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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

4. Multicellular Fauna and Flora Organisms in Transition

Mao, Yanlan and Jeremy Green. Systems Morphodynamics. Philosophical Transactions of the Royal Society B. 372/20160505, 2017. An introduction by British biologists to an issue with this suggested title to represent current integral understandings of how organisms and evolutions form and flourish in concert.

McClusker, Derek.. Cellular Self-Organization. Molecular Biology of the Cell. 31/3, 2020. Two decades into the 21st century, a European Institute of Chemistry and Biology, Bordeaux researcher can post a strong, quantified endorsement of nature’s pervasive propensity to spontaneously organize her/his biochemical, physiological, developmental, metabolic processes across every class and phylum, Here is another instance into the 2020s of a robust proof of an intrinsic ecosmic genesis alongside a olden mechanical fixation that prohibits any such phenomenal qualities.

While the organization of inanimate systems such as gases or liquids is mainly thermodynamically, biological systems exhibit an organization that is far from a well-mixed equilibrium. The variable modes displayed by cells are evident in life’s dynamic processes including development, movement, and division. These anisotropies operate at different phases from the meso- to the nano-scale that can be seen to reflect a self-organization characteristic of living systems. Here, some examples of self-organization underlying cellular variabilities are reviewed. Given the technical challenges of doing this, some successful approaches to study their self-organization will also be considered. (Excerpt)

Self-organization appears to be an intrinsic property of GTPase-driven pathways. Energy dissipation in these systems enables the emergence of a highly dynamic state in which multiple system components become organized in space and time. These properties appear to endow cells with a timely responsiveness to rapid perturbations. It may be too early to perceive and predict general principles of self-organization, but the use of diverse experimental models and approaches is providing insight into Schrödinger’s wonder at the “organism’s astonishing gift of concentrating a ‘stream of order’ on itself”. (147)

Merle, Melody, et al. Precise and Scalable Self-Organization in Mammalian Pseudo-Embryos. arXiv:2303.17522. Pasteur Institute, Paris and Princeton University biologists achieve still another instance whereby life’s organic occasion before, and after reproduction proceeds to organize itself. By extension all this procreative fertility could be seen to occur within and due to an inherently natural genesis.

During embryonic development, reproducible gene expression patterns determine cellular fates in time and space, which are crucial in the earliest stages when the body plan and asymmetric body axes emerge. In flies and worms they achieve near-single-cell spatial precision, even for macroscopic patterns. However, we know little about accuracy in mammals. Using an in vitro model for gastruloids, we show that genetic patterns reproduce within 20% in protein concentration variability. Our results reveal precision, reproducibility, and size scaling for mammalian systems, which spontaneously arise in self-organizing cell aggregates and could thus be fundamental features of multicellularity. (Excerpt)

Michod, Richard and Denis Roze. Transitions in Individuality. Proceedings of the Royal Society of London B. 264/853, 1997. Noted more elsewhere, biologist Michod’s University of Arizona group contributes to the growing perception of a nested evolutionary scale of integral entities.

The evolution of multicellular organisms is the premier example of the integration of lower levels into a single, higher level individual….We provide an explicit two-locus genetic framework for understanding this transition in terms of the increase of cooperation among cells and the regulation of conflict within the emerging organism. (853)

Mietke, Alexander, et al. Self-Organized Shape Dynamics of Active Surfaces. Proceedings of the National Academy of Sciences. 116/1, 2019. We recall a decade ago when self-organization as a formative force in cellular development was rarely mentioned or factored in. Here MPI Physics of Complex Systems and Technical University of Dresden theorists add to its inherent contribution to physiological function and somatic vitality. May it also be said that some 65 years after WW II, a global human phenomenon can rise Phoenix-like to learn about cosmic life’s self-verification, and to so offset a looming WW III, achieve our common Earthwise understanding and affirmation.

Morphogenesis, the emergence of shape and form in biological systems, is a process that is fundamentally mechanochemical: Shape changes of material are driven by active mechanical forces that are generated by chemical processes, which in turn can be affected by the deformations and flows that occur. We provide a framework that integrates these interactions between the geometry of deforming materials and active processes in them by introducing the shape dynamics of self-organized active surfaces. We show that the tight coupling between surface mechanics and active processes gives rise to the spontaneous formation of nontrivial shapes, shape oscillations, and directed peristaltic motion. Our simple yet general description lays the foundation to explore the regulatory role of shape in morphogenetic processes. (Significance)

Minelli, Alessandro. Perspectives in Animal Phylogeny. Oxford: Oxford University Press, 2009. The University of Padova zoologist writes a well-reviewed survey of the leading conceptual edges of evolutionary biology. A summary highlights these findings and next steps: metazoan life forms unto a general hierarchical scale; organism development proceeds via local dynamic modules; we need move beyond an adultocentric focus; and an acknowledgement of how pervasive convergence is.

Read the other way around, we can take as the (admittedly, somewhat idealized) default state of living matter a condition of everlasting dynamics which, in multicellular organisms, easily translates into unlimited growth and fractal-like iteration of developmental patterning. (243)

Minelli, Alessandro. The Development of Animal Form. Cambridge: Cambridge University Press, 2003. A significant volume about rethinking how organisms grow to relative maturity. Rather than occurring along a fixed path legislated by a molecular program, many epigenetic forces are in play which builds in a stochastic flexibility. In this way developmental biology can affect the evolution of life, which can inform a reintegration of these disciplines. A further consequence is an expansion of focus from either the DNA or adult form of an organism to its entire life cycle.

Moen, Daniel, et al. Evolutionary Conservatism and Convergence Both Lead to Striking Similarity in Ecology, Morphology and Performance across Continents in Frogs. Proceeding of the Royal Society B. 280/20132156, 2013. Life scientists Moen and John Wiens, SUNY Stony Brook, and Duncan Irschick, University of Massachusetts, Amherst, achieve a uniquely comprehensive study that includes all these title aspects at once. As a result, a substantial affirmation can be made of nature’s seemingly innate propensity to repeat common patterns and behaviors everywhere across for life’s disparate yet oriented development and radiation.

Many clades contain ecologically and phenotypically similar species across continents, yet the processes generating this similarity are largely unstudied, leaving fundamental questions unanswered. Is similarity in morphology and performance across assemblages caused by evolutionary convergence or by biogeographic dispersal of evolutionarily conserved ecotypes? Does convergence to new ecological conditions erase evidence of past adaptation? Here, we analyse ecology, morphology and performance in frog assemblages from three continents (Asia, Australia and South America), assessing the importance of dispersal and convergent evolution in explaining similarity across regions.

We find three striking results. First, species using the same microhabitat type are highly similar in morphology and performance across both clades and continents. Second, some species on different continents owe their similarity to dispersal and evolutionary conservatism (rather than evolutionary convergence), even over vast temporal and spatial scales. Third, in one case, an ecologically specialized ancestor radiated into diverse ecotypes that have converged with those on other continents, largely erasing traces of past adaptation to their ancestral ecology. Overall, our study highlights the roles of both evolutionary conservatism and convergence in explaining similarity in species traits over large spatial and temporal scales and demonstrates a statistical framework for addressing these questions in other systems. (Abstract)

Many species are ecologically and morphologically similar to species in similar biomes on other continents. This pattern of among-continent similarity in species traits occurs across many ecological guilds, clades and biomes (e.g. placental and marsupial mammals, Mediterranean-climate plants and desert lizards. However, the ecological and evolutionary processes underlying this similarity are not well understood, and thus many fundamental questions in ecology and evolutionary biology remain unresolved. (1)

Naranjo-Ortiz, Miguel and Toni Gabaldon. Fungal Evolution: Cellular, Genomic and Metabolic Complexity. Biological Reviews. April, 2020. As the life sciences proceed apace to record the anatomic presence of networks everywhere, here Barcelona Institute of Science and Technology geneticists explore in detail how these prolific microorganisms can be an exemplary way to study this interlinked and communicative phenomena. Within a sense of a transitional emergence from nucleotides and prokaryotes to mobile, varigated organisms, the fungi family do indeed provide an iconic, valuable model.

The question of how phenotypic and genomic complexity are related and shaped through evolution is a central to animal and plant biology. Recently, fungi have emerged as an alternative system of much value because they present a broad and diverse range of phenotypic traits and many different shapes. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout their evolution. Similarly, fungal genomes have a diverse architecture with rapid changes in genome organization. We explore how the interplay of cellular, genomic and metabolic traits mediates the emergence of complex phenotypes. (Abstract)

Fungus compose a group of spore-producing organisms feeding on organic matter, including molds, yeast, mushrooms, and toadstools.

Newman, Stuart, et al. The Vertebrate Limb: An Evolving Complex of Self-Organizing Systems. Progress in Biophysics and Molecular Biology. 137/12, 2018. In a special issue on Biological Challenges in Morphogenesis, SN, New York Medical College, Tilmann Glimm, Western Washington University and Ramray Bhat, Indian Institute of Science describe the latest verifications which reveal how life draws on the same homologous formations in kind across the animal kingdoms from insects and birds to our human selves. See also Some Caveats to Mathematical Modeling in Biology by Scott Gilbert and The Extracellular Matrix as a Driving Force by Marta Linde-Medina and Ralph Marcucio.

Nicholson, Daniel. Organisms ≠ Machines. Studies in the History and Philosophy of Biological and Biomedical Sciences. 44/4, 2013. With these sciences burdened by a centuries old ruling metaphor of life defined and described by mechanistic terms, a Cohn Institute, Tel Aviv University, philosopher explains and calls for a much overdue corrective. How obvious the error when a comparison is as clearly drawn as this. Machines are externally made, passive, can be taken apart, with no vitality of their own. Organisms have an intrinsic, motive purpose, holistic by way of interdependent cellular organs, and so on. In our midst of a cosmic Copernican revolution from dead to alive, this negative conflation that tacitly controls and constrains scientific mindsets is in much need of resolve. For a contrast see, e.g., Marijuan, et al (2013) on ‘blind’ cellular machinery, or Marchetti, et al (2013) about the lively physics of “active matter.”

The machine conception of the organism (MCO) is one of the most pervasive notions in modern biology. However, it has not yet received much attention by philosophers of biology. The MCO has its origins in Cartesian natural philosophy, and it is based on the metaphorical redescription of the organism as a machine. In this paper I argue that although organisms and machines resemble each other in some basic respects, they are actually very different kinds of systems. I submit that the most significant difference between organisms and machines is that the former are intrinsically purposive whereas the latter are extrinsically purposive. Using this distinction as a starting point, I discuss a wide range of dissimilarities between organisms and machines that collectively lay bare the inadequacy of the MCO as a general theory of living systems. To account for the MCO’s prevalence in biology, I distinguish between its theoretical, heuristic, and rhetorical functions. I explain why the MCO is valuable when it is employed heuristically but not theoretically, and finally I illustrate the serious problems that arise from the rhetorical appeal to the MCO. (Abstract)

Nicholson, Jeremy, et al. The Challenges of Modeling Mammalian Biocomplexity. Nature Biotechnology. 22/10, 2004. From a special issue on Systems Biology, a case is made that complex organisms such as human beings ought to be appreciated as “superorganisms” composed on many types of functional microbes. By this approach, better methods of drug design and prescription can be achieved.

Highly complex animals such as humans can be considered ‘superorganisms’ with an internal ecosystem of diverse symbiotic macrobiota and parasites that have interactive metabolic processes. (1268)

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