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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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VI. Earth Life Emergence: Development of Body, Brain, Selves and Societies

4. Cellular Holobiont Symbiogenesis

Martin, William and Michael Russell. On the Origins of Cells: A Hypothesis for the Evolutionary Transitions from Abiotic Geochemistry to Chemoautotrophic Prokaryotes, and from Prokaryotes to Nucleated Cells. Philosophical Transcations of the Royal Society of London B. 358/77, 2003. An extensive, illustrated technical paper proposes that membrane-bounded, free-living cells arose out of an original, not free-living “universal ancestor.”

From our viewpoint, physical compartmentation from the environment and self-organization of self-contained redox reactions are the most conserved attributes of living things, hence inorganic matter with such attributes would be life’s most likely forebear. (77)

Mason, Alexander, et al. Mimicking Cellular Compartmentalization in a Hierarchical Protocell through Spontaneous Spatial Organization. ACS Central Science. Online July 3, 2019. We include this entry about synthetic cells in this section because it shows how these title findings of life’s scalar self-organization are well evident across cellular forms. Eight Eindhoven University of Technology chemists apply this natural archetype of bounded whole units composed of symbiotic members to intentionally scope out how new beneficial and benign procreations could be conceived to well serve person and planet.

A systemic feature of eukaryotic cells is the spatial organization of functional components through compartmentalization. Developing protocells with compartmentalized synthetic organelles is a critical step toward one of the core characteristics of cellular life. Here we demonstrate the bottom-up, multistep, noncovalent, assembly of rudimentary subcompartmentalized protocells through the spontaneous encapsulation of semipermeable, polymersome proto-organelles inside cell-sized coacervates. The coacervate microdroplets are membranized using tailor-made terpolymers, to complete the hierarchical self-assembly of protocells, a system that mimics both the condensed cytosol and the structure of a cell membrane. In this way, the spatial organization of enzymes can be finely tuned, leading to an enhancement of functionality. (Abstract)

Meinesz, Alexandre. How Life Began: Evolution’s Three Geneses. Chicago: University of Chicago, 2008. A University of Nice-Sophia Antipolis biologist goes on to elucidates the subsequent triune developments of prokaryotic bacteria, plant and animal cells, and the rise of multicellular forms. A view from sunny France that carefully explains and weaves contingency and convergence, self-organization and selection, with nods to theological imports.

Michod, Richard and Aurora Nedelcu. Cooperation and Conflict During the Unicellular-Multicellular and Prokaryotic-Eukaryotic Transitions. Moya, Andres and Enrique Font, eds. Evolution: From Molecules to Ecosystems. Oxford: Oxford University Press, 2004. In these basic stages, a general progression is discerned from a competitive interaction of components onto increasing cooperative mediation, which leads to the emergence of a whole entity. In so doing, a new evolutionary level of individuality is achieved.

Misteli, Tom. Concepts in Nuclear Architecture. BioEssays. 27/5, 2005. The active cell nucleus is a non-random array of genomic functions as a result of its constant self-organization.

Central to self-organizing systems is the high dynamic content and a relative promiscuity of interactions among components. The recent observations of the dynamics of numerous nuclear proteins in living cells clearly supports both of these premises. (483) The auto-reinforcing behavior of self-organizing systems may contribute greatly to the overall stability of nuclear structure and the functional status of the genome but, at the same time, the transient nature of virtually all protein-protein and protein-chromatin interactions may also poise the system for rapid change in response to external stimuli. Thus, the dynamic, self-organized, nature of nuclear organization is a fundamental, functionally essential property of the cell. (483)

Misteli, Tom. The Concept of Self-organization in Cellular Architecture. Journal of Cell Biology. 155/2, 2001. The paradigm shift to perceive the living cell as a dynamic, non-equilibrium concatenation of interacting components both in the cytoskeleton and other compartments and in the nucleus itself.

I suggest that self-organization is a more general mechanism for the formation, maintenance, and function of cellular organization that currently anticipated. (181)

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)

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)

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