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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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V. Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

3. Cellular Holobiont Symbiogenesis

Roughgarden, Joan, et al. Holobiont as Units of Selection and a Model of Their Population Dynamics and Evolution. Biological Theory. Online September, 2017. In 1991 the microbiologist Lynn Margulis (1938-2011) proposed this title term for organisms in truth as symbiotic assemblages. The concept which has lately gained import and usage is given wide exposition by Joan Roughgarden, University of Hawaii, Scott Gilbert, Swarthmore College, Eugene and Ilana Zilber-Rosenberg, Tel-Aviv University, and Elisabeth Lloyd, Indiana University. Herein holobionts are seen to possess integrated anatomical, physiological, developmental, interactive, genomic qualities and functions within an overall viability. A January 2018 MIT Press book Landscapes of Collectivity in the Life Sciences, edited by Snait Gissis, et al will provide a major statement. And as proof of the actual utility of this holobiont/genome perception, it is used in Our Gut Microbiome: The Evolving Inner Self by Paraq Kundu, et al in the journal Cell (171/7, 2017) without even citing these origins.

Holobionts, consisting of a host and diverse microbial symbionts, function as distinct biological entities anatomically, metabolically, immunologically, and developmentally. Symbionts can be transmitted from parent to offspring by a variety of vertical and horizontal methods. Holobionts can be considered levels of selection in evolution because they are well-defined interactors, replicators/reproducers, and manifestors of adaptation. An initial mathematical model is presented to help understand how holobionts evolve. The model offered combines the processes of horizontal symbiont transfer, within-host symbiont proliferation, vertical symbiont transmission, and holobiont selection. The model offers equations for the population dynamics and evolution of holobionts whose hologenomes differ in gene copy number, not in allelic or loci identity. The model may readily be extended to include variation among holobionts in the gene identities of both symbionts and host. (Abstract)

Ryan, Frank. Darwin’s Blind Spot: Evolution Beyond Natural Selection. Boston: Houghton Mifflin, 2002. A British physician extols the unappreciated presence and force of symbiotic assembly in the advancement of life.

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)

Sagan, Dorion. From Empedocles to Symbiogenesis: Lynn Margulis’s Revolutionary Influence on Evolutionary Biology. Biosystems. June, 2021. We cite this latest essay as a succinct record of her valient endeavor to break out of old male fixation into a vital sense of an animate procreation graced by a universal principle of positive, reciprocal conciliations between all phases of organic entities. Yet we have a world tearing itself apart due to violent oppositions, which is in desperate need for such a unifying scientific vision. I have heard and met Lynn in Amherst, in my opinion she could merit being the one woman who could rise to the status of a Newton or Darwin.

As a primary expositor of the work of Lynn Margulis collaborating with her over thirty years on over thirty books and forty articles, scientific and popular, I attempt here to summarize her unique and lasting influence on evolutionary biology. Describing life on Earth as the multi-billion-year evolution of microbial communities, from prokaryotes maintaining Earth's atmosphere away from thermodynamic equilibrium to all eukaryotes as polygenomic beings, Margulis's interdisciplinary work has deeply influenced multiple fields including systematics, theories of the evolution of metabolism, paleobiology, and biogeochemistry. Overturning the neo-Darwinist narrative that speciation almost always occurs by the gradual accumulation of random mutations, Margulis's work revives a discarded philosophical speculation of the pre-Socratic Empedocles, who suggested that Earth's early beings both merged and differentially reproduced. Margulis's curiosity-driven science, collaborative work ethic, status as a woman, embrace of novelty, philosophical stance, current status of her theories, and the proposal for a new science of symbiogenetics are among the topics examined. (Abstract excerpt)

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.

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