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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
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V. Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

Barbieri, Marcello. The Organic Codes: An Introduction to Semantic Biology. Cambridge: Cambridge University Press, 2003. A novel theory of evolution and embryology that emphasizes the information and meaning content at genetic, eukaryotic, multicellular and cultural linguistic stages. At each instance a new genetic-like code or “natural convention” complements natural selection. This is the original volume by the University of Ferrara biologist which enters these realizations of how pervasive coding functions are. A later section, Biosemiotics, now contain many entries that confirm and advance this prescient view.

The most important lesson is that language evolution was a combination of two parallel but different processes – evolution of words and evolution of grammatical rules – and this is a fitting model for the two different mechanisms of biological evolution that are proposed by the semantic theory. (237)

Barton, Nick and Jonathon Coe. On the Application of Statistical Physics to Evolutionary Biology. Journal of Theoretical Biology. 259/317, 2009. University of Edinburgh biologists find comparisons between physical phenomena and life’s developmental procession to an extent that alludes to a fertile, conducive cosmos.

There is a close analogy between statistical thermodynamics and the evolution of allele frequencies under mutation, selection and random drift. (317) This analogy with statistical thermodynamics brings together previous ideas in a general framework, and justifies a maximum entropy approximation to the dynamics of quantitative traits. (317) However, a close analogy can be made when we consider evolution as a stochastic process: classical thermodynamics is based on the aggregate behaviour of a large number of molecules, just as population genetics depends on the aggregate behaviour of many reproducing genes. (317)

Basler, Georg, et al. Evolutionary Significance of Metabolic Network Properties. Journal of the Royal Society Interface. Online November 30, 2011. University of Potsdam, University of Aberdeen and Max Planck Institute mathematical biologists propose and describe a reconception of life’s sequential emergence in terms of nature’s universal nonlinear complex systems. Which then augurs, one might add, as many other similar advances, for a 21st century genesis synthesis.

Complex networks have been successfully employed to represent different levels of biological systems, ranging from gene regulation to protein–protein interactions and metabolism. Network-based research has mainly focused on identifying unifying structural properties, such as small average path length, large clustering coefficient, heavy-tail degree distribution and hierarchical organization, viewed as requirements for efficient and robust system architectures. However, for biological networks, it is unclear to what extent these properties reflect the evolutionary history of the represented systems. Here, we show that the salient structural properties of six metabolic networks from all kingdoms of life may be inherently related to the evolution and functional organization of metabolism by employing network randomization under mass balance constraints. Contrary to the results from the common Markov-chain switching algorithm, our findings suggest the evolutionary importance of the small-world hypothesis as a fundamental design principle of complex networks. The approach may help us to determine the biologically meaningful properties that result from evolutionary pressure imposed on metabolism, such as the global impact of local reaction knockouts. (Abstract, 1)

To conclude, we proposed a novel method to reveal the relation between network properties and their evolutionary background by preserving the universal physical principles that constrain the design of metabolic networks. Any property that originates from evolutionary pressure, and thus relates to an important biological function, should not be observed in artificial metabolic networks, which evolved free of evolutionary pressure, but satisfy all relevant physical constraints. This should even hold for properties evolved from complex time-dependent phenomena, if they are reflected in the ultimately observed network. (6)

Bateson, Patrick. New Thinking about Biological Evolution. Biological Journal of the Linnean Society. 112/2, 2013. The senior University of Cambridge zoologist is tapping into and trying to express a growing awareness that historic revisions and advances are much underway about how life developed from chemicals and microbes to primates and us. In regard, four areas and approaches are noted – organisms seem able to “constrain” their subsequent states, the major transitions scale due to novel informational sources, an Evo-Devo reunion of evolution and embryology, and signs of Lamarck-like epigenetic influences. A 21st century genesis-like synthesis is thus gaining robustness and veracity in our midst.

The article focuses on the active role of the organism in the subsequent evolution of its descendants. Choice, control of the environment, adaptability, and mobility all play their part. This growth area in biology and other active centres of research on epigenetics and different forms of inheritance are re-invigorating evolutionary biology. Many evolutionary biologists have taken the view that an understanding of development is irrelevant to theories of evolution. However, the integration of several disciplines now suggests that the orthodoxy is misplaced. (Abstract)

My sense is that the theories of biological evolution have been reinvigorated by the convergence of different disciplines. The combination of developmental and behavioral biology, ecology, evolutionary biology, and now microbiology has shown how important the active roles of the organism are in the evolution of its descendants. The combination of molecular biology, palaeontology, and evolutionary biology has shown important an understanding of developmental biology is in explaining the constraints on variability and the direction of evolutionary change. In other words, evolutionary theory is evolving. (6)

Bateson, Patrick, et al. New Trends in Evolutionary Biology: Biological, Philosophical and Social Science Perspectives. Interface Focus. 7/5, 2017. With coauthors Nancy Cartwright, John Dupre, Kevin Laland and Denis Noble, a special issue from a Discussion Meeting of the British Academy and the Royal Society held in London, November 2016 is introduced. A main theme is that a scientific and philosophical correction is overdue from a past thing or substance “mechanism” emphasis to an integrative appreciation of creatively dynamic processes. The endeavor goes forth within a broad “extended synthesis” project so to include 21st century advances such as multiple nested scales, biological niches, epigenetics, pervasive symbiosis, biosemiotic information conveyance, and more. Some papers are Why an Extended Evolutionary Synthesis is Necessary by Gerd Muller, The Evolutionary Implications of Epigenetic Inheritance by Eva Jablonka, Biological Action in Read-Write Genome Evolution by James Shapiro, Extended Genomes: Symbiosis and Evolution by Gregory Hurst, The Metaphysics of Evolution by John Dupre, and A Second Inheritance System: The Extension of Biology Through Culture by Andrew Whiten, some abstracts next. A laudable endeavor, but an even wider cast remains to include major transitions, self-organizing complexities, a statistical physics basis, and so on.

Since the last major theoretical integration in evolutionary biology—the modern synthesis (MS) of the 1940s—the biosciences have made significant advances. The rise of molecular biology and evolutionary developmental biology, the recognition of ecological development, niche construction and multiple inheritance systems, the ‘-omics’ revolution and the science of systems biology, among other developments, have provided a wealth of new knowledge about the factors responsible for evolutionary change. Whereas the MS theory and its various amendments concentrate on genetic and adaptive variation in populations, the extended framework emphasizes the role of constructive processes, ecological interactions and systems dynamics in the evolution of organismal complexity as well as its social and cultural conditions. Single-level and unilinear causation is replaced by multilevel and reciprocal causation. Among other consequences, the extended framework overcomes many of the limitations of traditional gene-centric explanation and entails a revised understanding of the role of natural selection in the evolutionary process. (Muller Abstract)

Many of the most important evolutionary variations that generated phenotypic adaptations and originated novel taxa resulted from complex cellular activities affecting genome content and expression. These activities included (i) the symbiogenetic cell merger that produced the mitochondrion-bearing ancestor of all extant eukaryotes, (ii) symbiogenetic cell mergers that produced chloroplast-bearing ancestors of photosynthetic eukaryotes, and (iii) interspecific hybridizations and genome doublings that generated new species and adaptive radiations of higher plants and animals. Adaptive variations also involved horizontal DNA transfers and natural genetic engineering by mobile DNA elements to rewire regulatory networks, such as those essential to viviparous reproduction in mammals. The intersections of cell fusion activities, horizontal DNA transfers and natural genetic engineering of Read–Write genomes provide a rich molecular and biological foundation for understanding how ecological disruptions can stimulate productive, often abrupt, evolutionary transformations. (Shapiro Abstract)

This paper briefly describes process metaphysics, and argues that it is better suited for describing life than the more standard thing, or substance, metaphysics. (Dupre Abstract)

Batten, David, et al. Visions of Evolution: Self-organization Proposes What Natural Selection Disposes. Biological Theory. 3/1, 2008. Co-authors are Stanley Salthe and Fabio Boschetti. Batten and Boschetti are with the Australian CSIRO agency, while Salthe is a veteran visionary biologist. The paper begins with a review of seven optional evolutionary theories from Depew and Weber’s 1995 Darwinism Evolving. This leads to a condensation of such themes in order to articulate an inherent “generativity” prior to environmental culling. To do justice, an extended quote is cited.

To summarize, we propose a view according to which the relation between self-organization and natural selection can be divided into three stages: (1) during the first stage, the emergence of organization is a necessary requirement for natural selection to occur. Without organization, behaviors that can be selected upon are statistically so unlikely that the process cannot even start. In this situation, self-organization constrains selection. In other words, organization proposes what selection might dispose. (2) In the second stage, primordial forms of organization provide the material for natural selection to act upon, which in turn results in the development of increasingly complex forms of organization. Here natural selection provides specific constraints on self-organization. Selection passes on contexts for further self-organization. (3) In the third stage, the relationship (both competition and collaboration) between increasingly complex forms of organization and their impact on the environment affects the context within which natural selection can act (e.g., the current cultural selection occurring in human society could not be conceived in the context of the early primordial soup), making natural selection and self-organization complementary aspects of a single process. (26-27)

Bear, Greg. When Genes Go Walkabout. Proceedings of the American Philosophical Society. 148/3, 2004. The noted science fiction writer and author of Darwin’s Radio proposes that a radical evolutionary synthesis is in the air if many new advances can be gathered together. In addition to those in the quote, Bear cites migratory gene transfer, much learning everywhere, a penchant for cooperation and so on. See also his website www.gregbear.com, click on Biology and then The New Biology for another pertinent essay.

Collecting facts from many sources – including papers and texts by the excellent scientists speaking here today – I tried to assemble the outline of a modern appendix to Darwin, using ideas from disciplines not available in Darwin’s time: theories of networks, software design, information transfer and knowledge, and social communication – lots of communication. (325)

Bedau, Mark. The Evolution of Complexity. Barberousse, Anouk, et al, eds. Mapping the Future of Biology. Berlin: Springer, 2009. The Reed College philosopher makes a crucial contribution to any expansion of evolutionary theory by factoring in evident “complex adaptive system” dynamics that appear inherently at work prior to selection. Drawing on advances in “artificial life” computations, an inclusion of this “missing” dimension can at last serve to verify and explain life’s non-random, vectorial emergence. Along with Susan Oyama in the same volume, and many other similar efforts noted on this side, such an approach can begin to realize and qualify the generative essence of a parental cosmos to earth child genetic code.

Our starting point is merely the observation of a trend. But perhaps the trend is not just an accident. Perhaps it is an instance of some general regularity. The arrow of complexity hypothesis is the hypothesis that evolution inherently creates increasing complex adaptive organisms. (112) The arrow of complexity hypothesis states that this dynamical emergent process is a generic property of some class of evolving systems, rather that just an accident. (112)

The conclusion to draw from this is that biology needs new concepts, theories and models if it is to resolve the arrow of complexity hypothesis. My own hunch is that we are missing some key insight, some important new concept or process or mechanism, that will resolve why complexity grows over the course of evolution. (130) Fortunately, biology does have a new powerful tool for exploring answers to this question: the constructive models of soft artificial life. These models are essential for making progress on deep questions about complex adaptive systems, such as the arrow of complexity. (130)

Bedau, Mark and Carol Cleland, eds. The Nature of Life: Classical and Contemporary Perspectives from Philosophy and Science. Cambridge: Cambridge University Press, 2010. A collections of reprints with four sections; Classical Discussions of Life; The Origin and Extent of Natural Life; Artificial Life and Synthetic Biology; and Defining and Explaining Life. But it seems to labor, unawares, in the moribund machine paradigm wherein life and sentience has to make excuses for itself in an intrinsically barren multiverse. The papers then appear a loose, pedantic collection of sample takes from authors such as Aristotle, Descartes and Kant to Tibor Ganti, David Deamer, Margaret Boden, Lynn Margulis and Richard Dawkins.

Beinhocker, Eric. Evolution as Computation. Santa Fe Institute Working Papers. 10-12-037, November, 2010. In this online paper, slated to appear in the Journal of Institutional Economics, (online May 2011) the McKinsey Global Institute, London, economics theorist presses on to view the physical, biological, and societal universe in terms of and as due to iterative, algorithmic, informative processes. By so doing, the work continues the major project of his 2006 The Origin of Wealth toward a vital synthesis of “self-organization with a generalized Darwinism.” This waxing school perceives complex adaptive systems as a natural ‘software’ that drives or generates the amplifying scales of life’s regnant intricacy. In this theme, evolutionary landscapes are ‘searched’ to find optimum solutions, by which order rises from disorder. It is noted that from geneticist Sewall Wright 1930s prescience, this approach has grown in veracity and application, now conveniently fit for our computer age.

In the 1980s and 90s the computational view of evolution began to be connected with emerging work on complex systems, and self-organization (Kauffman, 1993), as well as rooted in fundamental work on dissipative thermodynamic systems by figures such as Erwin Schrödinger and Ilya Prigogine, as well as von Neuman’s work on self-replicating systems and cellular automata, and the physics of information. This led to a further interpretation of evolution as a bootstrapping algorithm that uses free energy to create order in complex systems. (4)

One can likewise think of biological evolution as a computational algorithmic process that runs on the substrate of DNA and the other chemical machinery of biological organisms, but evolution itself is a more general substrate-neutral algorithm. (6) Following Wright (1932) and the subsequent literature, evolution can be characterized as a form of search algorithm that recursively explores a combinatorial problem space seeking out solutions that are more fit than others according to some notion of fitness. (6)

Benetez, Mariana, et al, eds. Frontiers in Ecology, Evolution and Complexity. http://scifunam.fisica.unam.mx/mir/copit/. A 2014 volume in this online imprint of UNAM National Autonomous University of Mexico. Octavio Miramontes and Alfonso Valiente-Banuet are co-editors. With an Introduction by Stuart Kauffman, a broad array of essays such as Plant Community Ecology, Flower Complexity and Fractals, Networks in Agroecology, Nonlinearity in Population Ecology, Criticality in Gene Networks, and The Ecology of Human Linguistic Groups. Noted authors include Suzanna Manrubia, Jorge Bascompte, Og DeSouza, and Pablo Marquet.

Advances in molecular biology, remote sensing, systems biology, bioinformatics, non-linear science, the physics of complex systems and other fields have rendered a great amount of data that remain to be integrated into models and theories that are capable of accounting for the complexity of ecological systems and the evolutionary dynamics of life. It is thus necessary to provide a solid basis to discuss and reflect on these and other challenges both at the local and global scales. This volume aims to delineate an integrative and interdisciplinary view that suggests new avenues in research and teaching, critically discusses the scope of the diverse methods in the study of complex systems, and points at key open questions. Finally, this book will provide students and specialists with a collection of high quality open access essays that will contribute to integrate Ecology, Evolution and Complexity in the context of basic research and in the field of Sustainability Sciences.

Bentley, Alexander and Herbert Maschner. Stylistic Change as a Self-Organized Critical Phenomenon. Journal of Archaeological Method and Theory. 8/1, 2001. (The leading edge work of these anthropologists is noted more in other sections.) This article provides a good entry to complex adaptive systems, how these inherent dynamics impel life’s self-similar evolution and equally apply to its cultural phase.

The theory of self-organized criticality is important in that it implies that the evolution of complex systems may be driven more by interactions between agents that by external events or natural selection. (35) The evidence for self-organized criticality in evolution has centered on the fact that the fossil record exhibits power-law distributions of the magnitudes of extinction events and species lifetimes. (43)

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