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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

Ganesan, A. Epigenetics: The First 25 Centuries. Philosophical Transactions of the Royal Society B. Vol. 373/Iss. 1748, 2018. A University of East Anglia scientist introduces a collection from an European Union seminar Epigenetic Chemical Biology (Action CM 1406), held in London in May 2017. Some papers are Epigenetic Drug Discovery, Impact of Dietary Gut Microbial Metabolites on the Epigenome, and Protein Methyl/Transferase Inhibitors as Precision Cancer Therapeutics. With a Readers, Writers and Erasers subtitle, the broader intent of these advances was a new informed phase of palliative and biomedical innovations.

Epigenetics is a natural progression of genetics as it aims to understand how genes and other heritable elements are regulated in eukaryotic organisms. The history of epigenetics is briefly reviewed, together with the key issues in the field today. This themed issue brings together a diverse collection of interdisciplinary reviews and research articles that showcase the tremendous recent advances in epigenetic chemical biology and translational research into epigenetic drug discovery. (Abstract)

Epigenetics refers to dynamic changes that occur at the DNA, RNA and protein level in eukaryotes. Epigenetics is at the heart of gene regulation and determines which genes are activated or silenced. It is of great importance fundamentally and has many exciting translational aspects including therapeutics, diagnostics, stem cell research, microbial pathway engineering and agriculture. (Action CM 1406 Fact Sheet)

Gawne, Richard, et al. Unmodern Synthesis: Developmental Hierarchies and the Origin of Phenotypes. BioEssays. Online November, 2017. A review of many problems that beset the mid 20th century “modern” version, along with criticisms of present efforts to amend, revise, and extend. Once again the practitioners seem compromised by narrow, piecemeal views which do not allow a full worldwide survey which could include self-organizing complexities and a lot more.

The question of whether the modern evolutionary synthesis requires an extension has recently become a topic of discussion, and a source of controversy. We suggest that this debate is, for the most part, not about the modern synthesis at all. Rather, it is about the extent to which genetic mechanisms can be regarded as the primary determinants of phenotypic characters. We argue that the methodology of the modern evolutionary synthesis has been enormously successful, but does not provide an accurate characterization of the origin of phenotypes. For its part, the extended synthesis has yet to be transformed into a testable theory, and accordingly, has yielded few results. We conclude by suggesting that the origin of phenotypes can only be understood by integrating findings from all levels of the organismal hierarchy. (Abstract)

Gilbert, Scott and Jonathan Bard. Formalizing Theories of Development: A Fugue on the Orderliness of Change. Minelli, Alessandro and Thomas Pradeu, eds. Towards a Theory of Development. Oxford: Oxford University Press, 2014. The Swarthmore College embryologist and an emeritus University of Edinburgh physiologist propose a metaphor of a musical score for genetic endowment which via nested “recursive subroutines” can improvise and generate anatomical form and growth. As the synopsis notes, this interplay of score and symphony implies an upward and downward movement amenable to formal graph theory.

This chapter looks at developmental biology as performance. Each animal inherits score (the DNA), mechanisms for interpreting of the score, and mechanisms for improvisation should the score be deficient. Developmental causation is found to be both upwards from the genome, downward from the environment, and laterally between cells. Developmental plasticity, organicism, phenotypic heterogeneity, symbiotic co-development, and cytoplasmic localization are each examples of causation from the environment downward. Stereocomplementary relationships are the key components of most developmental interactions. These interactions can be placed into a formal language of graph theory. Morphogenesis can be depicted in the general structure, where nouns cover tissues, molecules and networks and verbs describe processes such as moves, differentiates, grows and apoptoses. This manner of depicting development emphasizes the distributed nature of causality in morphogenesis and can be annotated with associated information or IDs (e.g. cell types, publications, gene-expression data) that link to external online resources that may be regularly updated. This graph approach portrays dynamic processes as the drivers of developmental momentum, and, since the same processes are used many times during development, they can be viewed as modules whose underlying networks are genomic subroutines. (Oxford online summary)

Gilbert, Scott and Sahorta Sarkar. Embracing Complexity: Organicism for the 21st Century. Developmental Dynamics. 219/1, 2000. An attempt to recover the unity of evolution and embryology which goes beyond the 20th century emphasis on a reduction to physical or genetic fragemnts, atom or gene, by recognizing structural interrelations which generate emergent wholes. These elements do not exist in isolation and their contextual environment needs to be factored in. A reciprocity of discrete components and dynamic network is recommended, which is a description of a complex adaptive system.

Ginsburg, Simona and Eva Jablonka. The Teleological Transitions in Evolution: A Gantian View. Journal of Theoretical Biology. 381/55, 2015. An article in a special issue edited by Eors Szathmary about Tibor Ganti (1933-2009): Towards the Principles of Life and Systems Chemistry. Ganti was a Hungarian biochemist who conceived prescient models of life’s origin and nature, as expressed in his The Principles of Life (1971, 2003). Israeli philosophers of science reach across millennia to compare the current tripartite core of metabolism, replication, and membrane with Aristotle’s conception, and with Ganti’s “chemoton” version. In each case, akin to a nascent view of evolution as a neural learning process (search Kouvaris), an oriented manifestation of consciousness can be seen as the ascendant essence. See also Primordial Evolvability, and The Systems Persepctive at the Crossroads between Chemistry and Biology in this issue. By a philosophical reflection, “theoretical biology” quite assumes and requires the presence of a greater, procreative reality of which life, evolution, mind and human persons are an intended, comprehensible phenomenon.

We discuss Gánti׳s approach to the study of minimal living organization, and suggest that his methodology can be applied to the study of the two other major teleological systems described by Aristotle: minimal consciousness (sentience, experiencing) and rationality. We start by outlining Gánti׳s strategy for the case of life: listing the basic characteristics that any living system capable of open-ended evolution must satisfy, developing a dynamic model that instantiates these characteristics (the chemoton), and identifying a capacity of the system (unlimited heredity) that allows the system to dynamically persist over evolutionary time and to be used as a marker of the evolutionary transition to life. We apply Gánti׳s explanatory strategy to the evolutionary transition to minimal consciousness, suggest a transition marker (unlimited associative learning) and discuss the wider evolutionary and philosophical implications of this approach. (Abstract)

Gissis, Snait and Eva Jablonka, eds. Transformations of Lamarckism. Cambridge: MIT Press, 2011. With a subtitle “From Subtle Fluids to Molecular Biology” this volume would seem to be another review of Jean-Baptiste (1744-1829). But based on a 2009 International Workshop on the History and Philosophy of Science in Jerusalem upon the 200th anniversary of J-BL’s opus Philosophie Zoologique, also in the same year as the Darwin anniversaries, and with premier contributions across History, Modern Synthesis, Biology, Philosophy, and Ramifications areas, a significant statement of a 21st century biological revolution is made. And worth noting it is much a woman’s work. Plus the editors, Marion Lamb, Evelyn Fox Keller, Sonia Sultan, Minoo Rassoulzadegan, Simona Ginsburg, and others helped achieve a thorough, insightful edition. For its salient theme is to contrast with, and move beyond, the vested Darwinian mechanism of random, sterile selection alone.

In this regard, as a person of his Romantic age, Lamarck, along with Immanuel Kant (1724-1804) and many others, was a natural philosopher of a vital, dynamic milieu graced by an innate “pour de la nature,” a “power of life,” within a “physical” materiality that spontaneously organized into progressive developmental stages. As Gissis details in her paper, this view endorsed an internal direction, teleology, recapitulation, individually interactive agents, and so on, indeed as a universal gestation. These lights can illume some two centuries later to rehabilitate Lamarck, no longer shelved, as an exemplar of such prior self-organizational forces that the complex system sciences just now increasingly verify.

In this persuasion then, several nascent features are woven. As part of the current reconception of genetic phenomena, a “soft inheritance” via epigenesis, of which Jablonka and Lamb, along with presenter Scott Gilbert are advocates, is now appended. Mathematical biologists Stuart Newman and Ramray Bhat (see quote) evoke a revised vitalism whence matter expresses an inherent evolutionary fertility. These windows then open upon multiple, recurrent levels of life’s nested emergence, aided much by symbiotic assembles. Biophilosopher Ehud Lamm waxes on the whole genome as no longer a collection of genes, but rather a systemic web of dynamic, informative relations. Evelyn Fox Keller (quote) goes on to extol Lamarck as an astute precursor of “nonlinear dynamical systems” at the essence of a once and future, true to life, new evolutionary synthesis.

Lamarck’s own dangerous idea, then was the (dynamical) materialist one of bringing life into the realm of the physical. In the case of evolving multicellular organisms, the physical incorporates self-organization and self-generating complexity (autopoiesis, corresponding to Lamarck’s “power of life”). With increased knowledge of the evolutionary history of developmental systems, therefore, and a better understanding of the physics of complex materials, we can at last appreciate the power of Lamarck’s ideas as he speaks to us across the Darwinian divide. (Newman and Bhat, 166)

Since the turn of the twenty-first century, epigenetic inheritance – the inheritance of cellular phenotypic variations that are not dependent on differences in DNA base sequence – has become an important aspect of pure and applied biological research. In this chapter I present a brief overview of the history of cellular epigenetic inheritance, outline recent evidence showing that it is ubiquitous, and suggest how it legitimizes the notion that soft inheritance is part of heredity and evolution. (215) Dobzhansky’s famous dictum “Nothing in biology makes sense except in the light of evolution” is correct, but it needs to be extended and qualified , for nothing in evolution makes sense except in the light of development. (Jablonka, 224)

The neo-Darwinian synthesis of the twentieth century was concerned with the visible world of plants and animals over the last 550 million years of evolution. It said nothing of the microbial world, where the greatest biochemical and genetic diversity and largest biomass are found. (271) In the microbial realm, central tenets of Darwinism do not apply, and the mode and tempo of evolution resemble “Lamarckian processes” coupled with saltational change. (Jan Sapp, 271)

The examples in this chapter provide evidence that symbiosis and evolution are not separate phenomena. Evolution shapes and selects for symbiosis, while organisms in symbiotic relationships evolve to accommodate one another. Although there is tension between the needs of the individual organisms and the relationships among the symbionts, symbioses continue to exist, implying that symbiosis increases the overall fitness of the individual species involved. (Gilbert, 290)

Is it, in fact, possible to account for the emergence of natural design, of a “self” that can be said to organize – indeed, for the emergence of natural selection itself – from purely physical and chemical processes? Although Darwin did not himself attempt to answer this question, Lamarck did. In fact, one might say that Lamarck saw it as the central problem of evolution. Firmly rejecting any evocation of extranatural causes, he sought a purely physical account of the “power of life,” of its natural tendency to increase complexity, and of the origin of entities that could be said to self-organize.” (Keller, 359)

Glancy, Jonathan, et al. How Self-Organization Can Guide Evolution. Royal Society Open Science. Online November, 2016. Research studies of how rodents (rats and mice) huddle together to keep warm inspire University of Sheffield, Adaptive Behavior Research Group scientists to perceive this communal behavior as a generic case of natural self-organizing phenomena. This write-up follows their 2015 PLoS Computational Biology paper A Self-Organizing Model of Thermoregulatory Huddling (11/9). It concludes with a strong claim that life’s evolution actually appears to be guided by such an intrinsic formative force. Online concurrently with Peter Schuster essay (search), here is one more testament to a genesis synthesis. To wit, a later entry, Self-Organized Criticality in the Evolution of a Thermodynamic Model of Rodent Thermoregulatory Huddling by Stuart Wilson (PLoS Computational Biology 13/1, 2017), reports upon this further quality.

Self-organization and natural selection are fundamental forces that shape the natural world. Substantial progress in understanding how these forces interact has been made through the study of abstract models. Further progress may be made by identifying a model system in which the interaction between self-organization and selection can be investigated empirically. To this end, we investigate how the self-organizing thermoregulatory huddling behaviours displayed by many species of mammals might influence natural selection of the genetic components of metabolism. By applying a simple evolutionary algorithm to a well-established model of the interactions between environmental, morphological, physiological and behavioural components of thermoregulation, we arrive at a clear, but counterintuitive, prediction: rodents that are able to huddle together in cold environments should evolve a lower thermal conductance at a faster rate than animals reared in isolation. (2016 Abstract)

Endotherms such as rats and mice huddle together to keep warm. The huddle is considered to be an example of a self-organising system, because complex properties of the collective group behaviour are thought to emerge spontaneously through simple interactions between individuals. Groups of rodent pups display two such emergent properties. First, huddling undergoes a ‘phase transition’, such that pups start to aggregate rapidly as the temperature of the environment falls below a critical temperature. Second, the huddle maintains a constant ‘pup flow’, where cooler pups at the periphery continually displace warmer pups at the centre. (2015 Abstract)

Gontier, Nathalie. Converging Evolutionary Patterns in Life and Culture. Evolutionary Biology. Online October, 2016. The University of Lisbon philosopher of science introduces a special issue about an increasing notice of nature’s intrinsic, recurrent orderliness. Typical, entries are Cultural Evolution by Alex Mesoudi, Lateral and Vertical Transfer in Biology, Linguistics and Anthropology by Frank Kressing, The Symbiotic Self by Jan Sapp (search) and From the Cell to the Ecosystem by Ricardo Guerrero and Mercedes Berlanga.

The natural world demonstrates signs of spatial–temporal order, an order that appears to us through a series of recognizable, recurring and consecutive patterns, i.e. regularities in forms, functions, behaviors, events and processes. These patterns lend insight into the modes and tempos of evolution and thus into the units, levels, and mechanisms that underlie the evolutionary hierarchy. Contributors to this special issue analyze converging patterns in the biological and sociocultural realm across and beyond classic divisions between micro- and macro-evolution; horizontal/reticulate and vertical evolution; phylogeny, ontogeny and ecology; synchronic and diachronic sociocultural and linguistic research; and tree and network diagrams. Explanations are sought in complexity theory, major transitions of evolution, and process and mechanism approaches to change; and consequences for notions such as “life”, “species”, “biological individuality”, “units” and “levels” of evolution are given. (Abstract)

Gontier, Nathalie. How Macro-Evolutionary Studies Call for an Extended Synthesis. http://aaas.confex.com/aaas/2013/webprogram/Session5756.html. A session at the February 2013 Boston annual AAAS meeting, organized by the University of Lisbon philosopher. Speakers include Douglas Erwin “The Evolution of Evolution: Changing Dynamics in Macroevolution,” Folmer Bokma “Complexity and Limits to Change” and Gontier’s Punctuated Equilibria: A Universal Pattern in Life and Culture.”

When Eldredge and Gould formulated the punctuated equilibria theory, they put several macroevolutionary phenomena on the agenda that were not addressed by the early population geneticists and the founders of the Modern Synthesis. Their theory provides alternative scientific interpretations for the mode and tempo of evolution. Occurring gaps in the fossil record, or the lack of evidence for the existence of intermediate species, are understood as real. And some (living) fossils do not appear to undergo any significant evolutionary change for millions of years, which necessitates the study of stasis. Acknowledging that evolution can occur faster or slower than predicted by Neodarwinians has consequences for how we define species and for determining the levels of evolution. Macroevolutionary studies provide different species concepts and argue that evolution can occur at levels higher than the pheno- or genotype. Today, multiple scholars investigate the causes of evolutionary stasis as well as punctuations, macroevolutionary trends, and how evolution occurs at different hierarchies. In recent years, evidence for macroevolution is also provided from within the field of molecular biology, and the pattern of punctuated equilibrium has been proven to be present in neontological and even sociocultural evolutionary phenomena. The session will examine how macroevolutionary studies call for an extension of the Modern Synthesis and which methodologies and techniques enable the study of macroevolutionary events. (Synopsis)

Gontier, Nathalie and Michael Bradie. Evolutionary Epistemology: Two Research Avenues, Three Schools and a Single, Shared Agenda. Journal for General Philosophy of Science.. 52/2, 2021. University of Lisbon and Bowling Green State University, Ohio scholars edit this latest survey of philosophical endeavors about how to get a read and bead on life’s long developmental course that brought us to such ruminations. Among entries are Cognitive Niche Construction and Extragenetic Information: A Sense of Purposefulness in Evolution by Lorenzo Magnani, Jierarchies, Networks and Causality by N. Gontier, United in Diversity: An Organic Overview of Non-Adaptationist Evolutionary Epistemology by Marta Facoetti, and Principles of Information Processing and natural Learning in Biological Systems by Predrag Slijepcevidic.

This special issue is devoted to the impact and ramifications of current research in evolutionary epistemology, an inter- and multi- disciplinary areas that can be sorted into two inclusive research avenues. One approach is an expansive study of the appropriate comprehension of life’s evolution (see below). The other program, by turns, considers the evolution of epistemology. Since its 1990s origins, EE has adopted three schools of thought: adaptationist, non-adaptationist, and applied EE. Although diverse in outlook, these several versions share and advance similar agendas about how knowledge evolves and relates to the world. (Excerpt)

Biosphere as the Communicative Network The final task is to put all categories of biological systems in the context of the biosphere. Heinz von Foerster argued that information is a purely relational concept that can be actualized only when related to cognitive systems. If we accept his dictum and assume that the biosphere is the supersystem that accommodates all seven categories of biological systems, it becomes the network of communicative interactions between them. The totality of all communicative interactions in the biosphere may be termed the “interactome” as the distributed network of biological information that holds organism–environment altogether. (Predrag S., 240-241)

The term “Epistemology comes from the Greek “episteme” and “logos”. Episteme means knowledge and understanding while logos translates as account or reason. In all historic these historic cases (Plato to B. Russell), epistemology seeks to comprehend one or another kind of cognitive success. (Stanford Encyclopedia)

Goodwin, Brian. Beyond the Darwinian Paradigm. Ruse, Michael and Joseph Travis, eds. Evolution: the First Four Billion Years. Cambridge: Harvard University Press, 2009. In an anniversary volume to celebrate natural selection, an alternative view is included which if fully appreciated would impact and worry all the other chapters. As noted more in Current Vistas, Goodwin broaches an inherent mathematical generativity that Darwin could not have known, (although he did hold to Romantic sensibilities), which antecedes later external impacts. Which one might note changes everything one might note such as what kind of universe – moribund machine or quickening gestation – and defines our epochal shift work to sort this out.

On the basis of the examples presented and the general principles that govern nonlinear dynamics, I shall argue that the processes involved have the consequences that some forms are possible, while others are not. Understanding the origins of the forms that define different species therefore requires that we understand the dynamic processes that generate them, which are not those of natural selection. (300)

Goodwin, Brian. How the Leopard Changed Its Spots. New York: Scribner’s, 1994. From this British structural biologist, an innovative case for a “science of qualities” which can support a “lawful” organic evolution of morphological complexity along with a measure of altruistic behavior.

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