I. Planatural Genesis: A Phenomenal, PhiloSophia, Propaedutic, WumanWise, Participatory Endeavor

C. Our Earthumanity Envisions an Animate, Self-Organizing, Encoded Procreativity

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)

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)

Ellis, John, et al. Ellis, John, et al. Do we Owe our Existence to Gravitational Waves?. arXiv:2402.03593. John Ellis, Kings College London, Brian Fields, Center for Advanced Studies of the Universe, University of Illinois, and Rebecca Surman, University of Notre Dame engage a novel imagination, akin to Simon Conway Morris, which is not constrained by the vested verdict that no other reality exists on its own. Rather by way of an integral vista, certain celestial elements and conditions can be seen to have a necessary relation to our considerate presence, This is not “anthropic” as much as an ability to perceive independent phenomena without which human beings could not be here. Our point is that just a mindfulness to allow the very possibility, which has been excluded for the past male century, can reveal an innately animate genesis.

Two heavy elements essential to human biology are thought to have been produced by the astrophysical r-process, which occurs in neutron-rich environments: iodine is a constituent of thyroid hormones that affect many physiological processes, and bromine is essential for tissue development. Collisions of neutron stars (kilonovae) have been identified as sources of r-process elements including tellurium, which is adjacent to iodine in the periodic table, and the lanthanides. Neutron-star collisions arise from energy loss due to gravitational-wave emission, leading us to suggest that they have played a key role in enabling human life by producing these certain elements. (Abstract)

In nuclear astrophysics, the rapid neutron-capture process, also known as the r-process, is a set of nuclear reactions that is responsible for the creation of approximately half of the atomic nuclei heavier than iron, the "heavy elements"

I am fascinated by the "inner space/outer space" connections that link the science at the smallest and largest scales. My research focusses on highest-energy sites in such as the big bang, exploding stars (supernovae), and particles in space (cosmic rays). Understanding these processes and their interplay allows us to trace the history of matter over a temporal expanse. (Brian Fields)

Evans, Constantine, et al. Pattern Recognition in the Nucleation Kinetics of Non-Equilibrium Self-Assembly. Nature. 625/500, 2024. This intricate, frontier posting by Cal Tech and University of Chicago computational biologists including Erik Winfree is able to graphically describe an expansive, self-similar consistency from molecules all the way to minds. Its deep neural net operations are found to well apply across these domains to an extent life’s spatial and temporal developmental panorama and self-observation well appears as a procreative genesis.

Inspired by biology's best computer, the brain, neural networks achieve a profound reformulation of computational principles. Analogous high-dimensional, interconnected architectures also arise within information-processing molecular systems inside living cells,. Might neuromorphic collective modes be thus found broadly in other physical and chemical processes such as protein synthesis, metabolism, or structural self-assembly? Here we examine nucleation of animate structures to show that complex patterns can be classified similar to neural network computation. Specifically, we design a set of 917 DNA tiles that can self-assemble in three alternative ways such that competitive nucleation depends on the co-localization of tiles within the three structures. This success suggests that ubiquitous physical phenomena, such as nucleation, may hold powerful information processing capabilities when scaled up to more intricate systems. (Abstract excerpt)

Our work adds sophisticated information-processing as a new emergent phenomenon in which self-assembly gains programmable and potentially learnable phase boundaries to solve specific pattern recognition problems, analogous to earlier results for large
N neural networks. This neural network inspired perspective may help us recognize information processing in high dimensional molecular systems that are entangled within physical processes, whether in biology or in molecular
engineering: multicomponent liquid condensates, active matter, and other systems might have similar programmable and learnable phase boundaries.

Fabbro, Franco. Biological and Neuroscientific Foundations of Philosophy. London: Routledge, 2023. Into this year it seems a sage polyscholar is able to contribute his opus work as a whole scale course from matter, energy, space and time across Earth life’s evolutionary emergence all the way to our planetary intelligence. Chapters flow from Philutsophical Foundations of Science and the Origin of Knowledge to the Evolutionary History of Human Beings, Communication and Information, onto DNA as a Symbolic Domain of Life, and Psyche as a Domain of Imagination, and Language as Symbolic Sharing. With this current vantage, the author traces a central course as an increase in informational knowledge and relative literacy which then engenders more personal agency and shared imagination. Altogether the volume exemplifies an participatory perception that may just now be possible.

Written by an expert scholar, the book draws together different strands to explore how scientific and neuropsychological discoveries are vital to our understanding of mind. A philosophical paradigm moves beyond physics and mathematics to embrace more complex frames of the knowledge of psychology and biology. The work reflects on the symbolic dimensions of "information" that characterize DNA genetics and the linguistic psyche involved with cognitive sociality, communication and consciousness. (Publisher)


It has been said that all living organisms from bacteria to human beings that the genetic information is contained in the DNA, which is made up of two strands of nucleotides that wind in a helix around each other. It is possible to compare the sequence of nucleotides bases to the letters of the alphabet that follow one another in ordered combinations to form the words, phrased and chapters of a book. (116)

The genetic code represents a “symbolic order” of a fundamental and universal nature. We speak of “symbols” because the information contained in the DNA is “something that stands for something else.” This is the symbolic order that makes life all living beings possible. The characteristics of universality and indispensability place this order in the innermost of living organisms surrounded in human beings by the most external symbolic layers made up of psyche and language. (117)

Franco Fabbro is Affiliate Professor at the Sant’Anna School of Advances Studies, Pisa. He was full professor of physiology, child neuropsychiatry and clinical psychology at the University of Udine, Italy some thirty years after he graduated in medicine (1982) and specialized in neurology (1986).

From Computation to Life: The Challenge of a Science of Organization. www.walterfontana.zone/writings. This entry is the Inaugural Lecture for the Chair in Informatics and Computational Sciences 2019-2020 at the Collège de France, Paris by the veteran Harvard Medical School systems biologist (see website). He was notably the coauthor with Leo Buss of The Arrival of the Fittest (1994, search) about an innate evolutionary course. Some 25 years later, this richly composed edition proceeds to describe a deep integration of chemical phenomena with complexity theories and physical substrates which altogether can be expressed b informative computer programs. As the quotes convey, along with a catalytic force, the whole package can well presage a natural genesis synthesis with a global 2020s research agenda. For a current example, see Representing Catalytic Mechanisms with Rule Composition by Jakob Andersen, WF, et al at arXiv:2201.04515,

(3) In addition to statistical models, researchers also construct mechanistic models to gain insight into the dynamical processes that generate the system state reflected in the data. Analyzing the behavior of a molecular interaction network is helpful for understanding how and why a biological system might function. Such networks are modeled at various levels of abstraction. One recent approach represents each interaction as an instruction in a purpose-made programming language. A model then effectively represents a biological system as a program. This is more subtle than just using a computer; it is about representing a complex system using ideas from computation. (E-1)

(4) At a more fundamental level, many systems in nature are composed of components that mutually construct each other in a way that glues them together into a unit: metabolisms, cells, organisms, ecologies, cognitive systems, economies, cultures. All these systems are functional organizations. What kind of dynamics produces organizations of this sort? How much of their architecture is contingent and how much of it is inevitable? The idea of computation is the modern formalization of the idea of mechanism. However, unlike its predecessors, the clockwork and the steam engine, computation emphasizes a constructive aspect of interaction. (E-1)

Auto-catalysis is relevant in origin-of-life scenarios, because it concentrates the mass of a system in the autocatalytic loop, while suppressing many side reactions that could be a kinetic threat. It would be of great interest to understand whether, given hypotheses about the chemical substances and the chemical rules available 3.5–4 billion years ago, this cycle was the only solution in the accessible chemical space, or whether there are other paths. In other words: is the universality in the functional organization of metabolism that we observe today one of many options, or is it necessary? (E-11)

In closing, I would like to take in the whole picture. I tried to span an arc between three chemistries and representations of their interactions founded on ideas from computer science. When endowed with dynamics, all three give rise to aspects I associate with functional organization. At the beginning I asked about such aspects as self-maintaining organizations of logic whose change is constrained, the auto-catalytic chemical networks present in living systems, and the causal structures that organize the signaling processes in cells. These dynamics are a constructive force based on interactions that directly build new objects with new interactive properties. The challenge of a science of (chemical) organization consists in formalizing and understanding this constructive dynamics. (E-16, 17)

Frank, Adam, et al. Intelligence as a Planetary Scale Process. International Journal of Astrobiology. February, 2022. Veteran astroscholars AF, University of Rochester, David Grinspoon, Planetary Science Institute and Sara Walker, Arizona State University provide a latest admission, description and affirmation of the actual evolutionary emergence a worldwise cerebral faculty. As the quotes engage, a mindfulness to allow something going on by own agencies, such an appearance and fulfillment now becomes readily evident.

Intelligence is usually seen as an individual faculty. Here, we broaden the idea of intelligence as a collective group property and extend it to the planetary scale. We consider the ways in which a relative technological intelligence may represent a kind of planetary scale transition, much as the origin of life itself may be seen as a global phenomenon. Our approach follows many researchers today that the correct scale to understand key aspects of life and its evolution is planetary, beyond traditional focus on individual species. (Abstract excerpt)

A transition to planetary intelligence, as we described here, would achieve its operative presence at a global scale. Such a mindful world could steer the future evolution of Earth, acting in concert with and guided by a deep understanding of natural systems. If other civilizations that may exist in the universe undergo such a transition, we would expect to see a marked difference in their biosignatures due to a sustainable, global intelligence versus those that not been able to attain this emergent phase. (27)

We propose five properties required for a world to show knowing cognitive activity operating across planetary scales. These are: (1) emergence ,(2) dynamics of networks, (3) networks of semantic information, (4) appearance of complex adaptive systems, (5) autopioesis. Different degrees of these properties appear as a world evolves from abiotic (geosphere) to biotic (biosphere) to technologic (technosphere). (33)

Frank, Adam, et al. The Blind Spot: Why Science Cannot Ignore Human Experience.. Cambridge: MIT Press, 2024. . As this decade goes on, senior scholars AF, University of Rochester, MG, Dartmouth College and ET, University of British Columbia convened for some time to come to the realization that a main lacunae of 21st century thought was the exclusion of any human place and relevance in a cosmic to cultural scenario, which is then relegated to accidental. While scientific descriptions achieved by our sapient acumen run from muons to a multiverse, it is rarely imagined that our present learned occasion has any other phenomenal or participatory account.

In The Blind Spot, astrophysicist Adam Frank, cosmologist Marcelo Gleiser, and philosopher Evan Thompson call for a revolutionary scientific worldview which includes humanity as a vital part of objective truth. For centuries people have looked to science to tell us who we are, where we come from, and where we’re going, but without our own inclusion. This Blind Spot impedes our learning about the universe, quantum physics, life, AI, mind, consciousness, and Earth as a precious planet. As a result, we can view ourselves as an intended source of nature’s self-understanding, going forward in the new millennium.

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