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

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.

Muro, Enrique, et al. The emergence of eukaryotes as an evolutionary algorithmic phase transition. PNAS. 122/13, 2025. By virtue of new instrumental Universidad Politécnica de Madrid led by Jordi Bascompte can now illume and describe just how life’s long microbrial age was finally able to merge onward to nucleated eukaryiotic cells. As the quotes say, this advance was found to involve an mathemathic equations in the form of of algorithmic computations which fostered a novel, ascendant phase of symbiotic unions as long advocated by Lynn Margulis.

For half the history of life on Earth, the complexity of organisms was limited to prokaryotic cells such as contemporary bacteria. The process by which genes are activated was entirely regulated by proteins. This set up a limit on cellular complexity, as even larger proteins became computationally unfeasible. The eukaryotic cell with its membrane nucleus finally emerged due to a conserved process of gene growth and a change in genetic regulation. This increase in cellular complexity which occurred a relatively abrupt manner opened up the path toward multicellular organisms. (Significance)

The origin of eukaryotes represents one of the main events in evolution since it led to multicellular organisms. Yet, it remains unclear how existing regulatory mechanisms of gene activity were transformed to allow this increase in complexity. Here, we address analyze the length distribution of proteins for 6,000 species across the tree of life. We then found a scale-invariant relationship naturally originates through a multiplicative process of gene growth across the entire evolutionary history. Our results indicate that this original advance was due to an algorithmic phase transition similar to search algorithms involved in engendering larger proteins. (Abstract)

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)

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)

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