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

Holland, John. Biology’s Gift to a Complex World. The Scientist. September, 2008. The University of Michigan systems wizard recounts in this “Magazine of the Life Sciences” the steps and path that led to his several advances in complexity theory. Holland first realized it is the recombination of genes in reproduction, rather than random mutations, that is the main driving force of evolution. This factor was next appreciated to have a mathematical basis, which he conceived as the now widely employed “genetic algorithms.” With stints at the Santa Fe Institute, such innate genome dynamics could be further modeled as “complex adaptive systems” composed of individual agents engaged in communicative interaction, from which a higher order emerges. In an expansion beyond molecules, CAS phenomena can be seen universally present from neural networks to immune reactions to financial economies. A good summary of Holland’s corpus and the welling shift to a genesis evolutionary synthesis.

Hoyal Cuthill, Jennifer and Simon Conway Morris.. Fractal branching organizations of Ediacaran rangeomorph fronds reveal a lost Proterozoic body plan. PNAS. 111/36, 2014. Cambridge University paleobiologists report a pre-Cambrium presence of a physiological fractal geometry whose self-similarity served to improve creaturely sustenance.

Rangeomorph fronds characterize the late Ediacaran Period (575–541 Ma), representing some of the earliest large organisms. As such, they offer key insights into the early evolution of multicellular eukaryotes. However, their extraordinary branching morphology differs from other organisms and is highly enigmatic. Here we provide a unified mathematical model, allowing us to reconstruct 3D morphologies of 11 taxa and measure their functional properties. This reveals an adaptive radiation of fractal morphologies which maximized body surface area, consistent with diffusive nutrient uptake. Rangeomorphs were adaptively optimal for the low-competition, high-nutrient conditions of Ediacaran oceans. (Abstract)

Hsieh, Shannon, et al. The Phanerozoic Aftermath of the Cambrian Information Revolution. Paleobiology. 48/3, 2022. Akin to Cellular Self-Organization: An Overdrive in Cambrian Diversity by Filip Vujovic, et al in BioEssays (July 2022), University of Illinois, Chicago and University of Connecticut paleoecologists including Roy Plotnick achieve a similar perception of rapid, wide-spread cerebral and cognitive advances as organic forms suddenly leapt forward from simpler stages. Many studies from the Burgess Shale to Devonian phases of “nervous system complexities” provided an empirical basis. As a result, a graphic radiation can be sketched from no CNS to ganglia onto a relative brain. In their rare purview, soma and sensory together are seen to constitute life’s radical emergent, quicker transition (on its way to our late planetary reconstruction).

The Cambrian information revolution describes how biotic increases in signals, sensory abilities, behavioral interactions, and landscape spatial complexity led to a rapid increase in animal cognition concurrent with the Cambrian radiation. Here, we compare neural and cognitive complexity in pre- and post-Cambrian marine ecosystems. We do not find a trend in this regard, nor in macroscopic sense organs These results suggest that sophisticated information processing was already common in early Phanerozoic ecosystems, comparable with behavioral evidence from the trace fossil record. The overall rise in cognitive sophistication in the Cambrian was likely a unique event in the history of life. (Abstract)

Comparisons of faunal lists from Cambrian and post-Cambrian ecosystems reveal similarly high shares of animal genera with brains as well as macroscopic sensory organs. Our results show that the Cambrian radiation generated ecosystems that were “modern” in sensory- and information-processing complexity, comparable to ecosystems in the later Phanerozoic. A major difference, however, is that most sensorially and cognitively complex animals in the Cambrian were panarthropods, since chordates and mollusks had not yet diversified. In both Cambrian and recent times, nervous systems permitted a variety of life modes, but the most active are associated with brains, which first appear in the Cambrian. (414-415)

Hudnall, Kevin and Raissa D’Souza. What does the tree of life look like as it grows? Evolution and the multifractality of time.. Journal of Theoretical Biology. 607/112121, 2025. UC Davis bioscholars propose an innovative perception of life’s long creaturely, branching development after Darwin’s archetypal elm as an instantiation of an iterative self-similar fractal geometry. The article comes with an Animation video to depict such an arboreal growth on its mathematic way toward mammals and peoples. Our philoSophic interest continues on to evident implications in our Earthwinian era whereby life’s episodic emergence appears to have a phenomenal,
independent, orthogenetic essence. (See also Dragon kings in self-organized criticality systems at arXiv:2308.02658 for earlier work by Raissa D'Souza.)

By unifying foundational principles of modern biology, we develop a mathematical basis for growing tree of life. Contrary to the static phylogenetic tree, our model shows that life’s track is more like a Cantor dust where each stage is a fractal form. As a result, this variegated course is nested, dualistic and stochastic. Altogether, its shape appears as a random iterated function that generates convexly related sequences of Metazoan species. The multifractal nature implies that, for any two living entities, the time interval from their last common ancestor to the present moment is a fractal curve. (Excerpts)

Our anatomical view is obtained from three prime features. The first is a nested scale which follows from descent-with-modification. The second is duality as biological sets transition between singularities and populations. The third aspect is a random facet whereby phylogeny is a stochastic process. Hence the natural tree of life as a whole is multifractal in that it consists of many distinct monofractals. (11)

Raissa D'Souza is Associate Dean for Research of the College of Engineering and a Professor of Computer Science at the University of California, Davis and on the Science Board at the Santa Fe Institute. See her Wikipedia page for much more. Kevin Hudnall is in Biological Systems Engineering Graduate Group at UC Davis.

Huneman, Philippe. Revisiting Darwinian Teleology: A Case for Inclusive Fittness as Design Explanation. Studies in History and Philosophy of Biological and Biomedical Sciences. Online July, 2019. The University of Paris Sorbonne evolutionary theorist offers a latest attempt sort and clarify ways to view life’s relative appearance as having some innate directional course. That is to say, how to thread a narrow path between its olden mainstream rejection and the fact that something must be going on which resulted in our human presence.

Huneman, Philippe and Denis Walsh, eds. Challenging the Modern Synthesis: Adaptation, Development, and Inheritance. Oxford: Oxford University Press, 2017. While holding to these three areas, an authoritative cast such as David Depew, Etienne Danchin, Patrick Batson, Alan Love, Stuart Newman, and Francesca Merlin press the envelope from a physical basis to evo-devo and evolvability. But its narrow compass yet allows little notice of epigenetics, cooperation, convergence, or self-organization.

Since its origin in the early 20th century, the Modern Synthesis theory of evolution has grown to become the orthodox view on the process of organic evolution. Its central defining feature is the prominence it accords to genes in the explanation of evolutionary dynamics. Since the advent of the 21st century, however, the Modern Synthesis has been subject to repeated and sustained challenges. In the last two decades, evolutionary biology has witnessed unprecedented growth in the understanding of those processes that underwrite the development of organisms and the inheritance of characters. The original essays collected in this volume survey the various challenges to the Modern Synthesis arising from the new biology of the 21st century. (Publisher edits)

Ingold, Tim. Between Evolution and History: Biology, Culture, and the Myth of Human Origins. Wheeler, Michael, et al, eds. The Evolution of Cultural Entities. Proceedings of the British Academy, 2002. In an effort to understand and diagram kinship relations, a British social anthropologist proposes a new view of evolution beyond Darwinian context-independent variation, selection and population genetics in order to integrate the self-organizing activity of a relational, environmental field in which organisms actually live. Ingold provides a good summary of the larger revolution in biology and evolutionary theory as it adds complementary epigenetic, topological effects which can express the influence of dynamic developmental systems.

In brief, instead of thinking of evolution as the sequential modification, along one or more lines of descent, of the design specifications that are supposed to underwrite the construction of organisms or artifacts, we have to regard it as the unfolding of a total field of relationships – a web of life – with which forms come into being and are held in place. We can then see that what we are accustomed to call history, when speaking of human beings, is but one aspect of a total process of evolution that embraces the entire organic world. (43)

Jablonka, Eva. Extending Darwinism. Seed. October, 2008. The Tel Aviv University geneticist and author provides a concise guide to frontiers of evolutionary theory some 150 years after The Origin of Species. Although Charles could not have known of DNA genes, he got it as right as could be for the mid 19th century. The mid 20th century Modern Synthesis went on to integrate with Mendelian genetics, which still prevails today. An “epigenetic” revolution is now underway, for much more is actually going on than random mutations. With past co-author Marion Lamb, the metaphor of a musical score is of utility in this regard. While an original score abides, its expression or performance quite depends on the external arrangement, instruments, orchestra maestro, and so on. Denis Noble in The Music of Life also evokes this fertile analogy.

My colleagues and I have argued that various types of epigenetic inheritance have played key roles in all the major evolutionary transitions. For example, the symbiotic relations with bacteria that gave rise to modern cells would have been impossible without epigenetic mechanisms allowing their cell membranes to reproduce; cellular epigenetic inheritance mechanisms were necessary for the transition from single-celled creatures to complex multicellular organisms with many cell types; a new non-genetic system of information transmission (symbolic language) was crucial for the transition to human culture. (26)

Jablonka, Eva and Marion Lamb. Evolution in Four Dimensions. Cambridge: MIT Press, 2005. Jablonka, Tel Aviv University and Lamb, University of London, gather a decade of research and articles into a meticulous argument that much more is going on than molecular mutations and blind selection. In actuality, a sequence of “inheritance systems” can be observed from genetic to epigenetic, behavioral and symbolic-linguistic realms. This view is said to accord with the Major Transitions scale of Maynard Smith and Szathmary since it likewise describes new, more effective modes of hereditary information transfer. The organization of these systems is both modular and holistic as the transmission proceeds both vertically and horizontally among relative carriers. As genetic information gains better templates and modes of expression, it is increasingly under the active control of nucleated cell, animal, human person. Altogether the book provides a comprehensive synthesis which defines a revised evolutionary synthesis as the emergence of a genetic script from DNA to knowledge. But the authors cite a caveat: since it is “very improper” to suggest anything progressive, even though it might look that way, such is not the case. An updated Precis by the authors, with peer comments, can be found in Behavioral and Brain Sciences 30/353, 2007.

This significant contribution, along with the major evolutionary transitions scale, has gained much acceptance since as a standard model for all manner of studies. A 2014 second edition has now come out from MIT Press with extensive updates. A main advance is the recognition of epigenetic effects far beyond nucleotides, along with systems biology integrations and a renewed importance of developmental biology. Prolific findings of regulatory, neural, and societal networks further contribute to a comprehensive scenario. An affinity is cited with the innovative theories of geneticist James Shapiro in his 2013 Evolution: A View from the 21st Century. Further substantiation is recorded for our symbolic, linguistic dimensions, by which regnant life is becoming recognized as self-organizing in kind. A topical bibliography for the intervening years is also included.

Our basic claim is that biological thinking about heredity and evolution is undergoing a revolutionary change. What is emerging is a new synthesis, which challenges the gene-centered version of neo-Darwinism that has dominated biological thought for the last fifty years. (1)

This change in perspective is not peculiar to molecular biology. A more integrated, developmental view is now being adopted in many other areas of biology. Attention is focused less on the individual components of a system and more on their organization and the collective properties that emerge from their interactions. Disciplinary boundaries are being crossed, and subjects like behavioral epigenetics, ecological epigenetics, and cultural epigenetics, are growing. (2014, 378)

Jaeger, Johannes and Nick Monk. Bioattractors: Dynamical Systems Theory and the Evolution of Regulatory Processes. Journal of Physiology. 592/11, 2014. In this special issue, a Universitat Pompeu Fabra, Barcelona, systems biologist and a University of Sheffield mathematician offer an exercise in how to perceive and express the actual presence of such agency, as if the missing natural genotype prior to any selective winnowing. In a Glossary, “ontogeny” is defined as “the generation of being” which includes not only development but also metabolic and physiological processes that produce phenotypes. For a later synopsis by the authors, see Everything Flows: A Process Perspective on Life in EMBO Reports (16/9, 2015).

In this paper, we illustrate how dynamical systems theory can provide a unifying conceptual framework for evolution of biological regulatory systems. Our argument is that the genotype–phenotype map can be characterized by the phase portrait of the underlying regulatory process. We show how the geometric analysis of phase space connects Waddington's epigenetic landscape to recent computational approaches for the study of robustness and evolvability in network evolution. Finally, we demonstrate how the active, self‐organizing role of the environment in phenotypic evolution can be understood in terms of dynamical systems concepts. A systematic exploration of such systems will enable us to understand better the nature and origin of the phenotypic variability, which provides the substrate for evolution by natural selection. (Abstract excerpts)

Jaeger, Johannes and Nick Monk. Dynamic Modules in Metabolism, Cell and Developmental Biology. Interface Focus. April, 2021. A paper for an Interdisciplinary Approaches to Dynamics in Biology issue, Complexity Science Hub, Vienna and University of Sheffield systems biologists (search) advance their 2020s studies by more insights how nature’s complex adaptive system procreativity is composed of distinct modular units. As they proceed to nest and join into whole entities, their diversity can contribute vital features. An array of clever graphics conveys how effective this method is, and how consistently it is availed. A philoSophia view would strongly imply that all these innate appearances must arise from and exemplify a greater genesis. See also Homology of Process: Developmental Dynamics in Comparative Biology by James de Frisco and J. Jaeger in this same issue.

Modularity is an essential feature of any adaptive complex system. Phenotypic traits are modules in the sense that they have a distinguishable structure or function. Since phenotypic traits are the product of regulatory dynamics, the generative processes that constitute the genotype–phenotype map must also be modular. Here, we propose an approach that parses such a complex regulatory system into elementary activity-functions. We illustrate by way of examples from metabolism, cellular processes, as well as development and pattern formation. We argue that dynamical modules provide a shared conceptual foundation for developmental and evolutionary biology, and can found a new account of process homology, see also DiFrisco and Jaeger in this focus issue. (Abstract)

Jaeger, Johannes, et al. The Inheritance of Process: A Dynamical Systems Approach. Journal of Experimental Zoology B. 318/8, 2012. In this journal edited by Gunter Wagner, mathematical biologists Jaeger, Universtitat Pompeu Fabra, Barcelona, with David Irons, University of Sheffield, and Nick Monk, University of Nottingham, propose a concerted, innovative effort toward a 21st century developmental evolutionary synthesis, which many agree is overdue. As the quotes discuss, a missing theoretical basis is the presence of innate nonlinear complex phenomena, as much a factor as biomolecular genes. A major import is that such genotype-like self-organization is at work prior to post phenotype selection. In regard, this work accords with similar 2012 projects across nature such as D. Aerts, et al for quantum potentials, J. Schneider, et al, animal societies, and K. Doron, et al for cerebral processes, (search all) where each seeks to admit the active role of these independent, universally applicable propensities as they serve to join discrete elements into dynamic interconnective networks. As a precedent, the authors say that this synthesis would fulfill the vision of holistic biologist Brain Goodwin (search).

A central unresolved problem of evolutionary biology concerns the way in which evolution at the genotypic level relates to the evolution of phenotypes. This genotype–phenotype map involves developmental and physiological processes, which are complex and not well understood. In this study, we argue that an explicit treatment of this map in terms of dynamical systems theory can provide an integrated understanding of evolution and development. We use a simple conceptual model to illustrate how the regulatory dynamics of the genotype–phenotype map can be passed on from generation to generation, and how heredity itself can be treated as a dynamic process. Our model yields explanations for punctuated evolutionary dynamics, the difference between micro- and macroevolution, and for the role of the environment in major phenotypic transitions. We propose a quantitative research program in evolutionary developmental systems biology—combining experimental methods with mathematical modeling—which aims at elaborating our conceptual framework by applying it to a wide range of evolving developmental systems. This requires a large and sustained effort, which we believe is justified by the significant potential benefits of an extended evolutionary theory that uses dynamic molecular genetic data to reintegrate development and evolution. (Abstract)

This lack of unity and understanding is not simply an issue of incompatible research programs or insufficient evidence. We argue that the problem is conceptual: we urgently need a mechanistic understanding of the nature of phenotypic variability for inherited traits if we are to gain an integrative understanding of evolution. By mechanistic, we mean causative explanations – in terms of dynamic interactions between genes or other relevant factors – rather than correlations between genotypes and phenotypes. Here, we present an outline of such a conceptual framework, expanding on the earlier work by (Brian) Goodwin (which) treats development and heredity as two different aspects (occurring at different time scales) of the same underlying evolutionary process. (593)

Epigenetic processes – physiology and development – co-determine the phenotype of an organism. While it is hardly controversial to treat these processes in terms of their dynamics, we show that heredity can be interpreted as a dynamical system as well, and that it is dynamic process itself that is inherited. We adopt the view that development and heredity can be combined explicitly by introducing a simple conceptual model based on dynamical systems theory. This model illustrates how the regulatory architecture of a developmental system is passed from generation to generation, and acts to integrate genetic, maternal, and environmental factors to produce a phenotype, which in turn is the primary target of natural selection. This regulatory structure holds the central ground between evolution and development, genotype, and phenotype. (593)

Lastly, our work is an attempt at integrating the great variety of approaches and subjects that have been proposed to be central to an extended evolutionary synthesis. This extension not only expands the scope of the original theory of evolution, but also shifts its focus away from genes towards evolving developmental systems, embedded in their genetic and environmental context. Darwin’s original theory suffered from two great deficits. One was the lack of a theory of inheritance. The integration of genetics into evolutionary theory solved this. Now it is time to tackle the second one: the lack of a mechanistic theory on the nature of phenotypic variability. Such a theory is now achievable. It will enable us to establish empirically whether there are regularities, or even laws, governing major phenotypic transitions. (608)

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