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

3. Cellular Self-Organization and Holobiont Symbiogenesis

Dundr, Miroslav and Tom Misteli. Biogenesis of Nuclear Bodies. Cold Spring Harbor Perspectives in Biology. 2/12, 2010. In this new professional journal, Rosalind Franklin University of Medicine (Chicago) and National Cancer Institute researchers give real credence to self-organizing proclivities as an innate source of such “biogenesis.”

The nucleus is unique amongst cellular organelles in that it contains a myriad of discrete suborganelles. These nuclear bodies are morphologically and molecularly distinct entities, and they host specific nuclear processes. Although the mode of biogenesis appears to differ widely between individual nuclear bodies, several common design principles are emerging, particularly, the ability of nuclear bodies to form de novo, a role of RNA as a structural element and self-organization as a mode of formation. The controlled biogenesis of nuclear bodies is essential for faithful maintenance of nuclear architecture during the cell cycle and is an important part of cellular responses to intra- and extracellular events.

Dupre, John and Stephan Guttinger. Viruses as Living Processes. Studies in History and Philosophy of Biological and Biomedical Sciences. Online March, 2016. We cite this current paper by University of Exeter philosophers because in these mid 2010s, it evinces to the generative, defining presence of symbiotic processes across life’s emergent evolution. View papers by Scott Gilbert, Jan Sapp and others, which make a similar claim. But the intrepid founder of this concept from the 1970s, the late Lynn Margulis (1938-2011), had to put up with constant denials and rejections, e.g. from Richard Dawkins. In the past few years, life’s relational propensities have become accepted as a primary formative factor. This is a curious aspect of evolutionary theory when features such as convergence (McGhee, 2011) and teleology (Deacon, 2016) are inadmissible until a sudden reversal occurs.

The view that life is composed of distinct entities with well-defined boundaries has been undermined in recent years by the realisation of the near omnipresence of symbiosis. What had seemed to be intrinsically stable entities have turned out to be systems stabilised only by the interactions between a complex set of underlying processes. This has not only presented severe problems for our traditional understanding of biological individuality but has also led some to claim that we need to switch to a process ontology to be able adequately to understand biological systems. A large group of biological entities, however, has been excluded from these discussions, namely viruses. Viruses are usually portrayed as stable and distinct individuals that do not fit the more integrated and collaborative picture of nature implied by symbiosis. In this paper we will contest this view. We will first discuss recent findings in virology that show that viruses can be ‘nice’ and collaborate with their hosts, meaning that they form part of integrated biological systems and processes. We further offer various reasons why viruses should be seen as processes rather than things, or substances. Based on these two claims we will argue that, far from serving as a counterexample to it, viruses actually enable a deeper understanding of the fundamentally interconnected and collaborative nature of nature. (Abstract

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)

Giger, Gabriel, et al. Inducing novel endosymbioses by implanting bacteria in fungi. Nature. 635/415, 2024. Sixteen ETH Zurich biologists led by Julia Vorholt describe an innovative procedure to learn more about nature’s pervasive blendings of microbial components to mutual advantage. Although long marginalized, these cellular tendencies are now seen to be a prime evolutionary feature. This paper then adds further proof by way of their experimental, synthetic symbioses. See also Scientists Re-Create the Microbial Dance That Sparked Complex Life by Molly Herring in Quanta (January 3, 2025) for a science news review of this significant work.

Endosymbioses have impacted the evolution of life and shape the ecology of a wide range of species. Here we implant bacteria into the fungus Rhizopus microsporus to follow the fate of artificially induced endosymbioses. Continuous positive selection on endosymbiosis mitigated initial fitness constraints by orders of magnitude upon adaptive evolution. The bacterium produced rhizoxin congeners in its new host, demonstrating the transfer of a metabolic function through induced endosymbiosis. Single-cell implantation thus provides an experimental approach with opportunities for synthetic endosymbioses with desired traits. (Abstract)

Intracellular endosymbioses are extraordinarily intimate interactions between organisms. They join two complex metabolic networks in a compartmentalized manner and are subjected to natural selection as a unit. This metabolic integration predisposes endosymbioses to enable major transitions in evolution. Accommodating an endosymbiont can benefit the host by acquiring chemical defense systems, unlocking essential nutrients or new energy sources. (1)

In summary, we have successfully implanted live bacteria into a fungus. We found that adaptive evolution increased the stability of the induced endosymbiosis despite high initial costs. The ability to initiate endosymbioses and explore boundary conditions for stable inheritance will aid approaches towards designer endosymbionts and sheds light on the evolutionary forces shaping endosymbiogenesis. (7)

Examples of endosymbiosis are everywhere. Mitochondria, the energy factories in your cells, were once free-living bacteria. Photosynthetic plants owe their sun-spun sugars to the chloroplast, which was also originally an independent organism. Many insects get essential nutrients from bacteria that live inside them. And last year researchers discovered the “nitroplast,” an endosymbiont that helps some algae process nitrogen. (M. Herring)

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