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

Perc, Matjaz, et al. Evolutionary Dynamics of Group Interactions on Structured Populations. Journal of the Royal Society Interface. Online January, 2013. With animals of all fur, fin or feather now known to persistently form and survive better by way of cooperative societies, systems researchers Matjaz Perc, Slovenia, Jesus Gomez-Gardenes and Luis Floria, Spain, Attila Szolnoki, Hungary, and Yamir Moreno, Italy draw upon “statistical physics and network science” to quantify mathematical agencies that these assemblies consistently seem to manifest. A major resource in regard is the game theory approach of Martin Nowak (search) and colleagues, backed up by over 150 references. We cite this work as an exemplary 2012 contribution that notices both a universal repetition across such animal groupings, and their implications of an independent generative origin.

Interactions among living organisms, from bacteria colonies to human societies, are inherently more complex than interactions among particles and non-living matter. Group interactions are a particularly important and widespread class, representative of which is the public goods game. In addition, methods of statistical physics have proved valuable for studying pattern formation, equilibrium selection and self-organization in evolutionary games. Here, we review recent advances in the study of evolutionary dynamics of group interactions on top of structured populations, including lattices, complex networks and coevolutionary models. We also compare these results with those obtained on well-mixed populations. The review particularly highlights that the study of the dynamics of group interactions, like several other important equilibrium and non-equilibrium dynamical processes in biological, economical and social sciences, benefits from the synergy between statistical physics, network science and evolutionary game theory. (Abstract)

Pezzulo, Giovanni and Michael Levin. Top-Down Models in Biology: Explanation and Control of Complex Living Systems above the Molecular Level. Journal of the Royal Society Interface. Vol. 13/Iss. 124, 2016. A Tufts University biologist and a National Research Council, Italy cognitive psychologist consider benefits of perceiving organic, evolving systems from an integral, retrospective vantage. For example, the dynamic regulation of pattern formation in embryogenesis requires new approaches to understand how cells cooperate towards large-scale anatomical goal states. But the paper then worries, as much of evolutionary theory, that this view seems to admit a teleological quality, which is not there nor permitted. As usual there is no sense of any contextual, generative nature that all this manifest activity comes from.

The current paradigm in biology and regenerative medicine assumes that models are best specified in terms of molecules. Gene regulatory networks and protein interaction networks are sought as the best explanations. This has motivated the use of a mainly bottom-up modeling approach which focuses on the behavior of individual molecular components and their local interactions. The companion concept is that of emergence, and it thought that future developments in complexity science can explain the appearance of large-scale order, resulting from the events described by molecular models. (2) However, top-down models, which have been very effectively exploited in sciences such as physics, computer science and computational neuroscience, present a complementary strategy. Top-down approaches focus on system-wide states as causal actors in models and on the computational (or optimality) principles governing global system dynamics. (2)

Phillips, James. Self-Organized Networks: Darwinian Evolution of Dynein Rings, Stalks, and Stalk Heads. Proceedings of the National Academy of Sciences. 117/7799, 2020. In this integral year, a veteran Rutgers University biophysicist describes sees these cellular formations as good examples of how nature organizes and orders itself. Phillips finds this dynamic patterning to be so suitable and robust that its self-making method could appear as a natural “design.” See also Self-assembly, Buckling and Density-invariant Growth of Three-dimensional Vascular Networks by Julius Kirkegaard, et al in the Journal of the Royal Society Interface. (October 2019) and Self-Organized Networks with Long-Range Interactions by J. Phillips at arXiv:2008.08668 for similar views.

However, Eugene Koonin, et al have posted a concern entitled No Waves of Intelligent Design in PNAS (117/19639, 2020) that the author’s allusion to some “positive” process which goes on by itself is not merited, nor should it be. Phillips replies in the same issue with Evolution of Proteins is Darwinian, see third quote. We cite as an instance of opposite mindsets which either can allow something more in effect, or categorically reject any phenomenal procreation, which is the academic fixation. One could also cite Stephen Jay Gould vs. Simon Conway Morris about evolution, Stephen Weinberg or Andrei Linde in cosmology and so on, whence one’s viewpoint is a matter of personal opinion.

Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin, and dynein. Their positive Darwinian evolution enables them to approach optimized, universal functionality (self-organized criticality). Dynein binds to tubulin through two coiled coil stalks and a stalk head. The energy used to alter the head binding and propel cargo along tubulin is supplied by ATP. Here, we show how many details of this interaction by water waves can be quantified by thermodynamic scaling. (Abstract excerpt)

Dynein is a family of cytoskeletal motor proteins that move along microtubules in cells. They convert the chemical energy stored in ATP to mechanical work.

I am grateful to Koonin et al. (1) for highlighting the question of whether positive Darwinian evolution occurs at the molecular level, or only neutral evolution (generally accepted). In a series of papers, I have displayed evidence for positive Darwinian evolution of proteins, using a new hydropathic method based on statistical physics (self-organized criticality) and (synchronizable) network theory, (Phillips)

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)

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.

Raipal, 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.

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