ElShamah - Reason & Science: Defending ID and the Christian Worldview
Would you like to react to this message? Create an account in a few clicks or log in to continue.
ElShamah - Reason & Science: Defending ID and the Christian Worldview

Otangelo Grasso: This is my library, where I collect information and present arguments developed by myself that lead, in my view, to the Christian faith, creationism, and Intelligent Design as the best explanation for the origin of the physical world.

You are not connected. Please login or register

Evolution: Where Do Complex Organisms Come From?

Go to page : Previous  1, 2, 3, 4

Go down  Message [Page 4 of 4]



Examining 47 crucial processes that influence the development, structure, and function of organisms reveals some astonishing interconnections

The sheer complexity and intricate interdependence observed in biological systems provide a strong foundation for arguments in favor of Intelligent Design (ID). 

1. Harmony in Complexity

The vast array of processes, ranging from the microscopic level (like DNA methylation) to the macroscopic (like organogenesis), are so tightly interwoven that a disturbance in one can drastically impact another. This finely-tuned orchestration suggests a system that has been designed with precision and purpose, rather than one that arose from a series of unplanned, random events.

The Orchestration of Neurogenesis: A Study in Irreducibility and Interdependence

One of the most interconnected and illustrative examples in biology where 16 of 47 crucial processes that influence the development, structure, and function of organisms come into play is the development of the vertebrate nervous system, specifically the development and differentiation of neural stem cells (neurogenesis) in the neural tube. Let's explore how these processes are intertwined:

1. Cell Fate Determination and Lineage Specification (Cell differentiation): Neural stem cells have the potential to differentiate into neurons, astrocytes, or oligodendrocytes depending on the signals they receive.
2. Chromatin Dynamics and Epigenetic Codes: These mechanisms help decide whether a stem cell will become a neuron or another type of glial cell. They regulate accessibility to genes that push a cell toward a particular fate.
3. Gene Regulation Network: Networks of transcription factors decide cell fate in the neural tube, turning genes on or off in response to external cues.
4. Morphogen Gradients: Chemicals like Sonic Hedgehog (Shh) and Bone Morphogenetic Proteins (BMPs) create gradients across the neural tube, instructing cells about their position and consequently their fate.
5. Cell-Cell Communication: Cells in the developing neural tube communicate to ensure that the correct number of each cell type is produced.
6. Cell Migration and Chemotaxis: Newly formed neurons migrate to their proper positions in the neural tube, guided by various chemical cues.
7. Cell-Cycle Regulation: Neural stem cells undergo specific cell cycle dynamics that influence whether they proliferate or differentiate.
8. Apoptosis: In development, it’s normal for some neurons to die off. This pruning ensures that only neurons making proper connections survive.
9. Neuronal Pruning and Synaptogenesis: After migration, neurons make multiple connections, which are then refined through pruning and strengthened through synapse formation.
10. Signaling Pathways: Multiple signaling pathways, including Notch and Wnt, are involved in deciding neural stem cell fate and guiding neural development.
11. Noncoding RNA from Junk DNA and MicroRNA Regulation: These are involved in regulating various aspects of neurogenesis, from stem cell maintenance to neuronal differentiation.
12. Cell Polarity and Asymmetry: Helps decide how neural stem cells divide - whether they produce two stem cells, two differentiated cells, or one of each.
13. Cytoskeletal Arrays: Essential for the process of neuronal migration and the growth of axons and dendrites.
14. Cell-cell adhesion and the ECM: Neurons need to stick to each other and the extracellular matrix for proper migration and connection formation.
15. Hormones: As development progresses, hormones can influence the maturation of neural cells and their functional integration.
16. Ion Channels and Electromagnetic Fields: Neurons' functionality depends on ion channels. As they mature, they start to produce electrical activity, which can, in turn, influence neighboring cells.

The development of the vertebrate nervous system, particularly neurogenesis in the neural tube, is a marvel of intricate processes that seem to be woven together with precision. When we delve deep into these processes, the sheer complexity and fine-tuning observed present an argument for irreducibility and interdependence, challenging the evolutionary narrative of gradualism. Consider the choreography involved in Cell Fate Determination and Lineage Specification. For a neural stem cell to decide its fate as a neuron, astrocyte, or oligodendrocyte, it requires clear signaling. Now, these signals are not arbitrary. They are governed by the Chromatin Dynamics and Epigenetic Codes that regulate gene accessibility. Without this precise regulation, the stem cell would be directionless, indicating the irreducible nature of these processes. Similarly, the Gene Regulation Network, which turns genes on or off, is contingent upon external cues. But for a gene to be regulated, there has to be a language it understands, an intricate code. This network can't function without knowing which genes to regulate, and this information is encoded within it. This makes it evident that the gene's language and the regulatory network are inseparable.

Morphogen Gradients, which instruct cells about their position, are another marvel. For a gradient to make sense, cells need a mechanism to interpret the gradient – the difference between high and low concentrations and act accordingly. The gradient, without an interpretative mechanism, would just be a spread of chemicals. This emphasizes the inherent interdependence between signaling and response mechanisms. Cell-Cell Communication in the neural tube is another illustration. The sheer accuracy needed to ensure the right number of each cell type is produced points to a system that cannot be reduced any further. If any component is removed or malfunctions, the entire communication collapses. This intricate dance of processes continues with Cell Migration and Chemotaxis, Cell-Cycle Regulation, and Apoptosis. Each process is like a cog in a watch. Remove one, and the watch stops ticking. For instance, a neuron that migrates but doesn't undergo apoptosis might lead to an oversaturation of neurons, disrupting the fine balance needed for a functioning nervous system.

Neuronal Pruning and Synaptogenesis are another testament. Neurons create connections, but without the language of synaptogenesis and the mechanism of pruning, these connections would either be too many or too few, again disrupting balance. The multitude of Signaling Pathways, the Noncoding RNA, MicroRNA Regulation, and all other processes mentioned each have a specific role, a language they understand, and a code they operate upon. These codes, languages, and mechanisms are irreducibly complex. One without the other would collapse the system. For example, the Cytoskeletal Arrays, vital for neuronal migration, must understand the language of the signaling pathways guiding them. The Cell-cell adhesion and ECM must operate in tandem with hormonal signals. The precise timing, intensity, and nature of these interactions point to an orchestration that's hard to imagine evolving piecemeal. This observation becomes even more profound when we consider Ion Channels and Electromagnetic Fields. The language of electrical activity is not just a random firing of electrons. It's governed by precise codes, which in turn are influenced by numerous other factors. The argument, thus, is clear: The processes observed in neurogenesis, with their codes, languages, and signaling mechanisms, are so intertwined and interdependent that they appear to be parts of a well-orchestrated system, not just random evolutionary byproducts. Their interconnected nature and the fact that one without the other makes no functional sense suggest that they had to be instantiated and created all at once, fully operational, from the outset.

1. Temple, S. (2001). The development of neural stem cells. Nature, 414(6859), 112-117. Link. ( The paper by Temple (2001) is known for its discussion on the potential of neural stem cells and their differentiation. In general, the literature establishes that neural stem cells in the brain have the capacity to generate both neurons and glia, which includes astrocytes and oligodendrocytes. The differentiation paths these cells take are influenced by various factors including intrinsic genetic programs and extrinsic signals from the environment.)
2. Hsieh, J., & Gage, F. H. (2004). Epigenetic control of neural stem cell fate. Current Opinion in Genetics & Development, 14(5), 461-469. Link. (This paper delves into how epigenetic mechanisms, including chromatin modifications, influence the differentiation paths of neural stem cells. The study highlights the interplay between the chromatin state and the genetic programs that drive neural stem cells toward specific lineages, such as neurons or glial cells.)
3. Jessell, T. M. (2000). Neuronal specification in the spinal cord: inductive signals and transcriptional codes. Nature Reviews Genetics, 1(1), 20-29. Link. (This article explores the complex interplay of transcriptional networks in determining neuronal fate within the spinal cord. Jessell elaborates on how specific transcription factors are activated or repressed in response to extrinsic signals, orchestrating the diverse cell types seen in the mature neural tube.)
4. Briscoe, J., & Ericson, J. (2001). Specification of neuronal fates in the ventral neural tube. Current Opinion in Neurobiology, 11(1), 43-49. Link. (This paper delves into how morphogen gradients, notably those of Shh and BMPs, play pivotal roles in specifying neuronal subtypes in the ventral part of the neural tube. The authors detail the intricate interactions and feedback loops between these morphogens and the resultant cell fates.)
5. Kicheva, A., Bollenbach, T., Ribeiro, A., Valle, H. P., Lovell-Badge, R., Episkopou, V., & Briscoe, J. (2014). Coordination of progenitor specification and growth in mouse and chick spinal cord. Science, 345(6204), 1254927. Link. (This research delves into the intricacies of cell-cell communication within the developing neural tube. It elaborates on how cells coordinate to specify progenitors and manage growth, ensuring the balanced production of various neural cell types.)
6. Marín, O., & Rubenstein, J. L. (2001). A long, remarkable journey: tangential migration in the telencephalon. Nature Reviews Neuroscience, 2(11), 780-790. Link. (This review discusses the migratory routes and strategies employed by neurons, focusing on the telencephalon. The paper delves into the various molecular cues and factors guiding this essential neuronal migration.)
7. Salomoni, P., & Calegari, F. (2010). Cell cycle control of mammalian neural stem cells: putting a speed limit on G1. Trends in Cell Biology, 20(5), 233-243. Link. (This review article elaborates on the importance of cell-cycle regulation, particularly the G1 phase, in neural stem cells. The authors discuss how the length of the G1 phase can influence the decision of neural stem cells to either proliferate or initiate differentiation.)
8. Oppenheim, R. W. (1991). Cell death during development of the nervous system. Annual Review of Neuroscience, 14(1), 453-501. Link. (This comprehensive review elucidates the pivotal role of programmed cell death or apoptosis in the development of the nervous system. Oppenheim details how natural neuronal death plays a role in refining neural circuits, ensuring the survival of only those neurons that establish functional and proper synaptic connections.)
9. Huttenlocher, P. R., & Dabholkar, A. S. (1997). Regional differences in synaptogenesis in human cerebral cortex. Journal of Comparative Neurology, 387(2), 167-178. Link. (In this research, Huttenlocher and Dabholkar provide a detailed examination of the dynamic process of synaptogenesis in the human cerebral cortex. The study underscores the importance of synapse formation and refinement in establishing efficient neural circuits. It delves into how neurons make numerous connections post-migration, which are subsequently pruned to fine-tune neural networks.)
10. Kageyama, R., Ohtsuka, T., & Kobayashi, T. (2008). Roles of Hes genes in neural development. Development, Growth & Differentiation, 50(s1), S97-S103. Link. (This review sheds light on the roles of the Notch signaling pathway, particularly mediated through Hes genes, in neural development. The authors delve into the intricate mechanisms by which Notch signaling contributes to the determination of neural stem cell fate. The interplay with other signaling pathways, such as Wnt, is also touched upon, highlighting the orchestrated nature of neural development.)
11. Rajasethupathy, P., Antonov, I., Sheridan, R., Frey, S., Sander, C., Tuschl, T., & Kandel, E. R. (2012). A role for neuronal piRNAs in the epigenetic control of memory-related synaptic plasticity. Cell, 149(3), 693-707. Link. (This groundbreaking study investigates the involvement of piRNAs, a type of noncoding RNA, in synaptic plasticity and memory storage. The work demonstrates how piRNAs and their associated proteins play a role in the epigenetic changes linked to memory storage. It serves as evidence of the broader involvement of noncoding RNAs, often referred to as "junk DNA", in neurogenesis, underscoring their importance in both stem cell maintenance and neuronal differentiation.)
12. Knoblich, J. A. (2008). Mechanisms of asymmetric stem cell division. Cell, 132(4), 583-597. Link. (This comprehensive review delves into the molecular and cellular mechanisms underlying asymmetric stem cell divisions. The author provides a detailed exploration of how cell polarity and asymmetry dictate the outcomes of stem cell divisions, particularly in neural stem cells. It emphasizes the importance of such divisions in generating cellular diversity during neural development.)
13. Dent, E. W., & Gertler, F. B. (2003). Cytoskeletal dynamics and transport in growth cone motility and axon guidance. Neuron, 40(2), 209-227. Link. (This comprehensive review discusses the intricate dynamics of the cytoskeleton in growth cones, the specialized structures at the tips of growing axons. The authors provide insights into how the cytoskeletal elements, including actin and microtubules, drive growth cone motility and, by extension, axon guidance. The paper illustrates the essential role of the cytoskeleton in neuronal development, emphasizing its importance for neuronal migration and the growth of axons and dendrites.)
14. Franco, S. J., & Müller, U. (2011). Extracellular matrix functions during neuronal migration and lamination in the mammalian central nervous system. Developmental Neurobiology, 71(11), 889-900. Link. (This review delves into the significant role of the extracellular matrix (ECM) during the process of neuronal migration and the formation of laminar structures in the central nervous system. The authors explore the diverse array of ECM components and cell adhesion molecules that guide neurons in their migration and ensure their appropriate placement and connections within the developing neural circuitry.)
15. McEwen, B. S., & Akama, K. T. (2013). Hormones and the maturation of brain architecture. Progress in Brain Research, 195, 91-104. Link. (This research paper discusses how hormones play a pivotal role in the maturation and architectural remodeling of neural networks. The authors elucidate the multifaceted effects of hormones on neural plasticity, differentiation, and integration during both development and adulthood, emphasizing their significance in shaping the structure and function of the brain.)
16. Hille, B. (2001). Ionic channels of excitable membranes (3rd ed.). Sunderland, MA: Sinauer. Link. (This seminal book dives deep into the biology and function of ionic channels in excitable cells like neurons. Hille discusses the role these channels play in the generation and propagation of electrical signals, as well as how this activity can influence neighboring cells through various mechanisms, including electromagnetic fields. The insights provided in this book form a foundational understanding of neurophysiology.)

Evolution: Where Do Complex Organisms Come From? - Page 4 Sfdsf10

Premise 1: The development of the vertebrate nervous system, as seen in processes like neurogenesis in the neural tube, is an intricate orchestration of interconnected and interdependent mechanisms, ranging from chromatin dynamics to electromagnetic fields.
Premise 2: Systems of irreducible complexity, wherein every component is essential for functionality, cannot feasibly arise through gradual, piecemeal additions, as evolutionary mechanisms would necessitate.
Conclusion: Given the intricate and interdependent nature of the vertebrate nervous system's development and its irreducible complexity, it points more conclusively to an intelligently designed setup than to gradual evolutionary mechanisms.

Chromatin Dynamics and Epigenetic Codes

Chromatin Dynamics (Point 12): At the microscopic level, chromatin dynamics describes how DNA and proteins are organized within the nucleus. DNA wraps around histone proteins, forming nucleosomes. The compactness of this structure dictates whether genes are accessible for transcription or not. Changes in chromatin structure play an essential role in controlling which genes are active at any given time.
Epigenetic Codes (Point 17): Epigenetics encompasses changes in gene function that don't involve alterations to the underlying DNA sequence. One of the primary mechanisms for this is DNA methylation (Point 15), where methyl groups are added to the DNA, usually leading to gene silencing.

Interdependencies and Implications

Gene Regulation Network (Point 18): Chromatin dynamics and epigenetic modifications directly influence the gene regulatory networks. These modifications decide which genes are turned on or off, ensuring that cells have the appropriate responses to environmental cues.
Cell Fate Determination and Lineage Specification (Point 6): Epigenetic codes and chromatin remodeling play crucial roles in determining cell fate. For instance, a stem cell's decision to become a muscle cell versus a nerve cell can be influenced by these modifications.
Tissue Induction and Organogenesis (Point 47): Proper tissue and organ formation requires specific sets of genes to be activated in a timely and spatial manner. Chromatin dynamics and epigenetic modifications help coordinate these gene expression patterns, ensuring organs form correctly and functionally.

Given the interplay between chromatin dynamics and epigenetic codes, one can see the harmony in complexity. If chromatin isn't organized correctly, or if the epigenetic codes go awry, the ripple effects can be vast, impacting everything from individual cell functions to the development of entire organs. Such a tightly coordinated system, where microscopic modifications can influence macroscopic outcomes, speaks to a design with intricate precision and purpose.

2. A House of Cards

Many proponents of ID describe the cellular processes and systems as a "house of cards." In this analogy, removing one card (or disrupting a single process) may cause the entire structure to collapse. Such intricate dependencies make it hard to envision a gradual, step-by-step evolutionary development. How would the system function if even one of its myriad processes was not yet in place?

Let's take a look into Cell-Cell Communication and its relevance to many of the processes listed previously.

Cell-Cell Communication and the Notch Signaling Pathway

In multicellular organisms, cells don't function in isolation. They constantly communicate with one another to maintain harmony and respond to changes in the environment. One of the most studied pathways in this realm is the Notch signaling pathway.

How Notch Signaling Works

Activation: Notch signaling is initiated when a ligand from a neighboring cell binds to the Notch receptor of another cell.
Cleavage and Migration: This binding event causes two proteolytic cleavages of the Notch receptor. The second cleavage releases the Notch intracellular domain (NICD), which then migrates to the cell's nucleus.
Gene Expression: Once inside the nucleus, the NICD associates with other proteins and acts as a transcriptional activator, turning on genes that will affect the cell's fate.
Interdependencies and Systems Biology Implications:

Cell Differentiation (Point 6): Notch signaling plays a critical role in determining cell fate and ensuring cells differentiate into the types needed for proper tissue and organ function.
Pattern Formation (Point 36): The pathway helps establish patterns of cells in tissues, ensuring the right cells are in the right places.
Gene Regulation Network (Point 18): Notch signaling interfaces with numerous other pathways, making it a node in the complex web of cellular communication. Disruptions here can have cascading effects on numerous processes.
Tissue Induction and Organogenesis (Point 47): Proper tissue formation often requires communication between cells, with Notch signaling being pivotal for many of these interactions.

Considering the Notch signaling pathway alone, it's evident that its perturbation can disrupt multiple processes. From a systems biology perspective, if this pathway wasn't functioning correctly or was only partially developed, it's challenging to see how many critical developmental processes would proceed effectively. Its intricate ties to various cellular and developmental processes underscore the vast interconnectedness in biological systems.

3. Irreducible Complexity

A cornerstone of the ID argument is that many biological systems are "irreducibly complex." This means that they need all their parts to be present and functioning simultaneously to work. In the vast web of interconnected processes, where one relies on another to operate, the absence or malfunctioning of even one process would render the whole system dysfunctional. This poses significant challenges to the idea of gradual evolution: if a system needs all its parts to function, how could it evolve piecemeal over time?

Epigenetic Regulation and Gene Expression

Taking a look at the list of 47 points, there is a profound interdependence between "DNA Methylation" (Point 15), "Epigenetic Codes" (Point 17), "Gene Regulation Network" (Point 18), and "MicroRNA Regulation" (Point 27).

DNA Methylation (Point 15): This involves the addition of a methyl group to a cytosine base in DNA. Methylation typically suppresses gene transcription, and thus, it's a mechanism by which genes can be "turned off."
Epigenetic Codes (Point 17): Epigenetics refers to changes in gene function without altering the DNA sequence itself. Methylation is an epigenetic modification, but there are others, such as histone modifications, which can impact how tightly DNA is wound around histone proteins, thereby regulating gene accessibility and expression.
Gene Regulation Network (Point 18): This is a complex network of interactions between genes, typically involving transcription factors, enhancers, silencers, and other regulatory elements that control when, where, and how genes are expressed.
MicroRNA Regulation (Point 27): MicroRNAs are small RNA molecules that do not code for proteins. Instead, they regulate gene expression post-transcriptionally. They can bind to messenger RNA (mRNA) molecules and prevent them from being translated into proteins, or even lead to their degradation.

The interdependedness between these processes ensures precise control over gene expression. For an organism to develop and function properly, genes need to be turned on and off at the right times and in the right places. But consider this: if DNA methylation patterns are awry, then certain genes might be wrongly activated or suppressed. The gene regulatory network relies on correct epigenetic codes to function properly, and aberrant microRNA expression can disrupt the entire balance.  These systems' mutual dependencies make it challenging to envision how they could have evolved separately or in a stepwise fashion. For example, if a regulatory gene network evolved before the epigenetic controls were in place, how would it ensure precision in gene expression? If microRNAs emerged but the system to process them or the targets they bind to weren't present, would they confer any advantage?
This web of interdependence between epigenetic modifications, gene networks, and microRNA regulation exemplifies the intricacies and precision of cellular processes, underscoring the challenges faced by piecemeal evolutionary explanations.

4. The Language of Life

The cell operates with a myriad of 'codes' and 'languages.' From the genetic code in DNA to the intricate signaling pathways and feedback loops, cells communicate and operate in a way that is reminiscent of an intricately coded software program. The emergence of such a detailed and error-proof 'language system' from random events appears statistically implausible and points towards a designed system.

Neural Blueprint and Information Transfer

To showcase the interdependence within the 47 points, let's focus on the intricate processes associated with neural development and communication. Consider the following components:

Neural plate folding and convergence (Point 30): Early in development, the neural plate undergoes specific movements and foldings to form the neural tube, the precursor of the central nervous system. This requires accurate spatial organization.
Neurulation and Neural Tube Formation (Point 32): Once the neural plate has folded, it must properly close to form the neural tube. This structure eventually gives rise to the brain and spinal cord.
Cell-Cell Communication (Point 5): Cells must communicate effectively to coordinate these early developmental processes. Miscommunication or errors in signaling can lead to severe developmental defects.
Gene Regulation Network (Point 18): A precise network of gene interactions ensures that the right genes are activated (or suppressed) at the right times for neural tube formation.
Morphogen Gradients (Point 28): These are concentration gradients of substances that dictate tissue development. In the context of neural development, morphogens play critical roles in specifying which parts of the neural tube become the brain and which become the spinal cord.
Homeobox and Hox Genes (Point 22): These genes play a pivotal role in setting up the body plan of an embryo along its head-tail axis, including defining regions of the developing brain and spinal cord.

From a system's biology perspective, neural development is a marvel of coordination and communication. For the neural tube to form correctly, cells must communicate with each other, adhere to each other in specific ways, respond to morphogen gradients, and activate the right genes at the right times. All these processes are tightly interwoven, and a failure in one process can impact others. For instance, if the gene regulatory network doesn't activate the right set of genes due to some perturbation, it could potentially affect the morphogen gradients, which in turn might disturb the proper folding of the neural plate, leading to defects in neural tube formation. Given the intricate dance between these processes, it's hard to fathom how such a system could have evolved piecemeal. Without the precise coordination of these multiple factors, the entire process of neural development could be jeopardized. This mutual dependency paints a picture of an orchestrated design where all parts must work in concert for the successful creation of such a complex system.

5. Feedback Loops and Regulatory Mechanisms

The numerous feedback loops and regulatory mechanisms ensure that every cellular process is meticulously monitored and adjusted as necessary. The foresight required for such intricate regulation seems beyond the scope of random mutations and natural selection.

Tissue Development and Maintenance

Diving into the intricate world of cellular growth, differentiation, and communication, let's explore the interwoven dance of several processes from the 47 points:

Cell-Cycle Regulation (Point 3): Cells have inbuilt systems that control their growth and division. A cell must decide when to divide, based on numerous external and internal cues.
Apoptosis (Point 2): Paradoxically, while some cells are growing and dividing, others are programmed to die, ensuring that tissues are sculpted properly and potential rogue cells are eliminated.
Signaling Pathways (Point 40): These pathways relay extracellular signals to intracellular targets, determining whether a cell divides, differentiates, or dies.
Cell Fate Determination and Lineage Specification (Point 6): Within a developing tissue or organ, cells are assigned specific roles. This involves a complex interplay of signals that tell cells to differentiate into one type of cell versus another.
Epigenetic Codes (Point 17): These are modifications to the DNA or associated proteins that don't change the DNA sequence but control gene activity. Epigenetic changes can be induced by environmental factors and can influence cellular decisions like differentiation.
MicroRNA Regulation (Point 27): Small RNAs that don't code for protein but regulate other genes post-transcriptionally. These can fine-tune cellular responses by adjusting the levels of specific proteins in a cell.
Feedback Loops and Hormones (Point 23): Chemical messengers, like hormones, often function within feedback loops, where the output of a system acts as an input to control its behavior, ensuring homeostasis.
Tissue Induction and Organogenesis (Point 47): The formation of specific tissues and organs requires a concert of the above processes. Cells need to grow, communicate, decide their fate, differentiate, or even undergo programmed death, all under the watchful eyes of regulatory networks.
Morphogen Gradients (Point 28): Concentrations of specific molecules in an embryo provide cues to cells, guiding them in their development and spatial organization within tissues and organs.

In this intricate interdependence of cellular processes, each is indispensable. For tissue development and organogenesis to occur correctly, cells need the right mix of growth signals, differentiation cues, and spatial information. If signaling pathways go awry, it can lead to unchecked growth or improper differentiation. If apoptosis doesn't function correctly, it might lead to malformations or predispose tissues to cancers. If epigenetic codes aren't set right, genes essential for proper function might remain silent or get inappropriately activated. All these processes interlock in an elegant dance, each reliant on the other, ensuring that tissues and organs develop properly. Given the sheer complexity and the tight interdependence of these systems, one can argue the challenges it poses to a purely stepwise evolutionary process.

6. Information Storage and Retrieval

The cell's ability to store, retrieve, and implement vast amounts of information is unmatched. DNA, often likened to a data storage system, holds the blueprints for the entire organism. The intricate processes by which this information is accessed, read, and executed seem to be beyond the capacity of unguided evolutionary processes to produce.

Orchestrating Organism Development

Consider the awe-inspiring journey of a single fertilized egg (zygote) as it develops into a complex multicellular organism:

Oogenesis (Point 34) & Spermatogenesis (Point 42): The journey of life begins with the formation of gametes. These processes create the mature egg and sperm, each responsible for carrying half of the genetic information that will lead to a new organism. This initial formation of gametes is foundational to the progression of life.
Oocyte Maturation and Fertilization (Point 35): Following the formation of these gametes, the next step in the dance of life is their fusion. Once the oocyte and sperm unite, a zygote emerges, endowed with a complete set of DNA. This DNA is the architectural blueprint that directs the growth and development of the entire organism.
Gene Regulation Network (Point 18): As the zygote's journey begins, a need for orchestration arises. The gene regulation network offers this orchestration, a vast interconnected web of interactions, determining when, where, and how genes get expressed. This system can be visualized as a master conductor, deciding which sections of the orchestra play and at which moments.
Epigenetic Codes (Point 17): Complementing the conductor, there are specific markers, akin to bookmarks on our DNA, that dictate which musical notes (genes) are emphasized and which are muted. Epigenetic modifications ensure that certain genes are made accessible while others remain silent, all without altering the original score (DNA sequence).
MicroRNA Regulation (Point 27) & Noncoding RNA from Junk DNA (Point 33): Just as a symphony may require fine-tuning, these molecules offer a layer of adjustment to the genetic output after the primary transcript, enhancing or modulating the performance as necessary.
Cell-Cycle Regulation (Point 3): With the foundational notes set, the zygote embarks on a growth journey. This growth is meticulously orchestrated, ensuring that each cellular division is harmonious, with DNA replicated with precision.
Germ Layer Formation (Point 20): As this cellular symphony continues, differentiation begins, setting the stage for the future tissues and organs. Cells start aligning into three primary sections or layers: ectoderm, mesoderm, and endoderm, each layer contributing unique notes to the life song.
Cell Fate Determination and Lineage Specification (Point 6): Within these layers, the individual notes (cells) are further refined and specialized, ensuring that each plays its part in the evolving melody of life.
Signaling Pathways (Point 40) & Morphogen Gradients (Point 28): Communication becomes pivotal as cells continue to evolve and find their position in the overarching composition. These pathways and gradients act as messengers, ensuring each cell understands its role and positioning.
Tissue Induction and Organogenesis (Point 47): The crescendo approaches as cells, driven by unique cues, assemble to form the organs that are vital to life, such as the heart, lungs, and liver.
Cell-Cell Communication (Point 5) & Cell-cell adhesion and the ECM (Point 4): And as the composition reaches its zenith, for the entire system to function harmoniously, cells must communicate and connect, ensuring that every note is in place, creating a beautifully coordinated melody of life.

The life of an organism, as illustrated, is a complex interplay of various systems and processes, each building upon the other, forming a harmonious melody from inception to maturity. This journey, from a single cell to a fully formed organism, involves accessing, reading, and executing a vast amount of information stored within the DNA. At each step, multiple processes from the 47 points are at play, acting like meticulous architects interpreting and building a structure based on an intricate blueprint. Given the precision, coordination, and depth of information involved, it offers a profound reflection on the cell's unmatched information storage and retrieval system.

The intricate interdependence and sheer complexity observed in biological systems make it hard to reconcile with a purely evolutionary framework that relies on random mutations and natural selection. The precision, foresight, and harmony seen in these systems appear to be indicative of a design by an intelligent agent.

Interdependence and Intricacy in Biological Systems

When one looks at the formation and development of complex multicellular organisms, it's akin to witnessing a grand orchestra, where each musician (or process) plays an essential part in crafting a collective, harmonious sound. If even one musician is missing or plays out of tune, the entire performance can be compromised. Similarly, the 47 biological processes are so deeply interwoven that a disturbance or absence in even a single process can lead to systemic disruptions. 

Foundational Importance: Just as an orchestra requires foundational instruments like percussion to set the rhythm, processes such as Oogenesis, Spermatogenesis, and Oocyte Maturation and Fertilization set the stage for life's beginning. Without these processes, the journey wouldn't even commence.
Regulation and Coordination: Once the foundational processes are in place, the need for regulation and coordination becomes paramount. The Gene Regulation Network, MicroRNA Regulation, and Epigenetic Codes serve as the conductors and coordinators, ensuring each 'musician' performs at the right time and in harmony with others.
Specialization and Differentiation: As the performance unfolds, specialized instruments like woodwinds or strings introduce unique melodies. Similarly, the Germ Layer Formation and Cell Fate Determination ensure cells differentiate and specialize, adding complexity to the organism's developmental 'symphony'.
Communication: In any orchestra, musicians must listen to and be in sync with each other. The biological equivalents are the Signaling Pathways and Cell-Cell Communication, which guarantee that cells 'listen' to each other and respond appropriately, maintaining the organism's intricate harmony.
Structural Integrity: Just as each section of an orchestra relies on the structure and positioning of its musicians, processes like Cell-cell adhesion and the ECM ensure the physical structure and integrity of tissues and organs.
Systemic Harmony: Finally, all these processes need to work in tandem. Tissue Induction, Organogenesis, and other processes ensure the organism's 'performance' is harmonized from start to finish.

Implications for Evolution and Complexity

The interconnectedness and dependency of these processes pose intriguing questions about the evolution of complex life. The traditional evolutionary model suggests a gradual accumulation of beneficial mutations over time. However, when considering irreducible complexity, a challenge arises: How can systems that rely so heavily on the simultaneous functioning of multiple components evolve incrementally? Such systems seem to defy a piecemeal evolutionary development, as the system wouldn't function (or would offer no evolutionary advantage) until all components are present and working together. The development of multicellular organisms is a marvel of complexity, coordination, and precision, revealing the awe-inspiring intricacies of life.

The Fine Balance of Life

Redundancy and Flexibility: While it's true that the intricacies of these systems point towards an irreducible complexity, nature has also ingeniously incorporated redundancy and flexibility. There are instances where multiple processes can achieve a similar outcome or where systems have backup mechanisms. This 'buffer' allows organisms to survive and adapt in fluctuating environments and under various stresses.
Fine-tuning: These systems are optimized for efficiency and effectiveness. Each process, while essential, has likely been the subject of countless iterations, shaped by environmental pressures and interactions with other processes. This ongoing 'tuning' has resulted in the beautifully orchestrated dance of cellular and molecular events we observe today.
The Starting Point of Complexity:  If even the most primitive unicellular organisms required a subset of these 47 processes to survive, then how could such complexity arise spontaneously without guidance? The leap from non-life to even the simplest life form is monumental, given the intricate machinery required at the cellular level. Such complexity, right from the beginning, suggests a purposefully designed set up. 
The Problem of Incremental Evolution:  How can a partial system, that's non-functional until fully formed, provide a selective advantage? Without the advantage, the process won't be 'selected' and thus, won't evolve. If the machinery of the cell works like a finely tuned watch, missing one gear might render it non-functional. Evolutionary processes can't favor non-functional or less functional states.
The Interconnectedness Challenge: The interconnected nature of the 47 processes outlined implies that changes in one system could have ripple effects across others. A random mutation in one part might require synchronized changes in several others to maintain functionality. Such a level of concurrent and harmonized change seems beyond the capabilities of random mutation and natural selection.
Plasticity and Pre-programming: The capacity for organisms to adapt to their environment is often touted as evidence for evolution. However,  this plasticity is evidence of pre-programmed adaptability—a foresight that allows organisms to respond to changing environments. Rather than being proof of random evolution, this built-in adaptability may suggest a designer who anticipated the varied and dynamic environments the organism would encounter.
Information Theory: One significant point is the infusion of information into the DNA. Information, as we understand it in other realms (like coding or linguistics), typically arises from intelligence. The intricate and specific information carried in the DNA, guiding the myriad of processes in the organism, is clear evidence of an intelligent input.




Processes involved in embryogenesis


● Of the 47 crucial developmental processes that determine an organism's shape and function, approximately half (24) play a direct role in embryogenesis. These 24 processes are mutually reliant, each interacting with one or multiple of its counterparts. Furthermore: 

● At least 12 epigenetic codes,  10 biological manufacturing codes, 21 signaling pathways, and 16 regulatory codes, are directly involved in embryogenesis.
● At least 12 epigenetic processes crosstalk with each other. So do 10 biological manufacturing codes, 20 signaling pathways, and 25 regulatory codes. 
 At least 15 epigenetic and manufacturing codes crosstalk, so do 15 epigenetic and signaling codes, 14 epigenetic and regulatory codes, 14 manufacturing and signaling codes, 11 manufacturing and regulatory codes, and 10 signaling, and regulatory codes.

Davidson, E. H. (2011): 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.  
Evolutionary bioscience as regulatory systems biology. Developmental Biology, 357(1), 35-40. Davidson, E. H. (2011) Link. (This paper delves into the interplay of evolutionary biology and regulatory systems, exploring their interconnectedness.)

Epigenetic Codes control gene expression without changing the underlying DNA sequence. Missing or altered epigenetic codes would lead to aberrant gene expression, possibly leading to developmental abnormalities or halting embryonic development altogether. Biological Manufacturing Codes refer to processes that produce essential molecules and structures for the cell. A disruption would impair the cell's ability to produce necessary components, potentially leading to cell death or malfunction. Signaling pathways help cells communicate and coordinate during development. Missing pathways would mean that cells don't receive essential developmental cues, potentially leading to structural abnormalities or a failure in organ and tissue formation. Regulatory Codes ensure that genes are turned on or off at the right times and places. Disruptions would result in genes being expressed at the wrong time or in the wrong cells, leading to developmental anomalies. Within-Codes Crosstalk (e.g., Epigenetic with Epigenetic): These interactions help fine-tune cellular processes. Disrupted crosstalk could lead to imbalances in cellular function, similar to the effects of missing individual codes. Between-Codes Crosstalk (e.g., Epigenetic with Manufacturing): These interactions often involve one process modulating another. If this modulation is lost, it would result in unregulated or improperly regulated cellular activities, leading to developmental malfunctions or halted embryogenesis.

Epigenetic and Manufacturing: A disruption here might affect how cellular structures and molecules are produced in response to epigenetic signals, potentially affecting cell differentiation or function.
Epigenetic and Signaling: Missing interactions could prevent cells from properly responding to developmental signals based on epigenetic status, leading to issues like improper cell migration or differentiation.
Epigenetic and Regulatory: This could disrupt the timing and location of gene expression in response to epigenetic cues, affecting how and where cells develop and differentiate.
Manufacturing and Signaling: Cells might not produce the right structures or molecules in response to developmental signals, possibly leading to structural or functional abnormalities.
Manufacturing and Regulatory: Disruption could affect how cellular products are made in response to gene regulatory signals, which might affect cell function or differentiation.
Signaling and Regulation: This could disrupt how cells interpret and respond to developmental cues at the gene regulation level, leading to improper development.

Any disruption or absence of these codes and their crosstalks would lead to a range of outcomes, from minor developmental abnormalities to lethal phenotypes. The specific impact would depend on the exact nature of the disruption and its context within the developing embryo.

Embryogenesis is a deeply intricate process that unfolds within a complex network of regulatory, signaling, epigenetic, and manufacturing systems. The profound coordination and complexity of these processes raise significant questions about how such a sophisticated system came into existence. The elaborate interplay between the various codes and pathways highlights a crucial point: the components of the system are interdependent. Without the presence of one, the others lose their functional significance. For instance, the epigenetic codes that control gene expression without changing the DNA sequence are essential. In their absence, the signaling pathways, no matter how well-structured, could not effectively relay their messages, leading to developmental anomalies. Conversely, without these signaling pathways, the cues relayed through the epigenetic codes would find no recipient, rendering them redundant. Biological Manufacturing Codes showcase another layer of this intricacy. These codes ensure that the cell produces essential molecules and structures. But what would be the point of these codes without the regulatory codes to turn genes on and off at the right times and in the right places? It would be like having a manufacturing plant with the capacity to produce, but no understanding of when and what to produce. This brings us to the fundamental argument: could these systems have evolved step by step in an evolutionary process? If one component of the system was to develop without the others, it would likely bear no function, as its role is contingent on the presence of the others. How then would natural selection favor and preserve such non-functional intermediate stages? Imagine a signaling pathway evolving without the regulatory codes to interpret the signals. It would be akin to developing a sophisticated telecommunications system in a world where no one has a phone. Or consider the development of the Biological Manufacturing Codes without the presence of epigenetic codes. It would be equivalent to having factories equipped with machinery, but no blueprint or plan to dictate the manufacturing process. This interconnectedness suggests that a piecemeal, stepwise emergence of these systems is not just improbable but virtually, and yes, even practically, in the realm of the impossible. The entire orchestration of embryogenesis evidences clearly the necessity of a holistic emergence rather than a gradual assembly. Moreover, the transition from one species to another, as in the example of an ape-like creature evolving coordinated development into Homo sapiens, appears fraught with challenges. Each species has a unique set of developmental processes. A mere tweak in one process would have absolutely catastrophic consequences. The simultaneous evolution of all these codes and pathways, without causing adverse effects, is extremely improbable. Each intricate process, with its codes and signals, would need to transform in sync with the others, maintaining the balance and harmony essential for embryonic development. In light of this, the profound complexity and coordination observed in embryogenesis are indicative of a system that was thoughtfully orchestrated, where each component was specifically designed to function in harmony with the others. This perspective underscores the idea that such intricacy and precision are unlikely to be the products of random, evolutionary, but nonetheless, unguided processes. The orchestration of embryogenesis bears the hallmark of purposeful design maybe like no other, showcasing a masterful interplay of systems that work seamlessly together.

Embryogenesis, with its vast array of processes and pathways, stands as a testament to the intricacy and complexity inherent in biological systems. The profound interconnectivity and finely tuned coordination observed in the developmental pathways suggest a system that appears to be irreducibly complex. In the context of embryogenesis, this concept can be applied to the interplay of epigenetic codes, biological manufacturing codes, signaling pathways, and regulatory codes. The epigenetic codes, responsible for controlling gene expression without altering the DNA sequence, are intricately linked with the biological manufacturing codes, which dictate how essential molecules and structures for a cell are produced. Without these specific instructions, the cell would be unable to produce the necessary components for its function, leading to abnormalities or cessation of development. This speaks to the point that the epigenetic codes and manufacturing processes are not only interdependent but are also irreducible in their complexity. If one process is hampered or missing, the entire system collapses. These play pivotal roles in ensuring that the developmental process progresses seamlessly. Missing signaling pathways would prevent cells from receiving crucial developmental cues, leading to anomalies. On the other hand, disruptions in regulatory codes could lead to genes being expressed at inappropriate times or places. These two elements are intricately woven together, and neither can function in isolation. For instance, without the signaling pathways, the regulatory codes would lack information on when and where to activate or inhibit gene expression. Crosstalk is an essential aspect of these systems, ensuring that each part communicates effectively with the others. This communication is vital for the seamless operation of cellular functions. For instance, the crosstalk between epigenetic and manufacturing codes ensures that cellular structures and molecules are produced in response to epigenetic signals. Similarly, the interplay between manufacturing and signaling ensures that cells produce the correct structures or molecules in response to developmental signals. This high degree of interdependence suggests that the system would fail if even one of these codes or signaling pathways was missing or malfunctioning. Given this deeply entrenched complexity, the evolution of such a system in a stepwise manner is not feasible. If intermediate stages bore no function, then by evolutionary standards, they would not be preserved or selected for. This poses a challenge: How could these pathways, codes, and processes have evolved piece by piece if the absence of any single piece would result in a non-functional or lethal phenotype? Furthermore, if we consider the development and differentiation of species, it seems improbable that such intricate processes could undergo substantial modification without catastrophic results. Taking the example of a chimp evolving into Homo sapiens, the entire system would need a coordinated overhaul of the various codes and signaling pathways. Even minor modifications could result in significant developmental anomalies. Consequently,  such systems, with their intricate designs, elaborate coordination, and sheer complexity, point to a design that is both intelligent and purposeful. The apparent irreducibility and interdependence of these systems make it hard to envision them being the product of a series of evolutionary accidents. Instead, they seem to underscore the notion of a sophisticated architecture underlying the wondrous process of life.

Premise 1: All processes vital to embryogenesis are intricately interconnected and rely on the proper function of each individual part (as evidenced by the interplay of epigenetic codes, manufacturing codes, signaling pathways, and regulatory codes).
Premise 2: Disruption or malfunction in any of these interconnected processes leads to catastrophic developmental consequences, as there is minimal flexibility within the system.
Conclusion: Therefore, the holistic integrity and functionality of embryogenesis are contingent upon the precise and uninterrupted coordination of all its constituent processes.

1. Oogenesis: Formation of the egg cell, the starting point of embryogenesis. The successful culmination of oogenesis sets the stage for Oocyte Maturation and Fertilization, ensuring a viable egg for the subsequent stages of embryogenesis.
2. Egg-Polarity Genes: Set up initial axes for the developing embryo. These genes lay the foundation upon which Regional specification and Pattern Formation rely to ensure a coherent body plan.
3. Oocyte Maturation and Fertilization: Initiates embryogenesis upon fertilization. The fertilization process is influenced by the conditions set by Epigenetic Codes and requires cues from the Gene Regulation Network for embryonic development.
4. Gene Regulation Network: Determines when and where genes are expressed, impacting processes such as Photoreceptor Development and Neural Crest Cell Migration by dictating their spatiotemporal formation.
5. Epigenetic Codes: Influence gene expression without altering the DNA sequence. They complement Gene Regulation Networks and play a role in events like Oogenesis and Oocyte Maturation and Fertilization.
6. Cell-Cell adhesion and the ECM: Crucial for tissue formation. The structural cohesion provided by these elements is integral for processes like Germ Layer Formation and Neurulation and Neural Tube Formation.
7. Cell Polarity and Asymmetry: Important for directed cell divisions. The establishment of cellular directionality is foundational for the workings of Egg-Polarity Genes, which dictate the initial embryo axes.
8. Germ Layer Formation (Gastrulation): Leads to the embryo's primary tissue layers. The layers form the basis for Cell Fate Determination and Lineage Specification, guiding cells towards specialization.
9. Cell Fate Determination and Lineage Specification (Cell differentiation): This process is underpinned by Germ Layer Formation, relying on prior tissue layer establishment, and it requires the Gene Regulation Network for precise differentiation.
10. Stem Cell Regulation and Differentiation: Stem cells give rise to other cells, working closely with Cell Fate Determination and Lineage Specification to produce varied cell types.
11. Homeobox and Hox Genes: Their role in body plans is contingent on initial guidance from Egg-Polarity Genes and further influences stages like Tissue Induction and Organogenesis.
12. Morphogen Gradients: These gradients, while guiding Cell-Cell Adhesion and the ECM, also integrate with Signaling Pathways to provide differentiation cues.
13. Segmentation and Somitogenesis: The establishment of body segments relies on instructions from Homeobox and Hox Genes and the foundation provided by Germ Layer Formation.
14. Neurulation and Neural Tube Formation: These events set the stage for Neural Crest cell migration, with the refinement from Apoptosis ensuring optimal nervous system development.
15. Neural Crest Cells Migration: Their migration and differentiation are based on prior activities of Neurulation and Neural Tube Formation and are guided by the Gene Regulation Network.
16. Neural plate folding and convergence: Setting the stage for Neurulation and Neural Tube Formation, this process also interacts closely with Cell Polarity and Asymmetry to achieve the right structure.
17. Photoreceptor development: The differentiation of these cells is directed by the Gene Regulation Network, ensuring they form at the right time and place.
18. Angiogenesis and Vasculogenesis: Blood vessels form and provide nutrients to developing tissues. Without Cell-Cell Adhesion and the ECM, the vessels wouldn't have the structural framework to form correctly. The specificity of cells sticking together relies on cues from the Morphogen Gradients and the Signaling Pathways.
19. Tissue Induction and Organogenesis: Stem cells, as part of Stem Cell Regulation and Differentiation, play a significant role in organ formation, and the processes here are also reliant on Signaling Pathways to specify organ types.
20. Pattern Formation: The organized arrangement of tissues leans on the initial conditions set by Egg-Polarity Genes and is further refined by Segmentation and Somitogenesis.
21. Regional specification: Along with Pattern Formation, regional specification ensures correct tissue and organ placement, guided by cues from Signaling Pathways.
22. Signaling Pathways: Their influence is seen in most embryogenic stages, from initiating Oocyte Maturation and Fertilization to guiding Cell Fate Determination and Lineage Specification.
23. Spatiotemporal gene expression: Acting in tandem with the Gene Regulation Network, this dictates the timing and location of formation processes like Photoreceptor Development.
24. Apoptosis: Beyond its role in Neurulation and Neural Tube Formation, apoptosis works with Signaling Pathways to refine structures across embryogenesis.

Epigenetic Codes involved in embryogenesis. This list encapsulates the core mechanisms:

1. DNA Methylation: A process where a methyl group is added to the DNA molecule, commonly leading to gene silencing. Occurs predominantly at CpG dinucleotides.
2. Histone Acetylation: Addition of an acetyl group to histones, generally leading to an open chromatin structure and active gene transcription.
3. Histone Methylation: Addition of a methyl group to histones, which can either activate or repress gene transcription depending on the specific histone and lysine or arginine residue being methylated.
4. Histone Phosphorylation: The addition of a phosphate group to histones, often associated with chromosome condensation during cell division.
5. Histone Ubiquitination: The process of adding a ubiquitin-protein to histones, which can be involved in both gene activation and repression.
6. Non-Coding RNA Regulation: Involves RNA molecules, such as microRNAs (miRNAs), long non-coding RNAs (lncRNAs), and Piwi-interacting RNAs (piRNAs) that don't code for proteins but can regulate gene expression at various levels.
7. Genomic Imprinting: A type of epigenetic inheritance where only one parental allele is expressed, and the other is silenced.
8. Chromatin Remodeling: Changes in the chromatin structure, which influence gene accessibility and expression, are achieved through complexes like SWI/SNF.
9. Histone Variants: Non-canonical histone proteins that can replace standard histones in the nucleosome, leading to altered chromatin structure and function.
10. RNA Methylation: Addition of a methyl group to certain RNA molecules, impacting their stability, localization, and function.
11. Histone Deacetylation: Removal of acetyl groups from histones by histone deacetylases (HDACs), typically leading to chromatin compaction and gene repression.
12. DNA Hydroxymethylation: Conversion of methylated cytosine to hydroxymethylcytosine, often associated with active transcriptional states.

Crosstalk among Epigenetic processes

Epigenetic modifications or processes, are tightly interconnected in cells and orchestrate the fine-tuned regulation of gene expression. Many of these mechanisms do not operate in isolation and frequently "crosstalk" with each other. Here's a summary of the crosstalk between the listed epigenetic processes:

1. DNA Methylation & Histone Modifications: DNA methylation, especially in CpG-rich regions, can attract proteins that read these marks and subsequently recruit histone deacetylases (HDACs), leading to histone deacetylation and a repressed chromatin state. Conversely, certain histone modifications can attract enzymes influencing DNA methylation status.
2. Histone Acetylation & Methylation: These two can either collaborate or oppose each other. For example, H3K9ac (histone H3 acetylated at lysine 9) is a mark of active transcription, while H3K9me3 (histone H3 tri-methylated at lysine 9) is typically linked with gene silencing.
3. Non-Coding RNA Regulation & DNA Methylation: Some long non-coding RNAs (lncRNAs) can guide DNA methyltransferases to particular gene loci, causing DNA methylation and subsequent gene repression.
4. Non-Coding RNA Regulation & Histone Modifications: Several lncRNAs and miRNAs engage with chromatin-modifying enzymes to either deposit or eliminate histone marks, influencing gene expression.
5. Histone Ubiquitination & DNA Methylation: Histone ubiquitination, especially on histone H2A, seems to be linked with DNA methylation levels, notably during DNA repair mechanisms.
6. Histone Ubiquitination & Chromatin Remodeling: The ubiquitination of histones can attract SWI/SNF chromatin remodeling complexes, altering nucleosome positioning and gene expression.
7. Chromatin Remodeling & Histone Modifications: SWI/SNF complexes and other chromatin remodelers can either ease or obstruct the placement or removal of specific histone marks, influencing gene accessibility.
8. Genomic Imprinting & DNA Methylation: Imprinted genes often associate with differentially methylated regions (DMRs) that are established during imprinting.

Biological Manufacturing Codes, address the ways cells use codes and languages to"manufacture" proteins and other essential components.:

1. Genetic Code: The set of rules by which information encoded in genetic material (DNA or RNA sequences) is translated into proteins (amino acid sequences) by living cells.
2. Codon Usage: Refers to the frequency with which particular codons are used to encode specific amino acids within genes.
3. tRNA Charging: The attachment of a specific amino acid to its corresponding tRNA molecule, a process essential for protein synthesis.
4. Ribosomal Decoding: The process by which ribosomes read codons in mRNA to synthesize proteins.
5. Signal Peptide Codes: Short (3-60 amino acids long) continuous sequences of amino acids that direct the post-translational transport of proteins.
6. Post-translational Modifications: Covalent processing events that change the properties of a protein by adding or removing chemical groups (like phosphates, methyls, or carbohydrates).
7. Protein Folding Codes: The inherent information in a protein sequence that dictates its 3D structure and folding pattern.
8. Splice Codes: Rules governing alternative splicing of pre-mRNA, leading to different mature mRNA molecules and, therefore, different proteins.
9. RNA Editing Codes: Modifications to RNA sequences that introduce changes not encoded in the DNA, affecting the properties or functions of the resultant proteins.
10. Glycosylation Codes: Rules governing the attachment of specific carbohydrate structures to proteins or lipids, affecting their stability, localization, and interactions.

Biological Manufacturing Codes Crosstalk

Biological Manufacturing Codes, which refer to fundamental molecular processes in cells, inherently communicate and crosstalk with each other. This crosstalk is vital to ensure the proper and coordinated functioning of cellular machinery. These crosstalk examples represent just a small fraction of the numerous intricate interactions that occur within cells. The cell is a highly coordinated and regulated environment, where countless processes communicate to maintain homeostasis and respond to external signals. Following is a detailed breakdown, highlighting how each of the manufacturing processes might crosstalk with each other:

1. DNA Replication & Transcription: DNA replication and transcription compete for the same DNA template. Excessive transcription can hinder replication fork progression, leading to DNA damage. Conversely, the presence of a replication fork can interrupt transcription.
2. DNA Replication & Translation: While these processes happen in different cellular compartments (nucleus vs. cytoplasm in eukaryotes), disruptions in DNA replication can lead to cell cycle arrest, which in turn could influence translation efficiency.
3. Transcription & Translation: In eukaryotes, transcription and RNA processing in the nucleus produce mature mRNA, which then gets translated in the cytoplasm. In prokaryotes, transcription and translation are coupled, meaning that as an mRNA strand is being synthesized, ribosomes can immediately begin translating it.
4. Transcription & Post-Translational Modifications: Transcription determines the type and quantity of proteins produced. Post-translational modifications can feedback to influence transcription factors and chromatin modifiers, influencing gene expression.
5. Translation & Lipid Biosynthesis: Many proteins produced through translation are enzymes that participate in lipid biosynthesis. Moreover, lipid compositions of membranes can influence the localization and function of ribosomes.
6. Lipid Biosynthesis & Carbohydrate Synthesis: Certain carbohydrates are components of complex lipids. Additionally, lipid-derived signaling molecules can influence carbohydrate metabolism pathways.
7. RNA Processing & Translation: Proper RNA processing, including capping, splicing, and polyadenylation, is crucial for mRNA stability and efficient translation.
8. Post-Translational Modifications & Lipid Biosynthesis: Modifications such as lipidation of proteins (like prenylation or myristoylation) anchor them to membranes, influencing protein localization and function.
9. Carbohydrate Synthesis & Translation: Some proteins produced by translation are enzymes involved in carbohydrate synthesis. Moreover, glycosylation, a type of carbohydrate synthesis, is a significant post-translational modification.
10. RNA Processing & Post-Translational Modifications: Certain non-coding RNAs produced during RNA processing can influence post-translational modifications by regulating the availability or activity of modifying enzymes.

Signaling Pathways and Codes in Embryogenesis:

Embryogenesis involves numerous signaling pathways and "codes." These pathways govern various aspects of development, ranging from cell differentiation to organ formation. Here's an exhaustive list of some of the most critical signaling pathways, but it's worth noting that while this list is comprehensive, ongoing research means new pathways and deeper understandings of existing pathways may emerge over time:

1. Notch Signaling Pathway: Crucial for cell-cell communication, influencing cell differentiation, proliferation, and apoptotic events.
2. Wnt Signaling Pathway: Plays a role in cell proliferation, migration, differentiation, and polarity.
3. Hedgehog (Hh) Signaling Pathway: Regulates aspects of embryonic development, including limb formation.
4. TGF-β Signaling Pathway: Involved in cell growth, cell differentiation, apoptosis, cellular homeostasis, and other cellular functions.
5. BMP (Bone Morphogenetic Protein) Signaling: Crucial for bone and cartilage formation.
6. FGF (Fibroblast Growth Factor) Signaling: Influences limb and neural development.
7. JAK-STAT Signaling Pathway: Mediates responses to interferons and a variety of other cytokines.
8. Retinoic Acid Signaling: Governs various stages of development, including neural differentiation.
9. Ephrin Signaling: Plays a role in the migration of cells and the development of their projected pathways.
10. MAPK/ERK Pathway: Transduces signals from receptors on the cell surface to DNA in the nucleus.
11. PI3K-Akt Signaling Pathway: Regulates critical cell functions like transcription, translation, proliferation, growth, and survival.
12. Delta-Notch Signaling: Critical for determining cell fates during embryogenesis.
13. Nodal Signaling: Essential for the formation of mesoderm and the patterning of the left-right axis.
14. mTOR Signaling: Regulates cell growth, cell proliferation, cell motility, cell survival, protein synthesis, autophagy, and transcription.
15. Cadherin Signaling: Plays a role in cell adhesion and in ensuring cells develop in the correct tissues.
16. Integrin Signaling Pathway: Regulates cell adhesion, migration, differentiation, proliferation, and apoptosis.
17. NF-kB Signaling Pathway: Plays a role in inflammation, immunity, cell proliferation, differentiation, and survival.
18. Sonic Hedgehog (Shh) Signaling: Vital for patterning during embryonic development.
19. VEGF (Vascular Endothelial Growth Factor) Signaling: Key to the formation of blood vessels (angiogenesis).
20. GPCR (G-protein-coupled receptor) Signaling: GPCRs are a large family of cell surface receptors that respond to a variety of external signals.
21. Calcium Signaling: Governs many processes like muscle contraction, neurotransmitter release, and cell growth.

Signaling Pathways Crosstalk
Crosstalk among signaling pathways is integral to achieving coordinated cellular responses. The following overview provides just a snapshot of the vast interplay between these pathways. The exact nature of interactions can depend on cell type, developmental stage, and external conditions. Here, in a concise manner, is an overview of how these pathways potentially communicate:

1. Notch and Wnt Signaling: Both pathways influence each other, especially during processes like cell differentiation. They can mutually inhibit or potentiate the effects of the other, depending on the cellular context.
2. Wnt and BMP Signaling: The Wnt pathway can activate or inhibit BMP signaling, influencing processes like cell differentiation and growth.
3. Hedgehog and TGF-β Signaling: Hedgehog signaling can influence the TGF-β pathway, particularly in development and cancer.
4. TGF-β and MAPK/ERK Pathway: TGF-β can activate the MAPK/ERK pathway, influencing cell growth and differentiation.
5. FGF and Notch Signaling: FGF signaling can modulate Notch pathway activities, especially in neurogenesis and angiogenesis.
6. JAK-STAT and PI3K-Akt Signaling: JAK-STAT activation often leads to PI3K-Akt pathway activation, especially in immune responses.
7. Retinoic Acid and FGF Signaling: Retinoic acid influences FGF signaling, particularly in neural differentiation.
8. Ephrin and Rho GTPases: Ephrin signaling often activates Rho GTPases, which can influence several of the listed pathways, such as PI3K-Akt and MAPK.
9. MAPK/ERK and PI3K-Akt Pathways: These two pathways can mutually regulate each other, often leading to coordinated control over cell growth and survival.
10. Delta-Notch and Nodal Signaling: Both pathways can influence mesoderm formation and can sometimes have antagonistic roles.
11. mTOR and PI3K-Akt Signaling: The PI3K-Akt pathway is a major upstream regulator of mTOR, governing cell growth and proliferation.
12. Cadherin and Wnt Signaling: Cadherins, being cell adhesion molecules, can influence the Wnt pathway, especially in processes like tissue boundary formation.
13. Integrin and FGF Signaling: Integrins can regulate FGF signaling, influencing processes like cell migration and wound healing.
14. NF-kB and Notch Signaling: Both pathways can regulate each other, often in the context of immune responses.
15. Sonic Hedgehog (Shh) and Wnt Signaling: Shh can influence Wnt signaling, especially during embryonic patterning.
16. VEGF and Notch Signaling: These pathways crosstalk during angiogenesis, determining vessel branching and density.
17. GPCR and Calcium Signaling: Activation of certain GPCRs can lead to an increase in intracellular calcium levels, influencing numerous cellular processes.
18. Hedgehog and Wnt Signaling: Both pathways interact in various developmental processes and in certain disease states like cancer.
19. BMP and Smad Signaling: BMP signals through Smad proteins, which are also part of the TGF-β signaling pathway.
20. PI3K-Akt and mTOR Signaling: PI3K-Akt can activate mTOR signaling, influencing cellular growth and metabolism.

Regulatory Codes in Embryogenesis

The term "regulatory codes" in embryogenesis typically refers to the combination of mechanisms, processes, and elements that control gene expression and activity. Regulatory elements, combined with various cellular processes, determine when and where specific genes are turned on or off during development.  The following list offers a comprehensive overview of the regulatory codes and systems involved in embryogenesis. However, as our understanding of genetics and developmental biology continues to evolve, new regulatory systems or more nuanced details about existing ones might emerge.

1. Promoters: DNA sequences located near the transcription start sites of genes; they determine where transcription by RNA polymerase begins.
2. Enhancers and Silencers: DNA sequences that, when bound by specific proteins (transcription factors), can increase (enhance) or decrease (silence) the transcription of specific genes.
3. Transcription Factors: Proteins that bind to DNA and influence the transcription of specific genes.
4. miRNA (microRNA): Small non-coding RNAs that regulate gene expression post-transcriptionally, usually by binding to and repressing the translation of target mRNAs.
5. lncRNA (long non-coding RNA): Longer RNA sequences that don't code for proteins but play roles in regulating various cellular processes, including chromatin remodeling and gene transcription.
6. Chromatin Remodeling: The dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory transcription machinery proteins, and thereby control gene expression.
7. DNA Methylation: The addition of a methyl group to the DNA, often leading to gene silencing.
8. Histone Modification: Post-translational modifications of histone proteins, such as methylation, acetylation, and phosphorylation, that influence gene expression.
9. RNA Splicing: The process by which introns are removed from the primary RNA transcript and exons are joined together to form a mature mRNA.
10. RNA Editing: The alteration of nucleotide sequences in an RNA molecule after it has been synthesized.
11. Alternative Polyadenylation: The process by which different poly(A) tails are added to the 3' end of an mRNA, which can influence mRNA stability, translation efficiency, and subcellular localization.
12. Ubiquitination: A process that tags proteins for degradation, altering their function or localization or promoting interactions with other proteins.
13. Phosphorylation: The addition of a phosphate group to a protein or other organic molecule, which can turn many protein enzymes on or off, thus altering their function.
14. Feedback Loops: Regulatory mechanisms in which a change in a parameter provides feedback that causes a counteracting change.
15. Morphogen Gradients: Concentration gradients of substances (morphogens) that can trigger distinct cellular responses at different threshold concentrations.
16. Gap Genes, Pair-Rule Genes, and Segment Polarity Genes: These genes define broad, then refined, then detailed areas of the embryo, respectively, and play a major role in segmentation during Drosophila embryogenesis.

Crosstalk Among Regulatory Codes in Embryogenesis

The regulatory codes in embryogenesis don't work in isolation; they frequently interact and influence each other, creating a tightly coordinated system that ensures proper development. This overview is a snapshot of potential interactions among regulatory codes. The exact nature and details of interactions can depend on the developmental stage, tissue type, and species-specific nuances. The embryonic regulatory network is intricate, and crosstalk between its components ensures robustness and precision in developmental processes. Here's a brief overview of how these regulatory elements and mechanisms might communicate:

1. Promoters and Transcription Factors: Transcription factors bind to specific sequences on promoters to either initiate or suppress transcription.
2. Enhancers/Silencers and Transcription Factors: Enhancers and silencers function primarily by attracting transcription factors, which in turn modulate gene transcription.
3. miRNA and mRNA: miRNAs latch onto mRNAs, adjusting their stability or translation and, by extension, affecting post-transcriptional gene expression.
4. lncRNA and Chromatin Remodeling: Certain lncRNAs have the capability to call chromatin remodeling complexes to particular genomic areas, affecting gene accessibility and transcription.
5. DNA Methylation and Histone Modification: Both mechanisms often collaborate to dictate chromatin structure and gene expression. DNA methylation can impact histone modifications, and the reverse is also true.
6. RNA Splicing and RNA Editing: Both processes are known to modify the sequence and therefore the function of mRNA. Some RNA splicing decisions can be influenced by RNA editing episodes.
7. Alternative Polyadenylation and miRNA: The selected poly(A) site can determine the presence or absence of miRNA binding sites on an mRNA, which can impact its regulation by miRNAs.
8. Ubiquitination and Phosphorylation: Both function as post-translational modifications. In some cases, phosphorylation might signal a protein to be tagged by ubiquitin and then broken down.
9. Feedback Loops and Morphogen Gradients: Cells interpreting morphogen gradients can trigger feedback loops that fine-tune and stabilize the interpretation of these gradients.
10. Histone Modification and Chromatin Remodeling: Alterations to histones can either attract or repel chromatin remodeling complexes, which subsequently influences the DNA's accessibility to the transcriptional machinery.
11. Transcription Factors and RNA Splicing: Some transcription factors have the capacity to influence alternative splicing decisions, thus impacting mRNA isoform creation.
12. Enhancers/Silencers and Chromatin Remodeling: The state of chromatin can determine the accessibility of enhancers and silencers, ultimately deciding if they can act upon their associated promoters.
13. Morphogen Gradients and Transcription Factors: Morphogens frequently work by managing the functionality or expression levels of transcription factors, which subsequently modulate downstream genes.
14. Gap Genes, Pair-Rule Genes, and Segment Polarity Genes: In Drosophila, these genes display a regulation hierarchy; gap genes are governed by maternal cues, which then manage pair-rule genes, which subsequently regulate segment polarity genes.
15. miRNA and Transcription Factors: miRNAs can target and dismantle mRNAs encoding transcription factors, while transcription factors can steer the expression of particular miRNAs.
16. Promoters and Enhancers/Silencers: Promoters, which are proximal to the transcription start sites, interact with distal enhancers and silencers to regulate gene transcription in a coordinated manner.
17. lncRNA and miRNA: Some lncRNAs act as sponges for miRNAs, thereby modulating the levels of miRNAs available to regulate target mRNAs.
18. RNA Editing and Alternative Polyadenylation: RNA editing events can alter the sequence used for polyadenylation, leading to different 3' ends on mRNAs.
19. Ubiquitination and miRNA: Protein degradation signaled by ubiquitination can influence the availability of factors important for miRNA processing or function.
20. Feedback Loops and RNA Splicing: Regulatory feedback loops can control the splicing machinery, determining the production of alternative spliced isoforms based on cellular conditions.
21. Morphogen Gradients and Chromatin Remodeling: The interpretation of morphogen gradients can lead to changes in chromatin structure, either promoting or inhibiting access to certain genes.
22. Histone Modification and DNA Methylation: The addition or removal of certain histone modifications can influence the recruitment of enzymes responsible for DNA methylation or demethylation.
23. Gap Genes and miRNA: Specific miRNAs can target gap genes for post-transcriptional regulation, adding an additional layer of control during embryogenesis.
24. Phosphorylation and Feedback Loops: The phosphorylation status of proteins within feedback loops can influence their activity, serving as a rapid switch to turn feedback mechanisms on or off.
25. RNA Splicing and lncRNA: Some lncRNAs can influence the splicing machinery or interact with splicing regulators, determining the inclusion or exclusion of exons in mature mRNAs.

Epigenetic and Manufacturing Crosstalk:

Here's an exhaustive list based on the provided format, detailing potential crosstalk between epigenetic mechanisms and manufacturing (signaling) pathways. This list provides a comprehensive overview of potential interactions, yet it's essential to recognize that while many of these interactions are established, others might be context-dependent or still under exploration in the scientific community.

1. DNA Methylation and Notch Signaling: Methylation patterns can influence the expression of genes in the Notch pathway, potentially modulating cell fate decisions and differentiation processes.
2. Histone Acetylation and Wnt Signaling: The acetylation status of histones can determine the accessibility and transcriptional activity of Wnt target genes, which play crucial roles in cell proliferation and fate determination.
3. Chromatin Remodeling and Hedgehog (Hh) Signaling: Chromatin remodeling activities can modulate the transcriptional responsiveness of Hh target genes, influencing tissue patterning and cellular differentiation.
4. Histone Methylation and TGF-β Signaling: Certain histone methylation patterns can affect the transcriptional output of genes downstream of TGF-β signaling, impacting cell growth and differentiation.
5. DNA Methylation and BMP Signaling: Methylation events can affect genes within the BMP pathway, influencing processes such as bone development and tissue repair.
6. Histone Phosphorylation and FGF Signaling: Phosphorylation events on histones might modulate the transcriptional activity of FGF-responsive genes, playing roles in wound healing and angiogenesis.
7. Chromatin Remodeling and JAK-STAT Signaling: The accessibility and transcriptional efficiency of JAK-STAT-responsive genes might hinge on the activities of chromatin remodeling complexes.
8. DNA Methylation and Retinoic Acid Signaling: Methylation patterns can influence the expression dynamics of genes responsive to retinoic acid, affecting processes like embryonic development and cellular differentiation.
9. Histone Deacetylation and Ephrin Signaling: Reduced acetylation on histones can potentially suppress the transcriptional activity of ephrin-responsive genes, impacting cellular migration and positioning.
10. Chromatin State and MAPK/ERK Pathway: The compactness or looseness of chromatin can affect how efficiently MAPK/ERK target genes are transcribed, influencing cell fate decisions.
11. DNA Methylation and PI3K-Akt Signaling: Methylation events on DNA sequences can influence genes within the PI3K-Akt pathway, affecting cell survival and proliferation.
12. Histone Ubiquitination and Delta-Notch Signaling: Ubiquitination events on histones can modulate the expression dynamics of Delta-Notch pathway components, potentially impacting cell-cell communication.
13. Chromatin Remodeling and Nodal Signaling: The transcriptional responsiveness of Nodal target genes might be influenced by chromatin remodeling activities.
14. Histone Methylation and mTOR Signaling: mTOR-responsive genes might be influenced by specific histone methylation events, affecting cellular growth and metabolism.
15. DNA Methylation and Cadherin Signaling: Methylation patterns on DNA might impact the transcription of cadherin genes, playing roles in cell-cell adhesion and tissue integrity.

Epigenetic and Signaling Crosstalk

Please note, that while the interactions listed below are based on known crosstalk between epigenetic mechanisms and signaling pathways, the intricate details and the extent of each interaction can vary across different cell types and organisms.

1. Histone Modification and TGF-β Signaling: Certain histone marks may influence the expression of genes regulated by TGF-β, playing pivotal roles in cell differentiation and proliferation.
2. Chromatin Remodeling and MAPK/ERK Pathway: Chromatin remodeling complexes can facilitate or inhibit the transcription of MAPK/ERK target genes, which are central to processes like cell growth and apoptosis.
3. DNA Methylation and JAK-STAT Signaling: Altered DNA methylation patterns can influence the expression dynamics of genes within the JAK-STAT pathway, potentially impacting immune responses and cell fate decisions.
4. Histone Acetylation and Wnt Signaling: The level of histone acetylation can modulate the transcriptional activity of Wnt target genes, affecting cell fate specification and tissue patterning.
5. Chromatin State and Hedgehog (Hh) Signaling: The accessibility of chromatin can impact the responsiveness of Hh target genes, influencing processes like limb development and tissue repair.
6. DNA Methylation and Notch Signaling: Methylation events on specific DNA sequences can determine the expression dynamics of genes in the Notch pathway, which governs cell differentiation and tissue patterning.
7. Histone Phosphorylation and PI3K-Akt Signaling: Phosphorylation events on histones might influence the transcriptional activity of genes responsive to PI3K-Akt signaling, affecting cell survival and metabolism.
8. Chromatin Remodeling and NF-κB Signaling: NF-κB target genes might require specific chromatin states, facilitated by remodeling complexes, to be efficiently transcribed, influencing immune responses and inflammation.
9. Histone Methylation and mTOR Signaling: Specific histone methylation patterns can influence the expression of mTOR-responsive genes, affecting cellular growth and nutrient sensing.
10. DNA Methylation and FGF Signaling: Methylation patterns can modulate the expression dynamics of genes within the FGF signaling pathway, impacting wound healing and angiogenesis.
11. Histone Deacetylation and BMP Signaling: The deacetylation state of histones can influence the transcriptional responsiveness of BMP target genes, which play roles in bone formation and cellular differentiation.
12. Chromatin State and Delta-Notch Signaling: The compaction or relaxation of chromatin might determine how efficiently Delta-Notch target genes are transcribed, potentially impacting cell-cell communication.
13. Histone Ubiquitination and Ephrin Signaling: Histone ubiquitination events can influence the transcription of ephrin-responsive genes, affecting cell migration and axon guidance.
14. Chromatin Remodeling and Retinoic Acid Signaling: Chromatin states can impact the transcriptional output of genes responsive to retinoic acid, influencing embryonic development and cellular differentiation.
15. DNA Methylation and Integrin Signaling: Methylation patterns on specific DNA sequences might influence the expression of integrin genes, affecting cell adhesion and migration.

Epigenetic and Regulatory Crosstalk

This list provides a glimpse of the potential crosstalk between epigenetic mechanisms and regulatory elements. The exact nature and implications of these interactions can vary across different cellular contexts and organisms.

1. miRNA Regulation and DNA Methylation: DNA methylation can silence miRNA genes, leading to altered miRNA profiles which can subsequently impact target gene expression.
2. Histone Deacetylation and Promoters: Histone deacetylation can compact chromatin, making gene promoters less accessible and thus reducing the potential for transcription initiation.
3. Histone Methylation and Enhancers: Certain histone methylation marks can either activate or repress enhancer regions, influencing the transcriptional activity of associated genes.
4. DNA Methylation and Transcription Factor Binding: Methylation at specific cytosines can prevent the binding of certain transcription factors, thereby altering gene expression patterns.
5. Chromatin Remodeling and Insulators: Chromatin remodeling can influence the effectiveness of insulator sequences, which demarcate transcriptionally active and inactive regions of the genome.
6. Histone Phosphorylation and RNA Polymerase II Activity: Phosphorylation of histone tails can influence the recruitment and progression of RNA polymerase II during transcription.
7. DNA Methylation and Splicing: Differential methylation in exonic regions can influence alternative splicing events, leading to diverse mRNA and protein isoforms.
8. Histone Acetylation and Locus Control Regions (LCRs): The acetylation state of histones can influence the activity of LCRs, which are regulatory sequences that control the expression of gene clusters.
9. Chromatin State and Silencers: The compaction or relaxation of chromatin can modulate the effectiveness of silencer elements, which downregulate the transcription of specific genes.
10. Histone Ubiquitination and Gene Termination: Ubiquitination of histones may play roles in signaling the proper termination of gene transcription.
11. DNA Methylation and 3’ UTR Regulation: Methylation patterns in 3' UTR regions can influence mRNA stability and translation efficiency.
12. Chromatin Remodeling and Super-Enhancers: Chromatin remodeling events can modulate the activity of super-enhancers, which are extended enhancer regions that control genes defining cell identity.
13. Histone Deacetylation and Gene Repressors: Histone deacetylation can enhance the binding and effectiveness of certain gene repressors.
14. DNA Methylation and Cis-regulatory Elements: DNA methylation patterns can influence the activity of cis-regulatory elements, thereby modulating gene expression in a spatial and temporal manner.

Manufacturing and Signaling Crosstalk

This list offers an overview of potential crosstalk between manufacturing processes (related to RNA and its modifications) and signaling pathways. Many of these interactions may depend on specific cellular contexts, and ongoing research continues to elucidate their complexities and implications.

1. Notch Signaling and RNA Splicing: Components of the Notch pathway can influence alternative splicing decisions, potentially affecting the production of various protein isoforms.
2. BMP Signaling and lncRNA: The BMP pathway might be influenced by lncRNAs that modulate the availability of BMP-responsive transcription factors or affect the stability of BMP-related transcripts.
3. Wnt Signaling and miRNA: Certain miRNAs can target components of the Wnt signaling pathway, influencing pathway activation or repression.
4. MAPK/ERK Pathway and CircRNAs: Some circRNAs might function as molecular sponges for miRNAs that target MAPK/ERK pathway components, thereby modulating pathway activity.
5. PI3K-Akt Signaling and RNA Methylation: RNA modifications, such as m^6A methylation, might influence the translation or stability of mRNAs related to the PI3K-Akt pathway.
6. Hedgehog (Hh) Signaling and RNA Transport: Proper localization and transport of Hh-related RNAs are crucial for gradient formation and signaling activity.
7. TGF-β Signaling and snoRNAs: Some snoRNAs might play roles in the post-transcriptional modifications of TGF-β pathway components, influencing signal transduction.
8. JAK-STAT Signaling and RNA Editing: RNA editing events might alter the coding sequence or regulatory regions of mRNAs involved in the JAK-STAT pathway, modulating signaling output.
9. mTOR Signaling and tRNA Modification: Modifications to tRNAs, such as pseudouridylation, can influence the translation efficiency of mTOR pathway components.
10. Delta-Notch Signaling and RNA Decay: The stability and decay rates of Delta-Notch-related mRNAs can impact the strength and duration of signaling.
11. Nodal Signaling and RNA Surveillance: Proper surveillance mechanisms ensure the fidelity of Nodal-related mRNAs, which is critical for pathway activation.

Manufacturing and Regulatory Crosstalk

This list encapsulates various potential crosstalk scenarios between manufacturing processes and regulatory elements. As always, the precise nature and impact of these interactions may vary based on cellular context and are areas of active research.

1. FGF Signaling and Enhancers: FGF-responsive genes are controlled by enhancer elements that respond to FGF signaling.
2. Wnt Signaling and Promoters: Certain promoters are activated in response to Wnt signaling, leading to the transcription of Wnt target genes.
3. TGF-β Signaling and Silencers: Some TGF-β responsive genes might be inhibited by silencers that are activated or deactivated in the presence of TGF-β signals.
4. Hedgehog (Hh) Signaling and miRNA: Hh signaling can modulate the expression of specific miRNAs that in turn influence the translation of Hh pathway components or target genes.
5. Notch Signaling and lncRNAs: lncRNAs might interact with the Notch signaling pathway by influencing the expression, stability, or translation of Notch target genes.
6. JAK-STAT Signaling and Enhancers: JAK-STAT-responsive genes may be modulated by specific enhancer elements that are sensitive to JAK-STAT pathway activation.
7. mTOR Signaling and Promoters: The mTOR signaling pathway can influence the activity of promoters related to cell growth, metabolism, and protein synthesis.
8. PI3K-Akt Signaling and Silencers: Silencer elements might downregulate genes when PI3K-Akt signaling is active, ensuring proper pathway regulation.
9. BMP Signaling and miRNA: BMP signaling can influence the expression of miRNAs that target BMP-responsive genes or BMP pathway components.
10. ERK Signaling and lncRNAs: Specific lncRNAs might modulate the ERK signaling pathway by affecting the transcription or translation of ERK-responsive genes.
11. Nodal Signaling and Enhancers: Enhancer elements responsive to Nodal signaling can activate genes critical for embryonic development and cell fate decisions.

Signaling and Regulatory Crosstalk

This list highlights various potential crosstalk mechanisms between signaling pathways and regulatory elements. The specifics of these interactions are still subjects of extensive research, and their outcomes might vary based on cellular context and external factors.

1. PI3K-Akt Signaling and Transcription Factors: The PI3K-Akt pathway can regulate the activity of certain transcription factors, determining their ability to bind DNA and control gene expression.
2. Wnt Signaling and miRNA: Wnt signaling can regulate the expression of specific miRNAs, which in turn can target mRNAs of Wnt-responsive genes.
3. Retinoic Acid Signaling and Histone Modification: Retinoic acid can influence histone modifications, which in turn control the expression of retinoic acid-responsive genes.
4. Notch Signaling and Enhancers: The Notch pathway can activate or repress enhancers that control the transcription of Notch target genes.
5. JAK-STAT Signaling and Silencers: JAK-STAT signaling might interact with silencers that downregulate unwanted or potentially harmful genes during an immune response.
6. Hedgehog Signaling and lncRNAs: Certain lncRNAs might be involved in the regulation of Hedgehog signaling by influencing the transcription or translation of pathway components.
7. mTOR Signaling and miRNA: The mTOR pathway can influence the expression of miRNAs that target genes involved in cell growth and metabolism.
8. TGF-β Signaling and Chromatin Remodeling: TGF-β signaling can lead to chromatin remodeling events that determine the accessibility of TGF-β-responsive genes.
9. BMP Signaling and Transcription Factor Binding Sites: BMP signaling might modulate the binding efficiency of transcription factors to their target sites, affecting BMP-responsive gene expression.
10. Nodal Signaling and Enhancer RNA: Nodal signaling can influence the production of enhancer RNAs (eRNAs) that facilitate the transcription of genes critical for embryonic development.
11. ERK Signaling and Histone Phosphorylation: ERK signaling can lead to the phosphorylation of histones, affecting the transcriptional activity of ERK-responsive genes.


Last edited by Otangelo on Sat Sep 16, 2023 11:52 pm; edited 5 times in total




What prevents the transition from micro to macroevolution?


Question: What barriers exist that may inhibit the progression from minor adaptive variations within a species to the emergence of entirely new species, or significant evolutionary transformations? In essence, what factors could potentially disrupt a seamless transition from microevolutionary processes to macroevolutionary outcomes? This has been traditionally a hard question to answer.

Response: The myriad developmental and regulatory processes underpinning the biology of organisms are both a testament to phenotypic plasticity and a set of constraints defining the spectrum of possible adaptation of life. These processes govern the structural and functional landscape of organisms. At the genetic level, mechanisms such as DNA methylation, chromatin dynamics, and noncoding RNA regulation shape the expression and regulation of genes. For instance, the DNA's organization within the nucleus, determined by chromatin dynamics, dictates the accessibility of genes for transcription. When these regulatory systems are perturbed significantly, it often leads to lethal or deleterious outcomes, thus constraining phenotypic diversity. At least 47 different mechanisms act synergistically to define the core attributes of organismal biology, encompassing form, development, regulation, and adaptation. Starting with organismal form, mechanisms like Angiogenesis and Vasculogenesis lay the groundwork for vital circulatory networks. Tissues and organs get their distinct shapes and structures from processes such as Cell-Cell Adhesion, Extracellular matrix-cell interactions (ECM) interaction, Pattern Formation, and Regional Specification. The intricacies of the cytoskeleton, driven by Cytoskeletal Arrays, bestow cells with structural integrity, facilitating movement and division. During developmental phases, events such as Gastrulation and Neurulation set the stage for germ layer formation and nervous system origination, respectively. Processes like Cell Fate Determination and Lineage Specification guide cells towards their specialized roles, while mechanisms like Morphogen Gradients and Signaling Pathways provide the cues for cells to follow developmental trajectories. Homeobox and Hox genes serve as master regulators in setting up the body's anterior-posterior axis, ensuring that each segment develops appropriately. Regulatory aspects within organisms rely heavily on molecular and cellular control systems. Chromatin Dynamics, DNA Methylation, and Epigenetic Codes modulate the accessibility and expression of genes. The Gene Regulation Network ensures that genes are expressed in harmony, and synchronized with the organism's needs. On a cellular level, Cell-Cycle Regulation maintains the balance between cell growth and division, while Cellular Senescence acts as a checkpoint, halting cells that might pose a risk. Systems like the Immune System Development arm the organism against external threats, while Hormonal pathways coordinate internal physiological processes.

For organisms to be adaptive, they must be responsive to internal and external changes. Cell Migration, Chemotaxis, and Neural Crest Cells Migration show the dynamic nature of cells, moving in response to specific cues. Mechanisms such as Ion Channels and Electromagnetic Fields modulate cellular responses to environmental stimuli. Feedback loops and checks established by Signaling Pathways and Spatiotemporal Gene Expression ensure that the organism responds accurately to temporal and spatial changes. Reproduction and generative processes, including Germ Cell Formation, Oogenesis, and Spermatogenesis, ensure the continuity of life, with specific checks and stages ensuring the creation of viable progeny. The influence of Microbiota and Symbiotic Relationships reminds us that organisms do not operate in isolation but are continually interacting with and being influenced by a myriad of external entities. Lastly, the dynamic nature of the genome, highlighted by Transposons and Retrotransposons, hints at the inherent plasticity and adaptability of life. But even as life changes and evolves, the orchestrated dance of these 47 mechanisms ensures a semblance of order, continuity, and coherence, but also a limited range of possible change. 

Developmental pathways play a pivotal role in ensuring a consistent sequence and pattern during an organism's formation. Processes such as gastrulation, neurulation, and segmentation are not mere sequences of events but are deeply integrated systems ensuring the appropriate development of tissues and organs. Major disruptions or alterations in these pathways could yield non-viable organisms, again demarcating boundaries of phenotypic plasticity and organismal possibilities. Furthermore, the functional constraints embedded in processes like angiogenesis, apoptosis, and hormonal regulation are vital. While these mechanisms ensure the proper physiological operation of an organism, significant deviations could disrupt these processes, making it untenable for the organism to maintain homeostasis. The role of foundational genes, particularly homeobox and Hox genes, cannot be understated. These genes, governing the anterior-posterior body plan of organisms, might undergo minor modifications over time. However, they resist the emergence of entirely novel body architectures, emphasizing the presence of phylogenetic constraints. Cellular and biochemical constraints manifest in the essential functions carried out by mechanisms like cell-cell adhesion, ion channels, and signaling pathways. These are not merely processes but foundational pillars supporting life's intricate web. A hypothetical new life form would face the monumental challenge of either adopting these systems or finding functionally equivalent alternatives. Reproduction, a cornerstone of life, also presents constraints. Processes central to sexual reproduction, like oogenesis and spermatogenesis, have a set framework. Significant alterations might result in reproductive barriers, which, while driving speciation, also delineate the limits of how divergent two organisms can be while still producing viable offspring. While evolution is proficient at modifying and diversifying life forms within the bounds set by these processes, these very processes define the extent of this plasticity. Over evolutionary timeframes, life might find novel pathways or modify existing ones, but the foundational principles, as defined by the processes listed, remain a consistent thread, shaping how life operates. This is exemplified, and well expressed by Davidson, a preeminent researcher in the field of Gene Regulatory Networks. He wrote: 

Davidson EH (2011): 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. 1

Micro-evolutionary adaptations typically manifest as subtle modifications within an established framework, ensuring the continuity and viability of an organism's lineage. These changes often arise in response to environmental pressures, facilitating enhanced survival without fundamentally altering the organism's foundational architecture. While these minor alterations can accumulate over time, they generally do not disrupt the central tenets of an organism's structure or functionality. Conversely, when we consider the realm of macro-evolution — where fundamental alterations to body plans and core biological systems are at play — the evolutionary landscape becomes significantly more complex. Changes of this magnitude venture into the heart of an organism's intricate biological network. Each component within this network is intricately connected to ensure optimal functionality. As a result, any profound alteration to one element has cascading implications for others, elevating the risk of unintended, detrimental consequences. This interconnected web of biological systems, processes, and structures has a built-in resilience against disruptions that could compromise the integrity of the organism. Genes responsible for governing these foundational attributes have safeguards. These protective mechanisms primarily manifest as robust negative feedback loops, ensuring that random genetic alterations that could destabilize essential functions are rapidly counteracted or negated. In essence, while evolution permits and even encourages variability, it also enforces boundaries to maintain the fundamental cohesiveness and functionality of life forms. Thus, while micro-evolutionary processes allow species to adapt and fine-tune their characteristics to ever-changing environments, the leap to macro-evolutionary shifts requires navigating a tightrope where the balance between innovation and functional integrity is paramount.

The biological realm offers a plethora of examples that highlight the principles of irreducibility, interdependence, and functional integration, underscoring the intricate nature of living systems. At the heart of this lies the concept of synergy, wherein multiple agents, mechanisms, players, or forces come together in a manner where their combined effect is significantly greater than if they operated independently. When we consider the cellular machinery and its myriad processes, it becomes evident that a holistic perspective, emphasizing the entire system rather than its individual parts, provides a clearer understanding. One cannot merely dissect the cell into its components and expect to grasp the full breadth of its operations. The emergent properties of cells — behaviors or capabilities that arise when all parts function as a cohesive unit — a testament to this systemic complexity. These properties aren't a feature of any single component but arise from the harmonious interactions of multiple parts. Consider the manufacturing, signaling, and regulatory codes of a cell. These codes, in essence, serve as languages that cells employ to produce proteins, communicate with other cells, and regulate their internal processes. These languages exemplify functional integration, as they are tightly interwoven and rely on one another. For instance, signaling pathways often depend on specific regulatory codes to ensure appropriate responses to external stimuli. Similarly, manufacturing codes rely on signals to modulate protein synthesis as per the cell's requirements. The concept of crosstalk between these codes is indispensable for the seamless operation of the cell, tissues, organs, organ systems, bodies, and even ecologies. It's much like an intricate dance where every step, turn, and spin is interconnected. Remove or alter one move, and the entire performance can fall apart. For instance, a signal to commence cell division must be in harmony with regulatory checks that ensure the cell is prepared for such a task. A disconnect here could lead to uncontrolled growth or cell death. From the perspective of the cell's development and operation, this tight-knit interdependence suggests that a stepwise evolution of these systems would be challenging. Each mechanism, language, or code system, in isolation, might not serve a functional purpose. For example, a signaling pathway without a corresponding regulatory mechanism might render the pathway dysfunctional, leading to cellular chaos. Therefore, these systems must have been instantiated all at once, fully operational, from scratch, for complex biological organisms to be viable. This is further bolstered by the presence of emergent properties in biological systems. These are characteristics that emerge when the system operates as a whole. It implies that the individual components alone, without their synergistic interactions, couldn't produce such properties. Moreover, cohesion within cellular processes mirrors the symbiotic relationships found in broader biological systems. Just as two organisms may coexist for mutual benefit, cellular mechanisms often operate in tandem, enhancing the overall efficiency and functionality of the cell. The idea of holism is profound in this context, emphasizing the importance of viewing the system as a composite rather than focusing solely on its individual parts. The complexity of life, characterized by synergy, emergent properties, functional integration, and interdependence, underscores the argument for a holistic approach to understanding biological systems. The intricacies suggest that the seamless operation of these systems may not merely be a byproduct of random, stepwise changes, but rather indicative of an intelligent orchestration of cohesive and synergistic components.

The distinction between microevolution and macroevolution, while both are embedded in the overarching theory of evolution, illuminates the different scales and types of change in the biological realm. Here are the key points highlighting why macroevolution cannot lead to macroevolution:

Functional Boundaries: Microevolutionary changes generally operate within the functional constraints of an organism, refining or adjusting existing traits without creating entirely new ones. Macroevolution, on the other hand, pertains to the emergence of entirely novel traits or significant alterations in body plans, which requires navigating a myriad of tightly interconnected biological systems.
Interconnectedness of Biological Systems: The intricate web of biological processes and systems, where each component is interconnected, means that profound alterations to one element can have cascading implications for others. Such a highly interconnected system resists drastic changes, as they could destabilize essential functions.
Negative Feedback Loops: Genes governing foundational attributes have protective mechanisms, like robust negative feedback loops, to counteract or negate random genetic alterations that might destabilize vital functions.
Irreducibility: Many biological systems and processes exhibit properties of irreducibility, meaning they need all their parts to function. This poses challenges for a stepwise evolution of these systems.
Emergent Properties: The complex interactions within biological systems lead to emergent properties that are not just the sum of individual components. These properties provide challenges for macroevolutionary transitions as they rely on the cohesion of multiple elements.
Holism and Synergy: The holistic nature of biological systems, where the combined effect of processes is significantly greater than their individual impacts, emphasizes the integrated nature of life. The introduction of significant new traits or systems would need to fit seamlessly into this holistic framework, which microevolutionary processes don't typically address.
Reproductive Barriers: Fundamental alterations in reproduction mechanisms could lead to reproductive barriers. While these might drive speciation, they also delineate the limits of divergence for producing viable offspring.
Phylogenetic Constraints: Foundational genes and processes, such as Hox genes that define the body plan of organisms, resist the emergence of entirely novel architectures, emphasizing inherent evolutionary boundaries.

While microevolution entails fine-tuning within existing functional and structural boundaries, macroevolution encompasses foundational shifts in those boundaries. The tight-knit interdependence, irreducibility, and emergent properties within biological systems present challenges for straightforward macroevolutionary transitions, highlighting why microevolutionary changes might not easily accumulate to result in macroevolutionary shifts.

1. Davidson EH (2011). EVOLUTIONARY BIOSCIENCE AS REGULATORY SYSTEMS BIOLOGY. Dev Biol, 357(1): 35–40. Link. (This paper delves into the interplay between evolutionary bioscience and regulatory systems biology, exploring the implications for our understanding of developmental and evolutionary processes.)

Evolution: Where Do Complex Organisms Come From? - Page 4 Image117

Last edited by Otangelo on Wed Oct 25, 2023 7:23 pm; edited 2 times in total




Most of the processes are controlled by genes or networks of signaling pathways. Each of these processes can be regulated by a complex interplay of numerous genes and signaling pathways, and this list is not exhaustive. This is a simplification and a selection of some key genes associated with each process. The actual number of genes and signaling pathways involved in each process is vast and often context-dependent.

1. Angiogenesis and Vasculogenesis: Formation of new blood vessels from pre-existing ones (angiogenesis) and de novo vessel formation (vasculogenesis). Genes involved: VEGF, FGF, and angiopoietins.
2. Apoptosis: Programmed cell death essential for removing unwanted cells. Genes involved: Bcl-2, Bax, caspases, and p53.
3. Cell-Cycle Regulation: Controls the progression of cells through the stages of growth and division. Genes involved: Cyclins, cyclin-dependent kinases (CDKs), p53, Rb.
4. Cell-cell adhesion and the ECM: Refers to how cells stick to each other and to the extracellular matrix. Genes involved: Cadherins, integrins, selectins, laminins.
5. Cell-Cell Communication: Cells communicate to coordinate their actions. Genes involved: Gap junction proteins like connexins; paracrine factors.
6. Cell Fate Determination and Lineage Specification: Process by which cells become specialized. Genes involved: Notch, Delta, Hedgehog, Wnt pathways.
7. Cell Migration and Chemotaxis: Movement of cells, guided by chemical gradients. Genes involved: Chemokine receptors, integrins.
8. Cell Polarity and Asymmetry: Defines cellular 'sides' or 'ends'. Genes involved: PAR proteins, Scribble complex.
9. Cellular Pluripotency: Cells can give rise to multiple cell types. Genes involved: Oct4, Nanog, Sox2.
10. Cellular Senescence: Stable cell cycle arrest. Genes involved: p53, Rb, p16INK4a.
11. Centrosomes: Organize microtubules and provide structure to cells. Genes involved: Centrin, pericentrin, gamma-tubulin.
12. Chromatin Dynamics: How DNA and proteins are organized in the nucleus. Genes involved: Histones H2A, H2B, H3, H4, HP1, SWI/SNF.
13. Cytokinesis: Physical process of cell division. Genes involved: Actin, myosin, RhoA, anillin.
14. Cytoskeletal Arrays: Framework of the cell. Genes involved: Actin, tubulin, keratins, vimentin.
15. DNA Methylation: Gene silencing. Genes involved: DNMT1, DNMT3A, DNMT3B.
16. Egg-Polarity Genes: Determine axes of the egg and organism. Genes involved: Bicoid, oskar, nanos, gurken.
17. Epigenetic Codes: Changes in gene function. Genes involved: EZH2, HDACs, HATs.
18. Gene Regulation Network: Interactions between genes. Genes involved are context-specific; transcription factors like MyoD for muscle cells, Pax6 for eye development.
19. Germ Cell Formation and Migration: Development and movement of reproductive cells. Genes involved: Vasa, Piwi, PLZF.
20. Germ Layer Formation (Gastrulation): Tissue layer development. Genes involved: Nodal, goosecoid, brachyury.
21. Histone PTMs: Modifications affecting DNA accessibility. Genes involved: Histone acetyltransferases, histone deacetylases, histone methyltransferases.
22. Homeobox and Hox Genes: Body plan control. Genes involved: HOXA, HOXB, HOXC, HOXD clusters.
23. Hormones: Bodily function coordination. Genes involved: Steroid hormone receptors, peptide hormone precursors.
24. Immune System Development: Immune cell formation. Genes involved: RAG1, RAG2, TCR, BCR.
25. Ion Channels and Electromagnetic Fields: Channels for ion flow. Genes involved: Voltage-gated sodium, potassium, and calcium channels.
26. Membrane Targets: Cell membrane processes. Genes involved: Ras, Rab, Rho GTPases.
27. MicroRNA Regulation: Post-transcriptional gene regulation. Genes involved: Dicer, Drosha, various miRNAs.
28. Morphogen Gradients: Tissue development concentration gradients. Genes involved: BMPs, Shh, Wnts.
29. Neural Crest Cells Migration: Movement of specific cells. Genes involved: SOX10, SLUG, SNAIL.
30. Neural plate folding and convergence: Neural tube formation. Genes involved: Shh, BMPs, FGFs.
31. Neuronal Pruning and Synaptogenesis: Neural connections. Genes involved: Neurexins, neuroligins, BDNF.
32. Neurulation and Neural Tube Formation: Neural tube development. Genes involved: Shh, Pax3, Pax7.
33. Noncoding RNA from Junk DNA: RNA with various functions. Genes involved: XIST, MALAT1, HOTAIR.
34. Oogenesis: Egg cell formation. Genes involved: ZP1, ZP2, ZP3.
35. Oocyte Maturation and Fertilization: Egg development and fusion with sperm. Genes involved: Mos, MPF, PLCzeta.
36. Pattern Formation: Cell/tissue arrangement. Genes involved: Dpp, Shh, FGFs.
37. Photoreceptor development: Light-detecting cells. Genes involved: Rhodopsin, opsin, PAX6.
38. Regional specification: Defining regions within tissues. Genes involved: Hox genes, Pax genes, Lim1.
39. Segmentation and Somitogenesis: Body segmentation. Genes involved: Notch, Delta, FGF8.
40. Signaling Pathways: Molecular events relay. Genes involved: Ras, Raf, MAPK.
41. Spatiotemporal gene expression: Time/place-specific gene expression. Genes involved: Clock, Bmal1, Period.
42. Spermatogenesis: Sperm cell formation. Genes involved: SYCP3, DAZ, BOULE.
43. Stem Cell Regulation and Differentiation: Stem cell fate control. Genes involved: Oct4, Sox2, Nanog.
44. Symbiotic Relationships and Microbiota Influence: Microbial interactions. Not typically governed by host genes directly but influenced by genes like NOD2, TLRs that recognize microbial elements.
45. Syncytium formation: Multinucleated cells. Genes involved: Myomaker, Myomerger.
46. Transposons and Retrotransposons: Mobile genetic elements. Genes involved: LINEs, SINEs, Alu sequences.
47. Tissue Induction and Organogenesis: Tissues/organs from undifferentiated cells. Genes involved: BMPs, FGFs, Wnts.





And here is the original research article (also open access), which deserves a round of applause:


Scroll down to Figure 5. Reflect on it for a few minutes.

THIS is the challenge, posed by Nature herself, for any theory of macroevolution. Mice have been mutated in nearly every way imaginable — by teratogenic chemicals, ionizing radiation, you name it — since the early decades of the 20th century. Jackson Laboratory, in Bar Harbor, Maine, which made the mouse the principal model system for mammalian biology, will soon celebrate its 100th anniversary (in 2029).

Yet the mice have stubbornly resisted becoming anything but mice — in the sense that wild-type Mus musculus still occupies the center point in the space within which all mutants are mapped. And the further away any mutant is located from that center point, the more problems it has. In short, the very last thing mice want to do is to macro-evolve. They have been telling us that for nearly 100 years.

In 1984, National Academy of Sciences geneticist Bruce Wallace, a PhD student of T.H. Dobzhansky at Columbia University, described the underlying functional logic of why this was the case (emphasis added):

"The Bauplan of an organism...can be thought of as the arrangement of genetic switches that control the course of the embryonic and subsequent development of the individual; such control must operate properly both in time generally and sequentially in the separately differentiated tissues. Selection, both natural and artificial, that leads to morphological change and other developmental modification does so by altering the settings and triggerings of these switches….The extreme difficulty encountered when attempting to transform one organism into another but still functional one lies in the difficulty in resetting a number of the many controlling switches in a manner that still allows for the individual's orderly (somatic) development.”

Figure 5 gives you all the visual (and functional logic) clues you need to understand why. Look at the control hierarchy as it cascades down towards the differentiated tissues and organs of the fully-developed animal, from the starting cell, the oocyte. This decision tree operates under constraints, and it has a target: a normal mouse. Random changes to the control logic tree will require compensating and coordinated changes throughout other parts of the tree. The earlier those random changes occur, the more parts of the tree they will affect.

Mice do not want to evolve. Not for any mystical or hard-to-understand reason; rather, given half a chance, they just want to be mice.


Sponsored content

Back to top  Message [Page 4 of 4]

Go to page : Previous  1, 2, 3, 4

Permissions in this forum:
You cannot reply to topics in this forum