V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An EarthWinian Genesis Synthesis
3. Cellular Self-Organization and Holobiont Symbiogenesis
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)
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)
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.
Singharoy, Abhishek, et al. Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell. 179/1098, 2019. At the culmination of the global 2010s, nineteen Arizona State University, Center for Applied Structural Discovery, molecular biologists present an illustrated report which proceeds to root life’s vesicular development phases deeply into a fertile physical substrate. In this expansive view, the scientific studies of cellular organisms which began decades, and centuries ago can now by way of detailed experiment, graphic display, and computational verity connect with a vital conducive ecosmos. From our late vantage, universe and human are rejoined as one and the same. As the quotes say, a further aspect is an advent and passage of a self-creative natural genesis to our collaborative, respectful, informed mitigation and continuance. A commentary herein is Dynamic Modeling of a 100 Million Atom Organelle at the Source of Life by Jean-David Rochaix (179/1012).
At the culmination of the global 2010s, nineteen Arizona State University, Center for Applied Structural Discovery, molecular biologists present an illustrated report which proceeds to root life’s vesicular development phases deeply into a fertile physical substrate. In this expansive view, the scientific studies of cellular organisms which began decades, and centuries ago can now by way of detailed experiment, graphic display, and computational verity connect with a vital conducive ecosmos. From our late vantage, universe and human are rejoined as one and the same. As the quotes say, a further aspect is an advent and passage of a self-creative natural genesis to our collaborative, respectful, informed mitigation and continuance. A commentary herein is Dynamic Modeling of a 100 Million Atom Organelle at the Source of Life by Jean-David Rochaix (179/1012).
Slijepcevic, Predrag. Serial Endosymbiosis Theory: From Biology to Astronomy and Back to the Origin of Life. Biosystems. April, 2021. Into this late year for a Symbiogenesis and Progressive Evolution issue, a Brunel University ecosmic philosopher (search) can post a widest-ranging survey and endorsement of nature’s propensity to combine into nested, mutually reciprocal units. The paper opens with an account of early Russian work, so as to proceed onto the lifetime contribution of Lynn Margulis (1938-2011) to quantify that such diverse unifications were a prime mover of life’s organismic development. The essay goes on to add Freeman Dyson’s later 1990s perception of symbiotic phenomena across interstellar and galactic reaches, along with Dyson’s 1999 Origins of Life book which finds such convergent, additive effects likewise in effect at this early stage.
Serial Endosymbiosis Theory, or SET, was conceived and developed by Lynn Margulis to best explain the origin of eukaryotic cells. In this paper, I focus on two aspects of SET. First, using the concept of “universal symbiogenesis”, proposed by Freeman Dyson to search for commonalities in astronomy and biology, I contend that SET can apply beyond eukaryogenesis. Second, I contrast a recent “viral eukaryogenesis” hypothesis, according to which the nucleus evolved from a complex DNA virus, with a view closer to SET, whence the nucleus evolved through the interplay of the archaeal host, the eubacterial symbiont, and a non-LTR transposon, or telomerase. (Abstract excerpt)
Smith, Eric and Harold Morowitz. Universality in Intermediary Metabolism. Proceedings of the National Academy of Sciences. 101/13168, 2004. The stoichiometry, energetics, and reaction concentration dependence of the reductive tricarboxylic acid cycle, via its network and autocatalytic properties, is proposed as a primordial metabolic core.
Widespread or universal structures and processes in cellular biochemistry are central to a coherent understanding of life, much as universality in physics has become central to understanding order in condensed-matter systems. (13168)
Sole, Ricard, et al. Synthetic Protocell Biology. Philosophical Transactions of the Royal Society B. 362/1727, 2007. The lead article in a dedicated issue on Towards the Artificial Cell, edited by Sole, Steen Rasmussen and Mark Bedau. Altogether the 13 papers cover the latest efforts to achieve in a laboratory a ‘minimal living system’ of generic cellular form. This requires both a ‘bottom up’ approach from self-assembling molecular components and a ‘top down’ method which simplifies cell genomes. For some comments, most authors are men who seem to engage such new creation as an engineering project. A common conflation of organicity with machinery results because there is no examination of what kind of nature abides, nor why, for what innate purpose, might human persons be able to take over biomaterial genesis. Other typical papers are Structural Analyses of a Hypothetical Minimal Metabolism by Toni Gabaldon, et al, Generic Darwinian Selection in Catalytic Protocell Assembles by Andreea Munteanu, et al, and Eors Szathmary on Coevolution of Metabolic Networks and Membranes.
The question here is: what are the conditions allowing a simple artificial protocell to reach reliable reproduction? Von Neumanns’ picture includes two key components of a complex adaptive system able to process information: hardware and software. In modern cells, software is carried by DNA, whereas proteins play the role of cellular hardware. (1730) Travelling from non-living to living matter means crossing a twilight zone: some transition domain where the preconditions for reliable cell replication (and thus life) exist. Although some steps need to be completed and some key processes are not yet understood, we are likely to see the success of synthetic cellular life soon at work over the next decade. (1736)