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

3. Cellular Holobiont Symbiogenesis

Thornburg, Zane, at al. Fundamental Behaviors Emerge from Simulations of a Living Minimal Cell. Cell. 185/345, 2022. A 15 member team mainly based at the University of Illinois achieves a novel depth and degree of analysis of life’s metabolic cellular basis. A four part graphic depicts the study range from internal processes, cell states, dynamic changes and onto whole-cell simulations. A news report appears in Quanta Magazine as Most Complete Simulation of a Cell Probes Life’s Hidden Rules by Yasemin Saplakoglu on February 24, 2022. By our PhiloSophia view, by a science spiral from individuals to such collaborative efforts, our Earthuman intelligence seems to carry out, as yet unawares, some natural participatory purpose to wholly quantify a self-cocreating genesis ecosmos. However might we peoples in this decade be able to realize this?

A kinetic model for a minimal bacterial cell offers quantitative insight into how the cell balances processes from metabolism to gene expression to growth. (In Brief)

We present a whole-cell fully dynamical kinetic model of a minimal cell with a reduced genome that has retained few regulatory proteins or small RNAs. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations reveal how the cell balances its metabolism, genetic information processes, growth, as a deeper view into the vital principles of life. (Abstract excerpt)

Tripp, Erin, et al. Reshaping Darwin’s Tree: Impact of the Symbiome. Trends in Ecology and Evolution. Online June, 2017. An eight member team from the University of Colorado, Rutgers University, Sun Yat-Sen University, Chinese Academy of Sciences, and the Chicago Botanical Garden perceive an “unfolding revolution” via the actual inclusion of symbiotic assemblies across life’s phylogenetic evolution. Its significance is cited as “a new way of exploring the world” as graced by nature’s propensities for mutually beneficial unions. The late Lynn Margulis and founding advocate of this prime phenomena would be pleased, gratified, and say “tell me about it.”

Much of the undescribed biodiversity on Earth is microbial, often in mutualistic or pathogenic associations. Physically associated and coevolving life forms comprise a symbiome. We propose that systematics research can accelerate progress in science by introducing a new framework for phylogenetic analysis of symbiomes, here termed SYMPHY (symbiome phylogenetics).

Varahan, Sriram, et al. Metabolic Constraints Drive Self-Organization of Specialized Cell Groups. eLife. June 26, 2019. Five Indian systems cell biologists contribute novel understandings of the many ways that cellular activities have a vitality of their own as they innately organize themselves into preferred states and solutions.

How phenotypically distinct states in isogenic cell populations appear and stably co-exist remains unresolved. We find that within a mature, clonal yeast colony in low glucose, cells arrange into metabolically disparate cell groups. Using this system, we model and experimentally identify metabolic constraints which drive such self-assembly. Our work suggests simple physico-chemical principles that determine how isogenic cells spontaneously self-organize into structured assemblies in complimentary, specialized states. (Abstract excerpt)

Wang, Xiaoliang and Dongyun Bai. Self-organization Principles of Cell Cycles and Gene Expressions in the Development of Cell Populations. arXiv:2105.07337. We cite this entry by Zhejiang University and Shanghai Jao Tong University biologists as an 2021 example of the worldwide acceptance of this universal generative spontaneity in effect across cellular living systems. But the evolutionary sciences remain stuck betwixt a textbook neoDarwinian random selection mode, and these major revisions and advances which have not yet come to form a genesis synthesis. It is our annotated anthology intent to report and document its actual achievement by its latest EarthWise personsphere transition.

A big challenge in current biology is to understand the exact self-organization mechanism underlying complex multi-physics which serve life’s processes. With multiscale computation from subcellular gene expressions to cell population dynamics based on first principles, we show that cell cycles can self-organize into the development of E. coli populations relying on the moving graded nutrient concentration profile. As a result, the statistical cell cycle distribution is forms into a universal function and shows a scale invariance. (Abstract excerpt).

Watson, Richard and Jordan Pollack. How Symbiosis Can Guide Evolution. Dario Floreano, et al, eds. Advances in Artificial Life. Berlin: Springer, 1999. Cooperative symbiotic unions can be recognized as a prime force if our perception can move beyond a narrow Darwinian gradualist view.

Despite being undeniably common, the phenomenon of symbiosis, and especially mutualism, has for the most part been treated as a curio; a transient aberration on the otherwise relentless path of mutually-exclusive competition between species. In contrast, enlightened evolutionary theory recognises symbiosis as an integral process, and a fundamental source of innovation, in evolution. (29)

West-Eberhard, Mary Anne. Modularity as a Universal Emergent Property of Biological Traits. Journal of Experimental Zoology B. Online November, 2019. In another response to John Bonner’s call to revise evolutionary theory due to major transitions, the senior Smithsonian Tropical Research Institute, University of Costa Rica field and theoretical biologist extols the formative importance of nature’s structural preference for a scale of self-contained whole units nested within larger, bounded entities. This deep propensity is then seen to serve all manner of biological features and viabilities.

Woese, Carl. Evolving Biological Organization. Sapp, Jan, ed. Microbial Phylogeny and Evolution. Oxford University Press, 2005. The veteran biologist continues to revision a more life-like science. An initial evolution of communal cells is seen to involve the “horizontal” exchange of genes, before their subsequent “vertical” transfer between sexual organisms. Because of these findings, the prokaryote model is called into question. Woese goes on to summarize eleven points about cellular evolution from the advent of translation from nucleic to peptide sequence, to more community and complexity, which then set the stage for Darwinian individuals.

The science of biology enters the twenty-first century in turmoil, in a state of conceptual disarray, although at first glance this is far from apparent. (99) The time has come to shift biology’s focus from trying to understand organisms solely by dissecting them into their parts to trying to understand the fundamental nature of biological organization, of biological form. (100) The organism is not a machine! (100)

…what can be taken as reasonable starting points for developing a concept of the evolution of cellular organization? There are three such points. The first is horizontal gene transfer, which…is the essence of cellular evolution. The second is the nature of the cellular translation apparatus, for the evolutions of translation and cellular organization are part and parcel of one another. The third is the fact that the cell and its evolution are complex dynamic systems/processes. Eventually, our understanding of cellular evolution (and of evolution in general) will be in terms of complex dynamics systems. (104)

Woese, Carl. On the Evolution of Cells. Proceedings of the National Academy of Sciences. 99/13, 2002. This pioneer researcher finds the origin of cellular organization arises from an ecosystem-like community of diverse cell designs which share novel features. This is informed by ‘horizontal gene transfers’ which constitutes ‘a universal genetic code.’ Evolution began in earnest when these cells gained the capacity for ‘symbolic representation’ as it opened vast new niches. Woese then sees human language as its latest manifestation.

Yong, Ed. I Contain Multitudes: The Microbes Within Us and a Grander View of Life. New York: Ecco Books, 2016. An award-winning science writer reveals the prolific internal bacterial colonies which are a vital basis of our bodily and Earthly sustenance. Indeed, the whole course of life’s evolution could be seen as a “Microbiocene” age.

Yukalov, Viacheslav, et al. New Approach to Modeling Symbiosis in Biological and Social Systems. arXiv:1408.0111. As an example of the current conceptual synthesis of communal life with physical matter, with Elizaveta Yukalova and Didier Sornette, ETH Zurich information theorists explain nature’s pervasive tendency to form mutually beneficial groupings in terms of statistical mechanics. Some keywords are: mathematical models of symbiosis, nonlinear differential equations, dynamics of coexisting species, dynamical system bifurcations. And the deeper implication, a step rarely taken, is to realize and affirm an independent source program for this universal complementarity of entity and empathy.

Zilber-Rosenberg, Ilana and Eugene Rosenberg. Role of Microorganisms in the Evolution of Animals and Plants: The Hologenome Theory of Evolution. FEMS Mcirobiology Review. 32/5, 2013. Open University of Israel and Tel Aviv University scientists pick up on growing realizations that symbiotic associations pervade and foster every domain of biology and evolution from animals and plants to ecosystems. In this paper, this common phenomena is seen to extend even to their genomic source. Search Lynn Margulis for its foundations, and Jan Sapp, Scott Gilbert, and Alfred Tauber, for the latest ramifications. A 2013 book length treatment The Hologenome Concept by the authors has now come out from Springer.

We present here the hologenome theory of evolution, which considers the holobiont (the animal or plant with all of its associated microorganisms) as a unit of selection in evolution. The hologenome is defined as the sum of the genetic information of the host and its microbiota. The theory is based on four generalizations: (1) All animals and plants establish symbiotic relationships with microorganisms. (2) Symbiotic microorganisms are transmitted between generations. (3) The association between host and symbionts affects the fitness of the holobiont within its environment. (4) Variation in the hologenome can be brought about by changes in either the host or the microbiota genomes; under environmental stress, the symbiotic microbial community can change rapidly. These points taken together suggest that the genetic wealth of diverse microbial symbionts can play an important role both in adaptation and in evolution of higher organisms. During periods of rapid changes in the environment, the diverse microbial symbiont community can aid the holobiont in surviving, multiplying and buying the time necessary for the host genome to evolve. The distinguishing feature of the hologenome theory is that it considers all of the diverse microbiota associated with the animal or the plant as part of the evolving holobiont. Thus, the hologenome theory fits within the framework of the ‘superorganism’ proposed by Wilson and Sober. (Abstract)

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