V. Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWinian Genesis Synthesis
Callebaut, Werner, ed. Biological Theory. Cambridge: MIT Press, 2006. A new journal which plans to integrate developmental, evolutionary and cognitive aspects. The first issue, Winter 2006, is available on the publishers website and contains a wide array of inaugural articles. But an observation seems in order – while in physics a theoretical basis is understood, biology has long had to make excuses for one, (earlier such journals have come and gone) for within our materialist cosmos, life is, incorrectly, held to appear and evolve so haphazardly that it could not have a lawful dimension.
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)
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 assemblyť 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), â€śsympathy groupâ€ť (~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 â€śrevealed that evolution can and does repeat itself at the levels of structures and patterns as well as individual genes.â€ť The repetition of structure and patterns is discussed next starting from a biological position and reformulated as a vocabulary of â€śrepeated assembly.â€ť (239)
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,
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?
…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)
Carroll, Sean B. Evo-Devo and an Expanding Evolutionary Synthesis. Cell. 134/1, 2008. A leading researcher and communicator provides a cogent review, subtitled A Genetic Theory of Morphological Evolution, on the interactive reunion and meld of development and phylogeny. Salient tenets are said to include: mosaic pleiotropy, ancestral genetic complexity, deep homology, heterotopy, vast cis-regulatory modularity and networks, and the conservation of gene tool-kits.