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

3. Cellular Self-Organization and Holobiont Symbiogenesis

Misteli, Tom. The Inner Life of the Genome. Scientific American. February, 2011. A popular article by the National Cancer Institute geneticist which can serve as a capsule of the frontiers of biology. New understandings of the cell nucleus, from his own group and other researchers, identify components, as per the quote, that seem to know what they are doing. While “machinery” and “factory” metaphors are used, it is said that such activities are not mechanically instructed but seem to organize themselves by the active, mutual interests of their constituents. Closer to truth, it increasingly appears that something is going on by itself, if the possibility could even be admitted, and accommodated by a conducive, evidential cosmos that is essentially organic and developmental in kind.

Aided by new 3-D imaging technology that allows us to peer deeper than ever into the living cell, we have discovered a startlingly vibrant ecosystem. In the nucleus, chromosomes physically interact with neighboring chromosomes, genes on those chromosomes migrate to different nuclear locations depending on what they need to accomplish, and molecules that regulate gene activity congregate in bustling hubs. (68) Instead I have proposed that nuclear positioning is self-organizing, somewhat like middle school students forming cliques because they are drawn together by mutual interests, not because they were instructed to associate by parents or teachers. In this view, the location of genes and chromosomes inside the nucleus springs from their activity and is not determined by some external organizing machinery. (72)

Mitchison, Timothy and Christine Field. Self-Organization of Cellular Units. Annual Review of Cell and Developmental Biology. Volume 37/October, 2021. In this forthcoming volume, Harvard Medical School researchers illustrate the historic paradigm shift within biological science. At present a vested, mechanistic version via natural selection alone, sans any teleological aim, exists side by side with these worldwise perceptions due to this deeper, innate agency. This paper offers an expansive array of real, quantified, instances, see also Tom Misteli for a 21st century chronicle. It is an aim of Natural Genesis to help inform, clear up, untangle and facilitate this overdue resolve. The current conflation could be one reason that vaccines are so misunderstood.

The purpose of this review is to explore self-organizing mechanisms that pattern microtubules (MTs) and spatially organize animal cell cytoplasm. We start with conceptual distinctions between self-organizing and templating mechanisms for subcellular organization. We then discuss how self-organization generates radial MT arrays and cell centers such as autocatalytic MT nucleation. We end by discussing shared mechanisms and principles for the MT-based self-organization of cellular units. (Abstract excerpt)

Moger-Reischer,, R. Z. Evolution of a Minimal Cell. Nature. 620/122, 2023. Nine biologists at the Craig Venter Institute, Indiana University, and ASU, gain new insights into basic cellular facilities by virtue of novel conceptions. See also a review Even Synthetic Life Forms With a Tiny Genome Can Evolve in Quanta on August 10.

Possessing only essential genes, a minimal cell can reveal mechanisms and processes that are critical for the persistence and stability of life1,2. Here we report on how an engineered minimal cell3,4 contends with the forces of evolution compared with the Mycoplasma mycoides non-minimal cell from which it was synthetically derived. Our findings demonstrate that natural selection can rapidly increase the fitness of one of the simplest autonomously growing organisms. Understanding how species with small genomes overcome evolutionary challenges provides vital views into the persistence of host-associated endosymbionts, the stability of streamlined chassis for biotechnology and the targeted refinement of synthetically engineered

Mojica, Nelly Selem, et al. Cellular Bauplans: Evolving Unicellular Forms by Means of Julia Sets and Pickover Biomorphs. BioSystems. 98/1, 2009. Spanish mathematical biologists including Pedro Marijuan propose that computer graphical capabilities (Biomorphs are life-like fractals found by Clifford Pickover) lately allow the perception in cellular realms, similar to archetypal animals, of inherent shapes that will appear prior to any post-selection.

The universe of cellular forms has received scarce attention by mainstream neo-Darwinian views. The possibility that a fundamental trait of biological order may consist upon, or be guided by, developmental processes not completely amenable to natural selection was more akin to previous epochs of biological thought, i.e. the “bauplan” discussion. (19)

Monk, N.A.M. Unravelling Nature’s Networks. Biochemical Society Transactions. 31/6, 2003. A review of new insights into biochemical reactions, cell architecture and metabolism and intercellular processes gained by the application of general complexity and network theories. At this cellular level, the universal properties of hierarchy, modular components and activities, invariance, and so on are in full effect. These approaches inform a promising new phase of research cited as …the post-genomic mission of understanding the cell as a complex dynamical system. (1457)

A prominent feature of biochemical networks is the fact that they appear to be scale-free, such that sub-networks of all sizes have the same statistical properties. A network is classified as scale-free if the distribution of degrees of its nodes (where the degree of a node is the number of edges (links) to/from that node) follows a power law. (1458)
A strong candidate for a central organizational principle is modularity. The existence of modules can be seen on many levels, examples being organelles and signal transduction pathways. (1458)

Moran, Nancy. Symbiosis as an Adaptive Process and Source of Phenotypic Complexity. Proceedings of the National Academy of Sciences. 104/Supplement 1, 2007. In this instance, a University of Arizona biologist contends that symbiotic unions of mutual aid are rife across organic domains from genomes to societies, as they serve to generate an increasing viable intricacy. This agency on its own, beyond mute mutation, akin to modularity and networking, represents another independent cause of cooperative emergence.

Nalaban, Valeriu, et al. Quantifying Emergence and Self-Organization of Enterobacter cloacae Microbial Communities. Nature Scientific Reports. 8/12416, 2020. We cite this entry by University of Southern California bioengineers as an example of the late 2010s full scale admission of these innate title forces and forms as they serve to distinguish and pervade life’s oriented gestation.

From microbial communities to cancer cells, many complex collectives embody emergent and self-organising behaviour. As a result, cells develop composite features such as formation of aggregates or expression of specific genes due to cell-cell interactions. Currently, we lack a universal mathematics to analyze the collective behaviour of biological swarms. We propose a multifractal inspired framework to measure the degree of emergent self-organisation from scarce spatial data and apply it to evolution of the arrangement of Enterobacter cloacae aggregates. Our method could identify these patterns and dynamics changes within the bacterial population. (Abstract)

Norris, Vic and Robert Root-Bernstein. The Eukaryotic Cell Originated in the Integration and Redistribution of Hyperstructures from Communities of Prokaryotic Cells Based on Molecular Complementarity. International Journal of Molecular Sciences. 10/2611, 2009. A University of Rouen biologist and the Michigan State University psychologist expand the main view that cellular life originated due to discrete components such as nucleotides and bacteria alone. Rather, an integrational milieu, an ecological whole system, is in equal existence as it repeatedly served to self-organize such entities into this evolutionary procession. Robert Root-Bernstein has pursued this theme for over a decade and here achieves a robust update, see also Alex Hunding, et al, for further confirmation.

In the “ecosystems-first” approach to the origins of life, networks of non-covalent assemblies of molecules (composomes), rather than individual protocells, evolved under the constraints of molecular complementarity. Composomes evolved into the hyperstructures of modern bacteria. We extend the ecosystems-first approach to explain the origin of eukaryotic cells through the integration of mixed populations of bacteria. We suggest that mutualism and symbiosis resulted in cellular mergers entailing the loss of redundant hyperstructures, the uncoupling of transcription and translation, and the emergence of introns and multiple chromosomes. (Abstract 2611)

In order to understand our argument, it is necessary to think of evolution not as the elaboration of individual traits, but as selection for more and more efficient ecologies. Thus, we propose that eukaryotic species did not evolve from elaboration or complexification of individual prokaryotic species, but rather that individual eukaryotic species evolved by integration and simplification from communities of diverse prokaryotes. (2612)

Palmer, Jeffrey, organizer. Symbiosis as an Evolutionary Driver: Mergers of Cells and Genomes. http://www.aaas.org/meetings/2009/program/lectures/topical.shtml.. From this web page, click on Program Planner, then on Browse, next on the Category. At the 2009 American Association for the Advancement of Science meeting in Chicago, a session under “Biological Science and Genomics” with this notable abstract. Palmer of Indiana University, along with Dalhousie University’s John Archibald, and Nancy Moran of the University of Arizona will speak. A broader AAAS overall program than in past years, it is worth searching among the many topics.

The endosymbiotic “hypothesis” for the origin of plastids and mitochondria from once free-living cyanobacteria and proteobacteria is now textbook “fact,” yet many fascinating aspects of the subsequent evolution of these organelles and their genomes have only recently been revealed thanks to the power of genomics. These include the following: mitochondrial genomes have repeatedly been lost during eukaryotic evolution, with the resulting organelles barely recognizable as endosymbionts; secondary, tertiary, etc., eukaryotic-eukaryotic symbioses have spread plastids and photosynthesis to the far corners of the eukaryotic world, leading to Russian Doll cells containing genes derived from up to a dozen different eukaryotic and endosymbiont genomes; the contribution of the original bacterial genome to the proteome of many mitochondria is remarkably dwarfed by that of the host eukaryotic genome; much has been learned about mechanisms of the functional transfer of organelle genes to the nucleus, as well as its remarkably punctuated tempo and pattern; and plant mitochondrial genes (and sometimes whole genomes) are transferred horizontally surprisingly often. Scientists are also only beginning to appreciate the ubiquity and metabolic diversity of latter-day symbioses of bacteria among eukaryotes. Bacterial symbionts of insects are best studied and display a remarkable range of genome sizes and gene repertoires, with some quite possibly having “crossed the line” from endosymbionts to organelles.

Pereira, Luisa, et al. A Symbiogenic Way in the Origin of Life. Seckbach, Joseph, ed. Genesis - In the Beginning. Dordrecht: Springer, 2012. With coauthors Telma Rodrigues and Francisco Carrapico, University of Lisbon biologists contribute an extensive chapter which makes a good case for the presence and inclusion of an evolutionary propensity for such “reticulated,” cooperative mutuality. Within the book’s Astrobiology theme, decades of symbiotic research and confirmation augur for the recognition of such a prior, creative force to Darwinian competition and selection alone. Indeed it is noted that Darwin actually noted this by his use of the term “concurrency” for these effects. As the quotes convey, such witness of a “universal symbiogenesis” (search Gontier) via a complementarity of agental and relational phases from pre-life forward quite appears as another result of nature’s innate self-organization.

The symbiogenic concept allows an innovative approach to the origin and evolution of life, with applicability to life’s initial stages, and capable of being a fundamental rule in life’s establishment and development on Earth and elsewhere. We suggest a naturalistic explanation for the origin of life, through the evolution of complex and adaptative systems, with synergistic, cooperative and symbiogenic mechanisms, guiding chemical evolution through its constraints. (729) We believe this definition allows different phenomena to be regarded as symbiogenic, and that universal symbiogenesis provides us with a general analytical tool for the immense interactions among different entities, namely the prebiotic and biotic entities. The symbiogenesis concept, through universal symbiogenesis, can be applied to the prebiotic evolutive context, beyond the biotic one, as a new paradigm shift in evolution. The science of complexity defies the selectionist hegemony, by arguing that such a long-term trend toward increasing complexity suggests the presence of additional mechanism(s). (729)

We believe that cooperative and synergistic processes were responsible, using terrestrial and extraterrestrial materials, for the creation of a large prebiotic pool, closely related to geochemical contexts, and intense interactions within. Most likely, a series of synergistic and cooperative effects produced a wide source of creativity, and functional advantages that pushed the emergence of complex and functionally integrated biological systems, through the evolution of self-organization and autocatalysis. It was only after this biochemical evolution of structures, which produced the informational capabilities necessary to self-replication, that the Darwinian mechanisms could arise. (739)

Pradeu, Thomas. A Mixed Self: The Role of Symbiosis in Development. Biological Theory. 6/1, 2012. In a thematic issue on how organisms develop, a Paris-Sorbonne University philosopher of biology argues for an expanded view of individuals. Rather than a closed system, creatures abide in and horizontally interact with environments. Mutualities, often bacterial, expand such selves into such reciprocal communities.

Since the 1950s, the common view of development has been internalist: development is seen as the result of the unfolding of potentialities already present in the egg cell. In this article, I show that this view is incorrect because of the crucial influence of the environment on development. I focus on a fascinating example, that of the role played by symbioses in development, especially bacterial symbioses, a phenomenon found in virtually all organisms (plants, invertebrates, and vertebrates). I claim that we must consequently modify our conception of the boundaries of the developing entity, and I show how immunology can help us in accomplishing this task. I conclude that the developing entity encompasses many elements traditionally seen as “foreign,” while I reject the idea that there is no possible distinction between the organism and its environment. (Abstract, 80)

Prosdocimi, Francisco, et al. The Theory of Chemical Symbiosis: A Margulian View for the Emergence of Biological Systems. Acta Biotheoretica. 69/1, 2021. We note this entry by Universidade Federal do Rio de Janeiro, Universidad Nacional Autónoma de México and Universidade Federal do Rio de Janeiro, Universidade Federal da Paraíba, Brazil biochemists as an example of how symbiotic phenomena are being found in increasingly widespread areas as in this case of life’s origins. As the title cites, some ten years after Lynn Margulis’ passing, there is strong effort is going forth to give prime credit to her four decades of study, explanation and defense.

The theory of chemical symbiosis (TCS) suggests that biological systems started with the collaboration of two polymeric molecules existing in early Earth: nucleic acids and peptides. Chemical symbiosis emerged when RNA-like nucleic acid polymers happened to fold into 3D structures capable to bind amino acids together, forming a proto peptidyl-transferase center. TCS suggests that there is no chicken-and-egg problem into the emergence of biological systems as RNAs and peptides were of equal importance to the origin of life. Life has initially emerged when these two macromolecules started to interact in molecular symbiosis. Mutualism is the strongest force in biology, capable to create novelties by emergent principles; on which the whole is bigger than the sum of the parts. (Abstract excerpt)

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