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

3. Cellular Self-Organization and Holobiont Symbiogenesis

Chen, Irene and Peter Walde. From Self-Assembled Vesicles to Protocells. Cold Spring Harbor Perspectives in Biology. 2/7, 2011. Harvard and ETH, Zurich, systems biologists help affirm life’s constant propensity toward “compartmentalization,” the formation at every nested scale of bounded, whole entities from these primal precursors to all manner of cells, organisms, and on to cellular-like communities.

Self-assembled vesicles are essential components of primitive cells. We review the importance of vesicles during the origins of life, fundamental thermodynamics and kinetics of self-assembly, and experimental models of simple vesicles, focusing on prebiotically plausible fatty acids and their derivatives. We review recent work on interactions of simple vesicles with RNA and other studies of the transition from vesicles to protocells. Finally we discuss current challenges in understanding the biophysics of protocells, as well as conceptual questions in information transmission and self-replication.

Chiu, Lynn and Scott Gilbert. The Birth of the Holobiont: Multi-Species Birthing Through Mutual Scaffolding and Niche Construction. Biosemiotics. Online March, 2015. The University of Missouri philosopher and Swarthmore College biologist neatly weave these aspects into novel evolutionary and developmental perceptions. As the quotes say, an individual organism is never an island, rather ones selfhood is a melange of microbes, organelles, anatomy and physiology in an environment. In this view the natal event joins mother, infant and microbiome in a symbiotic symphony. See also Developing Scaffolds (Caporael, 2014) and a special issue of this journal for which this article was written.

Holobionts are multicellular eukaryotes with multiple species of persistent symbionts. They are not individuals in the genetic sense — composed of and regulated by the same genome — but they are anatomical, physiological, developmental, immunological, and evolutionary units, evolved from a shared relationship between different species. We argue that many of the interactions between human and microbiota symbionts and the reproductive process of a new holobiont are best understood as instances of reciprocal scaffolding of developmental processes and mutual construction of developmental, ecological, and evolutionary niches.

We are evolutionarily, physiologically, and developmentally integrated holobiont systems, strung together through mutual reliance (developmental scaffolding) and mutual construction (niche construction). Bringing the processes of niche construction and developmental scaffolding together to interpret holobiont birth conceptually scaffolds two new directions for research: (1) in niche construction, identifying the evolutionary implications of organisms actively constructing multiple overlapping niches and scaffolds, and (2) in Evolutionary Developmental Biology, characterizing evolutionary and ecological processes as developmental causes. (Abstract)

The holobiont is the symbiotic integration of a eukaryotic host with its persistent populations of symbionts. Humans are not individuals in the genetic sense — i.e., they are not composed of and regulated by the same genome. However, holobionts satisfy all five notions of biological individuality: they are anatomical, physiological, developmental, immunological, and evolutionary units, evolved from a shared relationship between different species. (3) In sum, the holobiont as a whole exhibits the features of a biological individual, but the parts of the holobiont are in a large part strung together through mutual reliance (developmental scaffolding) and mutual construction (niche construction). (4)

Biosemiotics is about information and communication in biology. The past decade has brought about remarkable new discoveries about relationships between and within organisms. One of the most revolutionary of these discoveries has been the importance of symbiotic signals used to build, maintain, and protect a holobiont. Developmental symbiosis merges embryology and ecology in inter-species webs of mutual and reciprocal communication. Birth is seen not as the origin of a new individual, but as the perpetuation of these organizing webs of signals between animals and microbes. (14)

Collens, Adena, et al. The Concept of the Hologenome, an Epigenetic Phenomenon, Challenges Aspects of the Modern Evolutionary Synthesis. Journal of Experimental Zoology B. Online November, 2019. In this issue of responses to John Bonner’s call to re‐evaluate evolutionary theory in light of major transitions scale, Smith College biologists including Laura Katz advocate a factoring in and appreciation of epigenesis, symbiosis, microbiome and their manifest holobiont unity. These novel, significant insights are then seen to imply a radically expanded, 21st century evolutionary synthesis.

Cornish-Bowden, Athel. Lynn Margulis and the Origin of the Eukaryotes. Journal of Theoretical Biology. 434/20, 2017. This is an introduction by a CNRS research director to an issue on the 50th anniversary of Lynn Margulis’ classic paper The Origin of Mitosing Cells. Among entries are Symbiosis in Eukaryotic Evolution, From Endosymbiosis to Holobionts, Life before LUCA and Darwinizing Gaia by authors such as Ford Doolittle, Antonio Lazcano, Naoki Sato, Juli Pereto, and Nick Lane. And we especially note Symbiogenesis: Beyond the Endosymbiosis Theory by Duur Aanen and Paul Eggleton. Lynn’s valiant mission until her passing in 2011 in support of life’s consistent persuasion to join into beneficial unions received scant appreciation and often derision at the time. It is now gratifying to see her vision and contribution gaining wide acceptance and integration as a central biological tenet.

Symbiogenesis, literally ‘becoming by living together’, refers to the crucial role of symbiosis in major evolutionary innovations. The term usually is reserved for the major transition to eukaryotes and to photosynthesising eukaryotic algae and plants by endosymbiosis. However, in some eukaryote lineages endosymbionts have been lost secondarily, showing that symbiosis can trigger a major evolutionary innovation. We evaluate this hypothesis for two innovations in termites: the role of flagellate gut protist symbionts in the transition to eusociality from cockroach-like ancestors, and non-gut associated symbionts in the transition to ‘higher’ termites, characterized by the absence of flagellate gut protists. In both cases we identify a crucial role for symbionts. We conclude that symbiogenesis is more broadly applicable than just for the endosymbiotic origin of eukaryotes and photosynthetic eukaryotes, and may be a useful concept to acknowledge the important role of symbiosis for evolutionary innovation.

Curatolta, Agnese, et al. Cooperative Pattern Formation in Multi-component Bacterial Systems through Reciprocal Motility Regulation. Nature Physics. 16/11, 2020. University of Paris, University of Hong Kong, and Shenzhen Institute of Synthetic Biology biomedical researchers provide another indication this current year of how much since 2000 that cellular, and evolutionary science has adopted the formative presence of complex self-organized dynamics. But as yet without an integral organic revolution (which this site tries to report) we are not able to appreciate and avail its natural procreativity. But we note that this biological article is in a physics journal, so progress is underway.

Self-organization is a prerequisite of biological complexity. At the population level, it amounts to spontaneously sorting different individuals through space and time. Here, we reveal a simple mechanism by which different populations of motile cells can self-organize through a reciprocal control of their motilities. (Abstract excerpt))

Self-organization is a hallmark of living systems that is observed at all scales. Coordinated behaviours are indeed required to regulate the spatial arrangements of specialized cell types to generate tissue patterning and form complex body layouts, but they are also crucial to the global organization of populations. In biology, metabolic interactions or competition for food offer standard self-organization mechanisms, which have been shown to be complemented by motility-based mechanisms such as chemotaxis. (1152)

De Villiers-Botha, Tanya and Paul Cilliers. The Complex “I”: The Formation of Identity in Complex Systems. Cilliers, Paul and Rika Preiser, eds. Complexity, Difference and Identity: An Ethical Perspective. Berlin: Springer, 2010. At the leading edge of complex adaptive system theory, with its generic interplay of elemental agent, relational communication, and nested organization, University of Stellenbosch, RSA, philosophers muse over consequent implications of who we are. Rather than isolate individuals, a reciprocity of both our own uniqueness, while situated in a necessary, vital, community context, is newly advised. John Collier’s apropos chapter is noted herein. But this natural complementarity of individual and group, a salutary synthesis of person, neighborhood and planet just being realized, begs an organically creative cosmos suffused with these essential, constant propensities.

Dehmelt, Leif and Philippe Bastiaens. Self-Organization in Cells. Meyer-Ortmanns, Hildegard and Stefan Thurner, eds. Principles of Evolution: From the Planck Epoch to Complex Multicellular Life. Berlin: Springer, 2011. Max Planck Institute of Molecular Physiology biologists join the chorus presently reinventing life’s essence as a dynamic, universal complex adaptive system. By such lights, which this volume engages, cells, creatures and people can be rerooted in an implied conducive cosmos.

Cells are dynamic, adaptable systems that operate far from thermodynamic equilibrium. Their function and structure is derived from complex biological mechanisms, which are based on several distinct organizational principles. On the one hand, master regulators, preformed templates or recipes can guide cellular structure and function. On the other hand, local interactions between fluctuating agents and growing work-in-progress can lead to de novo emergence of structures via self-organization. (219)
In a self-organized process, several entities can interact with each other, and team up to produce a behavior of the group as a whole. In such systems, the organizing entity is not imposed from outside, but rather internal to the system itself. In a simple definition, self-organization is a process in which a pattern at the global level emerges solely from numerous dynamic interactions among the lower-level components of the systems. Moreover, the rules specifying interactions among the system’s components are executed using local information, without reference to the global pattern. (220)

Del Bianco, Marta and Stefan Kepinski. Context, Specificity, and Self-Organization in Auxin Response. Cold Spring Harbor Perspectives in Biology. 3/1, 2011. In similar accord with Dundr and Misteli’s paper next, University of Leeds biologists report still another instance of the intrinsic presence and activity of this generative guidance.

Auxin is a simple molecule with a remarkable ability to control plant growth, differentiation, and morphogenesis. The mechanistic basis for this versatility appears to stem from the highly complex nature of the networks regulating auxin metabolism, transport and response. These heavily feedback-regulated and inter-dependent mechanisms are complicated in structure and complex in operation giving rise to a system with self-organizing properties capable of generating highly context-specific responses to auxin as a single, generic signal. (Abstract)

Di Talia, Stefano and Massimo Vergassola. Waves in Embryonic Developement. Annual Review of Biophysics. 51/327, 2022. We note work by Duke University Medical Center and Sorbonne University, Paris cell biologists to record this notice of active relational forces, along with all else, which are also vitally present in life’s gestation phase.

Embryonic development hinges on effective coordination of molecular events across space and time. Waves have recently emerged as constituting an ubiquitous mechanism that ensures rapid spreading of regulatory signals across embryos for the emergence of body plan structures. Here we review a recent quantitative work on signaling waves, along with an integral theory. We start with reaction–diffusion systems and move to excitable dynamics and then coupled oscillators. Our goal is to inspire experimental work that will elucidate waves in development and beyond. (Excerpt)

Dietert, Rodney. The Human Superorganism. New York: Dutton, 2016. The Cornell University immunotoxicologist writes a popular exposition of novel appreciations that our physiologic viability is due much to a beneficial holobiont symbiosis with bacterial multitudes.

Dundr, Miroslav and Tom Misteli. Biogenesis of Nuclear Bodies. Cold Spring Harbor Perspectives in Biology. 2/12, 2010. In this new professional journal, Rosalind Franklin University of Medicine (Chicago) and National Cancer Institute researchers give real credence to self-organizing proclivities as an innate source of such “biogenesis.”

The nucleus is unique amongst cellular organelles in that it contains a myriad of discrete suborganelles. These nuclear bodies are morphologically and molecularly distinct entities, and they host specific nuclear processes. Although the mode of biogenesis appears to differ widely between individual nuclear bodies, several common design principles are emerging, particularly, the ability of nuclear bodies to form de novo, a role of RNA as a structural element and self-organization as a mode of formation. The controlled biogenesis of nuclear bodies is essential for faithful maintenance of nuclear architecture during the cell cycle and is an important part of cellular responses to intra- and extracellular events.

Dupre, John and Stephan Guttinger. Viruses as Living Processes. Studies in History and Philosophy of Biological and Biomedical Sciences. Online March, 2016. We cite this current paper by University of Exeter philosophers because in these mid 2010s, it evinces to the generative, defining presence of symbiotic processes across life’s emergent evolution. View papers by Scott Gilbert, Jan Sapp and others, which make a similar claim. But the intrepid founder of this concept from the 1970s, the late Lynn Margulis (1938-2011), had to put up with constant denials and rejections, e.g. from Richard Dawkins. In the past few years, life’s relational propensities have become accepted as a primary formative factor. This is a curious aspect of evolutionary theory when features such as convergence (McGhee, 2011) and teleology (Deacon, 2016) are inadmissible until a sudden reversal occurs.

The view that life is composed of distinct entities with well-defined boundaries has been undermined in recent years by the realisation of the near omnipresence of symbiosis. What had seemed to be intrinsically stable entities have turned out to be systems stabilised only by the interactions between a complex set of underlying processes. This has not only presented severe problems for our traditional understanding of biological individuality but has also led some to claim that we need to switch to a process ontology to be able adequately to understand biological systems. A large group of biological entities, however, has been excluded from these discussions, namely viruses. Viruses are usually portrayed as stable and distinct individuals that do not fit the more integrated and collaborative picture of nature implied by symbiosis. In this paper we will contest this view. We will first discuss recent findings in virology that show that viruses can be ‘nice’ and collaborate with their hosts, meaning that they form part of integrated biological systems and processes. We further offer various reasons why viruses should be seen as processes rather than things, or substances. Based on these two claims we will argue that, far from serving as a counterexample to it, viruses actually enable a deeper understanding of the fundamentally interconnected and collaborative nature of nature. (Abstract

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