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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

Bloom, Mark and Jan Rychtar. Game-Theoretical Models in Biology. Boca Raton: CRC Press, 2013. City University, London, and University of North Carolina mathematicians strive to fill a present need for a comprehensive volume that covers the many ways by which game-like phenomena apply to and appear in living, evolving systems. A history is sketched from Richard Lewontin’s 1961 Evolution and the Theory of Games to a gamut of Static, Dynamic, Classical, Matrix, Nonlinear, Asymmetric, Multi-Player, Mating, and more, aspects. Future usage by agent-based models, a turn to multi-level selection, and so on, are noted. See also Complex Adaptive Systems and Game Theory in the journal Complexity (16/1, 2010).

Blount, Zachary, et al. Contingency and Determinism in Evolution: Replaying Life’s Tape. Science. 362/655, 2018. Some three decades ago Stephen Jay Gould claimed that in a bare environment of contingent selection only, sans any inherent source to guide life’s development, human-like sentient beings would not appear a second time. This extended paper by ZB and Richard Lenski, Michigan State University, and Jonathan Losos, Washington University, St. Louis (search each), which weaves results from past projects, implies that much evidence since bodes well for an opposite view. An historic shift toward a deep predictability accrues due to a consistent convergence across many lineages, which is notable in niche constructions, digital runs that produce these trends, and many anatomic and physiological cases. See for example How Fish Get Their Stripes Again and Again by Hugo Gante in Science (362/396, 2018) and Scalable Continuous Evolution of Genes at Mutation Rates above Genomic Error Thresholds by Arjun Ravikumar, et al at bioRxiv (May 3, 2018).

Historical processes display some degree of “contingency,” meaning their outcomes are sensitive to seemingly inconsequential events that can change the future. Unlike many other natural phenomena, evolution is a historical process. Evolutionary change is often driven by natural selection which works upon variation that arises by random mutation. Moreover, evolution has taken place within a planetary environment with a particular history of its own. Here we replicate populations in evolutionary “replay” experiments which often show parallel changes, especially in overall performance, although idiosyncratic outcomes can affect which of several evolutionary paths is taken. Comparative biologists have found many notable examples of convergent adaptation to similar conditions, but quantification of how frequently such convergence occurs is difficult. On balance, the evidence indicates that evolution tends to be surprisingly repeatable among closely related lineages, but disparate outcomes become more likely as the footprint of history grows deeper. (Abstract excerpts)

Bonduriansky, Russell and Troy Day. Extended Heredity: A New Understanding of Inheritance and Evolution. Princeton: Princeton University Press, 2018. A University of New South Wales biologist/ecologist and a Queen’s University, Canada mathematician/biologist, each a veteran researcher, make a thorough case for this 21st century epigenetic expansion of what is involved as life’s informational source code works its ways. Noted by Conrad Waddington in the 1960s, taken up by Eva Jablonka, Marion Lamb, and others in the 2000s, it is now established that much more is actually going on beyond nucleotides and regulations in the standard genome. Once again complements of discrete digital operations and systemic analogue integrations are seen in play, along with saying that these (prosody-like) epigenetic dynamics serve a meaningful content. As a result, rather than nuances, a fundamental revision in “our understanding of evolution” is in order. (But their oft use of “machinery” still begs a conducive organic cosmos to reach a genesis synthesis.)

A further contribution is to situate these findings within the major evolutionary transitions scale. Since “new forms of heredity” are seen to accompany each nested emergence, it is considered that as these collaborative understandings of epi/genetic phenomena grow in reach and veracity, they could constitute a novel phase of “nongenetic cultural inheritance.” For concurrent examples, see Epigenome in Early Mammalian Development: Inheritance, Reprogramming and Establishment by Qianhua Xu and Wei Xie in Trends in Genetics (28/3, 2018), and Epigenetics: The First 25 Centuries by A. Ganesan in Philosophical Transactions of the Royal Society B (volume 373, issue 1748), 2018,

For much of the twentieth century it was assumed that genes alone mediate the transmission of biological information across generations and provide the raw material for natural selection. In this contribution, leading evolutionary biologists Russell Bonduriansky and Troy Day challenge this premise. Drawing on the latest research, they demonstrate that what happens during our lifetimes can influence the features of our descendants. On the basis of these discoveries, an extended concept of heredity is advanced about how traits can and cannot be transmitted across generations. By examining the history of the gene-centered view in modern biology and reassessing fundamental tenets of evolutionary theory, it is shown that nongenetic inheritance - epigenetic, environmental, behavioral, and cultural factors - could play an important role in evolution. (Publisher)

For example, while genetic inheritance involves random transmission of factors that usually cannot be modified in consistent ways by the ambient environment, nongenetic inheritance involves the transmission of factor that can often respond in consistent ways to environmental conditions. Moreover, while genetic information in the cell nucleus is embodied in linear nucleotide sequences that can be liked to a digital information medium, the factors that we include within ontogenetic inheritance range from nucleotide sequences similar to those of nuclear DNA to quantitative, structural, environmental and behavioral forms of variation that embody analogue information. (18-19)

This reflects a basic difference between the way biological information is encoded in DNA sequences versus most nongenetic factors. As philosopher Peter Godfrey-Smith has emphasized, genetic information is stored in linear sequences of repeating units, whereas nongeentic hereditary information is largely analogue in nature. In this sense, DNA sequences are like the digital information storage used by computers while nongenetic factors function more like the tuning pegs on a violin. Several pegs that can be tuned independently of one another can store far more information than an equivalent number of on/off switches. (144)

Bonner, John T.. The Evolution of Evolution. Journal of Experimental Zoology B. 332/8, 2020. The Princeton University biologist (1920-2019) was an experimental and theoretical pioneer for over 60 years with regard to the developmental course of animal morphogenesis and beyond. His especial subject was slime molds, but akin to D’Arcy Thompson (search) his thought spread across life’s soma and senses and on to human beings. Among his many works are Why Size Matters (2011) and Randomness in Evolution (2013). This posthumous essay is a final clarification and initiative, quite against the mainstream as he notes. While selection is always present, an array of innate structural and metabolic factors are in basic, prior effect. Its significance merited commentaries such as by Stuart Newman, Scott Gilbert, and by Russell Powell and Maureen O”Malley, and others (search here and the journal postings).

In the past, most biologists, myself included, did not think of evolution as changing over time. The wonders of natural selection were always at hand and in operation once there was life. However, with reflection it became obvious that evolution has changed. Life’s course can be separated into four phases, or eras. The first starts with the rise of life on earth, which led to single cells that multiply asexually. The second era takes advantage of sexual reproduction as evolution could now gallop forward because of more diverse offspring for natural selection. The third era begins with the introduction of multicellularity. In the fourth there is a radical innovation: the nervous system which forms in animals. This allowed major changes to proceed such as language that led to what we call civilization and no longer depends on the slow changes of gene‐controlled evolutionary steps. (Abstract)

Evolution has been from small to big, from simple to complex. Besides this obvious point, there has been another neglected but equally important trend in the control – or suppression - of the effect of randomness. In microorganisms, random events are common, but with the increase in size and complexity there has been a corresponding decrease in the role of chance. So there are three phenomena: the increase in size, the increase in complexity, and the decrease in the part played by randomness, all three go together during the course of evolution. (Randomness in Evolution, 7)

Borriello, Enrico, et al. Cell Phenotypes as Microstates of the GRN Dynamics. Journal of Experimental Zoology B. March, 2020. This frontier team of Arizona State University, Center for Biosocial Complex Systems polyscientists EB, Sara Walker, and Manfred Laubichler, with colleagues in other entries, continue to seek and express an implied mathematical source code for life’s oriented emergence. (If every organism has their own ontogenetic code, why should not the whole phylogenetic evolution have its similar evonomic endowment?) Akin to concurrent groups (see Hyunju Kim) attempts are made to finesse new approaches and methods, here an emphasis is on gene regulatory networks, so as to build a fuller case.

The two most fundamental processes describing change in biology - development and evolution - occur over widely different timescales, making them difficult to reconcile within a single frame. Development involves a temporal sequence of cell states controlled by a hierarchy of regulatory structures. It occurs over the lifetime of a single individual, and is associated to the gene expression level change of a given genotype. Evolution, by contrast entails genotypic change through the acquisition or loss of genes, and the emergence of new, environmentally selected phenotypes over the lifetimes of many individuals.

Here we present a model of regulatory network evolution that accounts for both timescales. We extend Boolean models of gene regulatory networks from only describing development to evolutionary processes so as to identify the phenotypes of the cells as the relevant macrostates of the GRN. A phenotype may now correspond to multiple attractors, and its formal definition no longer requires a fixed size for the genotype. This opens a quantitative study of the phenotypic change of a genotype, which is itself changing over evolutionary timescales. We show how specific phenotypes can be controlled by gene duplication events, and how gene duplication events lead to new regulatory structures via selection. It is these structures that enable control of macroscale patterning, as in development. (Abstract edits)

Boulter, Michael. Extinction: Evolution and the End of Man. New York: Columbia University Press, 2002. A paleontologist reviews a large database from the fossil record and finds it to exhibit a power-law fractal pattern. The same shape reappeared in each phylum that was tested. From these results it is theorized that evolution proceeds as a self-organized system. The author goes on to suggest that human beings are in the throes of an extinction process similar to earlier species, but now of our own making.

Bourgine, Paul and Annick Lesne, eds. Morphogenesis: Origins of Patterns and Shapes. Berlin: Springer, 2010. It is of interest that another country, in this case France, can hold a quite different view of evolutionary and embryonic phenomena. Paul Bourgine is a pioneer complex systems advocate, formerly at Ecole Polytechnique and other posts. Annick Lesne is a CNRS, Theoretical Physics of Condensed Matter Laboratory, Paris, senior scientist. This collection by French researchers which ranges from liquid crystals to urban topologies continues the project going back to Aristotle to situate life’s developmental ontogeny and phylogeny within a conducive physical nature. The work is akin to Jamie Davies’ Life Unfolding (2014) by explaining how physical and chemical agencies such as nonequilibrium dynamic systems, self-assembly, fractal geometry, scale invariance, cellular automata, epigenomics, provide a generative agency prior to selection.

A theme that flows through these works is a 21st century fulfillment of the prescience of D’Arcy Thompson, Erwin Schrodinger, Alan Turing, Conrad Waddington, Rene Thom, Max Delbruck, and others, who saw this evident connection. From Morphogenesis by Jonathon Bard in 1990 to the on-going “evo-devo” reunion, one can see a growing sense and veracity of life’s evolution once again as a procreative gestation. Through chapters such as Biological Self-Organization by Way of the Dynamics of Reactive Processes by James Tabony, From Epigenomic to Morphogenetic Emergence, Caroline Smet-Nocca, et al, Animal Morphodynamics by Nadine Peyrieras, and Systems of Cities and Levels of Organization by Denise Pumain, a strong case is forged. The Logic of Forms in the Light of Developmental Biology and Paleontology” by Didier Marchand goes on to state “The Major Body Plans: In the Early Cambrian, Quite Everything was Already in Place.”

What are the relations between the shape of a system of cities and that of fish school? Which events should happen in a cell in order that it participates to one of the finger of our hands? How to interpret the shape of a sand dune? This collective book written for the non-specialist addresses these questions and more generally, the fundamental issue of the emergence of forms and patterns in physical and living systems. It is a single book gathering the different aspects of morphogenesis and approaches developed in different disciplines on shape and pattern formation. Relying on the seminal works of D’Arcy Thompson, Alan Turing and René Thom, it confronts major examples like plant growth and shape, intra-cellular organization, evolution of living forms or motifs generated by crystals. A book essential to understand universal principles at work in the shapes and patterns surrounding us but also to avoid spurious analogies. (Publisher)

Braakman, Rogier and Eric Smith. The Compositional and Evolutionary Logic of Metabolism. Santa Fe Institute Working Paper. 12-08-11, July, 2012. SFI systems scientists, notable vitas appended, entertain theoretical ways to join, root, join, and source, life’s genomic and biological scales within the geological substrates from which they naturally arose. Metabolic networks, broadly conceived, are seen to have a prominent generative, homeostasis-like role in this regard. Within the major evolutionary transitions, their universal, independent dynamics then animate and recur across many levels. As Jeff Clune, et al (2012) attest from another angle, a sequential “recapitulation” becomes evident. The paper is now published in Physical Biology (10/1, February 2013).

In their Acknowledgements, the authors note their main mentor Harold Morowitz, who often advanced life’s metabolism as a premier quality. I first heard Harold speak in 1972 at the New School in NYC on “Biology as a Cosmological Science.” In 1987, Harold spoke at SFI, Stuart Kauffman was in the audience. I asked him there if he would address an annual meeting of the American Teilhard Association, which he did in 1991. His 1992 book was Beginnings of Cellular Life: Metabolism Recapitulates Biogenesis. After many years, exemplified by these incisive studies of Braakman and Smith, verifications of a fertile organic cosmos and earth are truly coming to life.

Metabolism is built on a foundation of organic chemistry, and employs structures and interactions at many scales. Despite these sources of complexity, metabolism also displays striking and robust regularities in the forms of modularity and hierarchy, which may be described compactly in terms of relatively few principles of composition. These regularities render metabolic architecture comprehensible as a system, and also suggests the order in which layers of that system came into existence. In addition metabolism also serves as a foundational layer in other hierarchies, up to at least the levels of cellular integration including bioenergetics and molecular replication, and trophic ecology. The recapitulation of patterns first seen in metabolism, in these higher levels, motivates us to interpret metabolism as a source of causation or constraint on many forms of organization in the biosphere. Many of the forms of modularity and hierarchy exhibited by metabolism are readily interpreted as stages in the emergence of catalytic control by living systems over organic chemistry, sometimes recapitulating or incorporating geochemical mechanisms. (Abstract)

In this review we identify a number of organizing principles behind the major universal structures and functions of metabolism. They provide a simple characterization of metabolic architecture, particularly in relation to microbial metabolism, ecology, and phylogeny, and the major (biogeochemical) transitions in evolution. We often find the same patterns of organization recapitulated at multiple scales of time, size, or complexity, and can trace these to specific underlying chemistry, network topology, or robustness mechanisms. (2)

Understanding either the emergence of life, or the robust persistence of the biosphere, requires understanding life’s capacity for exponential growth. Exponential growth results from proportional self-amplification of metabolic and other networks that have an “autocatalytic” topology. Network autocatalysis is a term used to describe a topological (stoichiometric) property of the substrate network of chemical reactions. In a catalytic network, one or more of the network intermediates is needed as a substrate to enable the pathway to connect to its inputs or to convert them to outputs, but the catalytic species is regenerated by the stage at which the pathway completes. Network-catalytic pathways must therefore incorporate feedback and comprise one or more loops with regard to the in ternally produced molecules. An autocatalytic network is a catalytic network augmented by further reactions that convert outputs to additional copies of the network catalyst, rendering the pathway self-amplifying. (6)

The most important message we hope to convey is the remarkable imprint left by very low-level chemical constraints, even up to very high levels of biological organization. Only seven carbon fixation modules, mostly determined by distinctive, metal-dependent carboxylation reactions, cover all known phylogenetic diversity and provide the building blocks for both autotrophic and heterotrophic metabolic innovation. A similar, small collection of organic or organometallic cofactor families have been the gateways that determine metabolic network structure from the earliest cells to the present. The number of these cofactors that we consider distinct may be somewhat further reduced if we recognize biosynthetic relatedness that leads to functional relatedness or cases of evolutionary convergence dominated by properties of elements. (40)

Eric Smith received a Ph.D. in Physics from the University of Texas at Austin in 1993. From 2000 he has worked at the Santa Fe Institute on problems of self-organization in thermal, chemical, and biological systems. A focus of his current work is the statistical mechanics of the transition from the geochemistry of the early earth to the first levels of biological organization. Rogier Braakman My scientific training grounds were the University of Amsterdam where I obtained a M.Sc. in Chemistry, and the California Institute of Technology where I completed a Ph.D. in Chemical Physics. My interests are broadly on how chemical organization evolves in nature. Currently I work on the logic and evolution of early bacterial metabolism and the origin of life using computational and theoretical methods. In the long-term my research goals are centered around developing conceptual frameworks that allow for a meaningful perspective on the evolution of chemical organization from cold dark interstellar clouds to complex multicellular organisms and ecosystems.

Brun-Usan,, Miguel, et al. Beyond Genotype-Phenotype Maps: Toward a Phenotype-Centered Perspective on Evolution. BioEssays. August, 2022. Lund University, Sweden, University of Southamption, UK and University of Lyon, France including Tobias Uller contribute a thorough, graphic hypothesis as a way to surmount the conflicts and misunderstandings that inhibit a viable union of life’s evolutionary aspects with the somatic development of organisms. The paper is much a result of a 2018 Integrating Development and Inheritance workshop at the Santa Fe Institute.

Evolutionary biology is paying increasing attention to the mechanisms that enable phenotypic plasticity, evolvability, and extra-genetic inheritance. Yet, there is a concern that these phenomena are not well integrated within evolutionary theory. Understanding their implications would require focusing on phenotypes and their variation, but this does not always fit well with the prevalent genetic representation that screens off developmental mechanisms. Here, we instead use development as a starting point, and represent it in a way that allows genetic, environmental and epigenetic sources of phenotypic variation to be independent. We show why this approach illumes the consequences of both genetic and non-genetic phenotype determinants, and note future areas of empirical and theoretical research

Calcott, Brett and Kim Sterelny, ed. The Major Transitions in Evolution Revisited. Cambridge: MIT Press, 2011. The volume is a decadal update upon this major theoretical advance, now much accepted, which still struggles with a nested scale of being and becoming from microbe to man at odds with prior Darwinian tenets. Players such as Daniel McShea, Samir Okasha, Peter Godfrey-Smith, and others wonder about its greater or lesser significance – is it really there, are the levels equal, what if anything drives its form, how about an evolving informational cause for each stage, and so on. While the overall pattern seems to evince an inherent self-organization, only one chapter by University of Adelaide philosopher Pamela Lyon touches upon complex dynamical systems.

A worthwhile extension, led by Richard Michod, is to recognize a relative manifest “individuality” across the processional sequence. By this view, an “Evolutionary Transition in Individuality” or ETI persuasion is considered in several essays. A summary retrospective by Eors Szathmary and Chrisantha Fernando goes on to note how this multilevel model has provided a working structure for life’s evolutionary emergence, which is currently spawning further ramifications with regard to neuronal, linguistic, behavioral areas.

In 1995, John Maynard Smith and Eörs Szathmáry published their influential book The Major Transitions in Evolution. The "transitions" that Maynard Smith and Szathmáry chose to describe all constituted major changes in the kinds of organisms that existed but, most important, these events also transformed the evolutionary process itself. The evolution of new levels of biological organization, such as chromosomes, cells, multicelled organisms, and complex social groups radically changed the kinds of individuals natural selection could act upon. Many of these events also produced revolutionary changes in the process of inheritance, by expanding the range and fidelity of transmission, establishing new inheritance channels, and developing more open-ended sources of variation. The contributors discuss different frameworks for understanding macroevolution, prokaryote evolution (the study of which has been aided by developments in molecular biology), and the complex evolution of multicellularity. (Publisher)

Callebaut, Werner and Diego Rasskin-Gutman, eds. Modularity: Understanding the Development and Evolution of Natural Complex Systems. Cambridge: MIT Press, 2005. After an Introduction: The Ubiquity of Modularity, three sections consider Evo-Devo: The Making of a Modular World, Evo-Patterns: Working Toward a Grammar of Forms, and Modularity of Mind and Culture. In the past decade, an array of research studies find that life evolves from genetic molecules to multicellular organisms, neural intelligence, and social commerce by way of individual modular components and processes. These results are seen to confirm the system theories of Nobel laureate Herbert Simon that such a nested hierarchy is the most economical method. This self-organizing structural tendency exists on its own prior to selection and provides another formative, and directional quality. A typical article by Daniel McShea and Carl Anderson, The Remodularization of the Organism, diagrams an emergent nest from prokaryotes to “individuated colony,” which is quite different from the aimless course of the Darwinian Modern Synthesis.

Patterns permeate nature at all levels of organization. From molecules in a cell to organs in a body, from animals in a colony to ecosystems in the biosphere, patterns exist everywhere. But patterns are also the realm of art and human enterprise. Thus, we recognize a sense of universality in patterns…. The fabulous limb of a dinosaur, the mighty limb of an elephant, and the gentle hand of Mona Lisa are all the product of millions of years of evolution, are all the same pattern. (Editors, 181) A striking feature of nature is the existence of common themes that recur over and over in fundamentally different systems. (181)

If modularity is an unavoidable design feature of organic life, then we should expect a series of phenomena to recur over and over in different lineages: seriality, redundancy, specialization, and integration. (Rasskin-Gutman, 209) Ever since the appearance of life on Earth, evolution has been operating over units of change constituting variations on the same theme. (210)

Callebaut, Werner, ed. Biological Theory. Cambridge: MIT Press, 2006. A new journal which plans to integrate developmental, evolutionary and cognitive aspects. The first issue, Winter 2006, is available on the publishers website and contains a wide array of inaugural articles. But an observation seems in order – while in physics a theoretical basis is understood, biology has long had to make excuses for one, (earlier such journals have come and gone) for within our materialist cosmos, life is, incorrectly, held to appear and evolve so haphazardly that it could not have a lawful dimension.

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