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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

Dennett, Daniel. Freedom Evolves. New York: Viking, 2003. The Tufts University philosopher of consciousness here defends the emergence of free will in evolution since this attribute possesses much survival value. Through insightful argument within a “naturalism” perspective, an increasing volition is seen to appear that is neither determined nor supplants the soul. It is worth contrasting this view with Dennett's 1995 book Darwin's Dangerous Idea which argued that vicarious selection is all that is going on.

Denton, Michael, et al. The Protein Folds as Platonic Forms: New Support for the Pre-Darwinian Conception of Evolution by Natural Law. Journal of Theoretical Biology. 219/3, 2002. A notable article because it attempts to set evolutionary theory in a philosophical context. The authors believe they have found in the geometries that protein molecules can take an evidence of “pre-existing” physical constraints. This approach is claimed to recover the pre-Darwinian mindset of the development of life as an expression of independent forms or archetypes (per Richard Owen) as ordained by natural law. These results counter the Darwinian view of natural selection by statistical chance alone by recognizing the presence of innate “constructional paths.” The work received notice in a short piece in the journal Nature, 410/417, 2002.

Depew, David and Bruce Weber. Darwinism Evolving. Cambridge: MIT Press, 1995. A large volume toward a more complete evolutionary synthesis by its expansion to include the “dynamical systems theory” of nonequilibrium thermodynamics, developmental paths, and innate self-organization.

Devitt, Michael. Resurrecting Biological Essentialism. Philosophy of Science. 75/3, 2008. It amazes how academia polarizes by opposing the evident, indispensible presence of an independent, universal source with groundless, aimless contingency. A prime reason that is rarely admitted is an overarching physical universe which does contain any creative agency. The CCNY philosopher bravely presses on by contending such an essence is broadly genetic in kind, which can then resolve the issue.

The article defends the doctrine that Linnaean taxa, including species, have essences that are, at least partly, underlying intrinsic, mostly genetic, properties. The consensus among philosophers of biology is that such essentialism is deeply wrong, indeed incompatible with Darwinism. I argue that biological generalizations about the morphology, physiology, and behavior of species require structural explanations that must advert to these essential properties. (Abstract, 344)

Di Bernardo, Mirko. Natural Selection and Self-Organization in Complex Adaptive Systems. Rivista di Biologia/Biology Forum. 103/1, 2010. Along with Gregorcic and Jerman in this journal and herein, a University of Rome biologist joins the worldwide effort to recast and reinform life’s evolutionary advance by way of such “immanent” natural laws. So is achieved one more indiciative melding and expansion via the universal presence of these genome-like dynamical propensities.

In the light of all that has been said, it is clear how Darwin’s theory, mostly centralized on the natural selection principle, does not take into account the deep self-organization processes, that is those processes characterized by a mysterious teleonomy. For this reason his theory is not able to explain those highly complex, unpredictable phenomena which cannot be measured by human reasons, such as the dynamic systems evolution and the stochastic processes of genic expression. (107)

Dokholyan, Nikolay and Eugene Shakhnovich. Scale-Free Evolution: From Proteins to Organisms. Koonin, Eugene, et al. Power Laws, Scale-Free Networks and Genome Biology. Berlin: Springer, 2007. Researchers at the University of North Carolina and Harvard University survey life’s complex emergence and find a deep, constant similarity across widely disparate domains. A common structure across many nested stages could then be the characteristic result from an inherent self-organization at work prior to selection. (See also Scaling Laws in the Functional Content of Genomes by Erik van Nimwegen in the present volume.) Be advised there is an earlier 2006 edition of the book with the same title. This evolution revolution due to an international collaboration is now itself becoming theoretically robust and augurs for a 21st century genesis synthesis.

An important consequence of this study was the observed correlation between the Darwinian divergent evolution of organisms and the evolution of proteins. Such correlation couples two basic biological scales – microscopic (proteins) and macroscopic (organisms). The fact that these scales are coupled suggests a truly scale-free evolution of molecules and organisms. It also signifies of the single unifying law that governs evolution of proteins and organisms. (99)

One striking observation is the scale-free organization of the PDUG – protein structural space – which is signified by hierarchical relations between structurally similar proteins. The emergence of power-law scaling of the PDUG connectivity is the result of evolutionary dynamics that is as robust at the scale of specific proteomes or at the scale of all organisms. The correlation between structural organization of proteomes and appearance of new organisms (speciation) also suggest a truly universal “scale-free” evolutionary dynamics, whereby the appearance of new protein fold families is parallel to appearance of new species. (102)

Doursat, Rene. The Growing Canvas of Biological Development. International Conference on Complex Systems. Quincy, MA, 2006. A University of Nevada, Reno, computer scientist finds embryos to develop due to an expanding lattice of gene regulatory networks which iteratively generate multiscale patterns. Doursat’s website, www.cse.unr.edu/~doursat, contains similar papers on self-organized neocortex networks. Abstracts and papers from this biannual six day meeting can be found at the New England Complex Systems Institute site: www.necsi.org.

The spontaneous making of an entire organism from a single cell is the epitome of a self-organizing, decentralized complex system. (1)

Duclos, Kevin, et al. Investigating the Evolution and Development of Biological Complexity under the Framework of Epigenetics. Evolution & Development. 21/5, 2019. University of Calgary biologists KD, Jesse Hendrikse and Heather Jamniczky first note an impasse with regard to explanations of life’s intricate emergence by the nucleotide code alone. It is here proposed that recently understood epigenetic influences might offer a promising broadening of these studies.

Dupre, John. The Role of Behaviour in the Recurrence of Biological Processes. Biological Journal of the Linnean Society. 112/2, 2014. In this special issue, the University of Exeter, Center for Genomics in Society, ethicist presses two main points. It is said that because of the arcane density of Alfred North Whitehead’s (1861-1947) writings, his holistic sense of an organically emerging universe has not be appreciated or availed. But in fact this respected “process philosophy” well expresses a deep essence of living systems. Again it is the spontaneous cellular and organism interactions that most distinguishes. It is then averred that such similar patterns and processes recur over and over in kind at each and every scale and case.

This paper examines the evolution of behaviour within a general perspective that sees evolution as the recurrence of processes, facilitated by a variety of behavioural and material inputs into development throughout the life cycle. The paper explores the ways in which behaviour is integrated into the reproduction of these developmental processes. One important conclusion of the analysis is that there is no reason to suppose that the rate of evolutionary change is limited, as evolutionary psychologists, in particular, have supposed, by the mechanisms for genetic transmission. This analysis also contributes to a broader picture which recognizes that biological entities are typically the sites of intersection of multiple processes, often on very different time scales. This is, indeed, a central reason why (more or less stabilized) processes must be treated as more fundamental than stable things in biology. The paper concludes with some reflections on how best to understand the flexibility of human nature. (Abstract)

First, I believe we should think of the biological world as most fundamentally and generally composed of processes rather than of individuals or organisms. I shall say a little about this below. Second, I take the central explanandum of evolutionary theory to be the recurrence of such processes. That is to say, what evolve are not just adult organisms, still less genomes but, rather, the full development cycles that connect sequences of such things. These developmental cycles are processes of which adult organisms are time slices, and genomes are parts of time slices. (306)

Edelmann, Jonathon and Michael Denton. The Uniqueness of Biological Self-Organization. Biology and Philosophy. 22/4, 2007. The phrase Natural Genesis first occurred to me from the work of New Zealand biologist Denton as a way to meld contingent selection with innate natural laws and forms. Here he is joined by an Oxford University doctoral candidate in theology to advance this once and future evolutionary vision whence life and human are rerooted in a conducive cosmos, functionally graced by creative temporal dynamics.

The pre-Darwinian conception of a special hierarchy of natural forms underlying the diversity of life and determining the major paths of evolution is consistent with the copious evidence for self-organization cited above. We find the parsimony and beauty of the idea that the basic forms of both the inorganic and the organic realms of nature may finally be shown to result form the same principle of self-organization immensely attractive and unifying. (598)

Erkurt, Murat. Emergence of Form in Embryogenesis. Journal of the Royal Society Interface. Vol.15/Iss.148, 2018. After noting a long history from Aristotle’s preformations to 19th century recapitulations, an Imperial College London mathematician factors in Turing reaction-diffusion, epigenetic influences, gene regulatory networks and a need to recognize “self-organizing operators.” Into the 21st century, by these novel sapiensphere additions life’s evolutionary developmental gestation at term gains a definitive credence.

The development of form in an embryo is the result of a series of topological and informational symmetry breakings. We introduce the vector–reaction–diffusion–drift (VRDD) system where the limit cycle of spatial dynamics is morphogen concentrations with Dirac delta-type distributions. We developed ‘fundamental forms’ from spherical blastula with a single organizing axis (rotational symmetry), double axis (mirror symmetry) and triple axis (no symmetry operator in three dimensions). Using our integrated simulation model with four layers (topological, physical, chemical and regulatory), we generated life-like forms such as hydra. Genotype–phenotype mapping was investigated with continuous and jump mutations. Our study can have applications in morphogenetic engineering, soft robotics and biomimetic design. (Abstract excerpt)

In this paper, we introduced the VRDD system as a novel concept which can generate bodyplans of fundamental forms by self-organization. We then elaborated on an FSM (finite-state machine) model of the genetic regulatory network. The result of VRDD combined with the FSM model is spatial cell differentiation during embryogenesis that can be used for hierarchical modelling of complicated forms. We have demonstrated that our concepts are capable of generating self-organized bodyplans from which we developed life-like organism forms in silico. (10)

Etxeberria, Arantza. Autopoiesis and Natural Drift: Genetic Information, Reproduction, and Evolution Revisited. Artifical Life. 10/3, 2004. The autopoietic processes are said to self-organize and maintain biological systems, where ”self” refers to its whole network of recursive processes, prior to selection effects. These innate dynamics are seen to exist independently of substrate and history.

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