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

Melo, Diogo, et al. Modularity: Genes, Development, and Evolution. Annual Review of Ecology, Evolution and Systematics. 47/463, 2016. Some two decades after life’s beneficial employ of modular components was first noticed (search Gunter Wagner), biologists Melo and Gabriel Marroig, University of Sau Paulo, with Arthur Porto, Washington University, and James Cheverud, Loyola University Chicago, commend their ubiquitous, essential presence across life’s dynamic organismic and phylogenetic development.

Modularity has become a central concept in evolutionary biology. A system is modular if it can be divided into multiple sets of strongly interacting parts that are relatively autonomous with respect to each other. This concept has been applied in developmental biology, in which modules either are different parts of the embryo that interact with each other, as with induction and morphogenesis, or are sets of interacting molecules that act independently in the patterning of multiple tissues. In this review, we focus on the role of variational modules in evolutionary processes. Variational modules are sets of traits that vary together and somewhat independently from other modules. (464)

Mesoudi, Alex, et al. Is Non-genetic Inheritance Just a Proximate Mechanism? A Corroboration of the Extended Evolutionary Synthesis. Biological Theory. Online February, 2012. It is not surprising that evolutionary theory, and most science itself, seems caught in the same rancor of strident positions and personalities as politics and climate change. This paper by eleven senior researchers - along with Mesoudi, Simon Blanchet, Anne Charmantier, Étienne Danchin, Laurel Fogarty, Eva Jablonka, Kevin Laland, Thomas J. H. Morgan, Gerd Müller, John Odling-Smee, and Benoît Pujol, from the UK, France, USA, Israel, and Austria – strongly confronts vested attacks on their nascent views of an expanded, pervasive sense of “genomic” influences. From a bevy of research findings beyond these authors, nucleotide genes are no longer “ultimate” with all other effects as peripheral “proximate.” Over the last decade what is considered “genetic” has shifted in emphasis from DNA molecules to AND regulatory networks, and onto epigenetic, neural, cognitive, behavioral, societal, and environmental effects. But these frontier findings have come under harsh criticism by old guard deniers and distorters, fixated on the 1950s modern synthesis, even though a 21st century major revision is widely called for. But the charge by British biologists Tom Dickins and Nick Barton that this project impugns “real science” is most rejected. A resolve might best be to proceed apace, which this site tries to report and document, toward a procreative genesis synthesis at home in a conducive cosmos, a once and future “universal gestation” that Charles Darwin and his day actually abided in.

What role does non-genetic inheritance play in evolution? In recent work we have independently and collectively argued that the existence and scope of non-genetic inheritance systems, including epigenetic inheritance, niche construction/ecological inheritance, and cultural inheritance—alongside certain other theory revisions—necessitates an extension to the neo-Darwinian Modern Synthesis (MS) in the form of an Extended Evolutionary Synthesis (EES). However, this argument has been challenged on the grounds that non-genetic inheritance systems are exclusively proximate mechanisms that serve the ultimate function of calibrating organisms to stochastic environments.

In this paper we defend our claims, pointing out that critics of the EES (1) conflate non-genetic inheritance with early 20th-century notions of soft inheritance; (2) misunderstand the nature of the EES in relation to the MS; (3) confuse individual phenotypic plasticity with trans-generational non-genetic inheritance; (4) fail to address the extensive theoretical and empirical literature which shows that non-genetic inheritance can generate novel targets for selection, create new genetic equilibria that would not exist in the absence of non-genetic inheritance, and generate phenotypic variation that is independent of genetic variation; (5) artificially limit ultimate explanations for traits to gene-based selection, which is unsatisfactory for phenotypic traits that originate and spread via non-genetic inheritance systems; and (6) fail to provide an explanation for biological organization. We conclude by noting ways in which we feel that an overly gene-centric theory of evolution is hindering progress in biology and other sciences. (Abstract)

Michod, Richard. Darwinian Dynamics. Princeton: Princeton University Press, 1999. The University of Arizona biologist elucidates the emergent, cooperative structures and processes of the new multiphase evolutionary theory.

Life exists as hierarchically nested levels of organization in which higher level units are composed of lower-level units (gene, chromosome, genome, cell, multicellular organism, society). My book is concerned with the study of cooperation and the principles that guide the emergence of higher levels of organization. I have tried to show that there is a common set of principles and problems that bind the study of levels of organization as disparate as the gene, the cell, the multicellular organism and whole societies. (xi)

Miller, William B.. Cognition, Information Fields and Hologenomic Entanglement: Evolution in Light and Shadow. Biology. 5/2, 2016. The author, a Northwestern University Medical School physician and artist now reside in Arizona and lists himself as an independent researcher. His 2013 book The Microcosm Within is available on Amazon, see www.themicrocosmwithin.com/author for more info. As included in a Beyond the Modern Evolutionary Synthesis collation, the paper is a good example of an incipient genesis synthesis by way of 21st century expansions into physical nature, an informational basis, a cerebral cast, along with an integral genomics from universe to microbes to human persons. For a further update see Biological Information Systems: Evolution as Cognition-Based Information Management in Progress in Biophysics and Molecular Biology (online December 2017)

As the prime unification of Darwinism and genetics, the Modern Synthesis continues to epitomize mainstay evolutionary theory. Many decades after its formulation, its anchor assumptions remain fixed: conflict between macro organic organisms and selection at that level represent the near totality of any evolutionary narrative. However, intervening research has revealed a less easily appraised cellular and microbial focus for eukaryotic existence. It is now established that all multicellular eukaryotic organisms are holobionts representing complex collaborations between the co-aligned microbiome of each eukaryote and its innate cells into extensive mixed cellular ecologies. Each of these ecological constituents has demonstrated faculties consistent with basal cognition. Consequently, an alternative hologenomic entanglement model is proposed with cognition at its center and conceptualized as Pervasive Information Fields within a quantum framework. Evolutionary development can then be reconsidered as being continuously based upon communication between self-referential constituencies reiterated at every scope and scale. (Abstract)

Minelli, Alessandro and Thomas Pradeu, eds. Towards a Theory of Development. Oxford: Oxford University Press, 2014. After two decades of a movement to reunite evolution and embryology, aka evo-devo, into the 2010s it is recognized that the project needs a more formal engagement. The editors, an emeritus University of Padova zoologist and a Paris-Sorbonne University philosopher of biology, assemble leading scientists to cover the range of issues such as morphogenetic fields, landscape metaphors, mechanisms, cell differentiation, selection effects, scaffolds, gene regulatory networks, and a microbial basis. Notable chapters could be General Theories of Evolution and Inheritance, but not Development? by Wallace Arthur, Physico-Genetics of Morphogenesis by Stuart Newman, and Formalizing Theories of Development by Scott Gilbert and Jonathan Bard (search).

Minugh-Purvis, Nancy and Kenneth McNamara, eds. Human Evolution Through Developmental Change. Baltimore: Johns Hopkins University Press, 2002. On the reunion of individual ontogeny and species phylogeny in light of variations in embryo developmental rate and timing, known as heterochrony.

Mitchell, Sandra. Biological Complexity and Integrative Pluralism. Cambridge: Cambridge University Press, 2003. A University of Pittsburgh philosopher of science argues for a better description of group level, superorganic selection as due to the effective action of complex dynamics. In this view, a self-organizing propensity necessarily exists prior to selective forces. As populations such as social insects organize themselves, the process spontaneously involves a specialization or division of tasks, which then facilitates sociality.

Self-organization refers to a family of agent-based model for generating “order” at a higher level from the interaction of components at a lower level without requiring the resulting structure be coded for in genetic blueprints or be solely a result of centralized control structures…..Division of labor emerged “spontaneously” from the self-organizing dynamics of our model. (38)

Morales, J. Serano, et al. From embryos to embryoids: How External Signals and Self-Organization Drive Embryonic Development. Stem Cell Reports. 16/1039, 2021. Into this decade, Andalusian Center for Developmental Biology, Seville, Spain researchers post a robust, graphic explanation of how even life’s gestational stages across Metazoan lineages can now be well appreciated to occur by nature’s universal procreative informed and guided agencies. The second quote is good recognition of the 21st century revolution.

Embryonic development has been seen as an inductive process directed by exogenous maternal inputs and extra-embryonic signals. Increasing evidence, however, is showing that embryogenesis involves endogenous self-organization. Recently, this self-organizing potential has been highlighted by a number of stem cell models known as embryoids that can recapitulate different aspects of embryogenesis in vitro. Here, we review these embryoid self-organizing behaviors and seek to reconcile them with classical knowledge of developmental biology. This analysis proceeds in support of embryonic development as a guided self-organizing process, which are controlled by both exogenous signals and endogenous self-organization. (Abstract)

In recent years, it has been shown that three-dimensional cultures of stem cells can spontaneously form complex biological structures that resemble organs (organoids) and embryos (embryoids). We are currently faced with the challenge of reconciling new evidence for embryonic self-organization with classical knowledge of developmental biology. We begin by presenting the different exogenous inputs and endogenous processes that control embryonic development. (1) Finally, we present a multidisciplinary approach to study embryonic self-organization, which combines experiments on embryoids, quantitative biology, and computational modeling. We conclude by proposing that a deeper knowledge on self-organization will be key to devise novel bioengineering strategies to control and improve embryoid development. (1)

Muller, Gerd and Stuart Newman. Editorial: Evolutionary Innovation and Morphological Novelty. Journal of Experimental Zoology. 304B/485, 2005. An introduction to a series of articles that cite advances in developmental biology (aka evo-devo) about a range of influences other than random mutation and selection as the deep source of novel Metazoan form.

Thus, while natural selection may act on any morphological variant which is associated with genetic variation, the origination of specific, phenotypic constructional elements depends on systems-level mechanisms which may act after, or even before the mutations with which they become associated by natural selection. (486) Recent appreciation of striking discordances between genetic and morphological evolution, unexpected phenotypic consequences (often none) of null mutations of key morphoregulatory genes, and new theoretical insights into self-organizing processes pertaining to living tissues, have focused new interest on generative mechanisms of biological form that extend beyond, and in turn, reflect back upon, the genetic level. (486)

Muller, Gerd and Stuart Newman, eds. Origination of Organismal Form. Cambridge: MIT Press, 2003. Darwinian evolution emphasizes incremental genetic change which applies to the maintenance and variation of morphology. How bodily form originates in the first place is not addressed, which requires a conceptual expansion to include epigenetic effects such as environmental, biochemical properties, geometric topologies and so on. These activities involve the dynamics of complex, self-organizing systems as a prior, generative factor to winnowing selection.

As the collected papers range over four areas – phylogenetics, genetics, development and morphological change – they portend a major revision in evolutionary theory. Much more than a gradual, contingent drift is going on. In this “post-genomic” synthesis the same body plans and organs repeat over and over (in terms of homology, homoplasy, modularity) which describes a more lawful, genesis-like process. In Newman's own paper, “From Physics to Development: The Evolution of Morphogenetic Mechanisms,” he observes that the earliest rudimentary organisms arose from and reflect their physical substrate.

Nachtomy, Ohad, et al. Leibnizian Organisms, Nested Individuals, and Units of Selection. Theory in Biosciences. 121/2, 2002. Gottfried Wilhelm Leibniz’s 17th century philosophy of life and nature as a hierarchical nest of symbiotic monads (individuals) provides a good historical context for new understandings of emergent evolutionary transitions which indeed take on this traditional structure.

This model stresses activity and pluralism: it accepts simultaneous co-existence of individuals at different levels, nested one within the other. (205)

Nehaniv, Christopher, ed. Mathematical and Computational Biology: Computational Morphogenesis, Hierarchical Complexity and Digital Evolution. Providence, RI: American Mathematical Society, 1997. Reports from a conference at the University of Aizu, Japan that gather many novel insights beginning to flow in from nonlinear theories.

Thus the workshop sought to provide a multi-disciplinary forum in which researchers from various fields could discuss and develop the ideas relating biology, symbiogenesis, autopoiesis, self-reproducing and self-maintaining systems, constructive biology, computational morphogenesis… (x-xi)

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