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

Stewart, Ian. Self-organization in Evolution. Philosophical Transactions of the Royal Society of London A. 361/1101, 2003. A mathematical perspective on the process of speciation to show how self-organizing effects are at work in fitness landscapes and symmetry-breaking bifurcations.

Stillman, Bruce, et al, eds. Evolution: The Molecular Landscape. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 2009. The proceedings of a Darwin anniversary conference with an international array of contributors across these sequential areas: Introduction, RNA and Proteins, Mutations, Selection and Adaptation, Diversity, Evolution of Systems, Evolution of Development, Domestication, Human Evolution, Social Interaction (denouement of intelligent design), and Human Society. Premier contributors include Janet Browne (Darwin biographer), Edward O. Wilson, Thomas Cech, Jack Szostak, Matt Ridley, and many others. Surely an edifice of evidence for life’s ancient, creaturely rise from molecule to mole to mankind.

But this august scientific achievement, with a vested reductive bent, sadly goes awry in its Summary by Brian Charlesworth, who laments in the quote over why people do not embrace it. One wonders why cannot a distinction be seen between these myriad, dovetailing field and experimental results, and such an unwarranted, default conclusion that only blind, aimless mechanism prevails? Of course being told we persons are just “impersonal machines” is publicly rejected, because it is the very wrong answer.

Evolution is probably the area of biology that probably attracts the most attention outside of the scientific community, and the question of the public understanding of evolution was also well represented at the Symposium. The idea that we are ourselves simply exceedingly complex machines, produced by impersonal evolutionary forces acting over billions of years, is still repugnant to many people, especially in the United States and the Islamic world, where fundamentalist religious beliefs are widely held. It is one of the paradoxes of our time that the country with the greatest concentration of scientific talent in the world is the only developed nation where a large fraction of the population espouses creationism, a doctrine that is tantamount to rejecting the scientific exploration of nature. (Charlesworth, 473)

Stoltzfus, Lev Yampolsky. Climbing Mount Probable: Mutation as a Cause of Nonrandomness in Evolution. Journal of Heredity. 100/5, 2009. In an earlier paper akin to Livnat 2013 above, NIST, Center for Advanced Research in Biotechnology, theorists revise Richard Dawkins’ “Mount Improbable” for his view of evolution to press a well-supported case that something actually does seem to be going on. But this is hard to articulate while trying to stay within “neoDarwinian” confines. Beyond just chance and contingency, or “shifting frequencies of population genetics,” an intrinsic “mutational bias” appears to be in prior, predictable effect. Life’s directional procession florescence is then due to these biased “inherent propensities.”

The classic view of evolution as ‘‘shifting gene frequencies’’ in the Modern Synthesis literally means that evolution is the modulation of existing variation (‘‘standing variation’’), as opposed to a ‘‘new mutations’’ view of evolution as a 2-step process of mutational origin followed by acceptance-or-rejection (via selection and drift). The latter view has received renewed attention, yet its implications for evolutionary causation still are not widely understood. We review theoretical results showing that this conception of evolution allows for a role of mutation as a cause of nonrandomness, a role that could be important but has been misconceived and associated misleadingly with neutral evolution. Specifically, biases in the introduction of variation, including mutational biases, may impose predictable biases on evolution, with no necessary dependence on neutrality.

As an example of how important such effects may be, we present a new analysis partitioning the variance in mean rates of amino acid replacement during human–chimpanzee divergence to components of codon mutation and amino acid exchangeability. The results indicate that mutational effects are not merely important but account for most of the variance explained. The challenge that such results pose for comparative genomics is to address mutational effects as a necessary part of any analysis of causal factors. To meet this challenge requires developing knowledge of mutation as a biological process, understanding how mutation imposes propensities on evolution, and applying methods of analysis that incorporate mutational effects. (Abstract)

Strohman, Richard. Maneuvering in the Complex Path from Genotype to Phenotype. Science. 296/701, 2002. The emeritus professor of molecular and cell biology at the University of California at Berkeley is a leader in articulating the nascent paradigm shift from particulate genes and selection alone to rule-based self-organizing systems as equally involved in a complementary fashion as genotype develops into organism. (And their existence then implies a different genesis universe.) More on Strohman’s views, and other researchers in this regard, can be found at: www.cswe.org/publications/jswe/03-2strohman.htm#t.

Human disease phenotypes are controlled not only by genes but by lawful self-organizing networks that display system-wide dynamics. (701) At the center of this effort is a need to understand the formal relationship between genes and proteins as agents, and the dynamics of the complex systems of which they are composed. (701)

Sukhoverhov, Anton and Nathalie Gontier. Non-Genetic Inheritance: Evolution above the Organismal Level. Biosystems. December, 2020. Kuban State Agrarian University, Russia and University of Lisbon (search NG papers) biophilosophers propose to expand upon extended evolutionary theories by moving on up life’s episodic emergent scale. In this broader view a constant impetus to form more nested cellular communities can become evident. The evident major transitions scale can thus be shifted toward this cooperative emphasis, and also accrue a reticulated, networked anatomy.

The article proposes to develop the Extended Evolutionary Synthesis (EES) by including phenomena that occur above the organismal level. We show that the current EES view is focused more on individual traits and less on community traits of biological, ecological, social, and cultural systems. In regard, we consider communities made up of interacting populations that occupy the same place in time and space, and for which the individual members can belong as the same or different species. Examples include biofilms, ant colonies, symbiotic associations in holobiont formation, and human societies. Our proposed communities model revises major transitions in evolution theory by adding the interplay between social traits and individual traits. (Abstract excerpt)

Suki, Bela. The Major Transitions of Life from a Network Perspective. Frontiers in Fractal Physiology. 3/Article 94, 2012. The major transitions theory (search Maynard) of an episodic, recurrent evolution from biomolecules to genomes, cells, mammals, brains, primates, and language, first proposed in 1995, has gained much acceptance. In the years since, a new nature has been realized as vitally suffused with complex, dynamical systems. A Boston University professor of Biomedical Engineering can now deftly elucidate the role of ubiquitous network topologies in this nested emergence, as the several quotes attest. In regard, the addition of these propensities leads to several implications. A generic sequence becomes apparent for stage changes akin to phase transitions in statistical physics. The dynamic recast of evolution then infers an iterative self-organization at work at each scale. Finally, from 2012, Bela Suki muses whether we might be in the midst of a further ascent to a worldwide humankind noopshere.

In an influential work, Maynard Smith and Szathmáry argued that the majority of the increase in complexity is not gradual, but it is associated with a few so-called major transitions along the way of the evolution of life. For each major transition, they identified specific mechanisms that could account for the change in complexity related to information transmission across generations. In this work, I propose that the sudden and unexpected improvement in the functionality of an organism that followed a major transition was enabled by a phase transition in the network structure associated with that function. The increase in complexity following a major transition is therefore directly linked to the emergence of a novel structure–function relation which altered the course of evolution. As a consequence, emergent phenomena arising from these network phase transitions can serve as a common organizing principle for understanding the major transitions. As specific examples, I analyze the emergence of life, the emergence of the genetic apparatus, the rise of the eukaryotic cells, the evolution of movement and mechanosensitivity, and the emergence of consciousness. (Abstract)

Here I will argue that the basis of the new kind of behavior post-transition is a fundamental change in the structure pre-transition. If each major transition can be linked to the emergence of a novel structure, then there man by a common mechanism behind these transitions related to the complexity of the underlying structural organization. (1) The theory of complexity has much to offer to understand life and its major transitions. Specifically, complexity deals with systems that show emergent behavior resulting from the interactions of many components or subunits of the system. A convenient way to discuss such systems is to consider the interactions among the units as a network. (1-2)

If we accept the notion that the structural basis of life is a network, then the “emergence” of living matter maybe associated with the emergence of a suitable network structure that allows processes associated with life. (4) Thus, network phenomena under non-equilibrium conditions mist have played a key role in the very first major transition, the origin of life, independent of the precise details of chemistry. (5)

As mentioned earlier, fractal structures and long-range correlated fluctuations naturally appear at the critical point during phase transitions providing thus an intriguing link between non-equilibrium conditions, ordered structures and the corresponding novel functions related to the major transitions of life. (9) If the major transition are indeed a network associated phase transition, then, to some extent, they should be independent of the details of the system. With regard to the first transition, the origin of life, does this suggest that a transition is likely to occur in any sufficiently rich soup of raw materials largely independent of the specifics of chemistry? Given the steady discovery of Earth-like planets, an important implication of this would be that some sort of a self-sustaining primitive life should abound in the universe. (10)

What is the expected impact of a new transition, biological or other, on human society? It is evident that even over the short time period of human evolution, various new networks have emerged and transitions occurred. A recent and perhaps most revolutionizing network in terms of human experience is the internet. As the complexity of the internet increases, is it possible to live through a phase transition such that the internet acquires some form of intelligence or consciousness? Also, consciousness is certainly an emergent phenomenon arising from the neural network connectivity of the brain. Could the human species undergo yet another phase transition? (11)

Svorcova, Jana and Anton Markos. Epigenetic Processes and the Evolution of Life. Boca Raton: CRC Press, 2019. Charles University, Prague theoretical biologists (search AM) achieve a consummate review to date of life’s oriented, stirring “planetogenesis.” The inclusive survey set within a biospheric milieu proceeds from rudimentary metabolic and/or replicator origins onto unicells and organisms, with an emphasis upon evolving phases of genetic heredity. An informational, semiotic quality is emphasized along with a pervasive symbiosis which leads to an I, Holobiont model. With all this in place, an extended evolutionary synthesis in the air is well scoped out.

The book covers the possible story of emergence of life and its subsequent evolution, emphasizing the necessary evolutionary step negotiation of a common "language set" which kept all inhabitants in the biosphere together, ensuring a basic level of understanding among them. The book focuses on "protocols of communication" (both genetic and epigenetic) representing norms shared and understood across the whole biosphere, enabling a plethora of holobiotic relationships. Cooperative nature of organismal evolution and epigenetic processes as a major force in evolution are also covered.

Szathmary, Eors. Toward Major Evolutionary Transition Theory 2.0. Proceedings of the National Academy of Sciences. 112/10104, 2015. A presentation at the October 2014 NAS Sackler Colloquium: Symbioses Becoming Permanent: The Origins and Evolutionary Trajectories of Organelles by the Eotvos University, Hungary, biologist and founder with John Maynard Smith in 1995 of this natural iterative scale. This 20 year review and update of nuances and verifications serves to aver its current mainstream acceptance. From protocells at life’s origin to nucleotides, eukaryotic cells, plastid organelles, organisms, eusocial cooperation onto symbolic human sapience, a nested sequence was facilitated in each case by a novel informational “inheritance system.” Gradual Darwinian selection is not mentioned, presently replaced by this axial oriented emergence, which quite bodes for a genesis synthesis.

The meeting was much about symbiotic unions as a prime source for life’s communal abidance, some other entries were Endosymbiosis and Its Implications for Evolutionary Theory by Maureen O’Malley, (Symbiotic Cell) and Major Evolutionary Transitions in Individuality by Stuart West, et al, (Enhanced Individuality). Szathmary has become a leading thinker in several areas such as life’s origin and edited a recent Journal of Theoretical Biology issue Tibor Ganti: Towards the Principles of Life and Systems Chemistry (381, 2015 search).

From Lower to Higher Level Evolutionary Units The first common feature is the transition from independent replicators to form higher level units: for example, genes ganged up in protocells, prokaryotes joined to constitute the eukaryotic cell, protist cells stacked together to form multicellular organisms, and so on. In order for such a transition to be successful, evolution at the lower level must be somehow constrained by the higher level. I adopt the view of (Andrew) Bourke (search), who suggested that major transitions should typically be cut into three phases: the formation, maintenance, and transformation of social groups. (10104)

Tarnita, Corina, et al. Evolutionary Construction by Staying Together and Coming Together. Journal of Theoretical Biology. 320/10, 2012. Social biologists Tarnita, Princeton University, with Clifford Taubes and Martin Nowak, Harvard University, continue their project to quantify the presence of mathematical, program-like lineaments in effect prior to selection which guide successful assemblies across animalian kingdoms. See also in the same journal (299/126, 2012) Prosperity is Associated with Instability in Dynamical Networks by Cavaliere, Matteo, et al, a team including Tarnita and Nowak. We cite abstracts from both papers to convey their content. Along with many like studies, it seems increasingly evident that some creative agency serves to promote salutary group cooperation as life evolves and quickens.

The evolutionary trajectory of life on earth is one of the increasing size and complexity. Yet the standard equations of evolutionary dynamics describe mutation and selection among similar organisms that compete on the same level of organization. Here we begin to outline a mathematical theory that might help to explore how evolution can be constructive, how natural selection can lead from lower to higher levels of organization. We distinguish two fundamental operations, which we call Staying Together and Coming Together. Staying together means that individuals form larger units by not separating after reproduction, while coming together means that independent individuals form aggregates. Staying together can lead to specialization and division of labor, but the developmental program must evolve in the basic unit.

Coming together can be creative by combining units with different properties. Both operations have been identified in the context of multicellularity, but they have been treated very similarly. Here we point out that staying together and coming together can be found at every level of biological construction and moreover that they face different evolutionary problems. The distinction is particularly clear in the context of cooperation and defection. For staying together the stability of cooperation takes the form of a developmental error threshold, while coming together leads to evolutionary games and requires a mechanism for the evolution of cooperation. We use our models to discuss simple aspects of the evolution of protocells, eukarya, multi-cellularity and animal societies. (Tarnita Abstract)

Social, biological and economic networks grow and decline with occasional fragmentation and re-formation, often explained in terms of external perturbations. We show that these phenomena can be a direct consequence of simple imitation and internal conflicts between ‘cooperators’ and ‘defectors’. We employ a game-theoretic model of dynamic network formation where successful individuals are more likely to be imitated by newcomers who adopt their strategies and copy their social network. We find that, despite using the same mechanism, cooperators promote well-connected highly prosperous networks and defectors cause the network to fragment and lose its prosperity; defectors are unable to maintain the highly connected networks they invade. Once the network is fragmented it can be reconstructed by a new invasion of cooperators, leading to the cycle of formation and fragmentation seen, for example, in bacterial communities and socio-economic networks. In this endless struggle between cooperators and defectors we observe that cooperation leads to prosperity, but prosperity is associated with instability. Cooperation is prosperous when the network has frequent formation and fragmentation. (Cavaliere Abstract)

Tauber, Alfred. Reframing Developmental Biology and Building Evolutionary Theory’s New Synthesis. Perspectives in Biology and Medicine. 53/2, 2010. The Boston University philosopher physician composes an essay review of Scott Gilbert and David Epel’s Ecological Developmental Biology (Sinauer, 2009) which extols how this marriage of evolution, embryology and ecology can express a deep instance of nature’s a complexly dynamic creativity. But the upshot, one might note, is far more than a revised theory, for what is really implied is a profoundly different genesis universe.

This orientation builds on the general intuition that evolution, development, metabolism, immune responsiveness, and neurological functions each require explanations of the plasticity, emergent phenomena, self-organization, and nonlinear, dynamic causation pathways characteristic of organic phenomena. Of course how the new biology is practiced varies from one discipline to the next, but the general movement towards multi-variant analyses, nonlinear dynamics, and holistic description suggests a unified theme that incorporates eco-evo-devo in this general theoretical and methodological movement of an integrative biology. (264)

Ten Tusscher, Kirsten. Of Mice and Plants: Comparative Developmental Systems Biology. Developmental Biology. Online November, 2018. While affinities between Metazoan fauna creatures are well proven, flora vegetation has not been similarly studied, or compared with animals. A Utrecht University computational developmental biologist here provides an initial survey of commonalities amongst plants and with regard to organisms. In collaboration with Paulien Hogeweg at UU and others, a case can be made because new biological systems and network organizations found across flora and fauna appear to exemplify the same structural source. The implication of independent, recurrent principles and process then becomes evident. See also In Silico Evo-Devo: Reconstructing Stages in the Evolution of Animal Segmentation by KtT, Renske Vroomans and Paulien Hogeweg in BMC EvoDevo (7/14, 2016).

Multicellular animals and plants represent independent evolutionary experiments with complex multicellular body plans. Differences in their life history, a mobile versus sessile lifestyle, and predominant embryonic vs. postembryonic development, have led to highly different anatomies. However, many intriguing parallels exist. Extension of the vertebrate body axis and its segmentation into somites has a striking resemblance to plant root growth and the prepatterning of lateral root competent sites. Likewise, plant shoot phyllotaxis displays is akin to vertebrate limb and digit patterning. Both plants and animals use complex signalling systems with systemic and local signals to fine tune and coordinate organ growth. Identification of these striking examples of convergent evolution provides support for the existence of general design principles: the idea that for particular patterning demands, evolution is likely to arrive at highly similar developmental patterning mechanisms. (Abstract excerpts)

Somites are body segments containing the same internal structures, clearly visible in invertebrates but also present in embryonic stages of vertebrates. Somites are transient, segmentally organized structures. In the vertebrate embryo, the somites contribute to multiple tissues, including the axial skeleton, skeletal and smooth muscles, dorsal dermis, tendons, ligaments, cartilage and adipose tissue. (Web definitions)

Toepfer, Georg. Teleology and its Constitutive Role for Biology as the Science of Organized Systems in Nature. Studies in History and Philosophy of Biological and Biomedical Sciences. Online July, 2011. For good reason, from Immanuel Kant to this late day, against all deniers and denouncers, the project continues to revive and articulate this once and future quintessence of life. Organisms are not machines. They proceed in gestation and growth toward their ordained state, seed to rose, egg to entity. A Humboldt University philosopher emphatically weighs in that unless this omission is corrected, we will never get limb, life and nature right. Please also view his publications page: http://www.georg-toepfer.de/

Nothing in biology makes sense, except in the light of teleology” – this could be the first sentence in a textbook about the methodology of biology. The fundamental concepts in biology, e.g. ‘organism’ and ‘ecosystem’, are only intelligible within a teleological approach. In the past, teleology has often been considered a methodological danger for science. One popular strategy to cope with teleological reasoning was to explain it by reference to the theory of evolution: functions were reconstructed as “selected effects”. But the theory of evolution obviously presupposes the existence of organisms as organized and regulated, i.e. functional systems. Therefore, evolutionary theory cannot provide the foundation for teleology.

The reason for the central methodological role of teleology for biology is not its potential to offer particular forms of (evolutionary) explanations for the presence of parts, but rather ontological: organisms and other basic biological entities do not exist as physical bodies do, as amounts of matter with a definite form. Rather, they are dynamical systems in stable equilibrium: despite changes of their matter and form (in metabolism and metamorphosis) they maintain their identity. What remains the same in these kinds of systems is their “organisation”, i.e. the causal pattern of interdependence of parts with certain effects of each part being relevant for the working of the system. Teleological analysis consists in the identification of these system-relevant effects and at the same time of the system as a whole. Therefore, the identity of biological systems cannot be specified without teleological reasoning. (Abstract)

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