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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
Recent Additions

I. Our Planatural Edition: A 21st Century PhiloSophia, Earthropo Ecosmic PediaVersion

C. An Earthumanity Era: A 2020s Cerebral Cyberspace Achieves a Worldwise Knowsphere Resource

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)

Evans, Constantine, et al. Pattern Recognition in the Nucleation Kinetics of Non-Equilibrium Self-Assembly. arXiv:2207.06399. 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)

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)

Furtak, Marcin, et al. The Forest, the Trees, or Both? Hierarchy and Interactions between Gist and Object Processing during Perception of Real-world Scenes. Cognition. Vol. 221, April, 2022. Into this year, Polish Academy of Sciences and Tel Aviv University neuropsychologists can draw upon their own research along with a review of past 21st century work to an extent that they can presently reach a strong conclusion. Taken together, these studies join our results in supporting the global to local accounts, suggesting that gist (field) is processed more readily, and earlier, than objects. (5) As reported across the website, a temporal sequence appears to go on for both evolution and an entity. A sighted occasion is viewed by way of these dual archetypal modes, whereby a contextual scene is perceived first, after which item details are noticed and situated.

The global-to-local theories of perception assume that the gist of a scene is computed early and automatically, whereas recognition of objects occurs at a later stage, requires attentional resources, and is primed by the representation of whole. To test these views, we investigated the sequence of gist- and object-recognition. We generally found that backgrounds were classified more accurately than foreground objects, while wider fields influenced object recognition. Thus these findings support global-to-local theories, implying that gists are more readily seen than details, and at an earlier stage. (Abstract excerpt)

Gagler, David, et al. Scaling Laws in Enzyme Function Reveal a New Kind of Biochemical Universalit. PNAS. 119/9, 2022. Arizona State University bioscientists including Sara Walker, Chris Kempes and Hyunju Kim enter a good example of novel Earthuman abilities which can now find life’s deeper phases to also be distinguished by common, recurrent, self-similar patterns as everywhere else. A further implication is that such a result can be traced to and rooted in physical phenomena. A section heading is Universal Scaling Laws Define the Behavior of Enzyme Classes Across Diverse Biochemical Systems. A graphic depicts how the same forms hold from Archaea and Bacteria to Eukaryotes and Metagenomes, independently of specific components. We wonder again at our emergent EarthWise faculty whom can just now come to these discoveries.

All life on Earth uses a shared set of chemical compounds and reactions which provides a detailed model for universal biochemistry. Here, we introduce a more generalizable concept that is more akin to the kind of universality found in physics. We show how enzyme functions form universality classes with common scaling behavior. Together, our results establish the existence of a new kind of biochemical universality, independent of the details of life on Earth’s component chemistry. (Abstract excerpt)

In physics, the notion of coarse-graining is critical to identifying universality classes, because it allows ignoring most details of individual systems in favor of uncovering systematic behavior across different systems. (3)

Garcia-Sanchez, Miguel, et al. The Emergence of Interstellar Molecular Complexity Explained by Interacting Networks. Proceedings of the National Academy of Sciences. 119/30, 2022. Centro de Astrobiologia (CSIC/INTA), Torrejon de Ardoz, Spain and Swedish University of Agricultural Science researchers including Jacobo Aguirre contribute a frontier synthesis by adding and applying such equally real and vitally present interlinking webworks to nature’s intrinsic formation of nodal biomolecules. This integration is achieved and demonstrated by through novel NetWorld algorithmic computations. As the quote says, an especial value accrues by virtue of a quantified perception of commonly recurrent processes and vivifying anatomies.

The road to life is punctuated by transitions toward complexity, from astrochemistry to biomolecules and eventually, to living organisms. But studies of these original phases remain a challenge to which complexity and network theory has not been much applied. We introduce a computational framework whereby simple networks simulate the most basic elements of life as they interact to form complex structures. We observe a resultant explosion of diversity when the parameter representing the environment reaches a critical value. While this model is abstract, its predictions well mimic the molecular evolution in the interstellar medium during the emergence of chemical complexity. Altogether our work suggests that the rules leading to biological complexity may be relatively simple as they engender universal patterns. (Abstract/Significance)

All in all, we believe that (i) the similarities between the results in [30], based on models that are firmly rooted in classical ecological theory and checked with real data, (ii) those obtained from molecular abundances in interstellar clouds, and (iii) the ones introduced by our computational environment, derived from a simple framework with no a priori ecological or chemical assumptions, are not coincidental. They instead hint that the long path from the creation of the basic prebiotic compounds in the interstellar medium to the origin of life and its evolution on the early Earth could show universal patterns and common phenomena at all scales and across all stages. (8)

Gontier, Nathalie, et al. Introduction: Language and Worldviews. Topoi. 41/3, 2022. University of Lisbon, Barcelona, Porto, Seville and Pavia scholars introduce the issue’s topical subject and survey some 15 contributions, see Abstract for more. Its reach by design traces all the way back to Animal Minds and the Evolution of Communication and Language. A major essay by the lead editor well summarizes, posted next. For example see Language: The Ultimate Artifact to Build, Develop and Update Worldviews by Lorenzo Magnani, The Work of Words: Poetry, Language and the Dawn of Community by Ricardo Santos-Alexandre and Language, Thought and the History of Science by Carmela Chateau-Smith. See also Evolutionary Epistemology by Nathalie Gontier and Michael Bradie in the Journal for General Philosophy of Science. (52/2, 2021) for an issue on this companion endeavor.

This special issue on Language and Worldviews grew out of a workshop on Language Throughout the Ages (Google) that was organized by the Applied Evolutionary Epistemology Lab (appeel.fc.ul.pt) at the University of Lisbon in 2019. Language and worldviews are favorite topoi for philosophers of language or mind, science, or religion, epistemology or logic. How language establishes, mediates, constructs, or enacts a contextual milieu amongst peoples, and between basic physical, sociocultural, and biological aspects is a huge, vital realm. (Excerpt)

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. See also Dynamics of Higher Order Networks by this collegial team including Matjaz Perc at arXiv:2203.06601 for a similar exercise.

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)

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