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V. Systems Evolution: A 21st Century 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.

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)

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. 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)

Aguirre, Jacobo, et al. On the Networked Architecture of Genotype Spaces and its Critical Effects on Molecular Evolution. Open Biology. July, 2018. In this Royal Society journal, Barcelona and Madrid systems theorists including Susanna Manrubia make a thorough case with over 200 references for a dynamic synthesis by way of ubiquitous network phenomena. The paper goes on to establish ways that these topologies can inherently arise from animate physical systems. Their presence is especially evident as whole genomes translate and array into creaturely physiologies. A “multlscape” is thus achieved with abilities to quickly adapt to external changes. In regard, a 21st century genesis revolution gains a broad outline by this deep inclusion of a complex, exemplary source as it arrays everywhere.

In this Royal Society journal, Barcelona and Madrid systems theorists including Susanna Manrubia make a thorough case with over 200 references for a dynamic synthesis by way of ubiquitous network phenomena. The paper goes on to establish ways that these topologies can inherently arise from animate physical systems. Their presence is especially evident as whole genomes translate and array into creaturely physiologies. A “multlscape” is thus achieved with abilities to quickly adapt to external changes. In regard, a 21st century genesis revolution gains a broad outline by this deep inclusion of a complex, exemplary source as it arrays everywhere.

Ananthaswamy, Anil. Chemistry Guides Evolution, Claims Theory. New Scientist. January 18, 2003. A report on scientists who believe that Earth’s early chemistry channeled life to form bounded vesicles and to proceed in a predictable way from cells to animals. A comment by Harold Morowitz sums up:

It’s part of a quiet paradigm revolution going on in biology, in which the radical randomness of Darwinism is being replaced by a much more scientific law-regulated emergence of life. (12)

Ao, Ping. Global View of Bionetwork Dynamics: Adaptive Landscape. Journal of Genetics and Genomics. 36/2, 2009. The emeritus University of Washington bioengineer is presently at the Systems Biology Laboratory, Shanghai Center for Systems Biomedicine. Also known as a “fitness landscape,” this popular map-like metaphor from Sewall Wright in 1932, variously by Theodosius Dobzhansky, George Simpson, Conrad Waddington, and others, attempts to graphically display the active evolutionary and organismic traverses, as if attractors, of creaturely genotypes and/or phenotypes. This 21st century survey covers five areas of population genetics, developmental biology, gene regulation and genetic switch, neural dynamics and computing, and protein folding via current complex network theories. For more background and discussion, see the edited volume The Adaptive Landscape in Evolutionary Biology, (Oxford UP, 2012) And while reading one wonders if a similar presence and expansion of such a ground of being and becoming might extended to life’s fertile celestial realms, as if a conducive cosmic spacescape.

Based on recent work, I will give a nontechnical brief review of a powerful quantitative concept in biology, adaptive landscape, initially proposed by S. Wright over 70 years ago, reintroduced by one of the founders of molecular biology and by others in different biological contexts, but apparently forgotten by modern biologists for many years. Nevertheless, this concept finds an increasingly important role in the development of systems biology and bionetwork dynamics modeling, from phage lambda genetic switch to endogenous network for cancer genesis and progression. It is an ideal quantification to describe the robustness and stability of bionetworks. Here, I will first introduce five landmark proposals in biology on this concept, to demonstrate an important common thread in theoretical biology. Then I will discuss a few recent results, focusing on the studies showing theoretical consistency of adaptive landscape. From the perspective of a working scientist and of what is needed logically for a dynamical theory when confronting empirical data, the adaptive landscape is useful both metaphorically and quantitatively, and has captured an essential aspect of biological dynamical processes. Though at the theoretical level the adaptive landscape must exist and it can be used across hierarchical boundaries in biology, many associated issues are indeed vague in their initial formulations and their quantitative realizations are not easy, and are good research topics for quantitative biologists. I will discuss three types of open problems associated with the adaptive landscape in a broader perspective. (Abstract)

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