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

Delisle, Richard, ed.. Natural Selection: Revisiting its Explanatory Role in Evolutionary Biology. Switzerland: Springer, 2021. The subject book is part of a new Springer series Evolutionary Biology: New Perspectives which is also edited by the University of Lethbridge, Canada philosopher. As the quotes allude, the intent is to gather and report a historic, overdue revolution far beyond Darwinism which is open to and can include the many advances of the later 20th century and in the 21st century. (See our Chapter V for a long litany and documentation.)

Evolutionary biology has been a remarkably dynamic area since its foundation. Its true complexity, however, has been concealed in the last 50 years under an assumed opposition between the "Extended Evolutionary Synthesis" and an "Alternative to the Evolutionary Synthesis". This multidisciplinary book series aims to move beyond the notion that the development of evolutionary biology is structured around a lasting tension between a Darwinian tradition and a non-Darwinian tradition, once dominated by categories like Darwinian Revolution, Eclipse of Darwinism, Evolutionary Synthesis, and Post-Synthetic Developments. (Series summary)

This book contests the general view that natural selection constitutes the explanatory core of evolutionary biology. It invites the reader to consider an alternative view which favors a more complete and multidimensional interpretation. The 1950s Modern Synthesis to date ihas two main bases: (1) Gradual evolution due to small genetic variations oriented by natural selection, a process leading to adaptation and (2) Evolutionary trends and speciation events as macroevolutionary events from processes and mechanisms occurring at a microevolutionary level. But if one reads the new papers herein by biologists, historians and philosophers, this decades old school is being set aside in preparation for a dynamic developmental paradigm. (Natural Selection)

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)

Doolittle, W. Ford. Darwinizing Gaia: Natural Selection and Multispecies Community Evolution. Cambridge: MIT Press,, 2024. The author is an esteemed biologist who for many years was a professor at Dalhousie University in Nova Scotia. But he was notably resistant since the 1980s to this view that living systems can regulate and maintain themselves on a planetary scale. Now four decades later when evolutionary understandings have moved beyond Darwinian strictures (W. Veit, et al), a more considerate acceptance is indeed possible. However, in so doing most of the book is a latest, thorough survey to date of these theoretical frontiers. Ten chapters such as Unresolved Conflicts in Darwinism, Holobiosis, Extended Phenotypes, Replicators and Interactors and especially Evolutionary Transitions in Individuality present a topical discussion of our mid-paradigm shift mix (per T. Kuhn) of both vested and replacement versions.

In the 1970s, James Lovelock's Gaia Hypothesis proposed that living organisms developed in tandem with their inorganic surroundings so to form a complex, self-regulating system. But evolutionary biologists still consider the theory problematic. In Darwinizing Gaia, W. Ford Doolittle, one of evolutionary and molecular biology's most prestigious thinkers, reformulates what evolution by natural selection is while legitimizing the controversial Gaia Hypothesis. As the first book attempting to reconcile Gaia with Darwinian thinking, and the first on persistence-based evolution, Doolittle's clear, innovative position broadens evolutionary theory by offering potential remedies for Gaia's theoretical challenges

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)

Duran-Nebreda, Salva, et al. Duran-Nebreda, Salva, et al. On the multiscale dynamics of punctuated evolution.. Trends in Ecology and Evolution. 39/8, 2024. Institut de Biologia Evolutiva, Barcelona, University of Tennessee, Vilnius University, Lithuania, American Museum of Natural History and Texas A&M University including Blai Vidiella, Sergi Valverde and Nils Eldredge himselfwho in 1972 along with Stephen Jay Gould formulated the original theory that life’s long developmental course seems to have proceeded by way of extended quiet periods interrupted by bursts of novel forms and properties. After a half century of wide and deep quantitative studies, this review indeed finds a broad semblance of such episodic patterns.

For five decades, paleontologists, paleobiologists, and ecologists have investigated patterns of punctuated equilibria in biology. Here, we step outside those fields and summarize recent advances in the theory of and evidence for this phenomena gathered from current observations in geology, molecular biology, genetics, anthropology, and sociotechnology. Altogether, our findings lead to a more general theory that we refer to as punctuated evolution. The quality of recent datasets support this expanded view in a way that can be modeled across a vast range from mass extinctions in ages past to the possible Anthropocene futures. (Abstract)

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