V. Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An Earthtwinian Genesis Synthesis

3. Cellular Self-Organization and Holobiont Symbiogenesis

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)

Sorensen, Megan, et al. Comparison of Independent Evolutionary Origins Reveals both Convergence and Divergence in the Metabolic Mechanisms of Symbiosis. Current Biology. 30/2, 2020. University of Sheffield, Exeter, and York biologists describe sophisticated experiments to elucidate the primary role played by nature’s tendency for all manner of cellular entities to join together in mutual benefit. Although difficult to recover because not readily evident, their procreative influence in life’s episodic emergence grows in importance. But in the article or references the life work of Lynn Margulis (1938-2011) as an advocate this vital feature, against much opposition, is not mentioned. A decade later one might imagine a second worldwide phase which at last confirms a universal symbiotic synthesis. See also a commentary Evolution: Convergent Pathways to Symbiosis by Levi Morran in the same issue.

Through the merger of previously independent lineages, symbiosis promotes the acquisition of new traits and exploitation of ecological niches, driving evolutionary innovation and vital ecosystem functions. In order to study this convergent process, independent we compared the metabolic mechanisms of two independent origins of Paramecium bursaria-Chlorella photosymbiosis using a reciprocal metabolomic pulse-chase method. This showed convergent patterns of nutrient exchange and utilization for host-derived nitrogen in the Chlorella genotypes and symbiont-derived carbon in the P. bursaria genotypes. Altogether our data suggests that the multiple origins of P. bursaria-Chlorella symbiosis use a convergent nutrient exchange. (Abstract excerpt)

Speijer, Dave. Debating Eukaryogenesis: Does Eukaryogenesis Presuppose Symbiosis Before Uptake? BioEssays. 42/2, 2020. The University of Amsterdam veteran biologist makes a strong case to date that life’s innate avail of beneficial assemblies at every stage reveals a persistent “symbiogenesis,” instead of an “autogenesis” by many small steps. Other “predator/prey” models are then also set aside. So it seems after decades of study, it can be said that this mutual “coadptation” method becomes most evident, and thus can traced to an earlier, onset phase. Further experiments are proposed, but in this consummate year, it does seem that a “universal symbiosis” proceeds apace through a developmental evolutionary gestation.

Eukaryotic origins are heavily debated. The author and others have proposed that they are linked with the arrival of a pre‐mitochondrion of alphaproteobacterial=like ancestry, in a so‐called symbiogenic scenario. The ensuing mutual adaptation of archaeal host and endosymbiont seems to have been a defining influence leading to the last eukaryotic common ancestor. An unresolved question deals with the means by which the bacterium ends up inside. Here the author argues that prior models share flaws, hence making them less likely, and that a “pre‐symbiotic stage” would have eased ongoing metabolic integration. I will speculate about the nature of the (endo) symbiosis that started eukaryotic evolution in the context of bacterial entry being a relatively “early” event. (Abstract excerpt)

Stephens, Andrea. Living Together. Trends in Ecology and Evolution. 37/7, 2022. A TREE editor introduces a latest review of nature’s avail of reciprocal unions at each and everywhere it can. Topical items are Mycorrhizal Traits, Lichen Symbioses, Host Influence of Symbiont Evolution, and more.

The term ‘symbiosis’ comes from Greek and means ‘living together.’ The articles in this special issue cover a range of topics about symbiotic relationships which are key to understanding life on Earth. The interacting partners modify each other’s behavior and physiology, which, in turn, alters their ecological dynamics. The ecology and evolution of life’s pervasive communions is key to understanding our planetary biodiversity.

Suarez, Javier and Vanessa Trivino. A Metaphysical Approach to Holobiont Individuality. Quaderns de Filosofia. 6/1, 2019. In this journal of the Societat de Filosofia del País Valencià, this entry by University of Barcelona and University of Murcia philosophers opens with Life on Earth does not walk alone. It is becoming evident nowadays that individuals do not exist in isolation apart from each other and their ecological region. Rather everyone’s internal, and external milieu and identity are actually a symbiotic, interactive unity between me and We, small and large, so as to compose a viable US. In regard a tripartite universal, iconome principle is thus being revealed.

Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, detractors argue that they are just chimeras or ecological communities. Both parties argue over what it takes for a “conglomerate” to be an individual from a biological point of view. This paper presents a meta-physical approach which draws on a conception of natural selection that supports the thesis that holobionts are units of selection which bear emergent traits and exert downward powers over the entities that compose them. In this vein, it is reasonable to conceive holobionts as emergent biological individuals. (Abstract excerpt)

Tekle, Yonas, et al. Molecular Data Are Transforming Hypotheses on the Origin and Diversification of Eukaryotes. BioScience. 59/6, 2009. Smith College (Tekle, Laura Katz) and University of Massachusetts at Amherst (Laura Wegener Parfrey) biologists provide a lengthy update to wit that the evolutionary occurrence of nucleated cells is better understood as due to a pervasive “chimeric” synthesis. All sorts of lateral, endosymbiotic, genetic, archaeal, and bacterial realms engaged in multilineal transfers and sharings are seen to engender the consequent myriads of cellular organisms.

Thornburg, Zane, at al. Fundamental Behaviors Emerge from Simulations of a Living Minimal Cell. Cell. 185/345, 2022. A 15 member team mainly based at the University of Illinois achieves a novel depth and degree of analysis of life’s metabolic cellular basis. A four part graphic depicts the study range from internal processes, cell states, dynamic changes and onto whole-cell simulations. A news report appears in Quanta Magazine as Most Complete Simulation of a Cell Probes Life’s Hidden Rules by Yasemin Saplakoglu on February 24, 2022. By our PhiloSophia view, by a science spiral from individuals to such collaborative efforts, our Earthuman intelligence seems to carry out, as yet unawares, some natural participatory purpose to wholly quantify a self-cocreating genesis ecosmos. However might we peoples in this decade be able to realize this?

A kinetic model for a minimal bacterial cell offers quantitative insight into how the cell balances processes from metabolism to gene expression to growth. (In Brief)

We present a whole-cell fully dynamical kinetic model of a minimal cell with a reduced genome that has retained few regulatory proteins or small RNAs. Time-dependent behaviors of concentrations and reaction fluxes from stochastic-deterministic simulations reveal how the cell balances its metabolism, genetic information processes, growth, as a deeper view into the vital principles of life. (Abstract excerpt)

Tripp, Erin, et al. Reshaping Darwin’s Tree: Impact of the Symbiome. Trends in Ecology and Evolution. Online June, 2017. An eight member team from the University of Colorado, Rutgers University, Sun Yat-Sen University, Chinese Academy of Sciences, and the Chicago Botanical Garden perceive an “unfolding revolution” via the actual inclusion of symbiotic assemblies across life’s phylogenetic evolution. Its significance is cited as “a new way of exploring the world” as graced by nature’s propensities for mutually beneficial unions. The late Lynn Margulis and founding advocate of this prime phenomena would be pleased, gratified, and say “tell me about it.”

Much of the undescribed biodiversity on Earth is microbial, often in mutualistic or pathogenic associations. Physically associated and coevolving life forms comprise a symbiome. We propose that systematics research can accelerate progress in science by introducing a new framework for phylogenetic analysis of symbiomes, here termed SYMPHY (symbiome phylogenetics).

Varahan, Sriram, et al. Metabolic Constraints Drive Self-Organization of Specialized Cell Groups. eLife. June 26, 2019. Five Indian systems cell biologists contribute novel understandings of the many ways that cellular activities have a vitality of their own as they innately organize themselves into preferred states and solutions.

How phenotypically distinct states in isogenic cell populations appear and stably co-exist remains unresolved. We find that within a mature, clonal yeast colony in low glucose, cells arrange into metabolically disparate cell groups. Using this system, we model and experimentally identify metabolic constraints which drive such self-assembly. Our work suggests simple physico-chemical principles that determine how isogenic cells spontaneously self-organize into structured assemblies in complimentary, specialized states. (Abstract excerpt)

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