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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 46 through 60 of 73 found.


Ecosmomics: An Independent Source Script of Generative, Self-Similar, Complex Network Systems

Cosmic Code > nonlinear > 2015 universal

Ge, Xiaofei, et al. Self-Organized Critical Dynamics of RNA Virus Evolution. arXiv:2204.08627. We cite this entry by Tsinghua University, Beijing and University of Paris researchers amongst a rush of nonlinear COVID studies which show how its etiologies can be deeply modeled complex network science. Once again, even in highly stressed, variegated disease pandemic, these mathematic dynamics seek and reside at a default condition poised between more or less relative order. A payoff would be that the past two intense years of such findings could result in methods to identify, prevent and control future epidemics

Studies of RNA virus (e.g., SARS-CoV-2) evolution are vital for understanding molecular evolution and medicine development but so far remain insufficient. Here, we characterize the RNA virus evolution as a physical system with absorbing states and avalanche behaviors. This approach maps biological data (e.g., phylogenetic tree and infection) to a general stochastic process which enables researchers to verify a self-organized criticality underlying RNA virus evolution. We find that SARS-CoV-2 exhibits scale-invariant avalanches as mean-field theory predicts. The lineages that emerge from such critical evolution coincidentally also match the Delta variant. (Abstract excerpt)

Cosmic Code > Genetic Info > DNA word

Zolyan, Suren. From Matter to Form: The Evolution of the Genetic Code as Semio-poiesis. Semiotica. March, 2022. A senior Russian linguist (search) considers how a better perception of nature’s deeply pervasive, self-similar, genomic procreativity can be attained by a turn to and inclusion of an informative biosemiotic essence.

We address issues of description of the origin and evolution of the genetic code from a semiotics standpoint. Developing the concept of code-poiesis introduced by (Marcello) Barbieri, a new idea of semio-poiesis is proposed. Such a recursive auto-referential processing of semiotic system could become a form of organization of the bio-world when notions of meaning are introduced into it. The description of the genetic code as a semiotic system (grammar and vocabulary) allows us to apply an internal reconstruction on the basis of heterogeneity so to explicate forms of coding and textualization. (Abstract excerpt)

The dual nature – biochemical and informational – of the genetic code and genome presupposes that one should be based on the principle of complementarity for its description (cf. Pattee 2007). As in the case of the waveparticle duality of physical entities, only when taken together will biochemical and informational descriptions represent a comprehensive state of affairs. The duality of genetic information will be represented through the double theoretical description. (18)

In philosophy, poiesis (from Ancient Greek) is the activity in which something is brought into being that did not exist before. It is a combined word for the making or formation some compound result. The term autopoiesis refers to a system capable of producing and maintaining itself.

Suren Zolyan: National Academy of Sciences of the Republic of Armenia, Yerevan, Armenia; Institute of Scientific Information on Social Sciences of the Russian Academy of Sciences, Moscow, Russia; and Immanuel Kant Baltic Federal University, Kaliningrad, Russia,

Life's Evolutionary Development Organizes Itself: A 2020s Genesis Synthesis

Quickening Evolution > Biosemiotics

Taborsky, Edwina. Rational Decision Making in Biological Systems. Biosystems. April, 2022. The veteran Canadian semiotics theorist (search) provides a latest integral articulation of life’s deeply encoded, communicative, textual essence. See also How an Information Perspective Helps Overcome the Challenge of Biology to Physics by Keith Farnsworth in this same journal and month as another example of this narrative nature appreciation.

This article presents an outline of biological systems that understands them as self-organizing informational or semiosic systems operating pragmatically and therefore intelligently with their environments. Peircean semiosis, a key analytic method, is a triadic networking function which can be seen as a fundamental natural process within the universe of energy, matter, and mind. In this regard, it generates all morphological forms, both material and conceptual, as they enable adaptation and evolution. (Abstract)

Semiosis is a transformative process of informational dynamics which operates within the physico-chemical, biological and conceptual realms. Semiosis functions as a complex network that enables adaptive morphological formation or spatiotemporal modes of existence. That is, my view of biological systems is that they are capable of self-description and self-measurement on themselves and their immediate environments. This defines them as complex adaptive systems such that they function within a tacit system of rational, self-organized, goal-directed and adaptively functional information processing. (15)

Quickening Evolution > Intel Ev

Czegel, Daniel, et al. Bayes and Darwin: How Replicator Populations Implement Bayesian Computations. BioEssays. 44/4, 2022. DC and Eors Szmathary, Institute of Evolution, Budapest, Hamza Glaffar, Cold Spring Harbor Laboratory and Joshua Tenenbaum, MIT, continue their project to perceive and identify life’s developmental emergence as primarily a cerebral, cognitive, knowledge-gaining occasion. It is argued that every organism across all Metazoan domains must be aware of, learn about and be able to predict their ever-changing environs so as to survive. Here bodily evolution (Darwin) and proactive mind (Bayes) are seen to advance in a parallel, reciprocal way. Their 2020s version can now be informed by novel probalistic, iterative, cognitive models. Writ large, a semblance of a self-educating, making, affirming, autocatalytic, proactive reality becomes evident. A premier feature is then a consilence of past reference and open future. See also Novelty and Imitation within the Brain by this group in Nature Scientific Reports (11:12513, 2021).

Bayesian learning theory and evolutionary theory both formalize adaptive competition dynamics in variable environments. What do they have in common and how do they differ? In this paper, we discuss structural and process analogies at a computational and an algorithmic-mechanical level. We point out mathematical equivalence and isomorphism between Bayesian update and replicator dynamics. We discuss how these mechanisms provide similar ways to adapt to stochastic conditions at multiple timescales. We thus find replicator populations to encode regularities so as to predict future environments. As a notable result, a unified view of the theories of learning and evolution can be achieved. (Abstract)

Quickening Evolution > Intel Ev

Czegel, Daniel, et al. Novelty and Imitation within the Brain: A Darwinian Neurodynamic Approach to Combinatorial Problems. Nature Scientific Reports. 11:12513, 2021. ). DC, Eors Szmathary, Marton Csillag, and Balint Futo, Institute of Evolution, Budapest, along with Hamza Glaffar, Cold Spring Harbor Laboratory post a latest version of their studies of life’s creaturely evolution as most involved with progressively gaining intelligence and knowledge so to best survive. See also Bayes and Darwin: How Replicator Populations Implement Bayesian Computations by this collegial team in BioEssay. (44/4, 2022.)

Efficient search in combinatorial spaces, such as those of possible action sequences, linguistic structures, or causal explanations, is an essential component of intelligence. Based our prior work, we propose that a Darwinian process, operating over sequential cycles of imperfect copying and selection of neural informational patterns, is a promising candidate. In teacher and learner settings, we demonstrate that the emerging Darwinian population of readout activity patterns can maintain and continually improve upon existing solutions A novel analysis method, neural phylogenies, is then proposed that displays the unfolding of the neural-evolutionary process. (Abstract excerpt)

Quickening Evolution > Teleology

Evolution on “Purpose:” Teleonomy in Living Systems.. Google tltle words. . This the name of an international June 2021 two day online meeting sponsored by the Linnean Society of London, since 1788 the premier naturalist endeavor. The main organizer was the biocomplexity theorist Peter Corning. The full site contains Abstracts for 20 presentations by leading scholars such as Stuartt Kauffman, Eva Jablonka, Denis Noble, Nathalie Gontier, Eugene Koonin, Stuart Newman, and James Shapiro. Various titles are Three Laws of Teleonometrics by Bernard Crespi, The Orgin of Goal-Directed Organization by Francis Heylighen, Teleonomy, Agency and Unity of Purpose by Samir Okasha and Teleophobia by Denis Walsh.

Living systems exhibit an internal teleology, the full implications of which have not been explored. This meeting will address various aspects of this phenomenon, including its scope and meaning, and its many forms and facets. Although it is now widely accepted that living systems exhibit an internal teleology, or teleonomy, the full implications of this distinctive biological property have yet to be explored. This online conference will seek to address various aspects of this important phenomenon, including the origins and history of the teleonomy concept, its scope and meaning, and its many forms and facets. Possible topics may include: an historical review of teleological thinking; teleolpgy in evolutionary theory; the nature of teleonomy and agency, genomes, semiotics, modeling teleonomic processes, in epigenesis, physiology, behavior natural selection and onto human evolution.. (Conference summary)

Teleology — the explanation of phenomena by appeal to the goals that they subserve — is widely thought to have been expunged from biology. The reasons offered for its putative banishment are numerous and varied — historical, conceptual, theoretical, metaphysical — and they are all wrong. There is no defensible reason for the teleophobia that holds contemporary biology in its grip. Furthermore, this fixation has had a deleterious effect on evolutionary theory. It has aided and abetted the shunting of organisms with natural purposes from evident developmental thinking. (Denis Walsh)

Quickening Evolution > Teleology

Dambricourt Malasse, Anne, ed.. Self-Organization as a New Paradigm in Evolutionary Biology. International: Springer, 2022. The editor is a senior paleo-anthropologist at the French National Center for Scientific Research. We have not yet seen its Table of Contents, but have already reviewed a significant chapter by Stuart Newman herein. As the book summary alludes, the volume is a first edition of a 2020s genesis synthesis within a revolutionary procreative ecosmos uniVerse with a spontaneous fertility all the way to a planetary progeny transition who might be able to realize and discover.

A new evolutionary synthesis is proceeding to integrate the scientific models of self-organization developed during the later 20th century based on the laws of physics, thermodynamics, and mathematics. This book shows how self-organization is now becoming integrated across a 21st century versions from life’s origins to our human phase. The first part pays attention to the modern observations in paleontology and biology, which include major theoreticians of the self-organization (d’Arcy Thompson, Henri Bergson, René Thom, Ilya Prigogine). The second presents different emergent evolutionary models including the sciences of complexity, the non-linear dynamical systems, fractals, attractors, epigenesis, and systems approaches with examples of the sciences of complexity and self-organization such as embryogenesis-morphogenesis phenomena. (Publisher)

Quickening Evolution > Teleology

Johnston, Iain, et al. Symmetry and Simplicity Spontaneously Emerge from the Algorithmic Nature of Evolution. PNAS. 119/11, 2022. Seven theorists mainly posted at Oxford University including Ard Louis and Chico Camargo consider how life’s ascendant occasion might be better understood as involving and due to computational processes. We note in this new section for its sense of some manner of code-script in effect. But the work still cites neoDarwinian “random mutations” which are then selected. See also Evolutionary Dynamics, Evolutionary Forces, and Robustness: A Nonequilibrium Statistical Mechanics Perspective by Riccardo Rao and Stanislas Leibler in PNAS (119/13, 2022.) A reader was Gunter Wagner, see his latest paper Body Plan Identity: A mechanistic Model with James DiFrisco in Evolutionary Biology (March 2022).

Engineers routinely design systems to be modular and symmetric in order to increase robustness and facilitate later alterations. Biological structures also frequently exhibit modularity and symmetry, but their origin is less well understood. However, evolution, unlike engineers, cannot plan ahead, and so these traits must also afford some selective advantage. Here we introduce a nonadaptive hypothesis based on an algorithmic picture of evolution. It suggests that symmetric structures arise because they require less information to encode and are more likely to appear through random mutations. Algorithmic information theory can thus predict that many genotype–phenotype maps are biased toward phenotypes with low descriptional complexity. We test and show that protein complexes, RNA structures, and a gene regulatory network exhibit an exponential bias toward simpler, more symmetric phenotypes. (Abstract excerpt)

Quickening Evolution > Teleology

Love, Alan and Max Dresow. Organizing Interdisciplinary Research on Purpose. BioScience. 72/4, 2022. University of Minnesota biologists provide an initial outline on this epochal, 20 million dollar, endeavor. Its biological purpose.org home site describes Cluster Projects such as Directionality in Genomics and Macroevolution and Evolutionary Origins and Transitions of Agency. Some typical researchers among many are Anya Plutynski (Agency in Development), Adi Livnat (Genomic Directions), and Richard Watson (Evolutionary and Organismal Goal-Directedness). A Scientific Board of Advisors includes Renee Duckworth, Walter Fontana, and Gunter Wagner.

There is a growing recognition that biological phenomena which suggest agency, directionality, or goal-directedness demand new conceptual frameworks that can translate into rigorous theoretical models and discriminating empirical tests. This project addresses the demand through a novel, interdisciplinary, large-scale program that combines philosophers, theoreticians, and experimentalists. (Project synopsis)

Call for Papers: Teleology for the 21st Century: Teleology used to be one of the central topics in metaphysics until well into the 19th century, but it is rarely discussed today. This lacuna is unfortunate, because the nature of goal-directedness has important implications about biological and human functions, naturalism, social science, the philosophy of mind, and much more. We are looking for innovative papers that shed light on what teleology is, either from a general metaphysical standpoint or in connection with some specific debate.

Quickening Evolution > Teleology

Newman, Stuart. Self-Organization in Embryonic Development. arXiv:2108.00532. This eprint posting by the veteran New York Medical College living systems theorist will be a chapter in Self-Organization as a New Paradigm in Evolutionary Biology, (Springer, July 2022). Search this site and his PubMed bibliography for many collegial pagers since the later 1990s. His lifetime endeavor has been to theorize, seek out and articulate the generative presence and effects of natural self-organizing forces across evolutionary and organism embryonic gestations. See also Form, Function, Agency: Sources of Natural Purpose in Animal Evolution by SN in EcoEvoRxiv (January 7, 2020) and Interplay of Mesoscale Physics and Agent-like Behavior in the Parallel Evolution of Aggregative Multicellularity by Juan Arias Del Angel, et al (with SN) in EvoDevo (11/21, 2020) for other recent entries.

"Self-organization" has taken hold in developmental biology such as in embryonic stem cells. While Immaneul Kant first introduced the phrase to describe the goal-directed properties of living systems, in modern use it has stood for complex forms and patterns than emerge through dynamical material processes. These effects also provide evolutionary templates for embryonic forms and morphological motifs of metazoan lineages. Embryos and organ primordia of animal species generate forms that thus esemble the outcomes of these physical effects. Using the examples of gastrulation, somitogenesis, and limb skeletal forms, I provide instances of, and a conceptual framework for, the relationships between basic physical and evolved types of developmental self-organization. (Abstract excerpt)

Quickening Evolution > Teleology

Rao, Riccardo and Stanislas Leibler. Evolutionary Dynamics, Evolutionary Forces, and Robustness: A Nonequilibrium Statistical Mechanics Perspective.. PNAS. 119/13, 2022. We cite this entry by Simons Center for Systems Biology, IAS, Princeton University and Laboratory of Living Matter, Rockefeller University, NYC researchers as a 2020s instance of how theories about life’s occasion and oriented, emergent course to our Earthuman retrospect are gaining deeper roots in an increasingly conducive physical substrate. Thus a genesis synthesis grows in depth, veracity and ecosmic expanse,

Any realistic evolutionary theory has to consider 1) the dynamics of organisms that reproduce heritable traits, 2) stochastic variations in these traits, and 3) the selection of those organisms that better survive and reproduce. Here, we introduce a general model of reproduction, variation and selection dynamics. Treating them as a nonequilibrium thermodynamic process better clarifies various forces that characterize evolution. One of Some of the detailed predictions of our model can be tested by quantitative laboratory experiments, similar to those performed in the past on evolving populations of proteins or viruses. (Abstract)

From a physicist’s point of view, evolution is an example of a nonequilibrium stochastic dynamical system. One of the main reasons why it is very different from dynamics studied in physics or chemical physics is that the reproduction of organisms is tightly connected with relatively precise, long-time inheritance. This allows the existence of stable variants that can better survive and reproduce than others, and thus allows organisms to evolve. Since the so-called evolutionary Modern Synthesis was deeply anchored in population genetics, mathematical models of evolutionary dynamics have mostly dealt with genetic variations. (5)

Earth Life Emergence: Development of Body, Brain, Selves and Societies

Earth Life > Nest > Microbial

Wang, Weijia, et al. The Impact of Individual Perceptual and Cognitive Factors on Collective States in a Fish School Model.. PLOS Computational Biology. March, 2022. University of Toulouse and Beijing Normal University researchers including Guy Theraulaz quantify how interactive behaviors become altogether coordinated for both member and group benefit. See also Global Dynamics of Microbial Communities Emerge from Local Interactions Rules by Simon Van Vliet, et al (Canada, Switzerland) in the same issue. We can once again note that in these papers, cases, and across the site, a definitive pattern and process can be seen in independent, recurrent effect. Phenotype-like communal entities over many scales arise from and are guided by an independent, universal, genotypic source code. But into 2022, these diverse entries in an open Public Library of Science are by researchers aware of work in their field, but still sans any sense of a novel Earthuman faculty learning on her/his own, nor of any phenomenal ecosmic universe reality they manifestly arise from.

Earth Life > Nest > Symbiotic

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)

Earth Life > Nest > Multicellular

Gosak, Marko, et al. Networks Behind the Morphology and Structural Design of Living Systems. Physics of Life Reviews. March, 2022. As a good example of timely abilities to achieve a convergent synthesis of nonlinear, animate complexities, five University of Maribor, Slovenia theorists including Matjaz Perc post a 40 page, 250 reference article with regard to life’s ubiquitous connectivities across every anatomic and physiological instance. For example intercellular and multicellular interaction patterns, fluid flows, neural nets and all else can be seen to exhibit similar topological dynamics. Today collaborative teams in every land, on a daily basis, altogether compose a speciesphere scientific endeavor going on by itself. But with insane carnage not far away, such a learning, thinking Earthuman faculty whom is achieving these revolutionary findings is still unknown. For such reasons, the evident presence of an independent, universal mathematic source in manifest effect still cannot be implied.

Advances in imaging techniques and biometric data methods have enabled us to apply the topological network properties to organelles, organs, and tissues, as well as the coordinations among them that yield a healthy, whole organism. We review research dedicated to these advances with a focus on networks between cells, the topology of multicellular structures, neural interactions, fluid transportation, and anatomies. The percolation of blood vessels, brain geometries, bone porosity, and relations between various parts of the human body are some examples we explore in detail. (Abstract excerpt))

Tools from the armamentarium of the complex network theory are nowadays recognized as a general and powerful theoretical framework for assessing real-world systems. Their wide applicability is to a significant extent a consequence of their natural suitability to represent and study the relations between individual components in virtually any discrete system. For these reasons, we are witnessing in the last two decades an explosion of multidisciplinary studies in which the complex network methods are applied to social sciences [223-229], linguistics [230-232], ecological systems [233-235], economics [236, 237], and a wide range of engineered and technological systems. (23)

Earth Life > Nest > Multicellular

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)

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