V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

Newman, Stuart. Inherency of Form and Function in Animal Development and Evolution. Frontiers in Physiology. Online June 19, 2019. As the Abstract describes, the New York Medical College cell biologist continues to advance his deep insights by which to appreciate life’s iterative anatomical and physiological emergence as arising from innate physical propensities. See also Inherency and Homomorphy in the Evolution of Development by SAN in Current Opinion in Genetics & Development (Vol. 37, August 2019).

I discuss recent work on the origins of morphology and cell-type diversification in Metazoa – collectively the animals – and propose a scenario for how these two features became integrated by way of a third set of cellular pattern formation processes. These inherent propensities to generate familiar forms and cell types are exhibited by present-day organisms. The structural motifs of animal bodies and organs, e.g., multilayered, hollow, elongated and segmented tissues, internal and external appendages, branched tubes, and modular endoskeletons, result from the recruitment of “generic” physical forces and mechanisms such as adhesion, contraction, polarity, chemical oscillation, and diffusion. Cellular pattern, mediated by released morphogens interacting with biochemically responsive and excitable tissues, drew on inherent self-organizing processes in proto-metazoans to transform clusters of holozoan cells into animal embryos. (Abstract excerpt)

Newman, Stuart. Physico-Genetic Determinants in the Evolution of Development. Science. 338/217, 2012. The New York Medical College cell biologist continues his project to admit and integrate the fundamental physical topologies and forces that serve to orient, guide, and constrain embryological maturation, both for individual ontogeny and species phylogeny. Akin to Mesoudi, et al above, this work is denounced by Jerry Coyne on the Huffington Post. Yet the next article in this issue, “A Dynamical-Systems View of Stem Cell Biology,” by Chikara Furusawa, Quantitative Biology Center, RIKEN, and Kunihiko Kaneko, University of Toyko, makes a similar case. A subsequent Letter in Science (339/646) by Kumar Selvarajoo and Masaru Tomita, Keio University systems biologists, cites this work as proof that innate “physical laws” play a strong formative role in life’s evolution and growth, and need be given their proper notice.

I propose that the origins of animal development lay in the mobilization of physical organizational effects that resulted when certain gene products of single-celled ancestors came to operate on the spatial scale of multicellular aggregates. (217) Many of the classic phenomena of early animal development – the formation and folding of distinct germ layers during gastrulation, the convergence and extension movements leading to embryo elongation, the formation of somites along the main axis of vertebrate embryos, the generation of the vertebrate limb skeleton, the arrangement of feathers and hairs – have been productively analyzed by mathematical and computational methods that treat morphological motifs as expected outcomes of physical processes that are generic, i.e., pertaining as well to certain nonliving, chemically active, viscoelastic materials. (217)

The idea that physics acted on early multicellular forms to define in broad strokes the patterns of development resolves several seemingly paradoxical aspects of the evolution of the animal phyla. These include the rapid emergence of nearly all of the metazoan body plans during the late Ediacaran-early Cambrian periods; the use of the same genetic tool kit to mediate similar morphogenetic processes in all animal phyla, however disparate; the recurrent appearance of a limited set of morphological motifs in all animal body plans and organ forms; and the relative insensitivity of phylum-associated morphological signatures to variations at stages of development before the multicellular one, when DPMs (dynamical patterning modules) come into play. (219)

Newman, Stuart and Gerd Muller. Origination and innovation in the Vertebrate Limb Skeleton: An Epigenetic Perspective. Journal of Experimental Zoology. 304B/593, 2005. Another example of significant rethinking and revision of the evolutionary synthesis, which increasingly looks like an oriented embryogenesis.

We suggest that the bauplan of the limb is based on an interplay of genetic and epigenetic processes; in particular, the self-organizing properties of precartilage mesenchymal tissue are proposed to provide the basis for its ability to generate regularly spaced nodules and rods of cartilage. (593) Rather that assuming that skeletal pattern is encoded in the embryo’s developmental repertoire by a hierarchy of gene-gene interactions, we suggest that it emerges from a complex system in which physical and other conditional, nonprogrammed (epigenetic) mechanisms of morphogenesis and pattern formation are also at play. (593-594)

Newman, Sturat. Inherent Forms and the Evolution of Evolution. Journal of Experimental Zoology B. Online August, 2019. The New York Medical College, Valhalla, theoretical experimentalist (search) has long studied and advocated the view that life’s creaturely forms arise from and manifest an intrinsic physical and mathematical basis. Here he comments on Bonner’s paper in this journal (June) which is a capsule of his 60 prolific years guided by this persuasion. In regard, Newman cites a growing trend to view the presence of the same structure, wing to limb, in descendent organisms. See also Inherency and Homomorphy in the Evolution of Development by SN in Current Opinion in Genetics (57/1, 2019), see third quote.

John Bonner presented a provocative conjecture that the means by which organisms evolve has itself evolved. The elements of his proposed model, namely the emergence of sex and enhanced selection pressures on larger multicellular forms, centers on a close mapping of genotypic to phenotypic change. He has also studied the intrinsic organizational properties of cell aggregates in social amoebae. By comparing the mechanistic bases of morphogenesis in the embryos of metazoans (animals), closely related holozoans, onto dictyostelids and volvocine algae, I conclude that understanding the evolution of multicellular evolution does indeed require knowledge of the inherent forms of diversifying lineages. (Abstract excerpt)

This approach stands outside of, but complements, the more gene-centric, adaptationist concepts of the major transitions in evolution scale, which are echoed in Bonner’s paper. As discussed her, and previously, the evolutionary transition from aggregates of unicellular organisms to the morphogenetically prolific Matazoa was a consequence of the acquisition of novel self-organizational capabilities, a factor that eludes selectionist explanatory frameworks. (6)

Inherency: The idea that aspects of the phenotype in development and evolution are latent in the organism’s material identity and that these features will spontaneously emerge if the conditions are appropriate.

Nghe, Philippe, et al. Predicting Evolution Using Regulatory Architecture. Annual Review of Biophysics. Volume 49, 2020. Seven bioscientists based in France, the Netherlands, UK, and USA consider how the latest convergent flow of systems, genomic, network, and more theories and methods, along with new instruments, seem to suggest an inherent, directional predictability for life’s long proactive development.

The causes of evolutionary constraint have remained somewhat elusive. Recently, a range of innovative approaches have leveraged mechanistic information on regulatory networks and cellular biology. These methods combine systems biology with population and single-cell models and new genetic tools which have been applied to a range of complex cellular functions and engineered networks. We review these developments, which are revealing the physical causes of epistasis at different levels of biological organization such as molecular recognition, a single regulatory network, and between networks. These advances seem to provide new indications of predictable features of evolutionary constraint. (Abstract excerpt)

Noble, Denis. The Future: Putting Humpty-Dumpty Together Again. Biochemical Society Transactions. 31/1, 2003. Rather than bottom up or top down methods, a call for a ‘middle-out’ approach that recognizes the effect of interactive networks and modularity in nature.

I think we can only say that we can the read the ‘Book of Life’ when we have succeeded in understanding how genes, and the proteins they code for, interact in cooperative ways in complex systems. This means that we must unravel and understand biological complexity, i.e. complement molecular reduction with higher-level integration. (156)

Noble, Denis. The Illusions of the Modern Synthesis. Biosemiotics. 14/1, 2021. The octogenarian Oxford University philosophical physiologist (search) continues his career quest to right the wrongs of this misguided theory which persists as the textbook version.. Indeed, a prime purpose of this Natural Genesis resource is to provide annotated documentation for an integral 21st century Genesis Evolutionary Synthesis. Noble’s view is that the MS was cobbled from mid-20th century opinions which took on its own gene-centric cast removed from actual realities. His main suggestion is that an emphasis on individual agencies whose proactive relational behaviors would replace prior passivities. His novel take struck a chord with commentators such as Signs of Consciousness? by Eva Jablonka, Agency and Choice in Evolution by Jonathon Delafield-Butt, The Plurality of Evolutionary Worldviews by Nathalie Gontier and Towards a Biosemiotic Theory of Evolution by Alexei Sharov, along with Tyler Volk, Louise Westling, Kalevi Kull. Aaron Gare and Guenther Witzany. Into these 2020s, whence a global sapiensphere may learn on her/his own (Charlotte and Charles EarthWin), such endeavors to get clear and correct on life’s oriented emergence make a vital contribution.

The Modern Synthesis (MS) has dominated biology for 80 years. It was first formulated in 1942, a decade before the major achievements of molecular biology, including the Double Helix and the Central Dogma (CD). These discoveries and concepts seemed to justify the genetic MS assumptions of accurate nucleotide replication, while the (DNA to RNA to Protein) CD was viewed as excluding the inheritance of acquired characteristics. This article examines the language of the MS to show how it is based on several misinterpretations of what molecular biology has found. In this regard, I cite these four Illusions: 1. Natural Selection; 2. The Weismann Barrier; 3. The Rejection of Darwin’s Gemmules; 4. The Central Dogma itself. An expansive multi-level view of life’s evolution avoids these miscues through the principle of biological relativity. (Abstract excerpt)

In this commentary I expand on the first of Noble’s illusions, the selection metaphor. Building on my work with Simona Ginsburg on the evolution of minimal consciousness, I argue that the existence of some complex sensory and motor patterns in the living world can be accounted for only through the evolution of conscious choice. (Jablonka)

Denis Noble has produced a succinct analysis of the ‘Illusions of the Modern Synthesis’. At the heart of the matter is the place of agency in organisms. This paper examines the nature of conscious agent action in organisms, and the role of affects in shaping agent choice. It examines the dual role these have in shaping evolution, and in the social worlds of scientists that shape evolutionary theory. Its central claim follows Noble, that agency is central to the structure of organisms, and raises careful consideration for the role animal agency and affective evaluations in biology, and in biologists. (Delafield-Butt)

The target article by Denis Noble is an excellent overview of the illusions of the Modern Synthesis that remain in textbooks. Overcoming these illusions shows the active role of organisms in the evolutionary process such as embryo development, epigenetic heredity, multilevel selection and niche construction. But what is still missing is the presence of individual agency, autonomy, semiosis, and goal-directedness. (Sharov)

Noble, Denis and Raymond Noble.. Understanding Living Systems.. Cambridge: Cambridge University Press, 2023. The esteemed octogenarian British brothers continue on message that a fixation on genes and mutation only is quite misguided, out of date and should be replaced such as Philip Ball does in his 2023 work How Life Works: A User’s Guide to the New Biology (herein).

Life is definitively purposive and creative. This book presents a paradigm shift in understanding living systems where the genome is not a code, blueprint or set of instructions. The authors show that gene-centrism misrepresents what genes are and how they are used by living systems. In fact, organisms make choices, influence their behaviour, development and evolution, and act as agents of natural selection. Reading this book will make you see life in a new light as a marvellous phenomenon.

Denis Noble is a British physiologist and biologist who held the Burdon Sanderson Chair of Cardiovascular Physiology at the University of Oxford from 1984 to 2004. Noble established The Third Way of Evolution project with James Shapiro which predicts that the entire modern synthesis will be replaced. Raymond Noble is Honorary Associate Professor at University College London.

Noble, Denis, et al. The Integration of Evolutionary Biology with Physiological Science. Journal of Physiology. 592/11, 2014. With coauthors Eva Jablonka, Michael Joyner, Gerd Muller and Stig Omholt, an introduction to an issue drawn from the 2013 International Union of Physiological Sciences (IUPS) Congress in Birmingham, England. Altogether it is agreed that a 21st century synthesis much beyond the 1950s “modern” version of Darwinian selection and random mutation is imperative. This content led to a Nature article Does Evolutionary Theory Need a Rethink? (514/161, 2014) as Point it does by the authors herein, and Counterpoint that all is fine from Greg Wray, Hopi Hoekstra, Doug Futuyma, and others. But as the papers listed show, a need remains for clarity and unity amongst the many voices and segments. For a good survey, Google “Physiology and the Revolution in Evolutionary Biology” for the IUPS keynote by Denis Noble on Voices from Oxford.

A notable sample could be Bioattractors: Dynamical Systems Theory and the Evolution of Regulatory Processes by Johannes Jaeger and Nick Monk (see below), Physiology of the Read-Write Genome by James Shapiro, The Biology of Developmental Plasticity by Patrick Bateson, et al, From Gene Action to Reactive Genomes by Evelyn Fox Keller, Form and Function Remixed by Stuart Newman, and Inheritance is Where Physiology Meets Evolution by Etienne Danchin and Arnaud Pocheville. A composite theme is a fulfillment of the evolution (phylogeny) and development (ontogeny, physiology) aka evo/devo, revival whence life’s long advance is indeed an embryonic gestation. A vital aspect is the presence of an independent, dynamic self-organization via genomic and epigenetic regulatory networks, in concert with environmental influences, prior to selection. In his talk, Noble endorses Shapiro’s view from his 2011 book (search) that there is nothing accidental about this, if we are able to admit, life quite knows what it is doing and becoming.

Norris, Vic and Patrick Amar. Chromosome Replication in Escherichia coli: Life on the Scales. Life. 76/706, 2011. University of Rouen and Universite Paris-Sud biologists offer insights on how a stratified biological evolution began because of “ecological” tendencies to form bounded vesicles, cells, and organisms made up of semi-autonomous components. A non-equilibrium thermodynamics is then seen to be driving this vibrant emergence. See also “Speculations on the Initiation of Chromosome Replication in Escherichia coli: The Dualism Hypothesis” by Norris in Medical Hypotheses (76/706, 2011).

At all levels of Life, systems evolve on the 'scales of equilibria'. At the level of bacteria, the individual cell must favor one of two opposing strategies and either take risks to grow or avoid risks to survive. It has been proposed in the Dualism hypothesis that the growth and survival strategies depend on non-equilibrium and equilibrium hyperstructures, respectively. (Abstract) Living systems are also highly structured. Indeed, in our "ecosystems-first", origins-of-life scenario, the most fundamental of living systems – cells – were highly structured right from the start. We have argued that this structuring takes the form of extensive macromolecular assemblies, termed hyperstructures, which are the descendants of the macromolecular aggregates, alias composomes, with which life began. (288)

At many levels, living systems are obliged to find compromises between the evolutionary virtues of growth and survival. We have proposed in the Dualism hypothesis that this quasi-universal need for a compromise solution results in Life on the scales of equilibria. In the case of bacteria, we have further proposed that a solution is provided by the cell cycle itself and that this entails the bacterium integrating (1) an intensity sensing that gives information about the non-equilibrium hyperstructures required for growth and (2) a quantity sensing that gives information about the equilibrium hyperstructures required for survival. (Conclusion)

Norris, Vic, et al. Modelling Biological Systems with Competitive Coherence.. Advances in Artificial Neural Systems. Article 703878, 2012. With life’s nested evolution and cognitive florescence now known as suffused by recurrent motifs and motives, Maurice Engel and Maurice Demarty, University of Rouen biologists go on to distill evidence for independent, universal patterns and generative “laws.” For an earlier take, see Vic Norris, et al “Hypercomplexity” in Acta Biotheoretica (53/313, 2005).

Many living systems, from cells to brains to governments, are controlled by the activity of a small subset of their constituents. It has been argued that coherence is of evolutionary advantage and that this active subset of constituents results from competition between two processes, a Next process that brings about coherence over time, and a Now process that brings about coherence between the interior and the exterior of the system at a particular time. This competition has been termed competitive coherence and has been implemented in a toy-learning program in order to clarify the concept and to generate—and ultimately test—new hypotheses covering subjects as diverse as complexity, emergence, DNA replication, global mutations, dreaming, bioputing (computing using either the parts of biological system or the entire biological system), and equilibrium and nonequilibrium structures. (Abstract)

The quest for universal laws in biology and other sciences has led to the development—and sometimes the acceptance—of concepts such as tensegrity, edge of chaos, small worlds, and self-organised criticality. In a different attempt to find a universal law in biology, one of us began working on the idea of network coherence in the seventies. This idea is related to neural networks which have indeed been proposed as important in generating phenotypes. The network coherence idea turned out to be scale-free and to address one of the most important problems that confronts bacteria, eukaryotic cells, collections of cells (including brains), and even social organisations. This problem is how a system can behave in (1) a coherent way over time so as to maintain historical continuity and (2) a coherent way at a particular time that makes sense in terms of both internal and environmental conditions. A possible solution would be for these systems to operate using the principle of competitive coherence. Given that living systems are complex or rather hypercomplex systems, characterised by emergent properties, we have speculated that competitive coherence has parameters useful for clarifying emergent properties and, perhaps, for classifying and quantifying types of complexity. We have further argued that competitive coherence might even be considered as the hallmark of life itself.

Norris, Vic, et al. New Approaches to the Problem of Generating Coherent, Reproducible Phenotypes. Theory in Biosciences. Online June, 2013. At the outset, it is worth noticing how certain nations, cultures, schools, can allow and profess a quite different evolutionary vision. An alternative vista is tacitly evident in a French milieu, broadly into Spain, Germany, Italy, and so on, where an enlivening and organizing force prior to selection alone is generally accepted. Here theoretical biologists and natural philosophers Norris, with Chislain Gangwe Nana, University of Rouen, and Jean-Nicolas Audinot, Public Research Centre “Gabriel Lippmann,” Luxembourg, describe life’s propensity to develop as a multi-level emergence to consistent viable forms and functions. In regard, Norris draws on his concept of “competitive coherence” of universally recurrent mode whence components such as genes or proteins survive and grow within a cellular membrane by a reciprocal benefit of entity and whole. In this view, life’s organic origin can be traced to and rooted in complementary physical and chemical principles. Search Norris, also Antoine Danchin and other colleagues, for more papers.

Fundamental, unresolved questions in biology include how a bacterium generates coherent phenotypes, how a population of bacteria generates a coherent set of such phenotypes, how the cell cycle is regulated and how life arose. To try to help answer these questions, we have developed the concepts of hyperstructures, competitive coherence and life on the scales of equilibria. Hyperstructures are large assemblies of macromolecules that perform functions. Competitive coherence describes the way in which organisations such as cells select a subset of their constituents to be active in determining their behaviour; this selection results from a competition between a process that is responsible for a historical coherence and another process responsible for coherence with the current environment. Life on the scales of equilibria describes how bacteria depend on the cell cycle to negotiate phenotype space and, in particular, to satisfy the conflicting constraints of having to grow in favourable conditions so as to reproduce yet not grow in hostile conditions so as to survive. (Abstract)

How do cells choose a few coherent, reproducible phenotypes out of the hyper-astronomical number apparently available to them? Trying to answer this question as theoretical biologist with integrative tendencies, has led me to develop new biological concepts such as competitive coherence, organisation at the level of hyperstructures, and Life on the Scales. My collaborators and I use these concepts to tackle other, related questions about the control and the function of the cell cycle, the marriage between metabolism and signalling, and the origins of life. We use a variety of approaches from mathematics and programming complemented by experiments based on Secondary Ion Mass Spectrometry. Spin-offs of our hypotheses include new techniques for bacterial and viral therapies, for studying phenotypic diversity at the level of single cells, for analysing individual DNA molecules and the molecules that associate with them, for biology-based computing, and perhaps even for a 'PCR of proteins'. In many of my activities, I try to act as a 'catalyst' within and across the disciplines and this has led me to collaborate with a couple of hundred scientists over the years. (Norris’ University of Rouen webpage)

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