V. Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWinian Genesis Synthesis
Etxeberria, Arantza. Autopoiesis and Natural Drift: Genetic Information, Reproduction, and Evolution Revisited. Artifical Life. 10/3, 2004. The autopoietic processes are said to self-organize and maintain biological systems, where ”self” refers to its whole network of recursive processes, prior to selection effects. These innate dynamics are seen to exist independently of substrate and history.
Fagerstrom, T., et al. Biologists Put on Mathematical Glasses. Science. 274/2039, 1996. With an opening nod to Galileo’s statement about the book of nature written in mathematics, four theoretical biologists make note of a dawning discovery and articulation of a universal pattern and process.
What causes Nature to build more complex things in a hierarchical manner with principles that are recurrent at all levels? Genes, for example, are integrated into genomes, cells into multicellular organisms, and individuals into societies. Recurrence of the same principle gives rise to ever higher forms of complex life in an apparently open-ended evolutionary process. (2039)
Fangerau, Heiner, et al, eds. Classification and Evolution in Biology, Linguistics and the History of Science. Stuttgart: Franz Steiner Verlag, 2013. A collection with chapters such as Reconstructing the Lateral Component of Language History and Genome Evolution Using Network Approaches which discern innate commonalities between these archetypal prescriptive realms.
While Darwin’s grand view of evolution has undergone many changes and shown up in many facets, there remains one outstanding common feature in its 150-year history: since the very beginning, branching trees have been the dominant scheme for representing evolutionary processes. Only recently, network models have gained ground reflecting contact-induced mixing or hybridization in evolutionary scenarios. In biology, research on prokaryote evolution indicates that lateral gene transfer is a major feature in the evolution of bacteria. In the field of linguistics, the mutual lexical and morphosyntactic borrowing between languages seems to be much more central for language evolution than the family tree model is likely to concede. In the humanities, networks are employed as an alternative to established phylogenetic models, to express the hybridization of cultural phenomena, concepts or the social structure of science. However, an interdisciplinary display of network analyses for evolutionary processes remains lacking. Therefore, this volume includes approaches studying the evolutionary dynamics of science, languages and genomes, all of which were based on methods incorporating network approaches.
Feigin, Charles, et al. The GRN Concept as a Guide for Evolutionary Developmental Biology. Journal of Experimental Zoology B. 340/2, 2023. In a special Animal Gene Regulatory Network Evolution section, see intro by Mark Rebeiz and Thomas Williams, Princeton University and University of Melbourne biologists provide a latest survey of the formative importance that these interconnective anatomies serve. As the quote says their active presence as they join and arrange nucleotides as life grows and quickens.
Organismal phenotypes result from inherited developmental programs, carried out during embryonic and juvenile life stages. These programs are not blank slates onto which natural selection can draw arbitrary forms. Rather, the mechanisms of development play an integral role in shaping phenotypic diversity and the evolutionary trajectories of species. The gene regulatory network (GRN) concept represents a potent tool for achieving this goal whose utility has grown along with advances in “omic” techniques. In this Perspective, we go on to discuss how experiments and projects can be designed and enhanced in light of the vital GRN concept. Finally, we show how the major steps of GRN model construction and experimental validation suggest generalizable workflows that can serve as a scaffold for project design.
Fernandez, Jose, et al. Emergent Diversity in an Open-Ended Evolving Virtual Community. Artificial Life. 18/2, 2012. We cite this as an example of growing abilities to simulate evolutionary and ecological communities by way of algorithmic, computational dynamics. With coauthors Daniel Lobo, Gema Martin, Francisco Vico, and Rene Doursat, University of Malaga and Ecole Polytechnique researchers study digital flora as multi-agent plants across genetic, developmental, and physiological domains. Diverse viable habitats are then seen to flourish via mutually interacting individuals within their biotic environment.
Thus, evolution is being increasingly studied through alternative approaches involving the theoretical reconstruction and simulation of living systems at multiple scales: genetic, cellular, developmental, population, and ecosystem. In particular, computational models have the great benefit of potentially producing a large number of experiments that can condense long evolutionary periods into short computing time frames, while making vast collections of data available for the analysis and extraction of relevant properties. (200)
Fields, Chris and Michael Levin. Scale-Free Biology: Integrating Evolutionary and Developmental Thinking. BioEssays. June, 2020. As a 2020 integrative phase goes forward, a veteran philosopher of biology now based in France and a Tufts University, Allen Discovery Center developmental biologist propose and scope out an array of unifying perspectives which are guided by an insight that life’s oriented emergence repeats in similar ways and means across the nested phases it engenders.
When the history of life on Earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life can also be seen as the development of life. Here some fruitful research directions suggested by this perspective are highlighted. Variation and selection become bidirectional information flows between scales, while “cooperation” and “competition” become scale relative. The language of communication, inference, and information processing are more useful than the language of causation to describe homogeneous and heterogeneous living systems. Emerging scale‐free theories such as predictive coding and active inference can provide conceptual tools for the study of a unified, multiscale dynamical system. (Abstract)
Fisher, Daniel. Asexual Evolution Waves: Fluctuations and Universality. Journal of Statistical Mechanics. Online January, 2013. Another article in the “Statistical Mechanics and the Dynamics of Evolution” issue noted in Nourmohammad below. Here a Stanford University biophysicist seems to find, allude to, in so many words, something is going on by itself. Could one ask what kind of greater reality does this such spontaneous structuring come from? And another deep insight might thus accord. As complexity science and statistical physics marry, it suggests that for a local existence, whether particle or person, a chancy contingency does go on, but for globally collective populations, a necessary “universality” of eventual, orderly patterning will prevail. (See also Christof Koch 2012) By this advisory, might we earth kinfolk join altogether, therefore choose to succeed, which may even influence our genesis cosmos amongst the stochastic multiverse?
In large asexual populations, multiple beneficial mutations arise in the population, compete, interfere with each other, and accumulate on the same genome, before any of them fix. The resulting dynamics, although studied by many authors, is still not fully understood, fundamentally because the effects of fluctuations due to the small numbers of the fittest individuals are large even in enormous populations. In this paper, branching processes and various asymptotic methods for analyzing the stochastic dynamics are further developed and used to obtain information on fluctuations, time dependence, and the distributions of sizes of subpopulations, jumps in the mean fitness, and other properties. The focus is on the behavior of a broad class of models: those with a distribution of selective advantages of available beneficial mutations that falls off more rapidly than exponentially. For such distributions, many aspects of the dynamics are universal—quantitatively so for extremely large populations. On the most important time scale that controls coalescent properties and fluctuations of the speed, the dynamics is reduced to a simple stochastic model that couples the peak and the high-fitness 'nose' of the fitness distribution. (Abstract)
Fodor, Jerry and Massimo Piattelli-Palmarini.
What Darwin Got Wrong.
New York: Farrar, Straus and Giroux,
What tangled webs we weave. These senior philosophers and cognitive scientists declare that the textbook gospel of “random mutation and adaptive selection” is a historical relic, and in no way an adequate explanation of how life evolves. But Ptolemaic epicycles are spun as the authors try to update and expand evolution within the tacit material machine paradigm. From the get-go (first quote) they claim that there is really no abiding, self-developmental nature to philosophize about in such a pointless, insensate universe. After some dense early chapters, an evo-devo window is rightly opened to admit the entire life span or ‘ontogenesis’ of an organism as where the evolutionary action is. For an example of further argumentation, Michael Ruse tears into the book in the March 7, 2010 issue of The Chronicle of Higher Education.
We therefore seek thoroughly naturalistic explanations of the facts of evolution, although we that they will turn out to be quite complex, as scientific explanations often are. It is our assumption that evolution is a mechanical process through and through. We take that to rule out not just divine causes but final causes, élan vital, entelechies, the interventions of extraterrestrial aliens and so forth. (xiii)
Fontana, Walter and Leo Buss. What Would be Conserved if ‘The Tape Were Played Twice’? Proceedings of the National Academy of Sciences. 91/757, 1994. A response to Stephen Jay Gould’s claim that if earth evolution happened again, because of blind variation and contingent selection as the only mechanism, human beings would not appear. But this article contends that the prior, independent existence of self-organizing dynamics, unknown to Darwin, introduces a novel source of emergent order. What would reoccur each time is the nested scale of self-maintaining organizations.
Moreover, separating the problem of the emergence of self-maintenance from the problem of self-reproduction leads to the realization that there exist routes to the generation of biological order other than that of natural selection. (761)
The Historical Nature of Biological Complexity and the Ineffectiveness of the Mathematical Approach.
Theory in Biosciences.
A University of Rome biotheorist clarifies and contributes to overdue, course correction, revisions of life’s inherent vitalities and oriented emergence as they naturally arise from biomolecules to ourselves. Four main aspects are identified as Organization, Individuality,
Contemporary scientific knowledge is mainly based on a reductionism epistemology and method. But its limitations prevent mathematical treatment of physical properties such as complex patterns and processes. The article will review the biological complexity debate and differences between living and inert matter. With these preparations, biological complexity can be viewed as a global, relational, and historical phenomenon at the individual and species level. (Abstract edits)
Frank, Steven. Natural Selection V: How to Read the Fundamental Equations of Evolutionary Change in Terms of Information Theory. Journal of Evolutionary Biology. 25/2377, 2012. The UC Irvine biologist continues his series of essays such as Selection vs. Transmission, Levels of Selection, and Kin Selection Theory. In Part V a reach is made to reorient life’s development in a more physical agreement with nature’s apparent essence and vitality by way of content and communication. As other areas, this somewhat statistical process seems akin to Bayesian probabilities (see below), which can illuminate how post-selection is involved.
The equations of evolutionary change by natural selection are commonly expressed in statistical terms. Fisher’s fundamental theorem emphasizes the variance in fitness. Quantitative genetics expresses selection with covariances and regressions. Population genetic equations depend on genetic variances. How can we read those statistical expressions with respect to the meaning of natural selection? One possibility is to relate the statistical expressions to the amount of information that populations accumulate by selection. However, the connection between selection and information theory has never been compelling. Here, I show the correct relations between statistical expressions for selection and information theory expressions for selection. Those relations link selection to the fundamental concepts of entropy and information in the theories of physics, statistics and communication. We can now read the equations of selection in terms of their natural meaning. Selection causes populations to accumulate information about the environment. (Abstract)
Fusco, Giuseppe, ed. Perspectives on Evolutionary and Developmental Biology. Padova: University of Padova Press, 2019. . This 420 page volume of essays for the Italian biologist and author Alessandro Minelli’s (search) 70th birthday is online in full, just Google title + Padova. With such entries a Towards a Developmental Biology of Holobionts by Scott Gilbert, An Evolutionary Biology for the 21st Century by Armin Moczek, Evo-Devo’s Challenge to the Modern Synthesis by Gerd Muller, The Evolutionary Relationships of Neural Structures in Arthropods by Angelika Stollewerk, Humans of the Middle Pleistocene by Giorgio Manzi, and Dynamic Structures in Evo-Devo by Johannes Jaeger, the work offers a latest evocation of this overdue (re)union of phylogeny and ontogeny. This 21st century synthesis is reinforced by a pervasive notice of symbiotic mutualities from eukaryotes to organisms and groups. In addition, a “self-constructing” essence is seen in process from physical origins to social peoples.
Evolutionary developmental biology (evo-devo) has revolutionized our understanding of why and how evolution unfolds the way it does. At the same time, much of evo-devo remains steeped in traditional perspectives and established dichotomies; these need to be overcome if evo-devo is to remain relevant in the coming century. In particular our conception of developmental evolution has to embrace the nature and consequences of developmental bias, the self-constructing nature of living systems, and the reciprocal interdependencies of development and environment in evolution. (Moczek abstract)