otangelo


Admin

Dr. Marc W. Kirschner (2005): This book is about the origins of novelty in evolution. The brain, the eye, and the hand are all anatomical forms that exquisitely serve function. They seem to reveal design. How could they have arisen? The vast diversity of organisms, from bacteria to fungi to plants and animals, all are of different design. How did they originate? Nothing in the inanimate world resembles them. All are novel. And yet novelty implies the creation of something from nothing—it has always defied explanation. How can small, random genetic changes be converted into complex useful innovations?

Mutation only changes what already exists. It does not create new anatomy, physiology, and behavior from nothing, so we need to know how readily one structure can be transmuted into another, particularly when we consider structures of intricate design and interdependent activities. With an understanding of how random genetic change is converted into useful innovation, a theory of novelty can be devised.

1. Dr. Marc W. Kirschner: The Plausibility of Life: Resolving Darwin's Dilemma 2005

Evolution: Where Do Complex Organisms Come From? 11111116

https://reasonandscience.catsboard.com

Otangelo


Admin

Alberch (1991) introduced the genotype-phenotype “mapping function” G => P which is much more complex than a one-to-one relation between genotype and phenotype: the same phenotype may be obtained from different combinations of genetic informational resources because of environmental plasticity, leading to Mosaic Pleiotropy, developmental bias, and developmental plasticity.

The term “epigenetics” is contested and used in a variety of ways. Bird (2007) suggests the following unifying definition of epigenetic events: the structural adaptation of chromosomal regions so as to register, signal or perpetuate altered activity states. These are features not directly governed by the genetic code but by the cellular context, and include DNA methylation, covalent modification of histone proteins (Jaenisch and Bird 2003), and RNA mediated DNA regulation (Mattick 2001, 2012). They are enabled by Gene Regulatory Networks (Carroll 2008) which themselves are the product of developmental processes based on the genes coding for their proteins. These are key actors in what occurs (Carroll 2005, 2008, Mattick 2012, Noble 2008a, Noble et al 2014), and are also selected in order to give the desired developmental results, leading to genetic inheritance processes. These multi-level evolutionary processes additionally select for metabolic networks, cell signalling networks, and proteins that enable the whole system to function (Wagner 2011, 2017).

Epigenetic Inheritance Processes:
Organisms transmit more than genes across generations, namely as well as the genome, the next generation inherits all the basic cellular machinery that underlies cell function and sets the context for reading the genetic code (Alberts et al 2007, Hofmeyr 2017). Noble (2008a) states this as follows: “There are two components to molecular inheritance: the genome DNA, which can be viewed as digital information, and the cellular machinery, which can, perhaps by contrast, be viewed as analogue information. … The egg cell machinery is just as molecular as the DNA. .. Both are used to enable the organism to capture and build the new molecules that enable it to develop, but the process involves a coding step in the case of DNA and proteins, while no such step is involved in the rest of the molecular inheritance. This is the essential difference.” 

Biological processes are complex phenomena that involve a multitude of steps and interactions between various molecular components. To truly understand these processes, we must provide a complete explanation that elucidates every relevant step involved in the process.

At the molecular level, biological processes are governed by a wide range of complex interactions that involve various proteins, enzymes, and other biomolecules. Understanding these interactions and how they work together to produce a specific outcome is crucial to gaining a complete understanding of biological processes.

Take the example of vision. While it was once thought that the anatomical structures of the eye were sufficient to explain how we see, we now know that a complete understanding of vision requires a molecular explanation. Specifically, we need to understand the interactions between 11-cis-retinal, rhodopsin, transducin, and phosphodiesterase that are involved in the process of vision.

Similarly, other biological processes such as digestion and immunity also involve complex molecular interactions that must be elucidated in order to gain a complete understanding of how they work. Merely looking at anatomical structures or invoking evolutionary theory is no longer sufficient to provide a complete explanation of these phenomena.

In fact, the fossil record, biogeography, and population genetics are also insufficient to explain the specific molecular interactions involved in these processes. While these areas of study can provide some insight into the evolution and distribution of species, they cannot provide a complete understanding of the molecular mechanisms involved in specific biological processes.

A satisfactory explanation of biological phenomena must include a molecular explanation that elucidates every relevant step involved in the process. Understanding these molecular interactions is crucial to gaining a complete understanding of biological processes and will lead to new discoveries and advancements in the field.

https://arxiv.org/ftp/arxiv/papers/1803/1803.10789.pdf

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution
https://www.cell.com/cell/fulltext/S0092-8674(08)00817-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS0092867408008179%3Fshowall%3Dtrue



Last edited by Otangelo on Mon Aug 28, 2023 11:24 am; edited 2 times in total

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