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

Pigliucci, Massimo. An Extended Synthesis for Evolutionary Biology. Annals of the New York Academy of Sciences. Vol. 1168, 2009. A chapter in this The Year in Evolutionary Biology 2009 edition written after the summer 2008 Altenberg workshop, chaired by MP, on an updated theory (proceedings in 2010 from MIT Press). An initial capsule history of evolutionary thought before Darwin to the mid 20th century Modern Synthesis sets the scene. Its nascent revision, not replacement mind you, is underway via more or less additions of contingency and/or necessity, multilevel selection, advanced population genetics, gene network properties, robust modularity, epigenetics, niche construction, self-organized emergence, phenotypic plasticity, and macroevolutionary patterns. A fine agenda, but the effort seems undercut by a preconcluded paradigm that denies any greater (ortho)genesis from which these properties and attributes may innately spring and can find deep explanation.

Pigliucci, Massimo. Do We Need an Extended Evolutionary Synthesis? Evolution. 61/12, 2007. Yes, which is increasingly in the air as a 21st century expansion of the 1950s Modern Synthesis that melded Darwin and Mendel. The State University of New York at Stony Brook biologist states and advances the argument. After a brief history, salient inclusions would be an organism’s development maturation, aka evo-devo, novel sources of epigenetic influence, and especially nature’s propensity to spontaneously complexify, which could add an original organizing force to complement later selection. Good groundwork to identify and join these factors, but a truly interdisciplinary, holistic vista would further blend symbiosis, major transitions, modularity, a vectorial intelligence, individuality, and many other gestational features. For reference, see also Phenotypic Integration, edited by Pigliucci and Katherine Preston (Oxford University Press, 2004).

The field began, in fact, as a theory of forms in Darwin’s days, and the major goal that an ESS will aim for is a unification of our theories of genes and of forms. This may be achieved through an organic grafting of novel concepts onto the foundational structure of the MS, particularly evolvability, phenotypic plasticity, epigenetic inheritance, complexity theory, and the theory of evolution in highly dimensional adaptive landscapes. (2743)

Natural selection, of course, would not thereby be denied, or even relegated to a secondary role, but would interact with self-organization to yield a more powerful theoretical architecture to finally merge the two major tendencies in the history of evolutionary biology: the pursuit of a theory of genes (or, more broadly, inheritance), and that of a theory of form. (2747)

Pigliucci, Massimo and Gerd Muller, eds. Evolution – the Extended Synthesis. Cambridge: MIT Press, 2010. Finally out after two years, the proceedings of the 2008 Altenberg Evolution conference. Although laudable papers by David Sloan Wilson, Eva Jablonka, and others are included, it appears that any sense of really modifying the Modern Synthesis was excluded and not permissible. For one example, "self-organization" is not even in the index. For an update, see The Extended Synthesis Debate in BioScience (64/6, 2014).

Plotkin, Henry. Evolutionary Worlds without End. Oxford: Oxford University Press, 2010. The emeritus University College London psychologist and author of works such as Evolution in Mind (1999) refutes an old but persistent claim that biological and human sciences cannot have intrinsic theories and laws like physics maintains. Indeed, in the 21st century, as evident across the life and cognitive sciences, novel appreciations are being found of deep, constant principles.

So, what is certain is that Rutherford as wrong. Science is not just physics and stamp collecting. Biology, and the social sciences nested within it, are sciences in their own right with the possibility of general theory that does not fall outside physics but of necessity goes beyond it, and which explains the astonishing variety of living forms that have existed, and do exist, on our planet. If there is life in other parts of the universe, and there likely is, then it too will have evolved and be evolving. If that life is sentient, imaginative and collective in the distribution of its knowledge forms and beliefs, then the notion of evolutionary worlds without end is what may be truly universal, and some part of that universality may be the set of general processes that drive these worlds. (190)

Powell, Russell and Maureen O’Malley. Metabolic and Microbial Perspectives on the “Evolution of Evolution". Journal of Experimental Zoology B. Online September, 2019. Boston University and University of Bordeaux philosophers of biology comment on John Bonner’s article with the above title (herein June) for a special issue. But this present paper, alongside structural biologist Bonner himself, Stuart Newman and Scott Gilbert, can illustrate a deep conceptual dichotomy. The major transitions model (see Abstract), along with the nested dimensions view of Eva Jablonka and Marion Lamb, and Newman who goes on to root life in a physical inherency, quite imply a directional procession. However P & O’M’s opening section is Broad Problem 1: Progressivism, which worries that these scalar views are at odds with past, vested denials of any teleological course and aim. As this quandary persists and resists, it begs a 21st century natural philosophy to sort out, clear up, and allow an actual evolutionary gestation to be realized. (See Powell’s new book Contingency and Convergence (MIT Press, Jan. 2020) for more.)

Identifying and theorizing major turning points in the history of life generates insights not only into epochal events but also the processes that bring them about. In his treatment of these issues, John Bonner identifies the evolution of sex, multicellularity, and nervous systems as enabling the “evolution of evolution,” which involves transformations in how life develops. By comparing his framework with two decades of major transitions scale theory, we identify some issues between Bonner's view and the prevailing literature. These problems include implicit progressivism, conceptual disunity, and a limited ability to explain major transformations. In contrast with the “vertical” focus on replication, hierarchy, and morphology that preoccupies most literature on major transitions, we propose a “horizontal” dimension in which metabolism and microbial innovations play an explanatory role in the broad‐scale organization of life. (Abstract)

Prokopenko, Mikhail, et al. Biological arrow of time: Emergence of tangled information hierarchies and self-modelling dynamics. arXiv:2409.12029. By later 2024, ten coauthors from astrophysicists to computational biologists at the University of Sydney, ASU, University of Sussex, UCL, and Oxford including Paul Davies, Joseph Lizier, Geraint Lewis and Fernando Rosas can now post a comprehensive application of 21st century complex network systems theory to an equally expansive synthesis of life’s evolutionary emergence to be at last able to discern a central, orthogenesis-like course. In regard, the major sequential transitions scale provides a definitive, vectorial ascent mostly distinguished by relative genetic prescriptions and regnant individuality at each nested stage. See also On the roles of function and selection in evolving systems by Michael Wong, et al at PNAS (120/43, 2023) for another current intimation.

We study open-ended evolution by focusing on computational and information-processing dynamics underlying major evolutionary transitions. In doing so, we consider biological organisms as hierarchical dynamical systems that generate regularities in their phase-spaces through interactions with an environment. These emergent information patterns can then be encoded within an organism. Our main conjecture is that when macro-scale patterns continue on to micro-scale components, it creates tensions between what is encodable at an evolutionary stage and what may be realisable in the environment. This computation-theoretic argument can then be seen to trace a biological arrow of time. (Abstract excerpt)

In consideration of what the nested transitions have in common, they each involve major changes in individuality and how it perpetuates itself by novel inheritance modes of storing and transmitting information. Examples include replicating molecules which form cells as independent replicators, the DNA genetic code and proteins as enzymes; prokaryotes evolving into eukaryotes with a nucleus, and so on towards multicellularity and eusociality, as well as language and sociocultural evolution. (3)
Finally, we suggested that the biological arrow of time generates an oriented course of “information self-creation” by way of three canonical elements of computation: information preservation (memory/storage), information modification (processing), and information usage (communication). We propose that, in terms of dynamical systems, it is precisely this defined quality that forms a dimension for major evolutionary transitions along the biological arrow of time (23)

Rainey, Paul. Is Evolution Predictable? New Scientist. June 14, 2003. Yes, because it is becoming increasingly realized that prior to Darwinian mutation and selection theres exist “basic design principles of complex systems” which generate “highly similar patterns of evolutionary change.” As a result, many processes with different starting points will converge on a similar result. If life’s tape is played over, there is a high probability that intelligent bipedal, binocular organisms will appear.

Rajpal, Hardik, et al. Quantifying Hierarchical Selection. arXiv:2310.20386. In this 2023 year, seven senior University College London and Pontificia Universidad Catolica de Chile (Pablo Marquet) system biologists including Henrik Jensen, Fernando Rosas and Pedro Mediano, are able to achieve definitive explanations for natural selection in effect on the higher-scale of colony and community groupings. In regard, the Tangled Nature model which Jensen and colleagues have worked out for some years, (search) serves as an explanatory basis.

At what level does selective pressure effectively act? When considering the reproductive dynamics of interacting and mutating agents, it has been debated whether selection should focus on the individual or does it emerge as a consequence of joint adaptation. Here we draw on recent information-theoretic data methods to study high-order structures -- such as groups of species -- in the collective dynamics of the Tangled Nature model of evolutionary ecology. Our results show that this theoretic version can lead to clusters of species that act as a selective group and acquire an informed agency. Overall, our findings support the relevance of hierarchies in evolutionary ecology as they arise from simpler processes of adaptation and selection. (Abstract)

We address these questions by way of information-theoretic tools applied to hierarchical selection in co-evolving species. The basic hypothesis behind these approaches is that if a group of individuals can enhance the prediction of their joint future, they can better adapt and thus survive. Building on these ideas, here we present analyses of simulations of co-evolution dynamics based on the well-studied Tangled Nature model, and investigate if there are conditions under which selection effectively acts at the level of groups of species instead of single species. (2)

Ramalho-Santos, Miguel. Stem Cells as Probabilistic Self-producing Entities. BioEssays. 26/9, 2004. A theoretical framework for stem cell biology based on the concept of autopoiesis as the essential process of self-production.

Reid, Robert G. B. Biological Emergences. Cambridge: MIT Press, 2007. An emeritus Professor of Biology at the University of Victoria, British Columbia writes his 500 page opus which may be the most significant contribution so far to a new evolutionary synthesis. Gaining in strength and credence over the past years, this major expansion beyond neoDarwinian mutation and selection to include the prior impetus of self-organizing dynamics appears to be reaching a critical cohesion. Reid discusses its many influences and evidences across biological realms such as symbiosis from bacteria to ecosystems, modularity, epigenesis, adaptability, connectivity, increasing complexity, and so on. The case is now sufficiently robust for a recovery of a directional “orthogenesis” as a “progressive” hierarchical nest of emergent whole entities. Natural selection, once the only force, fades before this novel “generative” agency. Along the way it is noted that cosmologists in search of a single equation are missing such ramifying biological propensities. While much collaborative translation remains, what is much “in the air” is not only an alternative theory but a view of life’s nested evolutionary genesis to its mindful human phase as meant to be.

Reiskind, Martha, et al. Nothing in Evolution Makes Sense Except in the Light of Biology. BioScience. 71/4, 2021. North Carolina State University, UT El Paso, University of Connecticut, Utah State University, and UT Austin biologists turn to Theodosius Dobzhansky’s 1974 statement as a guide for 2020s considerations about the mega-issue of whether life’s development is an independent, oriented, guided process, or just happenstance. By what method could a valid quantification be achieved? Recent findings of a repetitive convergence in kind from microbes to mammals is a good sign. See also What Prevents Mainstream Evolutionists from Teaching the Whole Truth about How Genomes Evolve? by James Shapiro and Denis Noble in Progress in Biophysics & Molecular Biology (May 2021) for another take. Both papers contain a long glossary of novel indications far beyond neoDarwinism, akin to our listing in Chapter V.

A key question in biology is the predictability of the evolutionary process. If we can correctly predict the outcome of evolution, we may be better equipped to anticipate and manage species’ adaptation to climate change, habitat loss, invasive species, or emerging infectious diseases, as well as improve our basic understanding of the history of life on Earth. In the present article, we ask the questions when, why, and if the outcome of future evolution is predictable. We first define predictable and then discuss two conflicting views: that evolution is inherently unpredictable and that evolution is predictable given the ability to collect the right data. (Abstract)

Relton, Caroline and George Davey Smith. Is Epidemology Ready for Epigenetics? International Journal of Epidemiology. 41/1, 2012. An editorial for a retrospective and review issue, seventy years after Conrad Waddington’s classic “The Epigenotype” article (Endeavor 1942). An array of papers by leading contributors such as Scott Gilbert, Eva Jablonka, and David Haig go on to cite a genetic and biological revolution to recognize how pervasive environmental and developmental influences are between genotype and phenotype. The expanded theory is extolled in other articles as a significant advance for medicine and public health. In regard, “epigenetics” broadly conceived could be seen, as noted by Jablonka and Ehud Lamm, to represent an admission of “network” interconnective, regulatory domains that join and link together all the discrete nucleotide genes.

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