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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

Baetu, Tudor. http://tudorbaetu.wordpress.com/publications. On this webpage by the University of Maryland philosopher can be accessed a flurry of pithy 2010 - 2012 papers such as British Journal for the Philosophy of Science, Genomic Programs as Mechanism Schemas: A Non-Reductionist Interpretation (from which the quote); Studies in History and Philosophy of Biological and Biomedical Sciences, Genes After the Human Genome Project; and Philosophy of Science, Mechanistic Constraints on Evolutionary Outcomes. If to surmise, something seems to be going on as life evolves to become more lively and smarter, a process and pattern that can’t be reduced or attributed to mechanism or selection alone. In regard it is broadly “programmatic” in a linguistic sort of way. Therefore a novel attentiveness is invited.

The discovery of gene rearrangement, nested genes, alternative promoters, alternative splicing, trans-splicing, RNA editing, frameshifting, alternate stop codons, polyproteins, and various other complications due to regulatory, post-transcriptional, and post-translational processing mechanisms pose a problem for the syntax-based gene concepts elaborated in the 1960s and 1970s. (650-651) The gist of these analogies with computer programs and hardwired electronic circuits is that the genome is organized as three nested levels of syntax-like DNA sequence motifs. (652) The gene level corresponds to the transcribed DNA. For the most part, genes act like independently processed modules because, once transcribed, their sequence is processed in accordance with the conserved sequences contained within their boundaries alone. (652)

In this article, I argued that genomic programs are best construed as abstract representations of the same sort as mechanism schemas and that, under this account, the program analogy is not reductionistic and does not ignore or underestimate the active contribution of epigenetic elements to phenotypes and development. In contrast to reductionistic interpretations equating genomic programs with recipes for constructing life, I argued that genomic programs are not representations of gene products or phenotypic outcomes, but rather sets of instructions for specific molecular mechanisms. (668)

Euro Evo Devo Vienna 2014. http://evodevo.eu/conferences/2014. A international meeting in July of the European Society for Evolutionary Developmental Biology that could be seen as a major, mature statement of this vital reunion on the way to a 21st century synthesis. Leading proponents such as Gunter Wagner, Etienne Danchin, Stuart Newman, Paula Mabee, Scott Gilbert, just about everyone it seems, will present the many ways that life’s evolution indeed is actually an embryonic gestation. A concurrent issue of Biological Theory will support, with an introduction Evo-Devo Shapes the Extended Synthesis by ESEDB president Gerd Muller. Typical symposia are Eco-Evo-Devo: Symbiosis and Epigenetic Inheritance, Bioinformatics and EvoDevo, and Cranial Neural Crest Populations across Developmental Systems.

Extended Evolutionary Synthesis. synergy.st-andrews.ac.uk/ees/the-project. A new website for a dedicated scientific endeavor to press on with a revised, updated evolutionary theory that many agree is overdue. A generous Templeton Foundation grant funds this vital project. It is overseen by Kevin Laland (search), a University of St. Andrews biologist, who assembled a premier team across four areas: Conceptual Issues, Evolutionary Innovations, Inclusive Inheritance, and Evolutionary Diversification. The research described will be carried by authorities such as Eva Jablonka, Gunter Wagner, Tim Lewens, Denis Noble, Ellen Clarke, Richard Watson, Jessica Flack, Andrew Gardner, many more. A summary article, Evolution Evolves, appears in the New Scientist for September 24, 2016. We quote it’s mission and sample phases.

The extended evolutionary synthesis (EES) is new way to think about and understand evolutionary phenomena that differs from the conception that has dominated evolutionary thinking since the 1930s (i.e., the modern synthesis). The EES does not replace traditional thinking, but rather can be deployed alongside it to stimulate research in evolutionary biology. It stands out in its emphasis on the role of developmental processes, which share with natural selection responsibility for the direction and rate of evolution, the diversity of life, and the process of adaptation. For example, the EES emphasizes that phenotypic variation is not random, that there is more to inheritance than genes, and that there are multiple routes to the adaptive fit between organisms and environments.

3. How evolution learns from experience: This project models the reciprocal interactions between long-term genetic evolution and short-term phenotypic plasticity, using a novel approach that exploits the parallels between learning and evolution. This will enable us to predict how plasticity shapes the evolution of developmental regulation and how this regulation biases genetic change. It will also shed light on how lineages maintain the ability to evolve as they become adapted.

22. Ecosystem networks and system-level functions: This theoretical project sets out to understand how inter-species interactions, through predation, competition and niche construction, are important for the stability and diversity of ecosystems. We are using connectionist learning theory to investigate the reciprocal interaction between the evolution of an ecological community and the non-living components of the ecosystem, exploring how this exchange influences the emergence of system-level functions.

International Society for the History, Philosophy, and Social Studies of Biology. www.ishpssb.org. This website has posted abstracts for its July 2005 conference at the University of Guelph in Ontario, which I attended. The biannual meeting, which covers all aspects of the biological, evolutionary and social sciences, is a good source for the latest theories, concepts and advances in these fields. It was last held in Brisbane, Australia, abstracts also on the site.

National Evolutionary Synthesis Center. www.nescent.org. A new consortium funded by the National Science Foundation and based in Durham, North Carolina intends to utilize the vast bioinformatics databases now being achieved to integrate molecular, developmental and phylogenetic studies.

Our goal is to help foster a grand synthesis of the biological disciplines through the unifying principle of descent with modification.

Schrodinger at 75 – The Future of Biology. www.tcd.ie/biosciences/whatislife. A September 2018 conference on the occasion of the Austrian-Irish Nobel physicist’s 1943 epic book What Is Life?. It is sponsored by Trinity College Dublin and held in the National Concert Hall. As Philip Ball cites in a retro-review in Nature (560/548, 2018), the work was a prescient “code-script” proposal (akin to Alan Turing) which initiated a long transition from physics and biogenetics being worlds apart to their current, active 2010s (re)unification. A stellar array of speakers includes Danielle Bassett, Leroy Hood, Christof Koch, Michael Gazzaniga, Linda Partridge, Nick Lane, and Svante Paabo.

The Third Way: Evolution in the Era of Genomics and Epigenomics. http://www.thethirdwayofevolution.com. Online since May 2014, this is a resource initiated by James Shapiro, Denis Noble and Raju Pookottil (see site) as a space for many diverse voices and authors who seek a viable alternative to intelligent design or Darwinian mutation and selection only. As the edited Rationale notes, and we seek to document, a 21st century, true to life synthesis is much in place if it could be gotten altogether. Among notable, enlisted advocates are Eva Jablonka, Scott Gilbert, Evelyn Fox Keller, Gerd Muller, Guenther Witzany, Wendy Wheeler, Eugene Koonin, Frantisek Baluska, Stuart Newman, Lynn Caporale, John Odling-Smee, Louise Westling, John Dupre, Kalevi Kull, Mae-Wan Ho, Ehud Lamm, Karin Moelling, and David Moore. Search each name here for writings, along with others under their People heading.

The vast majority of people believe that there are only two alternative ways to explain the origins of biological diversity. One way is Creationism that depends upon intervention by a divine Creator. The commonly accepted alternative is Neo-Darwinism, which is clearly naturalistic science but ignores much contemporary molecular evidence and invokes a set of unsupported assumptions about the accidental nature of hereditary variation. Neo-Darwinism ignores important rapid evolutionary processes such as symbiogenesis, horizontal DNA transfer, action of mobile DNA and epigenetic modifications. Moreover, some Neo-Darwinists have elevated Natural Selection into a unique creative force that solves all the difficult evolutionary problems without a real empirical basis.

Even today, the general public, and many scientists, are not aware of decades of research in evolutionary science, molecular biology and genome sequencing which provide alternative answers to how novel organisms have originated in the long history of life on earth. This web site is dedicated to making the results of that research available and to offering a forum to expose novel scientific thinking about the evolutionary process. The DNA record does not support the assertion that small random mutations are the main source of new and useful variations. Genomes merge, shrink and grow, acquire new DNA components, and modify their structures by well-documented cellular and biochemical processes. Most of the scientists referenced on this web site see evolution as a complex process with distinct mechanisms and stages rather than a phenomenon explainable by a small number of principles. (Rationale)

Manuel Viejo,, Jose and Mariano Sanjuán, eds.. Life and Mind: New Directions in the Philosophy of Biology and Cognitive Sciences. International: Springer, 2023. The editors are philosophers at the Autonomous University of Madrid. The volume is an eclectic survey of conceptual frontiers in four main areas: Animal and human cognition and Genetics, Teleology and Evolution. Some entries are Animal Understanding and Animal Self-Awareness, Incommensurability in Evolutionary Biology: The Extended Evolutionary Synthesis and Biological Teleology Beyond Natural Selection.

Abzhanov, Arkhat. The Old and New Faces of Morphology: The Legacy of D’Arcy Thompson’s Theory of Transformations and Laws of Growth. Development. 144/23, 2017. In a centennial issue upon D’Arcy’ Thompson’s classic On Growth and Form, an Imperial College London reader in evolution and developmental genetics praises from our late vantage how his espousal of innate physical forces and structural constraints in effect prior to natural selection is being verified by 21st century advances.

Taken as a whole, evidence suggests that the internal mechanisms , the famed Thompson’s ‘laws of growth,’ indeed exert a huge influence over morphological diversity and may explain much, perhaps most, of the increased generative capacity in certain avian and other animal clades to produce variation. Within this structural framework, one can better understand why D’Arcy Thompson was hesitant to explain the ‘profusion of forms’ in hummingbirds and other birds by means of natural selection alone. (4295)

Adami, Christoph. The Evolution of Biological Information: How Evolution Creates Complexity, from Viruses to Brains. Princeton: Princeton University Press, 2024. A senior authority in computational biology for over 20 years based at Michigan State University contributes his unique, 600 page opus. Its comprehensive chapters flow from the subject theory to biotic precursors, its genetic prescription, digital lab experiments, physiologic robustness, RNA origins, all the way to ascendant intelligence and social cooperation. As these aspects unfold in thorough turn they are braced by many equations.

An overall course becomes evident from the earliest replicants to metabolic biomolecules, cellular animals and relative linguistic knowledge. Although not a theme, it does trace a central trend that winds up with our sentient, observant selves. While Caleb Scharf and Yavul Harari write of algorithms that pass on from the human phase, for Adami the plot thickens and quickens as life’s genomic heredity proceeds from simple cells to neural cognizance. By 2024, a temporal progression may come into view of a procreative ecosmos were trying to decipher and read its own hereditary endowment.

In this final chapter I discussed three prime scales of life: how information is the key element that distinguishes life from nonlife, how the communication of information is the main factor that makes cooperation possible from cells to societies and how information is used to predict the future state of the world. Just as I wrote in the chapter introduction, once we look at biology in the light of information, it is hard not to see the fundamental importance of this concept. (519)

In this book, Christoph Adami adds a 21st century perspective to Darwinian evolution through the lens of an informational quality. This novel theoretical stance sheds light on how cells evolve to communicate, intelligence arises and viruses evolve drug resistance, By this account, information emerges as the central unifying principle which allows us to think about the origin of life on Earth and elsewhere. A leader in the field of computational biology, Adami especially considers the information theory of biomolecules and its content in genetic sequences and proteins. After viewing bacteria and digital organisms, he goes onto explain cooperation among cells, animals, and people. (MIT)

Christoph Adami is professor of microbiology and molecular genetics at Michigan State University. A pioneer in the application of methods from information theory to the study of evolution, he designed the Avida system that launched the use of digital life as a tool for investigating basic questions in evolutionary biology.

Adami, Christoph. What Is Complexity? BioEssays. 24/12, 2002. In an article for a special issue on “Modelling Complex Biological Systems,” a California Institute of Technology computer scientist perceives evolution as a nested hierarchy characterized by growing information content, aided by a natural selection for this quality.

It is probably more appropriate to say that evolution increases the amount of information a population harbors about its niche (and therefore, its physical complexity). (1089) Should we not expect an overall trend if evolution produces more and more diverse niches with more and more potential information? (1092)

Agrawal, Anurag. Toward a Predictive Framework for Convergent Evolution: Integrating Natural History, Genetic Mechanisms, and Consequences for the Diversity of Life. American Naturalist. 190/S1, 2017. In a supplement issue, the Cornell University biologist introduces this title endeavor which surveys the increasingly robust evidence for, and acceptance of, the recurrence of common forms and paths across animal kingdoms. The collected papers are from a 2016 American Society of Naturalists Symposium and include Pattern and Process in the Comparative Study of Convergent Evolution (D. Luke Mahler, et al), Evolutionary Scenarios and Primate natural History (Harry Greene) and Convergence and Divergence in a Long-Term Experiment with Bacteria (Richard Lenski).

A charm of biology as a scientific discipline is the diversity of life. Although this diversity can make laws of biology challenging to discover, several repeated patterns and general principles govern evolutionary diversification. Convergent evolution, the independent evolution of similar phenotypes, has been at the heart of one approach to understand generality in the evolutionary process. Yet understanding when and why organismal traits and strategies repeatedly evolve has been a central challenge. In this introductory article, I address these questions, review several generalizations about convergent evolution that have emerged over the past 15 years, and present a framework for advancing the study and interpretation of convergence. Perhaps the most important emerging conclusion is that the genetic mechanisms of convergent evolution are phylogenetically conserved; that is, more closely related species tend to share the same genetic basis of traits, even when independently evolved. Finally, I highlight how the articles in this special issue further develop concepts, methodologies, and case studies at the frontier of our understanding of the causes and consequences of convergent evolution. (Abstract excerpts)

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