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

Nourmohammad, Armita, et al. Evolution of Molecular Phenotypes under Stabilizing Selection. Journal of Statistical Mechanics. Online January, 2013. In a special issue on “Statistical Mechanics and the Dynamics of Evolution,” itself an historic convergence now underway, with coauthors Stephan Schiffels and Michael Lassig, University of Cologne biophysicists view life’s evolving dynamics as if something like an inherent mathematical source is in effect before post-selection. As the Abstract notes, an “independent” agency seems implicated, along with a sense of its “universal” application. These interdisciplinary studies portend a 21st century revolution in evolutionary theory, drive, and direction from random meander to an ordained orthogenesis, by virtue of a heretofore unknown or excluded genotype source. Some other papers are “Modelling Evolution in a Spatial Continuum” by Nick Barton, et al, “Finding the Boundary between Evolutionary Basins of Attraction, and Implications for (Sewall) Wright’s Fitness Landscape Analogy” by Dan Weinreich, Suzanne Sindi, and Richard A. Watson, and “Asexual Evolution Waves” by Daniel Fisher, reviewed above. A companion Journal of Statistical Physics, is on a similar track with special issues like “Statistical Mechanics and Biology” (144/2, 148/4, 2012) wherein, e.g., “Universality in Bacterial Colonies” by Juan Boanchela, et al, can be found.

Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype's genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes. (Abstract)

For complex traits, predictability turns out to depend on scale and on selection. There is little predictability at the genome level, because the total number of genotypes encoding a function trait is vastly larger than that realized in any on population. The equilibrium predictability is exponentially small in the number of trait sites, and populations evolving from a common ancestor will diverge through mutations at different sites. At the phenotypic level, the equilibrium predictability is related to the divergence-diversity ratio. It is small at neutrality, but under sufficiently strong stabilizing selection it can reach values of one. Hence, stabilizing selection generates predictability at the phenotypic level. (30)

Okasha, Samir. Evolution and the Levels of Selection. Oxford: Clarendon, 2006. A Bristol University philosopher of biology sorts through the literature on the current quantification that emergent life and nature does indeed scale as a nested hierarchy of wholes within wholes, wherein selection can work at a multiple of stages.

Orgogozo, Virginie. Replaying the Tape of Life in the Twenty-First Century. Interface Focus. 5/20150057, 2015. In 1991, Stephen Jay Gould famously stated that life’s evolution seems so chancy and contingent as due to selection alone, if it occurred again on Earth, a different outcome would result sans human beings. This claim has since caused much consternation and debate. Into the mid 2010s, the University of Paris Diderot, Institute Jacques Monod, Drosophila Evolution group leader contends that many findings such as repeatability in species’ phenotypes and genetic bases now imply an actual, much constrained course which would retrace in its inherent trajectory.

The question of whether outcomes of a replayed life's tape are predictable is now being addressed with an experimental approach, through a series of investigations dealing with smaller bouts of evolution. While it is too early to derive any definite conclusion, recent observations suggest that there are predictable portions within life's tape and that evolution might not be as unpredictable as once thought 25 years ago, when Stephen Jay Gould formulated his original question. (9

Ostachuk, Agustin. What is It Like to be a Crab? A Complex Network Analysis of Eucaridan Evolution. Evolutionary Biology. 46/2, 2019. In an entry which can exemplify a 2020s genesis synthesis, a National University of La Plata, Argentina biologist achieves a systems explanation of how this common crustacean came to form and develop. As the quotes say, a novel inclusion and application of nature’s pervasive topologies then provides a better explanation of how their skeletal carapace came to be. The result is seen as robust enough to be carried across Metazoan creatures because it implies an independent, generic anatomy and physiology. As the author noted in 2015 (search) new insights into an actual recapitulation process may also accrue. The entry illustrates a prime theoretical revision in our midst whence life’s long ascent from universe to us becomes braced by this vital, genetic-like mathematical source.

Eucaridan evolution involved a process starting from a body organization characterized by an elongate and cylindrical cephalothorax, a well-developed abdomen composed of swimming appendages, ending in a tail fan formed by flattened uropods and a telson. This process would lead to a body organization characterized by a shortened and depressed cephalothorax, and a reduced and ventrally folded abdomen. In this work, the evolution of the superorder Eucarida was studied using complex networks. A new definition of crab and its carcinization are given based on the results obtained. The evolution of the crab implied the formation of a triadic structure with high closeness centrality which represented a stable hierarchical core buried or enclosed in the topological structure of the network with its integrated and robust topology. (Abstract excerpts)

In this work, crustacean external morphology was abstracted as a network in which each individual morphological feature was considered as a node, and the edges among these nodes were established based on their physical connections. This representation and abstraction of the crab morphology as a network is considered to capture the evolutionary and developmental structural information of the whole organism. It represents the characteristic structure of a given organism, its architectural plan or Bauplan. The analysis of these different and successive plans yielded important results regarding the evolutionary trend of this group. In summary, this trend was involved an increase in complexity, integration and robustness. These models of crustaceans through complex network theory revealed important, unexpected and surprising features of their evolutionary process. (204)

Oyama, Susan. Compromising Positions: The Minding of Matter. Barberousse, Anouk, et al, eds. Mapping the Future of Biology. Berlin: Springer, 2009. The John Jay College developmental systems philosopher provides a generous guide to historic and current intimations that nature is literally informational, textual, somehow encoded, at its essence. Compare with Mark Bedau in the same volume as a frontier effort to get at this “missing” quality by which to truly achieve a 21st century synthesis. In so doing, parallels are drawn between “Logos: Divine Information,” as lately revived by “theistic evolutionists” such as John Haught, and “Biologos: Genetic Information,” with a potential promise to finally identify an intrinsic force “counter to chance.”

The primal Word, bringer of order and meaning to chaos, introduces a comparison of Divine Logos with what I call Biologos. Both involve notions of direction, guiding agency, creative purpose, and meaning – roughly, intentionality. In addition, saying the “same thing” in several languages implies meanings that are independent of their linguistic vehicles, suggesting another characteristic of Logos and many information concepts in biology: their transcendence of, indeed, domination of the material. (27)

Oyama, Susan, et al, eds. Cycles of Contingency. Cambridge: MIT Press, 2001. A broad array of essays explore the potential of developmental systems theory (DST) to move beyond particulate genetics. DST views the ontogeny of an organism as due to epigenetic cycles of interaction among a varied set of influences including DNA, cellular and organismic structural constraints together with social and ecological factors. These are more contingently constructed during embryonic development than predetermined.

Ozdemir, Vural, et al. Ready to Put Metadata on the Post-2015 Development Agenda? Linking Data Publications to Responsible Innovation and Science Diplomacy. OMICS: A Journal of Integrative Biology. 18/1, 2014. An international collaboration of 24 scientists and physicians from India, Turkey, Italy, the UK, USA, and far afield concerned with global health initiatives propose ways that this stream of biological and medical information be better organized and made more available. See also OMICS 2.0: A Practice Turn for 21st Century Science and Society by Vural Ozdemi in this journal (17/1, 2013).

Metadata refer to descriptions about data or as some put it, “data about data.” Metadata capture what happens on the backstage of science, on the trajectory from study conception, design, funding, implementation, and analysis to reporting. As the pursuit of knowledge broadens in the 21st century from traditional “science of whats” (data) to include “science of hows” (metadata), we analyze the ways in which metadata serve as a catalyst for responsible and open innovation, and by extension, science diplomacy. Such responsible innovation, as a collective learning process, has become a key component, for example, of the European Union's 80 billion Euro Horizon 2020 R&D Program from 2014–2020.

Looking ahead, OMICS: A Journal of Integrative Biology, is launching an initiative for a multi-omics metadata checklist that is flexible yet comprehensive, and will enable more complete utilization of single and multi-omics data sets through data harmonization and greater visibility and accessibility. The generation of metadata that shed light on how omics research is carried out, by whom and under what circumstances, will create an “intervention space” for integration of science with its socio-technical context. If we believe in science, then such reflexive qualities and commitments attained by availability of omics metadata are preconditions for a robust and socially attuned science, which can then remain broadly respected, independent, and responsibly innovative. (Abstract excerpts)

Defining OMICS: According to one etymological analysis, the suffix ‘ome’ is derived from the Sanskrit OM (‘completeness and fullness’). This is consistent with the ethos of integrative biology and the systems thinking embedded in data-intensive omics fields noted above, be it vaccinomics, pharmacogenomics, or public health genomics. The high-throughput omics data obtained in parallel from successive hierarchies of cell biology help discern systems diagnostics and therapeutics, taking into account the built-in molecular redundancies preserved in biology during the course of human evolution. (1)

Pah, Adam, et al. Use of a Global Metabolic Network to Curate Organismal Metabolic Network. Nature Scientific Reports. 3/1695, 2013. Via Google, the word Curate has dual meanings – “a person invested with the care or cure of souls,” or “to organize, sort, arrange, such as a museum.” A “Curator” is an overseer or caretaker. As the quotes explain, with Roger Guimera, A. M. Mustoe, and Luis Amaral, Northwestern University systems biologists propose a novel sophistication to further limn and parse complex genomes. As scientists proceed with this literacy project, as if “cosmic curators,” we seem to fulfill a phenomenal role as an intended agency by which a genesis uniVerse tries to consciously read its own genetic code.

The difficulty in annotating the vast amounts of biological information poses one of the greatest current challenges in biological research. The number of genomic, proteomic, and metabolomic datasets has increased dramatically over the last two decades, far outstripping the pace of curation efforts. Here, we tackle the challenge of curating metabolic network reconstructions. We predict organismal metabolic networks using sequence homology and a global metabolic network constructed from all available organismal networks. While sequence homology has been a standard to annotate metabolic networks it has been faulted for its lack of predictive power. We show, however, that when homology is used with a global metabolic network one is able to predict organismal metabolic networks that have enhanced network connectivity. Additionally, we compare the annotation behavior of current database curation efforts with our predictions and find that curation efforts are biased towards adding (rather than removing) reactions to organismal networks. (Abstract)

Paixao, Tiago, et al. Toward a Unifying Framework for Evolutionary Processes. Journal of Theoretical Biology. 383/28, 2015. A ten person Austrian, British, and German team that includes Nick Barton and Andrew Sutton propose to join the dual approaches of algorithmic computation and population genetics. The former involves agencies that search a relevant landscape, while the latter deals with dynamics of allele or genotype frequencies. A good part of the effort involves defining a consistent terminology for both aspects. By 2015, with advances and finesses, a viable synthesis, albeit with technical detail, can be broached.

The theory of population genetics and evolutionary computation have been evolving separately for nearly 30 years. Many results have been independently obtained in both fields and many others are unique to its respective field. We aim to bridge this gap by developing a unifying framework for evolutionary processes that allows both evolutionary algorithms and population genetics models to be cast in the same formal framework. The framework we present here decomposes the evolutionary process into its several components in order to facilitate the identification of similarities between different models. In particular, we propose a classification of evolutionary operators based on the defining properties of the different components. We cast several commonly used operators from both fields into this common framework. Using this, we map different evolutionary and genetic algorithms to different evolutionary regimes and identify candidates with the most potential for the translation of results between the fields. This provides a unified description of evolutionary processes and represents a stepping stone towards new tools and results to both fields. (Abstract)

Payne, Joshua, et al. RNA-mediated Gene Regulation is Less Evolvable than Transcriptional Regulation. Proceedings of the National Academy of Sciences. 115/E3481, 2018. In a paper that received science press notice, Payne, ETH Zurich, Fahad Khalid, Swiss Institute of Bioinformatics, and Andreas Wagner (search), University of Zurich evolutionary biologists make the case, akin to other current work (Daniels, Ouma), that along with nucleotides, transcriptional regulatory networks which turn genes on and off to achieve an informative creaturely genotype are of equal significance, maybe more so.

Cells regulate the activity of genes in a variety of ways. For example, they regulate transcription through DNA binding proteins called transcription factors, and they regulate mRNA stability and processing through RNA binding proteins. Based on current knowledge, transcriptional regulation is more widespread and is involved in many more evolutionary adaptations than posttranscriptional regulation. The reason could be that transcriptional regulation is studied more intensely. We suggest instead that transcriptional regulation harbors an intrinsic evolutionary advantage: when mutations change transcriptional regulation, they are more likely to bring forth novel patterns of such regulation. That is, transcriptional regulation is more evolvable. Our analysis suggests a reason why a specific kind of gene regulation is especially abundant in the living world. (Significance)

Pennisi, Elizabeth. Modernizing the Modern Synthesis. Science. 321/196, 2008. We use this news note to record the July 2008 select symposium at the Konrad Lorenz Institute in Altenberg, Austria, organized by Massimo Pigliucci and Gerd Muller, which discusses subject themes such as epigenetics, modularity, gene regulatory networks, and self-organization which now troubles the 1950’s version that joined Darwin and Mendel. Among the 16 attendees are Eva Jablonka, Stuart Newman, Gunter Wagner, Marc Kirschner, and Eors Szathmary. The meeting was to be under the radar but journalist Susan Mazur made it public in March on the New Zealand based Scoop site: www.scoop.co.nz/stories/HL0803/S00131.htm. She went on to interview everyone invited and others such as Richard Dawkins (not amused) and Stuart Kauffman (tell me about it), all of which is posted on this site. On the Rationally Speaking website, www.rationallyspeaking.blogspot.com, Piglucci has now provided a daily summary, along with commentaries. The citation below is the group’s summary statement. But the topical list does not include convergence, symbiosis, autopoiesis, a telic intelligence, emergence, and much else, let alone address an encompassing universe, wrongly seen as a machine. (See also Whitfield below for a later report.)

A group of 16 evolutionary biologists and philosophers of science convened at the Konrad Lorenz Institute for Evolution and Cognition Research in Altenberg (Austria) on July 11-13 to discuss the current status of evolutionary theory, and in particular a series of exciting empirical and conceptual advances that have marked the field in recent times. The new information includes findings from the continuing molecular biology revolution, as well as a large body of empirical knowledge on genetic variation in natural populations, phenotypic plasticity, phylogenetics, species-level stasis and punctuational evolution, and developmental biology, among others.

The new concepts include (but are not limited to): evolvability, developmental plasticity, phenotypic and genetic accommodation, punctuated evolution, phenotypic innovation, facilitated variation, epigenetic inheritance, and multi-level selection. By incorporating these new results and insights into our understanding of evolution, we believe that the explanatory power of evolutionary theory is greatly expanded within biology and beyond. As is the nature of science, some of the new ideas will stand the test of time, while others will be significantly modified. Nonetheless, there is much justified excitement in evolutionary biology these days. This is a propitious time to engage the scientific community in a vast interdisciplinary effort to further our understanding of how life evolves.

Pennisi, Elizabeth. Shaking Up the Tree of Life. Science. 354/817, 2016. A report on how current abilities to sequence organisms from microbes to fish, reptiles, birds, onto mammals, primates and us reveals a pervasive horizontal movement of genetic materials among closely related species, and also further afield. As a result, many animals, including humans are hybrid entities. The work of Princeton biologists Rosemary and James Grant to detect hybridization within avian lineages is highlighted. As a result, 2010s techniques by a worldwide science community are seen as wholly revising the tradition of distinct arboreal branches.

Biologists long ago accepted that microbes can swap DNA, and they are now coming to terms with rampant gene flow among more complex creatures. “A large percent of the genome is free to move around” notes Chris Jiggins, an evolutionary biologist at the University of Cambridge in the UK. This “really challenges our concept of what a species is.” As a result, where biologists once envisioned a tree of life, its branches forever distinct, many now see an interconnected web. (818)

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