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

Campbell, John O. Bayesian Inference and the World Mind. arXiv:1210.8031. The New Zealand physicist continues an interpretation of universe and human in terms of iterative probabilities. In addition a semiotic, informational aspect is availed whence one might imagine an evolutionary cosmos trying to perceive and recognize itself, as the second quote alludes.

Knowledge is a central concept within both Bayesian inference and the mathematical and philosophical program of logic and semiotics initiated by Charles Sanders Peirce and further developed by George Spencer-Brown and Louis Kauffman. The latter school is more philosophical than is usual with the practitioners of Bayesian inference and claims the existence of a world mind. When these two disciplines inform each other semiotics is provided with mathematical mechanism and Bayesian inference is seen to be closely related to the act of distinction, the fundamental basis of logic in the work of Spencer-Brown. This hybridization also suggests a definition for knowledge within Bayesian inference; a definition that has been curiously lacking. Given that Darwinian processes are physical implementations of Bayesian inference and are utilized within numerous scientific theories across a wide range of disciplines as mechanisms for the creation and evolution of knowledge we may view the conjunction of these theories, within universal Darwinism, as descriptive of a world mind. Placing the world mind in this context provides detailed support from the scientific literature and goes some way to refute the charges of mysticism which have been leveled at the semiotic approach. (Abstract)

Universal Darwinism also strives to provide insight into the details of the Darwinian process. We might view the fact that each of these many theories describe information processing systems designed to increase knowledge as evidence for the existence of a world mind and that a fundamental aspect of the universe is its evolving ability to know itself. (7)

Campos, Paulo and Viviane de Oliveira. Scale-free Networks in Evolution. Physica A. 325/3-4, 2003. A computer study of a replicating population of organisms exposed to mutation and selection finds that the connectivity between them self-organizes into a scale-free state, rather than a homogeneous pattern. This clustering is then seen to be similar to metabolic and internet networks.

Caporael, Linnda. Repeated Assembly. Rauscher, Frederick and Steven Scher, eds. Evolutionary Psychology: Alternative Approaches. Boston: Kluwer Academic, 2003. The RPI philosopher of biology and culture contributes to an expanding view of evolution as a multilevel nest from macromolecules to cells, organisms, groups and customs where the same patterns and processes recur at each stage. An update essay Revolutionary Darwinism in Grounding Sociality: Neurons, Mind, and Culture (Gun Semin and Gerald Echterhoff, eds., Psychology Press, 2011) goes on to situate nature’s emergent reiteration from zygote to literature within the major evolutionary transitions version.

Repeated assemblies are (a) recurrent, (b) entity-environment relations composed of (c) hierarchically organized (d) heterogenous components having (e) different temporal frequencies and scales of replication. (77) Instead of fictionalizing genes as souls and decision makers, repeated assembly draws on multilevel-evolutionary theory for a view of Darwinism as situated and relational. It emphasizes context, be it a cellular medium or a social medium; contingency, as the interactive relationship between events….and construction, through the self-organizing properties of recurrent resources (gametes, organisms, ecosystems, etc.). (85)

Caporael, Linnda. Revolutionary Darwinism: Sociality is the Ground. Semin, Gun and Gerald Echterhoof, eds. Grounding Sociality: Neurons, Mind and Culture. New York: Psychology Press, 2011. The concept of a repeated assembly� to explain ubiquitous cooperative groupings in an expansive evolution that the Rensselaer Polytechnic Institute professor of biological and cultural psychologies of science and technology has been advancing (search) here receives its most complete treatment. As the quotes aver, such viable patterns recur across the nested scale of major transitions, distinguished by a beneficial reciprocity of an entity or dyad within communal settings from localities and populations to macrodemes. A further parsing is seen to affirm Robin Dunbar's societal iteration (search) from individual (1, 2) to team or task group (5), “sympathy group� (~15), community (50-100), to larger collectives and today within worldwide humankind.

In contrast, from the evo-devo perspective, the phenotype results from the constructive interactions of events at different levels of organization as well as activity of the organism itself. While the (material) genes are necessary, they are not a sufficient resource in the self-organization and construction of an organism. Evo-devo has “revealed that evolution can and does repeat itself at the levels of structures and patterns as well as individual genes.� The repetition of structure and patterns is discussed next starting from a biological position and reformulated as a vocabulary of “repeated assembly.� (239)

The history of life is the history of several major transitions in the physical organization of biological phenomena. DNA molecules, chromosomes, and multicellular organisms are examples of the products of such reorganizations. The main characteristic of these major reorganizations is that entities capable of self-replication before reorganization are replicated as part of a larger entity after reorganization. (240)

Thus, from the evo-devo perspective, the organism embodies multiple different level of selection. Macromolecules, cells, cell lineages, organisms, and groups are at different levels of the biological hierarchy and the result of major transitions in the evolution of life. Evolution and development result from the outcome of conflicts and synergisms at different levels of organization. Note that individuals and groups constitute two levels of biological organization and development for humans. This is a far richer perspective than the gene’s eye view, in which the phenotype is taken for granted. (240)

The essential point is that people do dwell within collectively shared landscapes. Some of these are self-organizing demic structures of unrelated people where face-to-face socialization into the community is still required for acquiring the skills and values of the community. The superordinate groups of modern humans are smooth-textured aggregates of individuals or exchanging dyads that the thin description of society supposes. Instead, fractal-like structures calling on the same activity patterns of previous generations form lumpy social networks, some held together by the loose ties of shared traits, and others by the generative functions of demic structure. Such uniquely human processes have an evolutionary history that is grounded in repeatedly assembled – and observable – instantiations of bodies, tasks, group, size, and coordination. (255)

Caporael, Linnda, et al, eds. Developing Scaffolds in Evolution, Culture, and Cognition. Cambridge: MIT Press, 2013. With coeditors James Griesemer and William Wimsatt, a volume that tries to work this rather inorganic framework into life’s development, maintenance, and encephalization. A array of authors such as Stuart Newman, Eva Jablonka, James A. Evans, Pamela Lyon, and Georg Theiner try to employ to represent intermediate states which when no longer necessary are removed. The chapter that most intrigued was Evolution, Groups, and Scaffolded Minds by the Rensselaer Polytechnic Institute philosopher Linnda Caporael where she restates her theory that life advances by “repeated assemblies” in kind of a constant form and function, quote below. This nascent perception is similar, for example, to that of Vic Norris (2015).

Biological entities are hierarchically organized (DNA, cells, tissues, organisms, groups) in nested part/whole relationships, and organisms are the contingently developmental result of various genetic and epigenetic resources (genes, nutrition, oxygen, artifacts, language environment, social roles.) Thus, repeated assembly points to recurrences that we can observe – recurrences from generation to generation as well as recurrence across cultures. Not only do organisms repeatedly assemble, but so also do the products of organisms, including human ideas, artifacts, and cultural practices. (59) Repeated assemblies (definition) are recurrent entity-environment relations composed of hierarchically organized, heterogeneous components (which may themselves be repeated assemblies) having differing temporal scales and cycles of replication. (59)

Caporale, Lynn. Darwin in the Genome. New York: McGraw Hill, 2002. An earlier contribution to the growing realization that not all mutations occur with no other guiding context. Rather a persistent bias seems at work toward gene alterations that are of adaptive value to the subject organism. This theme is extensively taken up by, e.g., Kirschner and Gerhart in their new book, and implies a non-random, oriented evolution.

Caporale, Lynn. Natural Selection and the Emergence of a Mutation Phenotype. Annual Review of Microbiology. 57/467, 2003. Inklings of a 21st century evolutionary synthesis from the growing notice that genetic systems are not completely haphazard but evolve due to predictable, repeated pathways.

With examples from variations in bacterial surface proteins to the vertebrate immune response, it is clear that a great deal of genetic change is better than “random” with respect to its potential effect on survival. Indeed, some potentially useful mutations are so probable that they can be viewed as being encoded implicitly in the genome. An updated evolutionary theory includes emergence, under selective pressure, of genomic information that affects the probability of different classes of mutation, with consequences for genome survival. (467)

Caporale, Lynn Helena and John Doyle. In Darwinian Evolution, Feedback from Natural Selection Leads to Biased Mutations. Annals of the New York Academy of Sciences. Online September, 2013. Lynn Caporale, an independent consultant for drug discovery and functional genomics, joins with John Doyle who professes Control and Dynamical Systems at CalTech, to enlist the engineering concept of “protocols” – “sets of rules by which components interact to create new level of functionality” – to genetic transcriptions. By this novel approach, life’s long development gains further credence as an inherently nonrandom procession, which it is alluded Charles Darwin originally had in mind. See also Dr. Caporale’s “Overview of the Creative Genome” introduction to the 2012 Annals Volume 1267 Effects of Genome Structure and Sequence on Variation and Evolution. and her 2006 edited work The Implicit Genome (search).

Natural selection provides feedback through which information about the environment and its recurring challenges is captured, inherited, and accumulated within genomes in the form of variations that contribute to survival. The variation upon which natural selection acts is generally described as “random.” Yet evidence has been mounting for decades, from such phenomena as mutation hotspots, horizontal gene transfer, and highly mutable repetitive sequences, that variation is far from the simplifying idealization of random processes as white (uniform in space and time and independent of the environment or context). This paper focuses on what is known about the generation and control of mutational variation, emphasizing that it is not uniform across the genome or in time, not unstructured with respect to survival, and is neither memoryless nor independent of the (also far from white) environment. We suggest that, as opposed to frequentist methods, Bayesian analysis could capture the evolution of nonuniform probabilities of distinct classes of mutation, and argue not only that the locations, styles, and timing of real mutations are not correctly modeled as generated by a white noise random process, but that such a process would be inconsistent with evolutionary theory. (Abstract)

Caporale, Lynn, ed. The Implicit Genome. Oxford: Oxford University Press, 2006. This work, along with Neumann-Held, Eva and Christoph Rehmann-Sutter, eds. Genes in Development: Re-reading the Molecular Paradigm. is noted here as salient contributions to a rising genesis synthesis. Both have extensive reviews in the Emergent Genetic Information section.

Carroll, Sean B. Endless Forms Most Beautiful. New York: Norton, 2005. For some twenty years the study of individual embryology – ontogeny – has been converging with evolutionary biology – phylogeny. Originally unified in the later 19th century, research agendas caused these fields to separate in the 20th century. Lately a cross fertilization of developmental and evolutionary theory, aka evo-devo, is causing a major reunion. Carroll, a biologist at the University of Wisconsin, Madison and a leading researcher in this regard, explains a prime reason is a new understanding of the genetic code. The recent sequencing of the human genome, along with many other creatures, reveals that people and chimpanzees have an almost identical molecular DNA, while even worms have 50% of these genes. How then does animal diversity arise?

The answer is a master, regulatory system, known as homeotic or Homeobox genes, from the Greek for similar, which acts to switch on and off specific genes that encode for proteins during embryonic gestation. The same “tool kit gene” controls the fin on a fish, wing on a bird, or human arm, and has been in effect since the origin of cellular life. A constant modularity, division of labor and serial repetition is also recognized in both anatomical and cerebral domains. These revolutionary findings are seen to compose a third synthesis, after the Darwinian and Modern, to radically (re)join embryo and evolution in life’s grand procession.
And by these novel, composite insights, evolution is no longer without direction or progress, rather the same convergent path of ramifying complexity and cognition will be traced each time. But we note that the work is heavy in mechanical metaphors, a cell is still a “machine,” so a shift to an organic genesis cosmos remains.

…this book tells the story of the enormous diversity that has been created from combining a small number of common ingredients. (xi) The discovery of the ancient genetic tool kit is irrefutable evidence of the descent and modification of animals, including humans, from a simple common ancestor. (10) These two groups of animals (vertebrates and arthropods) …are constructed of repeated assemblages of similar parts. Is there a connection between modularity of design and the success in evolutionary diversification? I certainly think so. (26) The first part of this book has set the stage by illustrating four critical ideas about animal development – the modularity of animal architecture, the genetic tool kit for building animals, the geography of the embryo, and the genetic switches that determine the coordinates of tool kit gene action in the embryo. (134)

By focusing on the drama of the evolution of form, and illustrating how changes in development and genes are the basis of evolution, the deep principles underlying the unity and diversity of life emerge. (283) Some prominent scientists have argued that if we could rewind the tape of life and start over again, the result would be a totally different world from that which exists today. They are wrong. Tool kit genes conserve the essence of animals, and they react to ecological cues in very consistent ways. (book jacket)

Carroll, Sean B. The Origins of Form. Natural History. November, 2005. An article in a special issue on “The New Darwinism” to coincide with a major exhibition on Darwin at the American Museum of Natural History. But Carroll goes on to say that natural selection alone, the basis of the modern synthesis, is insufficient to explain how organisms arise and change. Rather the answers lie in the pursuit of evolutionary developmental biology – aka embryology, evo-devo – whose advances have brought a novel understanding of an inherent genetic direction. Instead of new genes appearing along the way to spawn diverse forms, or homo sapiens, an ancient, original set of genes is rearranged and “repurposed.” Organisms thus have a common genetic endowment or “tool-kit” whereby “old” genes find new applications, somewhat like repositioning letters in a paragraph. By the ubiquity of these strategic Hox genes, animal forms are seen as variations on an archetypal body plan (Bauplan), not haphazard inventions. But Richard Dawkins’ lead article, The Illusion of Design, says neoDarwinism means the “nonrandom survival (selection) of randomly varying heredity.” So much work remains to sort out these options, which this site is trying to document.

Cavalier-Smith, Thomas. Origin of Animal Multicellularity: Precursors, causes, consequences—the choanoflagellate/sponge transition, neurogenesis and the Cambrian explosion. Philosophical Transactions of the Royal Society B. Vol.372/Iss.1713, 2016. At this advanced stage of our descriptive reconstruction of the myriad evolutionary creatures who came before us, the emeritus Oxford University zoologist presents an intricate page size diagram: Cell structure divergence in phagotrophic non-amoeboid flagellates provided the basis for evolving animals, fungi, plants and chromists.

Evolving multicellularity is easy, especially in phototrophs and osmotrophs whose multicells feed like unicells. Evolving animals was much harder and unique; probably only one pathway via benthic ‘zoophytes’ with pelagic ciliated larvae allowed trophic continuity from phagocytic protozoa to gut-endowed animals. Choanoflagellate protozoa produced sponges. Converting sponge flask cells mediating larval settling to synaptically controlled nematocysts arguably made Cnidaria. I replace Haeckel's gastraea theory by a sponge/coelenterate/bilaterian pathway: Placozoa, hydrozoan diploblasty and ctenophores were secondary; stem anthozoan developmental mutations arguably independently generated coelomate bilateria and ctenophores. I emphasize animal origin's conceptual aspects (selective, developmental) related to feeding modes, cell structure, phylogeny of related protozoa, sequence evidence, ecology and palaeontology. (Abstract)

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