I. Planatural PhiloSophia: An Integral View of a Phenomenal, Independent, Procreative Actuality

C. Our Earthumanity Glimpses a Familiar, Ecorganic, Evogenesis, Ecode Universality and Vital Purpose

Canup, Robin and Philip Christensen, Co-Chairs. Origins, Worlds and Life: A Decadal Strategy for Planetary Science and Astrobiology. Washington, DC: National Academy of Sciences, 2022. The online posting is a thorough, graphic, 700+ page volume all about this ambitious 2023 to 2032 USA research project, with many global inputs. A paper edition will appear next year. It even considers “Planetary Defense” against astro objects. An Earthuman basis is conveyed by some 600 White Paper topical proposals across a wise span such as A Solar System Space Telescope, New Planetary Data Ecosystems Centers, and Cryogenic Comet Sample Return. Specific chapters cover Evolution of Protoplanetary Disks, Global Atmospheres, Magnetospheres, Moons, and Climate, on to Exoplanets, Dynamic Habitability and Life Elsewhere, along with program plans, equity concerns and so on. Many sections discuss spaceflight missions in this period and beyond

In regard, “A Table of Twelve Priority Scientific Questions” in accord with subject matter such as What Mechanisms Dispersed the Nebula and What are Giant Planets Made Of often recurs. Many sections come with an extensive reference list. But as one reads along, by any natural (Earthural) philoSophia it ought to be asked why we capable, collaborative Earthlings are embarking on this vast exploratory venture at all. To gain any such sense, a revolutionary ecosmos genesis neds to be appropriated which seems involved with its own self-quantification, decipherment, and recorded description. By these lights an integral self-discovery and recognition could be achieved. And within a Participatory UniVerse model, a decisive act of aware, informed self-selection and affirmation becomes possible.

STATEMENT OF TASK: The Space Studies Board shall establish a survey committee to develop a comprehensive science and mission strategy for planetary science that updates and extends the Board’s current solar system exploration decadal survey, Vision and Voyages for Planetary Science in the Decade 2013-2022. The new decadal survey shall broadly canvas the field of space and ground-based planetary science to determine the current state of knowledge and identify the most important scientific questions to be addressed during the interval. In addition, it will address relevant programmatic and implementation issues of interest to NASA and the National Science Foundation.

Q(uestion) 9.2 What are the Energy Sources that Life can Exploit on Earth and Other Planets?, (4-29); Q 9.1 How Did Early Earth Environments and Prebiotic Pathways Co-Evolve and Give Rise to Life and What Major Milestones in Earth History Were Coincident with Major Transitions in the Abundance, Quality, and/or Complexity of Life? (12-5); Q11.1 What Is the Extent of Molecular Complexity (e.g., Size, Heteroatom Diversity, Structure, Pathway Assembly Index) and Degree of Organization (e.g., Isomeric Preference, Polymerization) that Can Be Generated Abiotically Under Habitable Conditions? (14-4)

Q 11. Life Elsewhere: Expanding the search to include the possibility of life ‘not as we know it’ requires further technical and conceptual maturation, including advances in statistical methods, scaling laws, information theory, and probabilistic approaches. Understanding the relationship between the geochemical environment and the prebiotic pathways that can give rise to life requires cooperation among diverse disciplines that extends beyond the traditional platform to include geochemists, atmospheric chemists, geologists, geophysicists, astronomers, mission scientists and engineers, and astrobiologists, among others. (11-1)

Cavagna, Andrea, et al. Natural Swarms in 3.99 Dimensions. arXiv:2107.04432. Eight physicists from Italy and Argentina including Irene Giardina provide a further quantitative basis for the universal presence of optimum member-group integral behaviors which can be rooted in statistical physics. A definitive explanation can they be derived from Renormalization Group theories about relations between nested active scales. As the authors note, their advance is the first time that such a specific connection has been made.

The dynamical critical exponent z of natural swarms is calculated using the renormalization group. To order \epsilon = 4-d, a novel fixed point emerges, where both off-equilibrium activity and mode-coupling inertial interactions are relevant. In three dimensions the critical exponent at the new fixed point is z=1.3, in fair agreement with experiments. (Abstract)

Collective behaviour is found in a wide variety of biological systems from clusters of bacteria and colonies of cells, up to insects, bird flocks, and vertebrate groups. A unifying ingredient, which can be based in statistical physics, is the presence of strong, consistent correlations. Studies of avian flight, fish schools, mammal herds, swarms, microbes and proteins have found that the correlation length is much larger than the microscopic scales. Another key hallmark of statistical physics is dynamic scaling, which has been verified in many of these occasions. the case of natural swarms of insects. (1)

Within statistical physics, strong correlations and scaling laws are the two stepping stones leading to the Renormalization Group (RG): when we coarse-grain short-wavelength fluctuations, the parameters of different models flow towards one common fixed point ruling their large-scale behaviour. RG fixed points therefore organize the macroscopic behavior of strongly correlated systems into few universality classes. Biology is vastly more complex than physics, but the widespread presence of strong correlations and the validity of scaling laws cannot be considered a coincidence. They rather call for an exploration of the correlation-scaling-RG path also in collective biological systems. (1)

Cech, Thomas. The Catalyst: RNA and the Quest to Unlock Life's Deepest Secrets. New York: Norton, 2024. The 1989 Nobel chemist has been at the center of a revolutionary shift in genetic science from an original emphasis on DNA to its companion biomolecule ribonucleic acid RNA. The thematic story is about realizations of a wide array of features which have given it a significant role in many metabolic functions. A recent merit is to provide a vaccine base during the COVID pandemic. But our interest also lies with the title concept which can identify life’s deep propensity to consistently initiate and perpetuate its own procreative course, seemingly within a catalytic ecosmos.

As an example of current advances on this frontier, we cite BEACON: Benchmark for Comprehensive RNA Tasks and Language Models by Yuchen Ren, et al at arXiv:2406.10391 and RNAFlow: RNA Structure & Sequence Design via Inverse Folding-Based Flow Matching by Divya Nori and Wengong Jin at arXiv:2405.18768.

For over half a century, DNA has reigned in the popular imagination as the “secret of life.” But over the past decades, a quiet revolution has taken place. The biochemist Thomas Cech and a diverse cast of scientists have revealed that RNA, long overlooked as the passive servant of DNA, sits at the center of biology. In The Catalyst, Cech finally brings together years of research to demonstrate that RNA is the true key to understanding life on Earth, from its very origins to our future in the twenty-first century. The Catalyst moves from the early experiments to Cech’s own findings that it can catalyze cellular reactions and on to novel biotechnologies. The work glimpses how RNA-powered therapies such as CRISPR that can RNA rewrite the code of life and mRNA vaccines that have saved millions during the pandemic. BOOK

I tell the story of RNA in two parts: the first is how RNA revealed itself as life’s great catalyst. We begin in the 1950s with the experiments that un covered how RNA orchestrates the construction of the proteins that perform most of the essential functions in living organisms. Then we see how RNA is responsible for helping us humans do so much with our DNA jnformation. From there, the story takes a personal turn. I recount how my team discovered catalyric RNA called riboenzynes. (13)

Thomas Robert Cech (born December 8, 1947) is an American chemist who shared the 1989 Nobel Prize in Chemistry with Sidney Altman, for their discovery of the catalytic properties of RNA. He is also the president of Howard Hughes Medical Institute.

Chanu, Athokpam, et al. Analysis of the Structural Complexity of Crab Nebula Observed at Radio and Infrared Frequencies using a Multifractal Approach. arXiv:2206.04717. We cite this entry by Jawaharlal Nehru University, School of Computational and Integrative Sciences, Indian Institute of Astrophysics, and Tata Institute of Fundamental Research investigators for its self-similar content and as an example of deep human proclivities to carry out such studies wherever possible. A reference list harks back to Per Bak who in 1988 proposed a “physics of fractals” and “self-organized criticality.”

Into these 2020s, a convergent revolutionary discovery of a common, familial ecosmos can be attributed to a collaborative Earthuman sapience. In regard, an aware “planatural philoSophia” view might wonder how these mathematic, anatomy/physiology patternings get there in the first place. Why are we peoples moved and capable to learn all this? At this fraught moment, on this site we seek to support an evident presence of a greater phenomenal genesis with its own encoded course from universe to me + We = US.

The Crab nebula exhibits complex morphological patterns at different observing frequencies. We carry out a systematic investigation using imaging data at radio and infrared frequencies. For our analysis, we use standard multifractal detrended fluctuation analysis (MFDFA). We find long-range, power-law correlations, as expected from the physics of supernova evolution. Consequently, its multifractal properties originate from the probability density function as well as different correlations of large and small fluctuation values. Our analysis thus provides a fresh perspective on the morphology of the Crab nebula from a statistical physics viewpoint. (Abstract excerpt)

Cornish-Bowden, Athel and Maria Cardenas. The Essence of Life Revisited. Theory in Biosciences. 141/2, 2022. We locate this entry by Aix Marseille University, CNRS biotheorists amongst various current endeavors to consider and maybe resolve the deepest issue of something more or nothing else. It opens with past views of inevitability or randomness, e,g, Jacques Monod vs. Christian deDuve, and onto how a understandings of an evident catalytic self-organization form life origin could reveal a natural emergence. The authors ask whether novel theoretical bases can lead to an answer, which seems to involve a finesse of both motive agencies and post happenings. See also, e.g., Emergence, Construction or Unlikely? by Stuart Bartlett and Michael Wong at arXiv:2303.08018 for more wonderings.

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 mainly a cerebral, cognitive learning advance. It is argued that every organism across all Metazoan domains must be primarily able to be aware of and predict their ever-changing environs. By this view, bodily evolution (Darwin) and proactive mind (Bayes) need proceed in a parallel way. Here, this 2020s version is informed and braced by probalistic, iterative, cognitive models or versions. Writ large, once again an outline of a self-educating, making, affirming, autocatalytic participant reality can become evident as a complementarity of past reference and open future.

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)

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)

da Costa, Luciano. On Similarity. arXiv:2111.02803. We cite this 2021 entry by the senior University of Sao Paulo complexity theorist (search) as a way to record his steady flow of wide-ranging, collegial papers since the early 2000s. Another reason is a present burst of studies over a topical span from enzymes to texts and cities. By this work, along with many other worldwide contributions, 21st century nonlinear systems science altogether seems to have reached an integral convergence. Into the 2020s, a consistent natural recurrence of common patterns and processes, forms and flows, has now become quite evident everywhere.

In regard, the revolutionary outlines of an innate, organic evolutionary genesis can be expressed. By some affinity with a each one of us, a genetic-like universal, independent, network code source is found in self-organizing effect across every spatial and temporal domain. Its constant generative influence then serves to inform and exemplify itself in each phenotype-like occasion from galaxies to geckos. A familial, indeed Taoist, image becomes portrayed as an archetypal part/wave = light, DNA/AND = genome, bigender complementarity so as to compose a whole beingness in community.

In further regard, see also Coincidence Complex Networks by L. da Costa in Journal of Physics: Complexity (3/1, 2022), Enzyme Similarity Networks at 2205.0516) Text Characterization Based on Recurrence Networks by Souza, Barbara, et al. (2201.06665, see review) A Similarity Approach to Cities and Features by Da Costa and Eric Tokuda (2202.08301), City Motifs as Revealed by Similarity (2204.09104) and Neuromorphic Networks as Revealed by Features Similarity by A. Benatti, et al at 2207.10571.

The neural criticality hypothesis states that the brain may be poised in a critical state at a boundary between different types of dynamics. Many studies show that critical systems tend to exhibit optimal computational property. Here, we provide an account of the mathematical and physical foundations of criticality. We then review and discuss recent experimental studies so to identify important next steps to be taken, along with connections to other fields. (2111.02803 excerpt)

Many complex systems reveal intricate characteristics taking place at several scales of time and space. In particular, texts are distinguished by a hierarchical structure that can be studied by multi-scale concepts and methods. Effective approaches can emphasize words with more informational content. Here we advance this work with a focus on mesoscopic representations of networks. We extend this domain to textual narratives wherein recurrent relationships among parts of speech (subject, verb and direct object) form connections among sequential pieces (e.g., paragraphs). (2201.06665 excerpt)

Dambricourt Malasse, Anne, ed. Self-Organization as a New Paradigm in Evolutionary Biology. International: Springer Frontiers, 2022. The editor is a senior paleo-anthropologist at the French National Center for Scientific Research. The volume appears in a new Springer series Evolutionary Biology: New Perspectives (search Richard Delisle) and can represent a latest, strongly evident affirmation of this missing innate, common source force for life’s oriented, emergent development. In regard the work well serves to establish an absent, animating, informative, genome-like basis which can at last inform, explain, qualify and brace a valid 2020s genesis synthesis within a revolutionary ecosmos uniVerse.

We note these chapters to convey the book’s inclusive reach and deep veracity: Self-Organization Meets Evolution: Ernst Haeckel and Abiogenesis (Georgy Levit and Uwe Hossfeld, see review), Self-Organization in Embryonic Development (Stuart Newman, search), Biological Evolution of Microorganisms (Werner Arber) From Dissipative Structures to Biological Evolution: A Thermodynamic Perspective (Dilip Kondepudi, et al, see review), and Quantum Fractal Thermodynamics to Describe the Log-Periodicity Law in Species Evolution and Human Organizations (Diogo Queiros-Conde, et al). Anne Malasse then posts a final wrap as Sapiens and Cognition: The Last Threshold of Self-Organized and Self-Memorizing Increasing Complexity.

A new evolutionary synthesis is proceeding to integrate the scientific models of self-organization in occurrence since the later 20th century as based on the laws of physics, thermodynamics, and mathematics. This book shows how self-organization is by now integrated across a 21st century span from life’s origins to our human phase. The first part attends to the modern observations in paleontology and biology, with prior presciences such as Immanuel Kant, d’Arcy Thompson, Henri Bergson, and Ilya Prigogine. The second part views emergent evolutionary models drawn from the complexity sciences, the non-linear dynamical systems, fractals, attractors, epigenesis, and other system approaches such as embryogenesis-morphogenesis phenomena. (Publisher)

Global warming, anthropocene extinctions along with astrobiology efforts to look for primitive life forms are prompting thinkers to view life’s evolution as the prime reality for species biodiversity and indeed our own civilization. This discernment leads to better understandings of the origin of the organization of dynamic forms and processes from the smallest cellular unit to the most complex interactions within the organism and then between organisms. Such novel insights and vista just coming into view can illume over geological and cosmic time scales how principles of self-organization of complex systems and generic laws of adaptation and complexification are at procreative work. (Anne Malasse, The Origin and Evolution of Living Organisms: A Convergence between Old and New Paradigms.)

Daniels, Bryan, et al. Identifying a Developmental Transition in Honey Bees Using Gene Expression Data. bioRxiv, November 7, 2022. A latest paper by Arizona State University and Banner Health, Phoenix complexity theorists including Robert Page describes how dynamic genome studies now reveal critically poised bistable states even in this prescriptive phase. This –omic occurrence of self-organized criticalities can well establish nature’s 2020s universal preference for this optimum poise. See also Social Networks Predict the Life and Death of Honey Bees by Benjamin Wile, et al in Nature Communications 12/1, 2021 and Self-Organization and the Evolution of Division of Labor by R. Page and Sandra Mitchell in Apidologie (29/1, 1998).

In many organisms, interactions among genes lead to multiple functional states, while other interactions can transition into new modes, maybe by way of critical bifurcations in dynamical systems. Here, we develop a statistical theory to identify a bistability near a transition event from gene expression data. We apply the method to honey bees where a known developmental occurrence between bees performing tasks in the nest and leaving to forage. Our approach is able to predict the emergence of bistability and link it to genes involved in the behavioral transition. (Abstract excerpt)

Social insects represent well-known examples of adaptive collective systems, combining the efforts of many individual actors to produce robust and adaptive aggregate behavior. The allocation of tasks to individuals often displays a sophisticated organization that promotes collective success. This distributed coordination of effort is the result of a complicated process reaching from the level of gene regulation to social relations. (1) To summarize, the generality of this phenomenology suggests that such critical transitions may be a common mechanism within biology, making use of the emergent properties of strongly interacting dynamical networks to generate reproducible diversity. (14)

Dantas, Christine. Ergodic Concepts for a Self-Organizing Trivalent Spin Network. Annalen der Physik.. 536/10, 2024. We cite this latest paper by a National Institute for Space Research, Sao Paolo astrophysicist for its advanced meld of nonlinear science and quantum theories which then provides a further illumination of nature’s preferred state of a critical balance. In this case its formulation is a mathematical construct due to Roger Penrose. By virtue of these multiple 2024 findings from these deepest realms al the way to cerebral chimeras, a whole scale universality is being filled in and fleshed out.

We also want to record its historic occasion in this original European scientific journal from 1798 which some 326 years later into our 21st century global phase (all volumes and issues now online) may at last by sufficient content like this have reached an actual discovery event. See also her prior paper Ergodic Concepts for a Self-Organizing Trivalent Spin Network: A Path to (2+1)-dimensional Black Hole Entropy at arXiv:2305.16009, It is our aim in PediaPedia Earthica to gather, document report and bring to public awareness.

From a dynamical systems point of view, a trivalent spin network model in Loop Quantum Gravity is considered, which presents self-organized criticality (SOC), arising from a spin propagation dynamics. A partition function is obtained for the domains of stability connecting gauge non-invariant avalanches, leading to an entropy formula for the asymptotic SOC state. The microscopic origin of this SOC entropy is therefore given by the excitation-relaxation spin dynamics in the avalanche cycle. The puncturing of trivalent spin networks (TSN) edges participating in the avalanche are counted in terms of an ensemble perimeter over the implicit avalanches.

In physics, a spin network is a type of diagram which can be used to represent states and interactions between particles and fields in quantum mechanics. From a mathematical perspective, the diagrams are a concise way to represent multilinear functions and functions between representations of matrix groups.

Del Santo, Flavio and Nicolas Gisin. Creative and geometric times in physics, mathematics, logic, and philosophy. arXiv:2404.06566. University of Geneva natural scholars offer an insightful way so as to appreciate something constructive going on by itself. The phrase “creative time” is drawn from Henri Bergson a century earlier.

We propose a distinction between two concepts of time that play a role in physics: geometric and creative. The former is the time of deterministic physics and merely parametrizes a given evolution. The latter is characterized by real change, i.e. novel formation when a non-necessary event becomes occurs in an indeterministic physics. This allows us to cite a naturalistic presence as the moment that separates the potential future from the determined past. We discuss how these two concepts find applications in classical and intuitionistic mathematics and in classical and multivalued tensed logic. (Abstract).

There is almost nothing that we perceive so ubiquitously than the passage of time. And yet our most successful physical theories still struggle to make sense of this concept in an unequivocal way. Actually, modern physics has relegated time to play a less and less special role [1]. However, in the words of Ilya Prigogine, “no formulation of the laws of nature that does not take into account this constructive role of time can ever be satisfactory.” (1)

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