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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

3. Cellular Self-Organization and Holobiont Symbiogenesis

Dyson, Freeman. The Evolution of Science. Andrew Fabian, ed. Evolution: Society, Science, and the Universe. Cambridge: Cambridge University Press, 1998. To illustrate how the evolution of the cosmos, science, and life develop in the same, consistent way, physicist/philosopher Dyson cites the occasion of prevalent symbiotic unions in both biological and celestial realms. That sentence was my original review some 20 years ago. Into 2021 for this Symbiosis section that has since grown from eukaryotic cells onto holobiont organisms and now worldwise findings of “universal symbiogenesis” (Gontier, Slijepcevic,, Igamberdiev, et al) one can indeed perceive and report its evidential fulfillment.

s a physical scientist, I am struck by the fact that the borrowing of concepts from biology into astronomy is valid on two levels. One can see in the sky many analogies between astronomical and biological processes, as I shal shortly demonstrate. And one can see similar analogies between intellectual and biological process in in the evolution and taxonomy of scientific disciplines. The evolution of the universe and the evolution of science can be described in the same language as the evolution of life. (118)

Elde, Nels, et al.. A Role for Convergent Evolution in the Secretory Life of Cells. Trends in Cell Biology. 17/4, 2007. Deep in biological journals a systems reconception is underway to witness how cellular communities employ similar structures and processes in widely different situations. In this case, complex organelles as specialized secretory vesicles or dense core granules are profusely evident across animal and ciliate lineages.

The role of convergent evolution in biological adaptation is increasingly appreciated. Many clear examples have been described at the level of individual proteins and for organismal morphology, and convergent mechanisms have even been invoked to account for similar community structures that are shared between ecosystems. (157) The traditional emphasis on divergent evolution might be due, at least in part, to a historical focus on a small number of model organisms and a failure to appreciate the rapid and extensive changes that occur in genomes. (162)

Embley, T. Martin and William Martin. Eukaryotic Evolution, Changes and Challenges. Nature. 440/623, 2006. Paired in this issue with the Gavin article below, an update on the role of mitochondrial organelles in the prokaryote to eukaryote transition. But again proteins are said to interact as “machinery,” so an inappropriate natural matrix persists.

Mitochondria in previously unknown biochemical manifestations seem to be universal among eukaryotes, modifying our views about the nature of the earliest eukaryotic cells and testifying to the importance of endosymbiosis in eukaryotic evolution. (623)

Feijen, Frida, et al. Evolutionary Dynamics of Mycorrhizal Symbiosis in Land Plant Diversification. Nature Scientific Reports. 8/10698, 2018. Now that such mutual floral and faunal assemblies, which were long ignored or denied, have become well accepted, Swiss and Dutch botanists can describe their vital presence and contribution to life’s developmental course. See also Unity in Diversity: Ancient Partnerships between Plants and Fungi by K. Field and S. Pressel in New Phytologist (Online April 2108).

Now that such mutual floral and faunal assemblies, which were long ignored or denied, have become well accepted, Swiss and Dutch botanists can describe their vital presence and contribution to life’s developmental course. See also Unity in Diversity: Ancient Partnerships between Plants and Fungi by K. Field and S. Pressel in New Phytologist (Online April 2108).

Frank, Steven. The Origin of Symbiotic Symbiosis. Journal of Theoretical Biology. 176/403, 1995. A review of a new integrative model to explain the evolution of mutually beneficial assemblies.

A dominant theme in the history of life has been the evolutionary innovations of cooperative symbioses: the first genomes near the origin of life, integrated prokaryotic cells, the complex symbiotic communities that evolved into modern eukaryotic cells, lichens, mycorrhizae, and so on. (403)

Frolov, Nikita\, et al. Self-Organization of Microtubules: Complexity Analysis of Emergent Patterns. arXiv:2305.00539. KU Leuven, Belgium cell biologists describe a realistic method into the 2020s to well integrate life’s physiological cellular phenomena with a deep formative substrate from which they evidentially arise. In addition, phase transitional scales can be seen to express dynamic critical states. See also Order from Chaos: How Mechanics Shape Epithelia and Promote Self-Organization by Filipe Vicente and Alba Diz-Munoz in Current Opinion in Systems Biology ( Vol. 32-33, March 2023).

Microtubules self-organize to form the cellular cytoskeleton, give cells their shape and play a crucial role in division and intracellular transport. A question remains if there is a good way to quantify these structures and gain new knowledge about the active physical principles of self-organization they exhibit. Here we introduce a entropy-based method to evaluate the formal complexity of spatial patterns emerging in an agent-based computational model of microtubule-motor interaction. We find that the proposed quantifier can discriminate between ordered, disordered, and intermediate states. Moreover, our study indicates that transitions in such a system are likely to exhibit properties of self-organized criticality. (Abstract)

Nature exploits fascinating self-organization principles to provide the mechanisms of life on different scales. Just as the maintenance of an ecosystem depends on populations of species cooperating or competing for shared resources, life at the cellular level is determined by the arrangement and interaction between its constituents, such as proteins, polymers, and organelles. (1)

Gavin, Anne-Claude, et al. Proteome Survey Reveals Modularity of the Yeast Cell Machinery. Nature. 440/631, 2006. An exemplary article with 32 authors from across Europe, worth several comments. With prokaryotic and eukaryotic cellular components now identified, the dynamic interrelations between them can be recognized. This approach reveals constant information-based, “cross-talk” processes whence similar modular encapsulation repeats over and over. A universality is here implied but a machine metaphor remains in use throughout. Scientists seem to proceed, mostly unbeknownst and to their disservice, within a physical universe conceived as a material mechanism, whereof life and mind is an interloper.

We first derived a ‘socio-affinity’ index that quantifies the propensity of proteins to form partnerships. (632) The degree of core-module cross-talk between functional categories highlights many known connections, such as that between protein synthesis, transcription and the cell cycle, in addition to others less well established. (634)
The (proteome) modularity is highly reminiscent of that seen elsewhere in nature, for example the combinatorial use of amino acids to build polypeptides, or domains to create proteins with complex biochemical properties. Modularity might very well represent a general attribute of living matter, with de novo invention being rare and reuse the norm. (635)

Gerardo, Nicole. Harnessing Evolution to Elucidate the Consequences of Symbiosis. PLoS Biology. Online February, 2015. A commentary by the Emory University biologist on the article Mutualism Breakdown by Amplification of Wolbachia Genes in the same issue by Ewa Chrostek and Luis Teixeira. We note for the contribution, and to show how symbiotic activities are now caccepted as the common rule, which the late Lynn Margulis valiantly advocated for decades.

Many organisms harbor microbial associates that have profound impacts on host traits. The phenotypic effect of symbionts on their hosts may include changes in development, reproduction, longevity, and defense against natural enemies. Determining the consequences of associating with a microbial symbiont requires experimental comparison of hosts with and without symbionts. Then, determining the mechanism by which symbionts alter these phenotypes can involve genomic, genetic, and evolutionary approaches; however, many host-associated symbionts are not amenable to genetic approaches that require cultivation of the microbe outside the host. In the current issue of PLOS Biology, Chrostek and Teixeira highlight an elegant approach to studying functional mechanisms of symbiont-conferred traits. They used directed experimental evolution to select for strains of Wolbachia wMelPop (a bacterial symbiont of fruit flies) that differed in copy number of a region of the genome suspected to underlie virulence. Their study highlights the power of exploiting alternative approaches when elucidating the functional impacts of symbiotic associations. (Abstract)

Geva-Zatorsky, Naama, et al. When Cultures Meet: The Landscape of “Social” Interactions between the Host and Its Indigenous Microbes. BioEssays. Online August, 2019. As this composite organism model gains use acceptance, with some resistance, N G-Z, Technicon-Israel Institute of Technology, with Eran Elinav and Sven Pettersson, Canadian Institute for Advanced Research, Toronto, provide a comparative sociological and cultural dimension. To paraphrase, we contain multitudes which in turn make up our integral persona, which is here cleverly enhanced and expanded to health, psychological, and urbane realms.

Animals exist as biodiverse composite organisms that include microbes, eukaryotic cells, and organs. Through an interdependent relationship and an inherent ability to transmit and reciprocate stimuli in a bidirectional way, a human body, aka holobiont, secures growth, health, and reproduction. In this review an overview is provided on the communications between microbes and their host in mutually nurturing biochemical, biological, and social interconnected relationships.. Nutrition, immunology, and sexual dimorphism have been traversed extensively to reflect on health and mind states, social interactions, and urbanization defects/effects. Finally, examples of molecular mechanisms potentially orchestrating these complex trans-kingdom interactions are provided. (Abstract excerpt)

Gilbert, Scott and Alfred Tauber. Rethinking Individuality: The Dialectics of the Holobiont. Biology & Philosophy. Online October, 2016. A Swarthmore College biologist and a Boston University philosopher (search each) continue their consideration of organisms, and human beings, as communal mutualities by way of populations of microbial entities. This entry views the immune system as a prime instance, aided by “the recent recognition of the ubiquity of symbiosis.” But concurrent articles in this journal such as Holobionts and the Ecology of Organisms: Multi-species Communities or Integrated Individuals? By Derek Skillings, and An Exploration of Holobiosis and Evolutionary Theory by Ford Doolittle and Austin Booth have quandaries and offer revisions.

However, this autonomous notion of individuality has proven inadequate both in terms of current understanding of organismic organization and more specifically in regards to immune functions in various capacities beyond its defensive role. Beyond the difficulties of defining the individual immunologically, the recent surge of interest in immune processes mediating mutualistic relationships has further challenged the notion of immune mediated individuality (under the guise of the ‘immune self’). Following this line of criticism, the challenge of reconsidering immunology’s guiding precepts is that most (if not all) ‘‘individual’’ animals are increasingly appreciated as being organized consortia of hundreds of species living in a symbiotic commune. What had been previously described as ‘‘individual organisms’’ are, in fact, multi-species/multi-lineage ‘‘holobionts,’’ composite organisms, whose physiology is a co-metabolism between the host and its microbiome, whose development is predicated upon signals derived from these commensal microorganisms, whose phenotype is predicated on microbial as well as host genes, and whose immune system recognizes these particular microbes as part of its ‘‘self.” (2)

Gilbert, Scott, et al. Eco-Evo-Devo: Developmental Symbiosis and Developmental Plasticity as Evolutionary Agents. Nature Reviews Genetics. 16/10, 2015. Gilbert, Swarthmore College, Thomas Bosch, Christian-Albrechts University, and Cristina Ledon-Rettig, Indiana University, propose an expanded synthesis as mutual symbiotic benefits become evident in every aspect of biology. A “phylosymbiosis” proceeds by a reciprocity of symbiont component and holobiont host, which then recapitulates throughout an evolutionary gestation. By an historical review from Charles Darwin and Karl Mobius to Lynn Margulis, Carl Woese, Nancy Moran, Margaret McFall-Ngal, and others, the revolution has been long in the making. A phenotypic organism thus is a composite of its animal genome, resident symbionts, and an abiotic environment. A succinct 2015 summary with 165 references.

The integration of research from developmental biology and ecology into evolutionary theory has given rise to a relatively new field, ecological evolutionary developmental biology (Eco-Evo-Devo). This field integrates and organizes concepts such as developmental symbiosis, developmental plasticity, genetic accommodation, extragenic inheritance and niche construction. This Review highlights the roles that developmental symbiosis and developmental plasticity have in evolution. Developmental symbiosis can generate particular organs, can produce selectable genetic variation for the entire animal, can provide mechanisms for reproductive isolation, and may have facilitated evolutionary transitions. Developmental plasticity is crucial for generating novel phenotypes, facilitating evolutionary transitions and altered ecosystem dynamics, and promoting adaptive variation through genetic accommodation and niche construction. In emphasizing such non-genomic mechanisms of selectable and heritable variation, Eco-Evo-Devo presents a new layer of evolutionary synthesis.

Giorgi, Franco, et al. The Egg as a Semiotic Gateway to Reproduction. Biosemiotics. Online September, 2013. Giorgi, University of Pisa, Luis Emilio Bruni, Aalborg University, Denmark, and Louis Goldberg, SUNY Buffalo, propose that an “oogenesis” oriented development from egg to I may best be understood by way of information conveyances in dual textually semiotic digital and analog modes.

The egg behaves as a prospective cell sustaining the developmental processes of the future embryo. In biosemiotic terms, this apparent teleonomic behaviour can be accounted for without referring to the exclusive causal role played by its genetic makeup. We envision two different processes that are uniquely found in the oocyte: (1) the first involves the mechanisms by which large amounts of mRNA accumulate in the ooplasm to establish the embryo axes prior to fertilization; (2) the second involves transfer of an excess of maternally supplied ribosomes to the oocyte to provide the future embryo with newly synthesized proteins. In this paper, we argue that the information required to sustain embryonic development is not due to any physical properties of the zygotic DNA and the maternal mRNAs, but to their spatially and temporally ordered relationship in the zygote’s internal space. (Abstract)

The oocyte itself is a topologically closed system since it is a cell bounded by a plasma membrane. The existence of such a boundary makes it possible for the oocyte to build up an internal organized ooplasm with an autoreferential character and to refer to the mother’s body as another entity occupying its external environment. This situation stems directly from the necessity to distinguish the content to be described, and eventually to be constructed as the internal organized structure of the oocyte, from its surroundings: a clear distinction between what could be defined as selfhood and everything else that is to be experienced as otherness. It follows that self-description is a pre-condition for the system to undergo self-replication. Self-description and self-replication are thus two key processes that together allow the oocyte to constitute a new emerging individuality distinct from the mother’s body and to maintain unaltered the species’ heritage from generation to generation. (2)

In conclusion, we have claimed a unique status for the oocyte. The single cell carries within it the digitalized memory of the history of the species in the form of a haploid chromosome set and the analogically organized ooplasm in the form of differentially distributed transcripts. Following fertilization, it is the interaction between the zygotic nuclei and the maternally generated transcripts that allows the developmental potential of the embryo to be fully unfolded, even though the structural organization of the ooplasm involves more than just their topological distribution. Many additional hierarchical levels constrain the context-dependent interpretations on local contingencies, as they gradually unfold from these prime interactions. (7)

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