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

Weiss, Kenneth and Anne Buchanan. The Mermaid’s Tale: Four Billion Years of Cooperation in the Making of Living Things. Cambridge: Harvard University Press, 2009. Eight principles of life are highlighted in this latest accessible essay by the Penn State anthropologists: inheritance with memory, modularity, solitary sequestration, interactive coding, contingency, chance, adaptability, cooperation. Their presence is well explained across a range of Evo, Devo, and Eco scales, but in the absence of any natural philosophy, these qualities cannot be attributed to or seen as springing from a greater genesis universe, as they indeed imply. Accordingly, as the quotes juxtapose, while a social reciprocity is cogently advanced, any inkling of an intrinsic progression is denied nor really permitted.

For our purposes, suffice it to say that on the Evo scale, life is a contingent, undirected, and largely unpredictable process. (35) Last but not least – or should we say last but perhaps most – the principles of life we have described imply a variety of forms of cooperation. Cooperation, that is, literally co-operation, refers to different components working together successfully by some criterion, including that of evolutionary viability. The signals that produce branching, modular, and hierarchically nested organization inherently work cooperatively – indeed, signaling means the co-expression of all the sending and receiving factors. Cooperative communication enables sequestered parts to be coordinated so that the system can function as a whole. (38)

If there is a single striking fact about genes, genomes, and how they work, it is that everything we have discussed involves, or even is based on, cooperative interaction. DNA, and the whole genetic system, is essentially one large cooperating set of various kinds of codes. (67) In the last chapter we showed the many ways in which genomes are inherently modular and segmented. Most kinds of modular coding elements, like amino acid codons or regulatory binding sites occur tens of thousands or even millions of times within a single genome. What is responsible for these modular elements? The answer, in a word, is chance. (70)

Wennekamp, Sebastian, et al. A Self-Organization Framework for Symmetry Breaking in the Mammalian Embryo. Nature Reviews Molecular Cell Biology. 14/7, 2013. European Molecular Biology Laboratory, Heidelberg, researchers including Francois Nedelec, contend that prior Pre-patterning, Inside-outside, and Cell polarity, models cannot adequately explain how embryos develop from fertilization. Something else and more must be in effect. Aided by new analytic technologies, an organic system that develops by way dynamic local interrelations between cellular activities is clearly evident. For a similar take, see The Role of Self-Organization in Developmental Evolution by Joseph Bozorgmehr in Theory in Bioscience (April 2014).

The mechanisms underlying the appearance of asymmetry between cells in the early embryo and consequently the specification of distinct cell lineages during mammalian development remain elusive. Recent experimental advances have revealed unexpected dynamics of and new complexity in this process. These findings can be integrated in a new unified framework that regards the early mammalian embryo as a self-organizing system. (Abstract)

Self organization can be defined as the formation of complex patterned structures from units of less complexity by local internal interactions, without referring to an external blueprint or template. These internal interactions typically form feedback loops, thereby conferring robustness to the system. Other common features found in self organizing systems are nonlinearity, symmetry breaking and the emergence of patterns from stochastic fluctuations. (456) We believe that the self-organization theory is a comprehensive approach to explain all observed phenomena in a quantitative manner. (456)

West, Geoffery, et al. Allometric Scaling of Metabolic Rate from Molecules and Mitochondria to Cells and Mammals. Proceedings of the National Academy of Sciences. 99/Supplement1/2473, 2002. A survey of fractal self-similarities throughout the biological kingdom.

West-Eberhard, Mary Jane. Development and Selection in Adaptive Evolution. Trends in Ecology and Evolution. 17/2, 2002. A senior biologist chides the either/or situation of random selection vs. complex dynamics and topological constraints and proposes their integration by way of the prior effect of self-organizing systems.

The interesting feature of self-organization is not that it can produce novel form without selection (all persistent developmental mechanisms have done that), but that every separate detail of structure need not be explained in terms of a separate mechanism with selection operating step-by-step to gradually assemble a complex and coherent whole. (65)

West-Eberhard, Mary Jane. Developmental Plasticity and Evolution. Oxford: Oxford University Press, 2003. A large volume which expands gene-based theory to include an organisms’ developmental dynamics and internal geometries, as they actively respond to changing environments.

Modularity, like the responsiveness that gives rise to it during development and evolution, is a universal property of living things and a fundamental determinant of how they evolve. Modularity refers to the properties of discreteness and dissociability among parts and integration within parts. (56)

Whitfield, John. Postmodern Evolution? Science. 455/281, 2008. A news report on the July 2008 Altenberg discussions of a revised evolutionary synthesis (see Pennisi in this section) that in retrospect offers a micro-capsule of current dilemmas. If it is pressed that neoDarwinian theories are insufficient, this becomes fodder of creationists. Muddling matters are tacit philosophies which decry that since all views are culturally relative, one theory is not better than another. Add to this vested positions often at odds among attendees and other commentators, along with a need to add self-organizing dynamics as a prior complement to selection, and a heady brew results. But many players are indeed aware it is vital that process and engagement goes forward.

Wilke, Claus and Christoph Adami. The Biology of Digital Organisms. Trends in Ecology & Evolution. 17/11, 2002. Self-replicating computer simulations bring a novel perspective by which to understand how organisms mutate and evolve in recurrent ways.

The similarity in the results between the E. coli and digital organisms is striking, and supports the hypothesis that many aspects of evolving systems are governed by general principles. (530)

Wilkins, Adam. Between “Design” and “Bricolage:” Genetics Networks, Levels of Selection, and Adaptive Evolution. Proceedings of the National Academy of Sciences. 104/Supplement 1, 2007. The British biologist and editor of the journal BioEssays finds that if a “network perspective” is adopted, as the quote notes, new insights to an innate, iterative predictability can be gained. What is then implied is a salient shift from aimless tinkering to signs, dare one allude as does Wilkins, of a design.

In this article, however, I will present the case that a genuine integration of network-thinking into evolutionary genetics can greatly enrich our understanding of evolutionary events. In…the final part, I will present an argument that a deeper understanding of particular genetics networks, in conjunction with an appreciation of the generic properties of such networks, can, in principle, permit a larger predictive, or retrodictive, element in evolutionary biology that has hitherto been possible. (8590)

To sum up: if one accepts this view of a molecular sequence of upward interactions, with the effects of mutational events feeding through from the DNA sequence level, at the lowest molecular levels, to that of network modules and networks, and selection screening downward through this hierarchy, then the nature of the gene tinkering process is seen to be much less haphazard that the process connoted by the term “bricolage,” having more built-in molecular constraints yet, at the same time, lacking the goal-directed nature of a process that is implied by the term “design.” (8592-8593)

Williams, R. and J. Frausto Da Silva. Evolution was Chemically Constrained. Journal of Theoretical Biology. 220/3, 2003. A nested repetition from microbes to human beings is in fact mandated by energy gradients which drive a sequenctial usage of chemicals from reducing to oxidizing environments.

The objective of this paper is to present a systems view of the major features of biological evolution based upon changes in internal chemistry and uses of cellular space, both of which it will be stated were dependent on the changing chemical environment. The account concerns the major developments from prokaryotes to eukaryotes, to multi-cellular organisms, to animals with nervous systems and a brain, and finally to human beings and their uses of chemical elements in space outside themselves. It will be stated that the changes were in an inevitable progression, and were not just due to blind chance… (323)

Wills, Peter. Informed Generation: Physical Origin and Biological Evolution of Genetic Codescript Interpreters. Journal of Theoretical Biology. 257/3, 2009. The University of Auckland biophysicist explains his project of finding an evolutionary alternative to selection alone. But this requires a different view of life’s physical substrate as more innately graced by nonlinear, self-organizing propensities which can then take on genetic-like qualities. This “inherent capacity” gives rise to a “self-generating interpreter” which (whom) reads and processes via “complex networks of cooperating units” informative genotypes into viable phenotypes. (See also a prior paper: Wills, P., et al “Genetic Information and Self-organized Criticality” in Europhysics Letters (68/6, 2004), and search 2013 for a later report. Peter Wills is also a noted environmental, peace, and Maori rights activist. In this present article he makes much progress toward an imminent 21st century synthesis newly rooted in a conducive genesis universe.

The principle of Informed Generation specifies the need for the spontaneous emergence and evolutionary development of self-organizing processes that generate phenotypes from genotypes. The principle of Informed Generation describes a ubiquitous feature of biological systems: without the prior existence of certain components or functionalities, which are required for the production of themselves and others, no configuration of genetic information that accumulated through Natural Selection could ever serve as a codescript for an organism. (345) It is proposed that Informed Generation represents a quite general process of evolutionary self-organization in biological systems whereby essentially irreversible transitions in the systems' dynamics take them to historically contingent, isolated states whose characteristics are determinants of biological specificity. (345)

The emergence of genetic coding at the origin of life demonstrates Informed Generation as a result of a symmetry-breaking non-equilibrium phase transition. (348) More generally, Informed Generation could occur as a result of self-organization within and among complex dynamic networks at all levels in the biological hierarchy: metabolism, protein interactions, genetic expression and control, intra- and inter- cellular signaling, biomass transfer and ecology. (348) The principle of Informed Generation is distinguished from all of these in that it characterizes biological self-organization as the automatic production of a self-generating interpreter of genetic information. (348)

Wilson, David Sloan and Edward O. Wilson. Rethinking the Theoretical Foundation of Sociobiology. Quarterly Review of Biology. 82/4, 2007. A significant conceptual synthesis reviewed in detail in Organic Societies.

Winther, Rasmus. Systemic Darwinism. Proceedings of the National Academy of Sciences. 105/11833, 2008. A University of California at Santa Cruz philosopher essays how a systems evolution might be laid out with regard to three aspects: Explanatory Pattern which can engage both natural Law and contingent Narrative; Levels of Selection that are both Organismic and Hierarchical; and Degree of Difference Among Units of the Same Type: Variational and Essentialist Thinking. With a detailed bibliography, a good entry to this rethinking and expansion.

Systemic Darwinism provides a significantly more general and integrative perspective on complex biological systems than systems Biology. First, it highlights the astounding ontological complexity of biological reality: dynamical self-organizing systems (composed of hierarchical networks of parts) are genealogical and can therefore undergo selection. Systemic Darwinism thus follows a “compositional paradigm” according to which complex systems together with their diverse hierarchical networks of parts – and not just basement parts – are considered the focus of biological investigation. (11833)

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