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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

Ryan, Frank. Genomic Creativity and Natural Selection. Biological Journal of the Linnean Society. 88/4, 2006. An expansion on his 2002 Darwin’s Blind Spot that cites, as the quote notes, an array of genetic and metabolic activities are at work prior to selection alone.

In the early 1930s, the synthesis of Darwinian natural selection, mutation, and Mendelian genetics gave rise to the paradigm of 'modern Darwinism', also known as 'neo-Darwinism'. But increasing knowledge of other mechanisms, including endosymbiosis, genetic and genomic duplication, polyploidy, hybridization, epigenetics, horizontal gene transfer in prokaryotes, and the modern synthesis of embryonic development and evolution, has widened our horizons to a diversity of possibilities for change. All of these can be gathered under the umbrella concept of 'genomic creativity', which, in partnership with natural selection, affords a more comprehensive modern explanation of evolution. (655)

Sapp, Jan. Evolution by Association. New York: Oxford University Press, 1994. A proficient history of the alternative view of the rise of life as due more to symbiotic cooperation than a “survival of the fittest” competition.

Sapp, Jan. Saltational Symbiosis. Theory in Biosciences. 129/2-3, 2010. In an issue on “Contemporary Evolutionary and Philosophical Theories” in search of a 21st century expansion of Darwinism, the York University biologist contends that the time has come, is overdue, for the full admission of life’s deep symbiotic propensities, which he has advanced for years in articles and books (search).

Symbiosis has long been associated with saltational evolutionary change in contradistinction to gradual Darwinian evolution based on gene mutations and recombination between individuals of a species, as well as with super-organismal views of the individual in contrast to the classical one-genome: one organism conception. Though they have often been dismissed, and overshadowed by Darwinian theory, suggestions that symbiosis and lateral gene transfer are fundamental mechanisms of evolutionary innovation are borne out today by molecular phylogenetic research. It is time to treat these processes as central principles of evolution. (125)

Sapp, Jan. The Structure of Microbial Evolutionary Theory. Studies in History and Philosophy of Biological and Biomedical Sciences. 38/4, 2007. In the issue’s Towards a Philosophy of Microbiology section, the York University biologist strives to place much more emphasis on a universal cellular symbiotic activity via bacterial gene transfer than selection alone. Such an admission would then transcend the vested version of discrete, random entities. Sapp, along with other authors such as James Shapiro, Pamela Lyon, and Carol Cleland, make the valid point that neo-Darwinian, modern synthesis theory has hardened in response to Intelligent Design, which makes it adverse to any alteration. For what is implied, as we often note, is not an amendment but a radical genesis universe.

Indeed, all eukaryotes are chimeric superorganisms comprised of organellar DNA, and that of other symbionts and viruses; all are polygenomic. (792)

Sapp, Jan. The Symbiotic Self. Evolutionary Biology. Online March, 2016. A cogent update on this now accepted symbiosis redefinition of communal organisms by the York University biologist. He has been a steady advocate along with the late Lynn Margulis, Scott Gilbert, Nathalie Gontier, and others noted in its bibliography.

The classical one genome-one organism conception of the individual is yielding today to a symbiotic conception of the organism. Microbial symbiosis is fundamental in our evolution, physiology and development. This notion, while not new, has been revitalized by advances in molecular methods for studying microbial diversity over the past decade. An ecological understanding of our microbial communities in health and disease supplements the venerable one germ-one disease conception of classical germ theory, and reinforces the view that nothing in biology makes sense except in light of symbiosis. (Abstract)

Sapp, Jan, ed. Microbial Phylogeny and Evolution. Oxford: Oxford University Press, 2005. A major volume on the essential bacterial realm: how it arose and evolved via symbiogenesis, forms communities, and fans out into the spreading tree of life. Contributors include Lynn Margulis, Michael Dolan, Harold Morowitz, Norman Pace, William Martin, Ford Doolittle, and Carl Woese, whose exemplary paper is noted below.

Sasai, Yoshiki. Cytosystems Dynamics in Self-Organization of Tissue Architecture. Nature. 493/318, 2013. In an extensive article for a Frontiers of Biology section, the RIKEN Center for Development Biology, Japan, Neurogenesis and Organogenesis Group director, provides a sophisticated explanation for and verification of spontaneous creativity as well exemplified by this cellular portal. These insights accrue from a cycle of Multiscale mathematical modeling, Multidirectional experimental reconstruction, and Multiplex measurement, aided by Petaflop computation, Single-cell omics, Multigene editing, and so on. Three modes of tissue formation are self-assembly, self-patterning, and self-driven morphogenesis, seen as arising from an independent “intrinsic order.” In this venerable journal, 144 years on, now worldwide in scope as if a “Global Mind,” might it be broached that collaborative humankind is on to something, rather than nothing, proceeding by its own creative agency, which portends our revolutionary witness of a genesis uniVerse and destiny? In regard, per the closing quote below, Yoshiki Sasai proposes a 21st century “emergence biology” able to engage and appreciate this profound vista of life’s dynamic evolutionary ascent.

Our knowledge of the principles by which organ architecture develops through complex collective cell behaviours is still limited. Recent work has shown that the shape of such complex tissues as the optic cup forms by self-organization in vitro from a homogeneous population of stem cells. Multicellular self-organization involves three basic processes that are crucial for the emergence of latent intrinsic order. Based on lessons from recent studies, cytosystems dynamics is proposed as a strategy for understanding collective multicellular behaviours, incorporating four-dimensional measurement, theoretical modelling and experimental reconstitution. (Abstract)

Local interactions are multiplex in tissue self-organization, therefore, a change in an element’s state could simultaneously cause an alteration in interacting rules. This means that the ‘epigenetic landscape’ in such a complex system is not static but rather has a self-evolving ‘diachronic’ nature. In this sense, its biology goes beyond simple structuralism and instead requires a post-structuralism viewpoint. To understand such complex self-organizing mechanisms, conventional cell-level systems biology – which seeks to have a comprehensive analysis of elements and formulation of their interactions in the network – is simply not applicable. Therefore, for a mechanistic understanding of the dynamic nature of a self-developing system, we need to introduce a paradigm shift. In other words, instead of the reductionism based, bottom-up, approach that describes all the details of a system, we need to deduce the core regulatory principles of systems dynamics from fragmented and discretized information. From this viewpoint, I discuss the prospect of a new direction in research for dynamic multicellular systems, which I propose as ‘cytosystems dynamics.’ (323)

The concept of core control modules may be analogous to the idea of acupoints in acupuncture or ‘tsubo’ (a similar concept in Japan), for which stimulation exerts strong global effects on the autonomic nervous system. In this analogy, by identifying and steering the ‘acupoints’ of cytosystems dynamics, the hope is to manipulate complex multicellular behaviours such as self-organization, and perhaps even design them for a new purpose. Given the advances in related technologies described in this Review, the time should be ripe for then new, challenging research field, for which I suggest the term emergence biology with a goal to steer a multicellular population with complex behaviours on the basis of an understanding of its cytosystems dynamics. (325)

Schwemmler, Werner. Symbiogenesis: A Macro-Mechanism of Evolution. Berlin: de Gruyter, 1989. A prescient, holistic reading of an evolutionary scale of symbiotic unions from their cosmic beginnings through biological, neural, and human social stages.

Seckbach, Joseph, ed. Symbiosis. Dordrecht: Kluwer Academic, 2002. An extensive volume about mutual beneficial associations with an emphasis on the formation of the eukaryotic cell.

Serra, Denise, et al. Self-Organization and Symmetry Breaking in Intestinal Organoid Development. Nature. 569/66, 2019. A 13 person team at Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland perform detailed studies which exemplify how cellular life can indeed be known to have a capacity to organize itself during its evolutionary development.

Intestinal organoids are complex three-dimensional structures that mimic the cell-type composition and tissue organization of the intestine by recapitulating the self-organizing ability of cell populations derived from a single intestinal stem cell. Our findings reveal how single cells exposed to a uniform growth-promoting environment have the intrinsic ability to generate emergent, self-organized behaviour that results in the formation of complex multicellular asymmetric structures. (Abstract excerpt)

Shahbazi, Marta, et al. Self-Organization of Stem Cells into Embryos: A Window on Early Mammalian Development. Science. 364/948, 2019. It is vital to make note in this late year of how much a natural self-organizing process has become wholly accepted in cell biology, which was rarely considered just a decade ago. In a special section about Organoids, Cambridge University and Rockefeller University led by Magdalena Zernicka-Goetz present a visual articulation of how organisms come to form and flourish by virtue of this intrinsic formative method. Within this website, whenever could it be possible to imagine life’s whole evolutionary development as a self-organizing embryonic gestation? See also in this issue Organoids by Design by Takebe and Wells, second Abstract.

Embryonic development is orchestrated by robust and complex regulatory mechanisms acting at different scales of organization. In vivo studies are challenging for mammals after implantation, owing to the small size and inaccessibility of the embryo. The generation of stem cell models of the embryo represents a powerful system with which to dissect this complexity. Control of geometry, modulation of the physical environment, and priming with chemical signals reveal the intrinsic capacity of embryonic stem cells to make patterns. Here, we review the principles of self-organization and how they set cells in motion to create an embryo. (Shahbazi Abstract)

Organoids are multicellular structures that can be derived from adult organs or pluripotent stem cells. Early versions of organoids range from simple epithelial structures to complex, disorganized tissues with large cellular diversity. The current challenge is to engineer cellular complexity into organoids in a controlled manner that results in organized assembly and acquisition of tissue function. We discuss how the next generation of organoids can be designed by means of an engineering-based narrative design to control patterning, assembly, morphogenesis, growth, and function. (Takebe Abstract)

Shapiro, James. Bringing Cell Action into Evolution. http://shapiro.bsd.uchicago.edu/Shapiro.2013.BringingCellActionIntoEvolution.html.. A pithy presentation by the University of Chicago geneticist (search) at the Earth, Life & System Symposium in honor of Lynn Margulis, Texas Tech University, September 2012, see citation above for more info. Its power point slides are also available on his publications web page.

Lynn Margulis was an indefatigable advocate of positive cell action in the evolutionary process. Lynn focused her work on observing real-time interactions between cells and advocating the major role of cell fusions and symbiogenesis in rapid evolutionary change. Confirmation of the mitochondrion and chloroplast in eukaryotic cells as descendants of well-defined prokaryotes was a major turning point away from the gradualist ideology that dominated evolutionary thinking for most of the 20th Century. Since then, we have come to appreciate more the major evolutionary roles of cell-cell interactions and cellular control of genome structure. The well-established phenomena of symbiosis, hybridization, horizontal DNA transfers, genome repair, and natural genetic engineering have revolutionized our understanding of genome variation. Rather than a series of accidents randomly changing a ROM (read-only memory) heredity system, we realize that active cell processes non-randomly restructure a RW (read-write) genomic storage system at all biological time scales.

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