IV. Ecosmomics: Independent Complex Network Systems, Computational Programs, Genetic Ecode Scripts

This central chapter will portray the genomic basis of a 21st century animate revolution by sorting into 2000, 2010, and 2020 phases. We do this to convey a scientific ascent from homo to anthropo and Earthropo sapience, along with how this subject field went through stages of early, disparate, individual takes onto a maturing clarity and coalescence. At present a distilled, convergent synthesis has come to discover a common, gender-based, naturome code with node, dot, entity and link, relate, group complements. Which then compose a third, viable family, flock and so on.

2000 - 2010: We ought to open with a referral to prior intimations. As noted in An Anthropocosmic Code, at the heart of wisdom is a luminous relation by which to relate Earth and heaven, human and Divine. This correspondence recurs at each scale and instance because everything arises from and epitomizes a singular, complementary source. Our engendered microcosm is thus an iconic reflection of a numinous macrocosm. The opus work, then as now, is to realize that this existant abide is distinguished by an innate, discernable quality. That is to say, it comes with a code we are made and meant to read and write. A favorite image is Yin and Yang, whose feminine and masculine aspects reside within a triune, familial whole.

But this portal was set aside as a 17th to 20th mechanical science (a necessary spiral turn) went on to reduce cosmos and matter to benthic particles and theories, sans nay identity or purpose. Only just now is a novel humankind compass finding an ordained multi-level, iterative arrangement, this time over the temporal expanse of an evolutionary genesis. Its late version is expressed by Rosetta-like translations of the sciences of nonlinear, self-organizing, networked complexity. Here is an indicative quotation from the day, followed brief entries to rudimentary topics and approaches, then just getting going.

In the 1980’s and 1990’s we are witnesses to a new paradigmatic shift in science. Theorists in many fields are moving away from linear, reductionist, simple cause-effect models toward confronting the challenges of complex adaptive systems. Such systems are found in fields as diverse as astrophysics and economics, cerebral neurobiochemistry and cognitive psychology. (Harold Morowitz, Jerome Singer)

Nonequilibrium Thermodynamics A theory of energy and information flow, usage, and dissipation for open living systems. (Ilya Prigogine)

Fractal Geometry Nature displays the same shapes and topologies with fractional dimensions at every scale. (Benoit Mandelbrot)

Complex Adaptive Systems Many agents (neurons, people) in local interaction, guided by rules or norms give rise to an emergent order. (John Holland, Murray Gell-Mann)

Self-Organization As these systems proceed without central direction, they arrange into a nested scale of whole entities. (Stuart Kauffman, et al)

Universality Similar self-organized complex adaptive network dynamics are found throughout nature from cosmos to civilization. (Eugene Stanley, Mark Buchanan)

Modularity Complex systems tend to form modular, symbiotic components and processes from genes to societies. (Herbert Simon, Gunter Wagner)

Autopoiesis Such bounded, animate systems make and maintain themselves by referring to an internal description. (Humberto Maturana, Francisco Varela)

Self-Organized Criticality Whereby complex dynamic systems seem to become poised at the edge of order and chaos. (Per Bak)

Scale-Free Networks Elemental nodes interlink from cellular metabolisms to ecosystems and the Internet. (Albert-Laszlo Barabasi, Duncan Watts)

Synergetics A more physically based theory of a universal self-organization. (Herman Haken, Scott Kelso)

Artificial Life Computer simulation of molecular, genetic, organic, social and economic societies and their evolution. (Chris Langton, Chris Adami)

Cellular Automata A computational process based on simple, algorithmic rules which self-assemble into an emergent order. (Stephen Wolfram)

Hierarchy Theory Evolving organisms and ecosystems deploy into a scalar sequence and arrangement. (Stan Salthe, Niles Eldredge)

Neural Networks The brain is built and works by multiple networks of neurons, synapses and axons in constant flux due to weighted inputs and experience. (John Hopfield, Stephen Grossberg)

Connectionism A cognitive theory of how neurons compute and handle information, aka parallel distributed processing. (David Rumelhart)

Synchronicity Phenomena from electrons and fireflies to planetary orbits synchronize in unison, which gives rise to orderly forms. (Steven Strogatz)

A vital observation is that few generic components or activities distinguish the ubiquitous system. Whether bacterial assemblies, financial investors or a scientific endeavor as we just saw, many entities interact, and communicate, guided by common rules and norms, from which an overall, adaptive organization arises . A reciprocal interplay of free agents and local interactions, nodes and links in network terms, can be indentified in each case. In this guise they can be seen to form complements of particulate and holistic, discrete and systematic, dot and connect phases.

As this natural activity goes through its cycle or spiral of self-emergence, a standard sequence is traced. In its initial stages, units or elements (microbes, neurons, organisms, researchers) propagate and compete. As densities increase, a modular division of labor occurs. Constant dialogue occurs whether by chemicals, electric potentials, behaviors or language. In time cooperation succeeds over competition. At a threshold of viable coherence, a new whole scale of relative individuality is achieved. We now move on to a 2010 writeup I did for readers who asked for an accessible, introductory survey.

2010 - 2020: As Habitable UniVerse above documents an ongoing revolution unto an organic genesis ecosmos, it ought to be an equivalent genetic code. A concurrent endeavor of theoretical mathematics across physical, biologic and cultural phases is indeed describing a natural uniVerse to human genotype. In response, I posted a Global Glossary of some 32 working terminologies, subject, personal views, and more within a broad nonlinear complex network systems approach. The topical array from 10 years before has is now reached a stage of gaining mature, evidential definitions. A good book introduction is Complexity: A Guided Tour by the Portland State University scientist Melanie Mitchell (Oxford, 2009). We open quotes from this work, a subject listing, which then can be sorted sorts into certain areas.

All the systems I described above consist of large networks of individual components (ants, cells, neurons, stock-buyers, Web-site creators), each typically following relative simple rules, with no central control or leader. It is the collective actions of vast numbers of components that give rise to the complex, hard to predict, and changing patterns of behavior that fascinate us. (12)

Now I can propose a definition of the term complex system: a system in which large networks of components with no central control and simple rules of operation give rise to complex collective behavior, sophisticated information processing, and adaptation via learning or evolution. (13)

Systems in which organized behavior arises without an internal or external controller or leader are sometimes called self-organizing. Since simple rules produce complex behavior in hard-to-predict ways, the macroscopic behavior of such systems is sometimes called emergent. Here is an alternative definition of a complex system: a system that exhibits nontrivial emergent and self-organizing behaviors. (13)

Agent-Based Modeling, Artificial Life, Autopoiesis, Biosemiotics, Cellular Automata, Chaos Theory, Complex Adaptive Systems, Computational Information, Developmental Systems Theory , Dissipative Structures, Dynamical Systems Theory, Econophysics, Emergence, Fractal Geometry, General Systems Theory, Hierarchy Theory, Multi-Agent Systems, Neural Networks, Non-equilibrium Thermodynamics, Nonlinear Phenomena, Renormalization Group Theory, Scale-Free Networks, Scale Invariance, Self-Organized Criticality, Self-Organization, Small-World Network, Statistical Physics, Swarm Intelligence, Synergetics, Synergy, Universality.

Generic Complex System Agent-Based Modeling, Complex Adaptive System, Multi-Agent Systems

Complexity Sciences Nonlinear Phenomena, (Dynamical) Chaos Theory, Emergence

Computer-Based Techniques Cellular Automata, (Digital) Computation Information, Swarm Intelligence

Earlier & Other Versions General Systems Theory, Statistical Physics, Nonequilibrium Thermodynamics, Renormalization Group Theory

Topological Aspects Fractal Geometry, Self-Similarity, Hierarchy, Scale Invariance

CS Features Self-Organization, Autopoiesis, Scale-Free Networks, Self-Organized Criticality, Synergy, Small World, Universality

Field Specific Approaches Dynamical Systems Theory (Evolution), Developmental Systems Theory (Psychology), Neural Networks (Brain), Biosemiotics (Language), Econophysics (Social)

Agent-Based Modeling “An agent-based model (ABM) is a class of simulations for the interactions of autonomous agents (both individual and collective entities such as organizations or groups) with a view to assessing their effects on the system as a whole. It combines elements of game theory, complex systems, emergence, computational sociology, multi-agent systems, and evolutionary programming. (Wikipedia) A tendency carried over from reductive particle or object analysis has been to place more weight on the entity or element component of a CS rather than the connections.

Artificial Life “While processes of self-organization, reproduction, learning, adaptation and evolution are in nature confined to the biological sphere, they can be duplicated in principle in computer simulations.” This approach researches via high speed computations how digital and analog equations are able to graphically simulate and model life from the bottom-up. Since organic forms do follow from genomic programs, it became rather easy to do.

Autopoiesis A neologism coined by Chilean biologists Humberto Maturana and Francisco Varela in the 1970s to emphasize how living systems are involved with “self-making” as they strive to maintain a bounded viability. This occurs by referring to and reapplying the internal descriptive processes that originally constituted them. In this view, all life from an original ur-protocell to multicellular organisms is characterized by a propensity to form and maintain closed entities with their own included meaning. An accessible book by these scholars is Tree of Knowledge (1992) while >i>The Enactive Mind by Varela, Evan Thompson, and Eleanor Rosch takes the theory to cognitive domains.

Biosemiotics “Biosemiotics is an interdisciplinary research agenda investigating the myriad forms of communication and signification found in and between living systems. It is thus the study of representation, meaning, sense, and the biological significance of codes and sign processes, from genetic code sequences to intercellular signaling processes to animal display behavior to human semiotic artifacts such as language and abstract symbolic thought.” (International Society for Biosemiotic Studies)

Cellular Automata Wikipedia has an extensive but technical posting for this computation driven approach. The term means the use of graphic “cells” or boxes to which one of two values are typically ascribed. As various software programs run they spin out highly intricate forms, some of which look a lot like organisms. A famous initiator and theorist is Stephen Wolfram as per his 2002 tome A New Science of Life.

Chaos Theory “A field of study in mathematics, physics, economics and philosophy to observe the behavior of dynamical systems that are highly sensitive to initial conditions, often referred to as the butterfly effect. Small differences in initial conditions yield widely diverging outcomes for chaotic systems, rendering long-term prediction generally not possible.” This misnomer has stuck since the 1980s from early inklings that apparently chaotic behavior actually exhibits mathematical regularities. James Gleick’s popular 1987 Chaosbook is a landmark introduction to the whole endeavor.

Complex Adaptive Systems Again CAS are distinguished by many semi-autonomous parts or entities engaged in relational interaction, via communication by tacit rules or norms, from which emerges novel, feasible, organizations. The presence of this complementarity might even be taken to infer masculine and feminine principles.

Computational Information “In physics and cosmology, digital physics is a collection of theoretical perspectives based on the premise that the universe is describable by information, and therefore computable.” All these areas involve hyperfast computers, so often slip into such as emphasis. In its purview, software algorithms iteratively and recursively which give rise to increasingly complex, material ‘hardware’ forms.

Developmental Systems Theory “Developmental systems theory (DST) is a collection of models of biological development and evolution that argue that the emphasis the modern evolutionary synthesis places on genes and natural selection as explanation of living structures and processes is inadequate. DST embraces a range of positions, from a need to include more explanatory reasons than genes and natural selection, to the view that evolutionary theory profoundly misconceives the nature of living processes.” A main formulator is biotheorist Susan Oyama’s 2001 work Cycles of Contingency.

Dissipative Structures A term associated with nonequilibrium thermodynamics with regard to open systems that receive and process energy and information to maintain and foster their viability with any excess dissipated. A closed system, by contrast, has no such outside inputs, and is a inappropriate standard carried over from inorganic, equilibrium phenomena studies.

Dynamical Systems Theory Another DST, this time as an employ of complexity insights by Indiana University psychologists Esther Thelen, Linda Smith, and others to study the kinetic, behavioral, linguistic and cognitive maturation of infants and children. The approach has caught on and is now used by many practitioners such as Scott Kelso, Alan Fogel, Marc Lewis, Kathleen Nelson, and in the Netherlands, Paul van Geert.

Econophysics An interdisciplinary field that combines statistical, many-body physics with nonlinear dynamics to illume complicated economics issues and policies. A main founder is Boston University systems sage Eugene Stanley. From tentative beginnings in the 1990s, the field has taken hold worldwide. The technical journal Physica A: Statistical Physics and others now contain many papers as an example of the welling meld of physics and complex systems.

Emergence “In philosophy, systems theory, science, and art, emergence is the way complex systems and patterns arise out of a multiplicity of relatively simple interactions. Emergence is central to the theories of integrative levels and of complex systems.” This abstract term for regnant, cognizant life is often posed as a positive alternative to a mechanical, reductive disassembly of nature. A prime expositor is theologian Philip Clayton, as conveyed in his Mind and Emergence: From Quantum to Consciousness (Oxford, 2004).

Fractal Geometry A fractal is "…a rough or fragmented geometric shape that can be split into parts, each of which is (at least approximately) a reduced-size copy of the whole.” A mathematical fractal results from a software equation or algorithm that is recursively run again and again. A fractal shape is too irregular to be described by planar Euclidean geometry, and has a ‘self-similar’ affinity across its myriad nested dimensions. Natural objects approximated by fractals are clouds, mountain ranges, lightning bolts, coastlines, snow flakes, flora like cauliflower and broccoli, and animal coloration patterns, that is just about everything.

General Systems Theory From the 1950s into the 1980s, along with its cousin cybernetics, this was the main school in prescient search for holistic integrations of an organismic nature. A tacit inspiration was the hope of finding a common code everywhere. An expositor was Ludwig Von Bertalanffy in a 1968 book by this title, another opus is Living Systems by James G. Miller (McGraw Hill, 1976).

Hierarchy Theory “Hierarchies are ordinations, as from smaller to larger, or from simpler to more complex. In science-related discourses there have been two forms of hierarchy theory, one based on scale (extension) and another on descriptive complexity (intension).” (Stan Salthe) This is an approach based on the conception that nature consistently arrays itself into scales of beings and becomings.

Multi-Agent Systems Another phrasing of a generic CAS, akin to ABS above, that may be variously adopted by a discipline, e.g. as Applied Anthropology used to model the spread of an epidemic in Baltimore. The phrase gives the impression of still another technique, which it is not.

Neural Networks Brain development and cognitive function has been a major area of CS application as cerebral anatomy and activity become exemplars of self-organization. In CalTech’s John Hopfield proposed the theory in 1982 to explain how neurons are entrained by way of synapses and axons into myriad webworks. As we think, neural nets ever change their ‘weights,’ emphasis, or presence based on the content they receive and convey. A computational version called artificial neural networks or ANN has found use in simulating ecosystems and many other areas.

Nonequilibrium Thermodynamics (This is an edited introduction from A Thermodynamics of Life.) “The sterile, mechanical universe of 19th century theories was conceived as a closed, isolated system tending to equilibrium. As predicted by the second law of thermodynamics, it inexorably expires as available energy is spent as entropy. But a recent revision is underway by which life has become known as an open system infused and organized by a flow of energy and information. The gloomy fate has been superseded by far-from-equilibrium version which can describe and qualify the florescent rise of life and its human phase.”

Nonlinear Phenomena “Nonlinear” has been a generic banner for complexity studies, in contrast to earlier, mainly physical sciences that understandably dealt with simpler “linear” cause and effect. But complex self-organization is not straight-forward, it is affected by small influences at its outset (e.g., the so-called butterfly effect), so that resultant forms and activities can be locally unpredictable. However, as Statistical Physics avers below, large-scale patterns tend to average out and are reliable in outcome.

Renormalization Group Theory “In theoretical physics, the renormalization group refers to a mathematical apparatus that allows one to investigate the changes of a physical system by views at different distance scales.” Renormalization group is formally related to "scale invariance," a symmetry that appears the same at all scales.” We cite this term, first used by the 1975 Nobel physicist Kenneth Wilson, because it occurs in some CS papers.

Scale-Free Networks Simpler object interconnections such as telephones are equal point to point, or ‘random graphs,’ with no characteristic geometry. In the late 1990s Notre Dame physicists Albert-Laszlo Barabasi and Reka Albert realized that nonlinear nature and society was actually graced by a distinctive type of arrangement whereof certain nodes or hubs had many links, while most other had only a few. This insight has since grown into a major field of complex system research. As a result, the same scale or form is repeated in self-similar fashion over and over, e.g., food webs, brains or social media. The Internet is a prime example, which might imply cerebral propensities.

Scale Invariance This is another phrase to denote CS propensities to repeat in kind again and again, often in a layered emergence of the same animate pattern and process. “Self-similarity” is also used to describe this recurrence. Its iconic representation would be geometric fractals, whose infinite repetition arises from iterations of mathematical, software-like equations. Such a constant recapitulation across every natural and social realm from galaxies to Gaia could be taken to infer the presence of an innate, implicate, cosmic genetic-like source.

Self-Organized Criticality A concept mainly from the late Danish scientist Per Bak, well told in his How Nature Works (Springer, 1996), to explain how natural phenomena seems to reside in a dynamic, creative state or zone poised between order and chaos. The phrase and theory is now widely used from origin of life studies to brain cerebration. As a comment, we include this quote from Complexity and Criticality (2005) by Kim Christensen and Nicholas Moloney, which notes a need to get clear, common definitions.

“The word `complexity' takes on a variety of meanings depending on the context, and its official definition is continuously being revised. This is because complexity is a rapidly developing field at the forefront of mathematics, physics, geophysics, economics and biology. And yet, nobody agrees on a clear and concise theoretical formalism with which to study complexity. For our purposes, complexity refers to the repeated application of simple rules in systems with many degrees of freedom that gives rise to emergent behaviour. Self-organized criticality is a cooperative feature emerging from the repeated application of the microscopic laws of a system of interacting parts.”

Self-Organization “The process where a structure or pattern appears in a system without a central authority or external direction. A globally coherent pattern appears from the local interaction of the elements that makes up the system, thus the organization is achieved in a way that is parallel and distributed. The most robust and unambiguous examples of self-organizing systems are from the physics of non-equilibrium processes. Self-organization is also relevant in chemistry, where it is also synonymous with self-assembly. The concept of self-organization is central to the description of biological systems, from the subcellular to the ecosystem level.” (Wikipedia)

“Self-organization is the spontaneous often seemingly purposeful formation of spatial, temporal, spatio-temporal structures or functions in systems composed of few or many components. In physics, chemistry and biology self-organization occurs in open systems driven away from thermal equilibrium. The process of self-organization can be found in many other fields also, such as economy, sociology, medicine, technology.” (Scholarpedia) As opposed to any mechanical or architectural artifact, which are made by outside control, or preset plans, an iconic property of complex systems is their ability to arrange into increasingly multifaceted forms and viability. A prime articulator has been the polymath physician Stuart Kauffman, in his brilliant writings over some 40 years.

Small-World Networks “In mathematics, physics and sociology a small-world network is a type of mathematical graph in which most nodes are not neighbors of one another, but most nodes can be reached from every other by a small number of hops or steps. Social networks, the connectivity of the Internet, and gene networks all exhibit small-world network characteristics.” Circa 1998 Duncan Watts and Stephen Strogatz came up with this mathematical model and name as another perspective on and attribute of scale-free networks, based on how close or remote “nodes” are to each other.

Statistical Physics “A condensed matter or many-body physics that endeavors to explain and predict the macroscopic properties and behavior of a system on the basis of known characteristics and interactions of its microscopic constituents, usually when the number of such constituents is very large. In the past years, the field has branched into complex systems because it was realized that both studied the spontaneous activity of many agents with relational behaviors. An entry example (2010) of this merger might be the Centre for Statistical Mechanics and Complexity, University of Rome, website (Google).

Swarm Intelligence An AI scheme that deals with natural and societal systems composed of many interactive ‘individuals’ that coordinate via distributed control, which engenders self-organization. Examples are colonies of ants and termites, schools of fish, flocks of birds, herds of land animals, along with some artifacts as robot motions.

Synergetics Another method to explain the formation and self-organization of patterns and structures in open systems far from thermodynamic equilibrium. It was fostered from the 1970s by Hermann Haken, a University of Stuttgart laser physicist. In its idiom, self-organization requires a 'macroscopic' system, consisting of many nonlinearly interacting subsystems. A Springer series in Synergetics has published dozens of technical volumes since 1977.

Synergy “Synergy, in general, may be defined as two or more agents working together to produce a result not obtainable by any of the agents independently.” We mention as abstraction in the mix, as used by Peter Corning in his Nature’s Magic: Synergy in Evolution and the Fate of Humankind(2003) about innate propensities for cooperation. Symbiosis would be another take.

Universality “In statistical mechanics, universality is the observation that there are properties for a large class of systems that are independent of the dynamical details of the system.” A word used across the sciences and humanities, which for complexity science means the same dynamical system in evidence from galaxies to genomes to Gaia. Its archetypal attributes would be many interactive agents, scale-free networks, and nested self-organization. If such a ubiquitous repetition can be succinctly articulated, it well infers an independent, creative source, and illumes, as wisdom teaches, nature’s manifest, illustrative repetition. Please see our new, extensive 2020 Introduction and throughout for a vital 21st century affirmation.

A Complex Systems Timeline This arcane array, whereof each vernacular phrase denotes a certain attribute, begs translation unto a familiar human and earth account, as our new introduction attempts. Historically, this movement began in the 1960s with the general systems theory school. A prescient 1980 work The Self-Organizing Universe by Erich Jantsch conveyed its promise. Another milestone was Mitchell Feigenbaum’s 1982 finding that apparent chaos, such as turbulent fluid flow, in fact exhibited mathematical regularities. A breakthrough 1987 book was James Gleick’s Chaos: Making a New Science, which brought the endeavor to popular awareness.

As the usual course, the 21st century complexity project diversified and morphed into technical detail and preferences, aided by computer capacities not before possible. Since the 2000s, scientific studies spread across all natural and societal realms from cosmos to civilization, from astrophysics and genomics to psychology and economics, as these novel insights brought a heretofore elusive theoretical explanation. Each domain from galactic clusters to life’s origin, animal behaviors, disease epidemics, conversational speech, and so on was found to exemplify a complex adaptive system of many interactive agents and interlinked nodes.

In mid course writings on nonlinear systems began to cite and include both modes of a dynamical, recurrent complexity (phenotype) which was so obvious that there must be inferred cause (genotype) from it all arose. Some examples are Self-Organization in Complex Ecosystems by Jordi Bascompte and Richard Sole (2006), and Marten Scheffer’s Critical Transition in Nature and Society (2009). A 2008 paper Collective Behavior in Animal Groups: Theoretical Models and Empirical Studies by Irene Giardina and colleagues at the University of Rome contends that since starling flocks or tuna schools are so composed of autonomous members in beneficial group formations, they clearly infer a mathematic and physical origin.

In the same period, researchers realized that complexity studies and statistical physics were actually dealing with the same phenomena, albeit with different approaches and terms. But what is not yet seen or possible at that time was a philosophia view of a self-creative universe with dual domains of emergent phenotype development and immanent genetic-like source.

Artime, Oriol and Manlio De Domenico. From the Origin of Life to Pandemics: Emergent Phenomena in Complex Systems. Philosophical Transactions of the Royal Society A. May 2022.

Azpeitia, Eugenio, et al. Cauliflower Fractal Forms Arise from Perturbations of Floral Gene Networks. Science. 373/192, 2021.

Bianconi, Ginestra, et al. Complex Systems in the Spotlight: Next Steps after the 2021 Nobel Prize in Physics. Journal of Physics: Complexity. 4/010201, 2023.

De Marzo, Giordano, et al. Quantifying the Unexpected: A Scientific Approach to Black Swans. Physical Review Research. 4/033079, 2022.

Krakauer, David, ed. Worlds Hidden in Plain Sight: The Evolving Idea of Complexity at the Santa Fe Institute 1984 – 2019. Santa Fe, NM: Santa Fe Institute Press, 2019.

Newman, Stuart. Self-Organization in Embryonic Development. arXiv:2108.00532.

Nguyen, Thank, et al. Spatial Patterns of Urban Landscapes in the Indian Punjab are Predicted by Fractal Theory. Nature Scientific Reports. 12/1819, 2022.

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A. A Procreative Ecode: An Ecosmome to Geonome Complementary Hereditary Endowment

The present entry is a circa 2018 – 2023 review and preview as an EarthSmart personsphere seems to reach a new phase of an integral convergent synthesis which closes on an actual discovery. This Planatural resource online since 2002 now covers 4,000 text pages with some 9,000 references across 85 sections. After the new, extensive Introduction above, here we enter another, latest survey with a current recital of its premises and rationales as a drafty, synoptic, outline proposal, so to ever gather so many aspects into natural narrative edification.

A Caveat Please recall that all this content is attributed to and drawn from a 21st century advent of a global person/sapiensphere whom might be learning and knowing on her/his own. Our premise is that such findings can be found across the scientific journals, if of a mind to allow and peruse. We record these writings are not my opinion but evidently there by themselves.

Altogether this reference resource entry has three modular parts. It opens with a 2023 EarthWise State of a Genesis UniVerse as an update survey of philosophia views and scientific achievements after the circa 2020 review above. The next section is Ecosmomics: 21 Century Studies of Independent, Generative, Self-Organized, Complex Adaptive Network Critical Systems. as an extensive 21st century retrospect of nonlinear, complexity science and statistical physics.

A 1990s – 2000 – 2015 period mostly engaged structural aspects by way of many interactive enties. Into the later 2010s, an increased perception and proof of a constant dynamic, cyclical activity began. By turns, a self-organized criticality, chimera oscillations, bistability, creative coherence became evident. Early on, neuroscientists found that cerebral faculties resided at an optimum poise of more or less order, inhibit or excite, and so on. By this 2023 year, a glimpse of a historic HumanEarth Discovery of a natural geneis graced and guided by one common, bigender, genetic-like ecode might at last be possible.



EARTHWISE 2022 STATE OF A GENESIS UNIVERSE

This ongoing review/preview is arranged inio several segments. It opens with a latest survey of apparent brain/mind-like cognitive qualities of a collective EarthSmart sapience. Our “second culture” Planatural PhiloSophia approach may then gather many convergent scientific aspects so as to envision an independent, abiding essence. As a main result, an array of revolutionary ecosmos uniVerse to EarthVersion features are recited as they just now reveal a unified, consistent procreative genesis. Its organic fertile, vitality arises from a self-organized, genomic-like code-script which energizes and informs a temporal course from uniVerse to us peoples.. We proceed with with a present glimpse fo a common, bigender, ciritical Naturome Ecode.

To continue, our rarest Earth has been able to support an evolutionary course of bodies, brains, intelligence, agency and selves to an extent it now appears as an episodic, unfolding, embryonic gestation. By this unique retrospect, an apparent Geonativity event at term is alluded to. But in the past few years, as Our EarthMost Occasion documents, a singular significance for our home bioplanet as a unique fittest candidate has arisen. By turns, if kinder wins over cinder, a sustainable Earthropocene era and ecocreative Ecosmocene futurity can open wide going forward.

Planatural PhiloSophia Wisdome

Major Evolutionary Emergent Transition At the ourset, a further stage might lately be seen in occurrence as it ascends to and closes over life’s planetary personsphere. Into these years, it has taken a while to recognize this as it may only now become evident.

Into 2023, new Major ETI section (V. A) entries, along with a special, extensive Human Socio-Cultural Evolution in Light of Evolutionary Transitions issue in Royal Society Philosophical Transactions B (February, see next), add a profound substantial credence for life's nested emergence from first occasions as vitality proceeds to rise by recurrent stages to just now close over our ovo/bio/neuro prodigious pediasphere.

Carmel, Yohay, et al. Human Socio-Cultural Evolution in Light of Evolutionary Transitions: Introduction to the Theme Issue. Royal Society Philosophical Transactions B. February 2023.

An EarthKinder Individuality As its Chap.V. Sect. A documents, each nested level from genes to peoples seems to take on a personal identity, often with a new genetic-like mode, as a new whole cellular grouping begins. We cite Planetary Progeny, KinderKind and so on in accord.

Global Earthificial Sapiensphere As a consequence, an equivalent brainy facility, as it self-organizes neural multiplexes can be seen as learning, gaining knowledge, and coming upon a real discovery by her/his own endeavor. But into later 2022 we add, an intense degree of hyper-active intelligent capacity has suddenly come into use by names such as generational AI, Large Language Models, chatGPT, see title module for references.

WholeWorld BiCameral Complementary Cognizance Such an implied, projected cerebral faculty (see Dan Graham, et al Chap. II, Sect C), ought to similarly take on archetypal discrete node and link relational phases. In this way a new, infant-like visionary encounter might accrue and occur on an KinderKind scale. We often cite a WumanWise essence so as to identify both halves of the mind, sky and uniVerse.

Sophia Sapiens: a Woman’s Ecosmos For these reasons, an ecological reproductive spacescape with an encoded fertility (From Eternity to Maternity) could well be viewed. As Gender Complements cites, a feminine competence uses each side join a fine acuity with a holistic, integral scene so as to achieve a meaningful witness. By another view, the olden philosophy term, aka PhiloSophia, could rightly be reversed as SophiaPhilo, so to note the primacy of a feminine field context, before particle objects.

Going on, it is imperative that an entrenched patriarchy be fully indicted as toxic egotist madmen brutalize, enslave, silence, any feminine quality. (Just read the daily Human Rights news.) Here is a fatal aberration of rapacious, barbaric violence that seems bent on a final Armageddon. Into 2023, Iranian, Afghan, all over suppression of women has harshly intensified, especially to block any education opportunities.


Phenomenal Knowledge To stay on message, a grand benefit would be a whole mindful ability to observe an independent existence with its own certain identity and
temporal course, (which left side men are unable to do), so tp allow this genesis vision. That is to say (as I have been told) we need to have a wherewithal to see something dynamic and formative going on by itself. Every facet of our occasion then gains a double dimension, whereof people become exemplary participants.

A Discovery Code Event For the time being, a note is made that a once and future concept that this universal presence, however vast, comes with a built-in way it is made and meant to be known by we Earthlings. Wuman and universe. microcosm and Macrocosm are one and the same as some manner of a familial ecosmos.

eLibrary of eCosmos Over the 21st century, as these qualities, features, occurrences reinforce over the 21st century, as the many topical website references attest, a worldwise edition of an open “accumulated knowledge repository” has come to envelope so as to provide an integral knowledge to guide us through. That is to say our Participatory role much involves an Iteracy Literacy achievement by way of its genetic-like hereditary code

A Procreative Family Ecosmos UniVerse

A Revolutionary Procreative Organic Ecosmos Universe We can now move on to an epochal encounter of an animate, innately fertile, “pregnant” (C. de Duve) emergent development as it altogether forms in our knowsphere midst. An olden left side, men only mode has wound up with a pointless morbidity, case closed, not even Ptolemaic. In regard, one can now gather and integrate many features and qualities that can just now be found across the literature.

But a comparison of these old and new moribund machine to an innate organic fertility views, it is important to note that our ascendant EarthVersion is distinguished by a second deep dimension of an immaterial, mathematic, genomic-like source. Particles are “pointless, “peoples” are surely not. This independent realm then carries an informative prescription so as to generate, self-organize, and impel phenotype-like phenomenal beings and becomings from uniVerse to our peopleVerse.

A Moon to MultiVerse Spacescape At this point, this 400 year historic expanse is known, in our home uniVerse, to be populated with a trillion or so galaxies, each with billions of vicarious stars. Since c. 2000, an epochal discovery of myriad stellar orrerys with some sextillion profligate global objects has occurred. A philosophia point could add that it is beginning to seem that an entire uniVerse may have a certain, knowable identity and temporal course of its own

Solar/Ovular Planetary Incubators Similarly, as the ExoEarths section reports, there are current inklings that these starry systems may have an overall conducive, life-bearing, evolutionary essence. As if sunny incubators, habitable (benign) mid-zones then favor longer-duration bioworlds (see Earth Alive) can give life a chance to evolve, develop, personify and maybe rise to become worldwise progeny.

A UniVersal Naturome Ecode

Ecosmomics: An Independent, Informative Genomic Source With an organic, fertile spacescape in place, an essential biological astro-milieu ought then be considerably graced with its own innate, genetic quality. This Chapter IV describes and documents many ways since the 1990s that such a mathematic, generative source cause has been found, quantified, explained and distilled to a common code. Thus a bigender familial form and its exemplary, omic/iconic result lately distinguishes everything and everyone with a heretofore unkonwn actual, factual image and significance.

Since the 1990s, complex adaptive systems, multiplex neural networks, cellular automata, fractal invariances, interactive agents, computational intelligences qualities have been found to infuse and inform every scale and instance from universe to us. A prime 21st century finding is that as these archetype modes (node/link, me/We) engage in communicative behaviors, they proceed to self-organize into emergent, viable patterns and processes into ensembles. In accord, a major achievement of our global genius in the 2020s is that a whole spatial and temporal recurrence in kind has been robustly proven.

In more regard, the full Natureome section next provides extensive references as this common result becomes evident over every depth and breath. A timeline from 2000 to 2015 to 2022 now defines a scientific sequence as many initial versions were clarified and melded into one iconic, biconic and triune animate unity (aka as yin/yand and Tao). These earlier years, focussed on a spatial-component complex adaptive systems phase (John Holland, Murrary Gell Mann) through to c. 2015. The node/link network theories and topologies over this period added more structural features.

However in the later 2010s, a second dynamic, reciprocal process became evident which this biological phenomena appears to seek and settle into. First cited in the 1970s by Stuart Kauffman, and the 1980s by Per Bak, one could note Dante Chialvo and Miguel Munoz (search names) today. This steady propensity has been dubbed a Self-Organized Criticality whence a temporal fluidity maintains a middle balance between more or less orderly, polar states. Altogether it seems that life knows best and prefers an active contrast between such archetypal modes for any organic or social instance.

Nature’s “sweet spot” poise. These 21st century anatomy and physiology, fractal and vitality, have been dubbed by this title (Chialvo) for this node/link, me/We, past/future golden mean. Another “Chimera” version (Anna Zakharova) is seen to reside in both phases at once. As a latest example, we cite Phase Transitions and Criticality in the Collective Behavior of Animals by Pawel Romanczuk and Bryan Daniels at (arXiv:2211.03879.) wherein Humboldt University and Arizona State University theorists conceive a convergent synthesis of these form and function proclivities. The paper will be a chapter for the 2023 Volume VII of the World Scientific series Order, Disorder, and Criticality, edited by Yuri Holovatch in Lviv, Ukraine.

Thus our historic, intended quest proceeds to gain a textual literacy (iteracy) that a natural narrative maybe written in so to discern an infinite affinity of an iconic, biconic, and triconic (yang, yin, Taome) scriptome For a specific example 2022 articles such as Self-Organized Critical Dynamics (B. Tadic, Dynamics 2/2/2022) and Universality of Functional Diversity Across Human Organizations (Vicky Yang, arXiv:2208.06487) among many more, attest to a consistent, genome-like exemplar from uniVerse to us peoples. And on this December 6, I come upon an especially apt synthetis Critical Phenomenon in Embryonic Organization by Camilla Autorino Camilla and Nicoletta Petridou in Current Opinion in Systems Biology (Vol. 31, Sept. 2022).

An Evolutionary Developmental Embryonic Gestation

With all this in place, we reach life’s Ecosmic and Earthly progression from spontaneous network origins all the way to a major planetary personsphere fultillment. From 2022, a once and future appreciation can arise in an animate, fecund, encoded procreativity. (Indeed in Darwin’s day, a popular theme was “universal gestation.”) But a 20th century study of skeletal bodies and a random modern synthesis led to its denial and demise. Nut we can now list an array of advances into a worldwise century which can reveal an oriented “genesis synthesis.”

As Chap. V enters in such detail, an informative source of a self-organizing, genetic-like code vivifies a reproductive course. By the 2020s, a nested major transitions scale of a cellular wholes extends all the way to our global resolve forms. Into this year, a new Chapter VI can describe a neural, cognitive encephalization which proceeds, thickens, learns, quickens, along with metabolism and morphology.

As this evolutionary ascent goes forth, a relative degree of individual proactive agency and behavior in cohesive groupings, aka creative union, fluoresces and flourishes. In addition, as Chap. V, D records, in 2019 the British Linnean Society and colleagues (Peter Corning, Stuart Newman) realized that it was no longer possible to ignore, or deny that a teleological, orthogenetic orientation was actually going on. (See Chapter V for many more reasons.)

An EarthWinian Celestial Optimization We make note of this broadly present selective process which has been found to extend across a natural genesis procreation. Please refer to Universal Evolution. Cosmopoiesis: An Autocatalytic, Self-Made Universe, Biteracy: Algorithmic Computation and other section for many citations. This novel feature will have major implications with regard to the Super Earth Nova and Earthernity concepts. But the question then arises as to what quality is nature’s genesis trying to select for? In some fundament way, it involves our reception and continuance of the ecosmome code program.


A PediaKind EarthDay A 1990 – 2020 – 2030 – 2060 GeoNativity Event

As our Planatural Genesis introduction above notes, the website considers, life’s long evolution can take on an actual identity as an embryonic developmental gestation. As on occasion in these essays, and by reference entries lately quantify, we cite some affinities between a person (mother) and a gravid bioglobe. As one may just follow this theme, three prime features might serve. As references by Karin Schwab, Hugo Largercrantz, Jean-Pierre Changeux and others cite, it has been found that at some point in the birth/hatch process each fetus awakens from a long dream sleep to their own self-consciousness. In an oviparous case, each hatchling has had to break their shell by their own initiative. Another aspect for any organism would be the reception, in some form, of their own personal genetic complementary code.


ECOSMOMICS: 21ST CENTURY STUDIES OF INDEPENDENT GENERATIVE, SELF-ORGANIZED, COMPLEX ADAPTIVE, NETWORK, CRITICAL SYSTEMS

Circa 1990s to 2015 Structural Features

As a way to express this occasion, we here trace the scientific origins, development, and a 2020s integral synthesis of self-active complexity phenomena by way of a 1990 to 2022 sequential orientation. In retrospect, this thirty year span can be sorted into 1990, 2000, 2005, 2010, 2015, 2018, 2020/2021 and 2022 phases so as to convey its divergent, convergent and now integrative fulfillment. By this late vista, a spiral transition from individuals to our present global collaborative success can be viewed.

As an apocalyptic madness and despair sets in, an intent of these new introductions is to attribute a concurrent knowledge edification to our emergent Earthuman personshpere sapience, aka a thinking and learning planet. As this website resource documents, a conceptual 21st century procreative ecosmic revolution seems underway. If of a mind to allow and view. An extant reality may then be revived from morbidity to organic life and peoples which is distinguished with an independent, informative, mathematical genetic code everywhere. Some 400 years after Galileo, a natural narrative might finally be known as written in a familial scriptomics.

1990 A subsequent major emergent evolutionary transition in individuality could be seen to begin with the end of the cold war standoff. I visited the Santa Fe Institute in 1987 where the complexity revolution was much initiated. Coincidentally an unprecedented era began whence worldwide communication, travel, and trade became increasingly possible. At the same while this epochal revision of complex, self-organizing, systems science takes of in depth and diversity. The parallel appearance of graphic computational abilities provided a vital component.

2000 Into this new century, and millennium (quite timely), personal laptop computers, faster mainframes, and Internet websites began to form an interlinked capacity. But Apple and Microsoft programs are rudimentary, Google, Amazon, et al are fledgling start-ups. The study of “nonlinear” dynamic phenomena in many guises such as complex adaptive systems, synergetics, automata, fractals, et al (see Chap. IV for an extensive survey) came to inform theoretical and experimental endeavors.

2005 Early stages of scientific publisher and academic library websites were just coming online. I still had to go to MIT to fetch paper books such as The Knowledge Grid (Hai Zhuge) and to Yale for Self-Organization and Evolution of Social and Biological Systems (Hemelrijk), This later collection was the first time that wherein entries from molecular and microbial domains to animal groups to languages began to report something similar going on at each instantiation.

2010 After a decade of interlinked hardware and software advances, along with more user access, scientific journals shifted to a paperless online presence. (My own view is that both human-scale paper and faster cyberspace modes should have been kept, especially so students. A worldwise sapiensphere began to form and intensify into billions of site content-filled sites such as encyclopedias. As this global facility stirred into a relative mind of her/his own (Daniel Graham 2021, et alia), by an evident consideration, it might be seen as commencing to learn on its (her/his) prodigious own. At this date, the presence of nature’s multiplex networks from neural to metabolic and celestial realms gained recognition.

2015 A phenomenal Ecopernican revolution enters a convergent phase of integrative synthesis. As quantum and classical systems united, astronomic raiments gained an active fertility, and life’s physiological, cellular and cognitive scales organized themselves, an independent code-script became well implied. A common informative, bigender-like source which served to form emergent vitalities could be readily distilled. Life’s symbiotic unions, and biosemiotic encodings also were also as a prime movers. In tandem, a historic advance in artificial intelligence (AI) occurred whereof brain-like neural nets were found to be a much better method.


A New Dynamic Activity Phase 2015 to 2020 to 2023

2018 A further quality could now be appreciated whence these natural patterns and processes were realized to seek and reside at a self-organized critical balance of entity and community modes. See Colloquium: Criticality and Dynamical Scaling in Living Systems by Miguel Munoz for a premier paper. At an accelerating pace, a strong recognition that an ecosmic universal genesis performs best at a dynamic bigender poise of neuron + synapse, me member + we group, DNA biomolecule + AND regulatory net, and ever on, became widely articulated.

2020/2021 As this EarthMinder intelligence may reach an epic moment of observant self-cognizance, our planetary progeny is now well informed and prepped to actually discover a natural genesis uniVerse to human/Wuman EarthVerse procreation. In accord, such a fertile organic spontaneity seems to be rooted in and spring from one, genetic-like (familial) program. A once and future UniVersality For a working word, a “Naturome” source code is dubbed as a once and future “Universality” by virtue of its whole scale recurrence. Search “Alexandria” for a December 2019 conference by this name, sponsored by the NSF director France Cordoba.

2022 At the same while that tragic horrors consume and imperil we peoples and whole Earth, by robust verifications in evidence everywhere, such a dispensation may at last be possible. As the prime references cited herein indicate, a new convergent phase distinguished by a uniVerse to humanVerse invariant scale and exemplary instance is newly evident. Here are three new, apropos citations.

Into 2022, three more significant quantifications about an optimum social preference of a member/group, conserve/create, compete/cooperate, past/future complementsarity which poise in a dynamic harmony. From Lebanon to Sri Lanka and everywhere else no guidance of how and why to live altogether exists, nor can any such basis even be imagined. Yet as these works attest, its Confucius or confusion. At this late hour, a natural, golden mean balance has at last been well proven.

As the Earth Learn 2022 introduction above, and the whole website recites, its singular edification is the presence of one, common iconic genotype-like pattern and process, form and function in kind. An archetypal array of particle/wave, DNA/AND, neuron/net, left/right brain, member/group define a bigender complementarity. Our title mentions Familial because altogether these identities make up a triality of light, genome, neorome, and so on. As Chapter IV documents, their dynamic activity is then found to prefer and reside a balanced poise between more or less order.

At this point in 2022 of real March Madness, when all degrees of senseless carnage are going on, it would serve to consider what such a concurrent UniVersality affirmation could well imply and inform. A common bigender, familial code is just coming to light which is found to be in self-similar, invariant effect across every spatial and temporal, stars to starlings, realm. By this integral verification, a true affinity between micro-ecosmic wuman beings and the entire macro-ecosmic procreative spacescape is becoming evident. As tradition has long averred, the whole, infinite uniVerse and our infinitesimal epitome are indeed one and the same.

2023 As this online subject content and more proceeds into another year, each chapter and section comes with a new notable reference list to replace the 2020 version. Going forward, a whole outline 2023 - 2030 module for especial contributions is now posted after An Earthumanity Era. As a strong sign that this vital poise view grows apace, a book version The Cortex and the Critical Point: Understanding the Power of Emergence. by John Beggs (see review below) has now been published, see review below.


As another way to evince how this significant perception has spread across the universe and Earthversion, here next is a citation litany from Integral Occasion all the way to Phenomenal Peoples. And all these entries are continually updated as they grow in breadth and depth.

INTEGRAL OCCASIONS
Artime, Oriol and Manlio De Domenico. From the Origin of Life to Pandemics: Emergent Phenomena in Complex Systems. Philosophical Transactions of the Royal Society A. May 2022.
Tadic, Bosiljka and Roderick Melnik. Self-Organized Critical Dynamics as a Key to Fundamental Features of Complexity in Physical, Biological and Social Networks. Dynamics. 2/2, 2022.
Chen, Luyao, et al. AI of Brain and Cognitive Sciences: From the Perspective of First Principles. arXiv:2301.08382.
Sanchez-Puig, Fernanda, et al. Heterogeneity Extends Criticality. arXiv.2208.06439. August 2022.
Villani, Marco, et al. Evolving Always-Critical Networks. Life. 10/3, 2020.

CELESTIAL REALMS
Kartvelishvili, Guram, et al. Self-Organized Critical Multiverse. arXiv:2003.12594.
Aschwanden, Markus. The Fractality of Astrophysical Self-Organized Criticality. arXiv:2203.12484.
Pereverzev, Sergey. Dark Matter Searches and Energy Accumulation and Release in Materials. arXiv:2212.13964.
Wei, Jun-Jie. Scale Invariance in X-ray Flares of Gamma-ray Bursts. arXiv:2212.08818.

QUANTUM, MATERIAL
Ohler, Simon, et al. Towards Learning Self-Organized Criticality of Rydberg Atoms using Graph Neural Networks. arXiv:2207.08927.
Mondal, Suman, et al. Self-Organized Criticality of Magnetic Avalanches in Disordered Ferrimagentic Material. arXiv:2210.05183.
Sherman, Nicholas, et al. Universality of Critical Dynamics with Finite Entanglement. arXiv:2301.09681.
Tsakmakidis, Kosmas, et al. Quantum Coherence-Driven Self-Organized Criticality. Science Advances. March 2018

EARTH SYSTEM
Smyth, William, et al. Self-Organized Criticality in Geophysical Turbulence. Nature Scientific Reports. 9/3747, 2019.
Jensen, Henrik. Brain, Rain and Forest Fires: What is Critical about Criticality: In Praise of the Correlation Function. Journal of Physics: Complexity. 2/032002, 2021.
Cheraghalizadeh, J., et al. Simulating Cumulus Clouds Based on Self-Organized Criticality. arXiv:2211.06111.

CELLULARITY
Zimatore, Giovanna, et al. Self-organization of Whole-gene Expression through Coordinated Chromatin Structural Transition. Biophysics Reviews. 2/031303, 2021.
Ge, Xiaofei, et al. Self-Organized Critical Dynamics of RNA Virus Evolution. arXiv:2204.08627.
Vidiella, Blai, et al. Engineering Self-Organized Criticality in Living Cells. Nature Communications. 12/4415, 2021.
Proverbio, Daniele, et al. Buffering in Cell Regulation Motifs Close to Criticality. arXiv:2212.08600.

ORGANISM AND COMMUNITY
Autorino, Camilla and Nicoletta Petridou. Critical Phenomenon in Embryonic Organization, Current Opinion in Systems Biology. Vol. 31, Sept. 2022.
Shpurov, Ivan and Tom Froese. Evidence of Critical Dynamics in Movements of Bees inside a Hive. Entropy. 24/12, 2022.
Schaposnik, Laura, et al. Animal Synchrony and Agent’s Segregation. arXiv:2212.07505.
Zamponi, Nahuel, et al. Scale Free Density and Fluctuations in the Dynamics of Large Microbial Ecosystems. arXiv:2206.12384.

CEREBRAL DYNAMICS
Tian, Yang, et al. Theoretical Foundations of Studying Criticality in the Brain. Network Neuroscience. 6/4, 2022.
Shettigan, Nandan, et al. On the Biophysical Complexity of Brain Dynamics. Dynamics. 2/2, 2022.
Plenz, Dietmar, et al. Self-Organized Criticality in the Brain. Frontiers in Physics. July 2021.
Magnasco, Marcelo. Robustness and Flexibility of Neural Function through Dynamical Criticality. Entropy. 24/5, 2022

HUMAN PHENOMENON
Tang, Xun and Huifang Ye. Metaphorical Language Change Change is Self-Organized Criticality. arXiv:2211.10709.
West, Bruce, et al. Relating Size and Functionality in Human Social Networks through Complexity. PNAS. 117/31, 2022.
Notarmuzi, Daniele, et al. Universality, Criticality and Complexity of Information Propagation in Social Media. arXiv:2109.00116.


ECODE 2023: EARTHKINDER READS A UNIVERSAL, INDEPENDENT ECOSMOME TO GEONOME EXEMPLARY ENDOWMENT

After our current Ecosmos to Earthmost status report, a 30 year complexity science progressive revolution can be seen to attain a convergent veracity via an infinite affinity. It is then incumbent to note that our collaborative sapience has in fact begun to glimpse and achieve a historic discovery of an actual greater genesis with its own phenomenal identity, ecode genetic-like essence, and a procreative purpose. As a way to express, we next gather an initial array of salient references with Independent Universality, Exemplary Epitomes and Earthropocene Geonome/Phenome sections.

An Ecosmome Independent Universality In an Creative Organic UniVerse, a major Earthumanity sapience has been able to perceive and decipher an independent, genetic-like, informative, source-script with a bigender, familial heredity in effect.

Artime, Oriol and Manlio De Domenico. From the Origin of Life to Pandemics: Emergent Phenomena in Complex Systems. Philosophical Transactions of the Royal Society A. May 2022.
When a large number of entities interact with each other and their environment, higher spatio-temporal outcomes often spontaneously arise. This emergent phenomenon holds for a broad range of complex systems from physical to biological and social related to collective behavior.

Allard, Antoine, et al. Geometric Description of Clustering in Directed Networks. arXiv:2302.09055.
Zhou, Zheng, et al. Fractal Quantum Phase Transitions: Critical Phenomena Beyond Renormalization. arXiv:2105.05851.

Goldbeter, Albert. Dissipative Structures in Biological Systems: Bistability, Oscillations, Spatial Patterns and Waves. Philosophical Transactions A. Vol. 276/20170376, 2018.
This review will discuss the conceptual relevance of dissipative structures as the dynamical bases for non-equilibrium self-organization in biological systems,

Bianconi, Ginestra. Multilayer Networks: Structure and Function. Oxford: Oxford University Press, 2018.
Zakharaova, Anna. Chimera Patterns in Networks. International: Springer, 2020.

Lopez, Roberto, et al. The Excitatory-Inhibitory Branching Process: Cortical Asynchronous States, Excitability, and Criticality. arXiv:2203.16374.
Voit, Maximilian and Hildegard Meyer-Ortmanns. Emerging Criticality at Bifurcation Points in Heteroclinic dynamics. Physical Review Research. 2/4, 2020.

Tadic, Bosiljka and Roderick Melnik. Self-Organized Critical Dynamics as a Key to Fundamental Features of Complexity in Physical, Biological and Social Networks. Dynamics. 2/2, 2022.
Studies of complex systems reveal collective behaviours that emerge due to self-organised critical fluctuations. By physical, biological, and social network exemplars, we show how a self-organised criticality occurs by way of reciprocal topologies and a driving force.

Wolfram, Stephen. The Physicalization of Metamathematics and Its Implications for the Foundations of Mathematics. arXiv:2204.05123.
But our Physics Project suggests that underneath everything there is a general abstract structuration and that our physical laws arise in an inexorable way from this informative basis.


Exemplary Epitomes Everywhere As the entire Planatural Genesis website has come to document, our EarthSmart transition has proceeded to report an invariant presence in kind from astrome, quantome and atome phases through life’s personal/planetary development to our humanEarth epitome.

Perc, Matjaz. Beauty in Artistic Expressions through the Eyes of Networks and Physics. Journal of the Royal Society Interface. March 11, 2020.

Berezhiani, Lasha, et al. The Complex Galactic Dynamics of Dark Matter Superfluidity. arXiv:2212.10577.
We consider self-interacting bosonic dark matter with superfluidity to show that optimum theory parameter space corresponds to thermalized dark matter halos.

Antonello, Priscila, et al. Self-organization of In Vitro Neuronal Assemblies Drives to Complexity Network Topology. eLife. 11/e74521, 2022.
Kulkarni, Suman, et al. Information Content of Note Transitions in the Music of J. S. Bach. arXiv:2301.00783.

Kocoglu, Cemile, et al. How Network-based Approaches can Complement Identification Studies in Frontotemporal Dementia. Trends in Genetics. 38/9, 2022. This review considers genetic approaches in FTD and network biology concepts to better identify complex neurological disease.

Ciss, Mamadou, et al. Description of the Cattle and Small Ruminants Trade Network in Senegal. arXiv:2301.11784.
We present a procedure based on temporal network theory to identify possible sentinel locations using two indicators: vulnerability and time of infection.
Pan, Yi-Ru, et al. Universality and Scaling in Complex Networks from Periods of Chinese History. Chaos. January 2023.

Sarkanych, Petro, et al. Network Analysis of the Kyiv Bylyny Cycle – East Slavic Epic Narratives. arXiv:2203.10399.
Witthaut, Dirk, et al. Collective Nonlinear Dynamics and Self-Organization in Decentalized Power Grids. Reviews of Modern Physics. February 2022.

Tadic, Bosilijka. Cyclical Trends of Network Load Fluctuations in Traffic Jams. Dynamics. 2/4, 2022.
The transport of information packets in complex networks is a prototype system for the study of traffic jamming, a nonlinear dynamic phenomenon that arises with increased traffic load and limited road capacity.

Fugenschuh, Marzena and Feng Fu. Overcoming Vaccine Hesitancy by Multiplex Social Network Targeting. arXiv:2302.07813.
Social factors of disease prevention are a main basis behavioral epidemiology. Our findings provide insight into network-based methods during a viral pandemic.

Gysi, Deisy and Katja Nowick. Construction, Comparison and Evolution of Networks in Life Sciences and Other Disciplines. Journal of the Royal Society Interface. May, 2020.
Network approaches apply in many fields for they display complex relationships between entities as well as group-level properties. Our focus is the life sciences across molecular, ecological, neuropsychological and evolutionary aspects.

Yang, Vicky Chuqiao, et al. Scaling and the Universality of Function Diversity across Human Organizations. arXiv:2208.06487.


Earthropocene Geonome/Phenome Vitality Here are initial reports of a double naturome ecode scenario that includes both an intrinsic, invormative guides and its (wo)manifest result from stars to starlings and our own cultural benefit going forward.

Grossberg, Stephen. Conscious Mind, Resonant Brain: How Each Brain Makes a Mind. New York: Oxford University Press,, 2022.

Araujo, Nuno, et al.. Steering Self-Organization through Confinement. arXiv:2204.10059.
These concepts arose in the late 20th century and define collective structures and patterns that arise from many interactive units, such as molecules, colloidal particles, cells, animals, pedestrians and so on.

Gagler, Dylan, et al. Scaling Laws in Enzyme Function Reveal a Biochemical Universality. PNAS. 119/9, 2022.
Ouellette, Nicholas. A Physics Perspective on Collective Animal Behavior. Physical Biology. 19/2, 2022.

Corbetta, Alessandro and Federico Toschi. Physics of Human Crowds. Annual Review of Condensed Physics. 14/311, 2023.
Understanding the behavior of human crowds is a key step toward a safer society and more livable cities. Despite the individual variability and will of single individuals, human crowds, from dilute to dense, invariably display a remarkable set of universal features and statistically reproducible behaviors.

Khanra, P., et al. Endowing Networks with Desired Symmetries and Modular Behavior. arXiv:2302.1548.

West, Geoffrey. Scale: The Universal Laws of Growth, Innovation, Sustainability, and the Pace of Life, in Organisms, Cities, Economies, and Companies. New York: Penguin, 2017.

Turker, Meliksah and Haluk Bingol. Multi-Layer Network Approach in Modeling Epidemics in an Urban Town. European Physical Journal B. February 2023.
In order to mitigate the negative impact of the epidemics, researchers viewed the pandemic using forecasting techniques and epidemics simulations on networks.


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View the 71 Bibliographic Entries

B. A Survey of Mathematic, Dynamic, Textual, Anatomic, Program-like, Self-Similar Aspects

Within this composite chapter all about our Earthwise revolutionary perception of a vital generative code domain, this topical section will first document the Network Physics revolution, as Albert Laszlo Barabasi (2012) cites, which now serves to join all the prior nodal elements. Biteracy: Natural Algorithome Programs considers this computational, algorithmic aspect. Similarly, A Rosetta Ecosmos Literacy reports how even our human verse and voice have become amenable to and influenced by complexity phenomena. With this in place, Universality Affirmations can describe the premier 2020 achievement of realizing, discerning and deciphering a common. iconic bigender complementarity and triality.

1. Network Physics: A Vital Interlinked Anatomy and Physiology

The first title phrase is meant to distinguish this 21st century scientific endeavor from a long, albeit necessary particle focus in this subject field. It reports the expansive witness of nature’s scale-free mode of dynamic interconnections everywhere, originally due much around 2000 to Albert-Laszlo Barabasi and Reka Albert, then Notre Dame University physicists, search each name. In contrast to prior random or Erdos-Renyi graphs, e.g., telephones, natural phenomena from galaxies to genomes, organisms, societies and languages are finely interconnected by a “preferential attachments and growth” of node elements and relational linkages. As such, they contain larger and smaller modules, hubs and communities with more influence. An ever growing list includes galactic and quantum networks, multiplex neural nets, animal and human groupings, onto power grids and Internet websites.

The initial model applied so well that it has, with much updating and expansion, been adopted by every scientific field and realm, as ALB notes in a 2012 Nature Physics article entitled The Network Takeover. Network Science texts by Mark Newman, Shlomo Havlin, Barabasi, and others show how robust this notice of equally real communicative interactions between parts, objects, entities has become. For one instance, their universal presence is evident when one can find daily arXiv e-print site postings such as The Network behind the Cosmic Web (1604.03236) and Mapping Out Narrative Structures and Dynamics Using Networks (1604.03029), where both papers cite these same principles. Publications such as Journal of Complex Networks and Network Neuroscience post theoretical advances such as multiplex core/periphery modes and simplical complexes, along with anatomy, physiology and biomedical applications.

2020: From the 2002 Statistical Mechanics of Complex Networks paper by Reka Albert and Albert-Laszlo Barabasi to The Network Takeover by ALB in 2010 to this bidecadal year, a novel Network Physics section with 143 entries can report a whole scale revolution about ecosmos to ecologies and economies has occurred. An organic universe to human genesis appears to be suffused by a heretofore unseen anatomic topology and connective physiology which embodies, joins, relates and vivifies its evolutionary procreation. From galactic clusters to protein metabolism, animal groupings and onto literary texts and especially cerebral cognition, a similar multiplex, neural net geometry is in proactive effect. Again all these phenomenal findings well imply an independent, universally exemplified, informed mathematical source.

2023: Within our novel title, the theoretic and empirical study of animate nature’s pervasive connectivities, as if an ecosmic anatomy and physiology, remains an intense collaborative activity. As many citations attest, a rush of current multiplex and metaplex contributions well portends a common universality from quantum to galactic to societal realms. Going forward, we mention Cemile Kocoglu, Dino Pitoski, Albert Barabasi and others who apply this attribute to practical diagnosies to much benefit

Aleta, Alberto and Yamir Moreno. Multllayer Networks in a Nutshell. Annual Review of Condensed Matter Physics. 10, 2019.
Battiston, Federico, et al. Network beyond Pairwise Interactions: Structure and Dynamics. Physics Reports. June, 2020.
Bianconi, Ginestra. Multilayer Networks: Structure and Function. Oxford: Oxford University Press, 2018.
Boguna, Marian, et al. Network Geometry. arXiv:2001.03241.
Chavalarias, David. From Inert Matter to the Global Society: Life as Multi-level Networks of Processes. Philosophical Transactions of the Royal Society B. February, 2020.
Duarte, Denise, et al. Representing Collective Thinking through Cognitive Networks. Journal of Complex Networks. 10/6, 2022.
Gysi, Deisy and Katja Nowick. Construction, Comparison and Evolution of Networks in Life Sciences and Other Disciplines. Journal of the Royal Society Interface. May, 2020.

Fortunato, Santo and Mark Newman. 20 Years of Network Community Detection. arXiv:2208.0111.
Frottier, Theo, et al. Harmonic Structures of Beethoven Quarters: A Complex Network Approach. arXiv:2201.08796.
Ghavasieh, A. and M. De Demonico. Statistical Physics of Network Structure and Information Dynamics. Journal of Physics: Complexity. February 2022.
Kostic, Daniel, et al. Unifying the Essential Concepts of Biological Networks. Philosophical Transactions of the Royal Society B. February, 2020.
Mariani, Manuel, et al. Nestedness in Complex Networks: Observation, Emergence, and Implications. Physics Reports. Volume 813, 2019.
Porter, Mason. Nonlinearity + Networks: A 2020 Vision. arXiv:1911.03805.
Siew, Cynthia, et al. Cognitive Network Science. Complexity. Art. 2108423, 2019.
Vespignani, Alessandro. Twenty Years of Network Science Nature. 558/528, 2018.

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2. Biteracy: Natural Algorithmic Computation

The present Cosmic Code chapter reports a broad array of scientific encounters with nature’s generative propensity to form evolutionary self-organizations of complexity and cognition. From our humankind vista, a revolutionary perception can be noticed of an independent, mathematical program-like agency in procreative effect. Here we collect a range of computational, algorithmic, information-based, cellular automata, meta-biology, evolutionary optimization, analog/digital software, DNA data and more entries. These endeavors often refer to Gottfried Leibniz, to Greece before, and later espeically to Alan Turing so as to trace a heritage in search of an “alphabetic calculus” and “Mathesis Universalis.” In regard, the perennial quest (magnum opus, great work) was in much part to decipher and read a natural logos, a constant source code to avail as an edifying guidance.

This introduction is a 2018 update because recent contributions seem at last to be reaching a robust affirmation. We might list Stephen Wolfram, Gregory Chaitin, Sara Walker, Hector Zenil, Enrico Borriello, Anne Condon, Leroy Cronin, Agoston Eiben, Hyunju Kim, Doug Moore, Paul Davies and more. The achievement is closing upon a common code program behind nature’s universal proclivity to become poised at a reciprocal self-organized criticality, see also Universality Affirmations herein.

Another aspect is in need of airing and review. The phrase “mindless mathematics” has been bandied about (Aguirre 2018), which infers that cosmic nature (or lack thereof) is bereft prescription or purpose. But in actuality a mathematical domain can take two different forms. One is a pure or applied mode, such as arithmetic. Each day on the arXiv preprint site some 200 entries appear under Mathematics. But its Computer Science section reports on computational software which does carry information. Each day some 300 contributions are listed. So we may have an arithmetic to which “mindless” might apply, and maybe an “algorithmetic” version that does contain, or has a fmindful capacity for narrative message.

And finally, we introduce “Biteracy,” a word which does not come up in a Google search. As the section title alludes, natural algorithms have roots in John Holland’s 1970’s original genetic version, with many extensions since, see Xin-She Yang. But we refer to John A. Wheeler’s familiar “bit to it” arc which courses from an informative (quantum) origin through an oriented evolution to vital human observers and recorders. An inference could be that we regnant peoples arrive as the way a participatory uniVerse learns to decipher, read, and intentionally take forth its own genomic endowment.

2020: A parallel, companion endeavor to complex systems science is this active field of computational program studies. From Alan Turing’s morphogenesis to Stephen Wolfram’s cellular automata, Gordana Dodig-Crnkovic’s informational basis and many more, a natural genesis is known to involve and be suffused by analog/digital (George Dyson 2020) codings. As they work their way, some manner of selective optimization seems to be going on. In its genetic algorithmic form (John Holland) a deep affinity becomes evident amongst this whole mathematic emergence.

2023: The endeavor to perceive a natural mathematic animation can be traced back to Alan Turing in the 1950s and Gottfried Leibniz long before. In our global 21st century, digital/analog versions spread across a wide spectrum. We cite an array of advocates below, and note Susan Stepney, George Dyson, Laura Schaposnik, Tanya Latty amongst many innovators.

Bernini, Andrea, et al. Process Calculi for Biological Processes. Natural Computing. 17/2, 2018.
Caucheteux, Charlotte and Jean-Remi King. Brains and Algorithms Partially Converge in Natural Language Processing. Communications Biology. 5/134, 2022.
Dowek, Gillis. Computation, Proof, Machine: Mathematics Enters a New Age. Cambridge: Cambridge University Press, 2015.
Dyson, George. Analogia: The Emergence of Technology beyond Programmable Control. New York: Farrar, Straus and Giroux, 2020.
Gregor, Karol and Frederic Besse. Self-Organizing Intelligent Matter: A Blueprint for an AI Generating Algorithm. arXiv:2010.07627.
Hsu, Sheryl, et al. A Physarum-inpsired Approach to the Euclidean Steiner Tree Problem. Nature Scientific Reports. 22/14536, 2022.

Krause, Andrew, et al. Recent Progress and Open Frontiers for Turing’s Theory of Morphogenesis. Philosophical Transactions of the Royal Society A. November, 2021.
Krenn, Mario, et al. Predicting the Future of AI with AI: An Exponent Growing Knowledge Network. arXiv:2210.00881.
Molina, Daniel, et al. Comprehensive Taxonomies of Nature-and Bio-inspired Optimization. Cognitive Computation. 12/897, 2020.
Nichol, Daniel, et al. Model Genotype-Phenotype Mappings and the Algorithmic Structure of Evolution. Journal of the Royal Society Interface.16/20190332, 2019.
Stepney, Susan and Andrew Adamatzky, eds. Inspired by Nature. International: Springer, 2018.
Wolfram, Stephen. The Physicalization of Metamathematics and Its Implications for the Foundations of Mathematics. arXiv:2204.05123.
.
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3. Iteracy: A Rosetta Ecosmos Textuality

This module began in 2004 as a place to convey perceptions of an innate natural textuality written in an edifying script that newly literate humans were invited and meant to decipher and read. Into the later 2000s, as the complexity sciences grew in veracity, it was realized that fractal scales and dynamic self-organizations could apply to and are ingrained across written literature and spoken conversation. This project has variously expanded in the 2010s to a quantum compositionality (Coecke, Aerts), a statistical physics basis (Burridge), mathematic patterns in mythologies (Kenna, et al), and so on. Other sections such as The Book of Naturome, An Informational Source and Emergent Genetic Information also have apropos citations.

2020: By this date many diverse studies have quantified that even our vernacular languages and written literature can necessarily be seen as reflections of nature’s independent complex, fractal network systems. As another aspect, an intrinsic textual literacy is found to have an expressed occasion from quantum compositions through the evolution of a relative accumulated knowledge repository all the way to our alphabetic paper volumes and now online ebook/ejournal modes.

Arias-Gonzalez, Ricardo. Writing, Proofreading and Editing in Information Theory. Entropy. 20/5, 2018.
Bost, Xavier and Vincent Labatut. Extraction and Analysis of Fictional Character Networks. ACM Computing Surveys. 52/5, 2019.
Burridge, James and Tamsin Blaxter. Spatial Evidence ther Language Change is not Neutral. arXiv:2006.07553.
Chai, Lucy and Danielle Bassett. Evolution of Semantic Networks in Biomedical Texts. arXiv:1810.10534.
Coecke, Bob. Compositionality as We See it Everywhere Around Us. arXiv:2110.05327..
Gallego, Angel and Roman Orus. The Physical Structure of Grammatical Correlations. arXiv:1708.01525.
Kenna, Ralph, et al, eds. Maths Meets Myths: Quantitative Approaches to Ancient Narratives. International: Springer, 2017.
Markovic, Rene, et al. Applying Network Theory to Fables: Complexity in Slovene Belles-Lettres. Journal of Complex Networks. 7/1, 2019.

Mufwene, Salikoko, et al. Complexity in Language: Developmental and Evolutionary Perspectives. Cambridge: Cambridge University Press, 2017
Najafi, Elham and Amir Darooneh. A New Universality Class in Corpus of Texts: A Statistical Physics Study. Physics Letters A. 382/1140, 2018.
Ramirez-Arellano, Aldo. Classification of Literary Works: Fractality and Complexity of the Narrative, Essay, and Research Article Entropy 22/8, 2020.
Souza, Barbara, et al. Text Characterization Based on Recurrence Networks. arXiv:2201.06665.
Stepney, Susan and Andrew Adamatzky, eds. Inspired by Nature. International: Springer, 2018.

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4. Universality Affirmations: A Critical Complementarity

This is a new 2016 section to report an increasing scientific witness and confirmation of an evolutionary developmental genesis that iteratively repeats itself in exemplary kind at every phase and instance from universe to us. A distillation is underway from self-organizing, complex adaptive network systems to a single, iconic particle/wave, DNA/AND, node/link complementarity and whole triality. So as we track the global literature, citations of a true “universality” are now being admitted. We cite next a summary for a 2018 Stochastic Models in Ecology and Evolutionary Biology conference, (search Venice), as a good example.

Living systems are characterized by the emergence of recurrent dynamical patterns at all scales of magnitude. Self-organized behaviors are observed both in large communities of microscopic components - like neural oscillations and gene network activity - as well as on larger levels - as predator-prey equilibria, to name a few. Such regularities are deemed to be universal in the sense they are due to common mechanisms, independent of the details of the system. This belief justifies investigation through quantitative models able to grasp key features while disregarding inessential complications.

Fast forward to 2020, this perception has become known as a “self-organized criticality” between opposite but reciprocal domains of more or less order in dynamic balance. As our worldwide learning curve rises, new entries from physics to neuroscience (Stuart Kauffman, William Bialek, Miguel Munoz, Dante Chialvo, et al) report that living systems seem to seek and prefer an active repose between such complementary states. These dual, polar states take on archetypal modes such as conserve and create, maintain and evolve. A technical version of this natural attractor is cited as a chimera condition (Zakharova, Bastidas, et al) whence “coherence and incoherence” coexist at the same time.

Another salient indication is the wide-ranging employ of (artificial) neural networks, along with genetic sequencing techniques, to study disparate realms from quantum phases to the gamut of cosmic, creaturely and societal realms. In similar regard, algorithmic, self-organizing map, astroinformatic, statistical physics, phylogenetic tree and other methods are being repurposed to quantify areas from galaxies and chemistry to language and ecosystems.

And it ought to be noticed that this epic discovery (see Ecosmomics intro) appears to imply and represent gender principles, yang and yin once again within a Taome trinity. How neat it would be if a bicameral sapiensphere learning on her/his own, could gain such 2020 binocular vision of a family ecosmos. And how wonderful if political parties locked destructive conflict could reinvent themselves as entity/empathy, animus/anima, particle/pattern, me + we = US mutually beneficial halves

2020: From the 1960s general systems theory, the Santa Fe Institute in the 1980s, many theoretical versions, the complexity science project was moved by an incentive to find a common source code that recurs in reliable self-similar kind everywhere. As the introduction above describes, only just now due to our global collaborations has an actual articulation and fulfillment been achieved.

Aschwanden, Markus. Self-Organized Criticality in Solar and Stellar Flares. arXiv:1906.05840.
Bala, Arun. Complementarity beyond Physics. Basingstoke, UK: Palgrave Macmillan, 2017.
Bastidas, Victor, et al. Chimera States in Quantum Mechanics. arXiv:1807.08056
Chialvo, Dante. Life at the Edge: Complexity and Criticality in Biological Function. arXiv:1810.11737.
Ge, Xiaofei, et al. Self-Organized Critical Dynamics of RNA Virus Evolution. arXiv:2204.08627.
Helmrich, Stephan, et al. Signatures of Self-Organized Criticality in an Ultracold Atomic Gas. Nature. 577/481, 2020.
Jensen, Henrik. Brain, Rain and Forest Fires: What is Critical about Criticality. Journal of Physics: Complexity. 2/032002, 2021.
Kartvelishvili, Guram, et al. The Self-Organized Critical Multiverse. arXiv:2003.12594.
Munoz, Miguel. Colloquium: Criticality and Dynamical Scaling in Living Systems. Reviews of Modern Physics. 90/031001, 2018.

Notarmuzi, Daniele, et al. Universality, Criticality and Complexity of Information Propagation in Social Media. arXiv:2109.00116.
Paraslesh, Fatemeh, et al. Chimeras Physics Reports. October 2020.
Plenz, Dietmar, et al. Self-Organized Criticality in the Brain. arXiv:2102.09124.
Sakurai, A., et al. Chimera Time-Crystalline Order in Quantum Spin Networks. arXiv:2103.00104.
Sanchez-Puig, Fernanda, et al. Heterogeneity Extends Criticality. arXiv.2208.06439. August 2022.
Tadic, Bosiljka and Roderick Melnik. Self-Organized Critical Dynamics as a Key to Fundamental Features of Complexity in Physical, Biological and Social Networks. Dynamics. 2/2, 2022.
Villani, Marco, et al. Evolving Always-Critical Networks. Life. 10/3, 2020.
Wilting, Jens and Viola Priesemann. 25 Years of Criticality in Neuroscience. arXiv:1903.05129.
Zakharova, Anna. Chimera Patterns in Networks. International: Springer, 2020.
Zamponi, Nahuel, et al. Scale-Free Density and Correlations Fluctions in the Dynamics of Microbial Ecosystems. arXiv:2206.12384.

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5. Common Code: A Further Report of Reliable, Invariant Occasions

By a 2020 wiseworld philoSophia view, many references cited in Parts III: Organic Universe, IV: Cosmomic Code and V: A Systems Evolution describe by an array of approaches and various terms an invariant presence of self-organized, network, complementary patterns and processes everywhere. This section serves to gather more reports which attest to a natural genesis by way of an independent, mathematic, one code system composed of certain dual agency/relation, node/link, member/group complements. In this manner, the universal naturome (cosmome to geonome) double duty becomes manifestly exemplified at each and every procreative stage. From protein webs to desert biotas, human cultures, microbes to a metropolis, onto the interstellar raiment, one same triality repeats over and over. We next post, for an example, a 2019 mission statement of the Santa Fe Institute.

SFI researchers endeavor to understand and unify the underlying, shared patterns in complex physical, biological, social, cultural, technological, and even possible astrobiological, worlds. Our global research network of scholars spans borders, departments, and disciplines, unifying curious minds steeped in rigorous logical, mathematical, and computational reasoning. As we reveal the unseen mechanisms and processes that shape these evolving worlds, we seek to use this understanding to promote the well-being of humankind and life on earth.

2020: As Universality Affirmations above and other places have reported and confirmed, by this binocular, bicameral year an archetypal complementarity within an integral triality has been found in relative kind everywhere. From digital + analog = source program, node + link + network, feminine + masculine = family, and proceeds ever on. In a self-similar ecosmos one universally iterated code is in effect and rises from particle + wave = light, left + right brain = cognizant knowledge all the way to me + We = US. In regard, we seek to enter and center this momentary fulfillment of our historic decipherment endeavor as a premier EarthMost accomplishment.

Amgalan, Anar, et al. Unique Scales Preserve Self-Similar Integrate-and-Fire Functionality of Neuronal Clusters. arXiv:2002.10568,
Araujo, Nuno, et al. Steering Self-Organization through Confinement. arXiv:2204.10059.
Asllani, Malbor, et al. A Universal Route to Pattern Formation. arXiv:1906.05946.
Caetano-Anolles, Derek, et al.Evolution of Macromolecular Structure: A ‘Double Tale’ of Biological Accretion. arXiv:1805.06487.
Frank, Steven and Jordi Bascompte. Invariance in Ecological Patterns. arXiv:1906.06979.
Gagler, David, et al. Scaling Laws in Enzyme Function Reveal a New Kind of Biochemical Universality. PNAS. 119/9, 2022.

Garcia-Ruiz, Ronald and Adam Vernon. Emergence of Simple Patterns in Many-Body Systems from Macroscopic Objects to the Atomic Nucleus. arXiv:1911.04819.
Kim, Hyunju, et al. Universal Scaling Across Biochemical Networks of Earth. Science Advances. 5/1, 2019.
Ribeiro, Tiago, et al. Scale-Free Dynamics in Animal Groups and Brain Networks. Frontiers in Systems Neuroscience. January, 2021.
Sinha, Saurabh, et al. Behavior-related Gene Regulatory Networks: A New Level of Organization in the Brain. PNAS 117/23270, 2020.
Tao, Terence. E pluribus unum: From Complexity, Universality Daedalus. 141/3, 2012.
Wurthner, Laeschkir, et al. Bridging Scales in a Multiscale Pattern-Forming System. arXiv:2111.12043.
Yang, Ruochen and Paul Bogdan. Controlling the Multifractal Generating Measures of Complex Networks. Nature Scientific Reports. 10/5541, 2020.

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C. Our Own HumanVerse (Epi) Genomic Heredity

In Part III, The Information Computation Turn, we saw how space, time, matter and energy is becoming seen as suffused by an informative, program-like quality. Part IV, Cosmic Code, went on to document such an independent procreative system, while Part V, A Quickening Evolution, reported humankind’s nascent integral synthesis of the oriented, gestation of life, mind and self-cognizance. This extensive Part VI, Earth Life Emergence, will attempt to show how these innate, genetic-like, complementary principles are in similar manifestation everywhere. To continue this scenario, its most familiar exemplar, of course, is the genome code that informs the form, function and life span of every organism and person. Since circa 2001, with the sequencing of the human genome, a whole scale revision has been underway as to what constitutes genetic phenomena, broadly considered, which is still being worked out. This section will try to chronicle the many concerted efforts, see also Systems Biology and Genetics above.

While the last half of the 20th century from the 1953 DNA double helix sought to find the nucleotide and associated biomolecules, as readers know, a “systems” turn has begun to study the equally present dynamic regulatory networks that connect all the pieces. In regard, what defines a “gene” is still in abeyance, e. g. strings of codons. With this expansion, a new aspect known as “epigenetics” has opened opens to many external, environmental influences in effect beyond a point molecular locus. So once again the universal complex archetypes of a discrete elemental mode - DNA, along with the interactive relations - AND, with their informative content and communication, are well exemplified.

With these advances, as readers know a multitude of “-omics” have sprung up and taken across every organic scientific field and stage. Proteome, metabolome, cellular interactome, a neural connectome, are among many, each distinguished by an interplay of nodes and links. Thus an emergent genetic phenomena accrues as a fertile cosmos becomes graced with a genome-like essence everywhere. As an example, the popular “major evolutionary transitions” emergence by John Maynard Smith and Eors Szathmary (search & shown next) whence life’s episodic procession from suitable biochemicals to our human phase is at each step facilitated by a novel informative basis. Its linguistic version, one could even say “languagome,” is covered in A Cultural Code.

2020: In 2000 genome sequencings were just possible, but prior point gene to disease or malady model was still in place. By 2010, it was realized that much more was going on beyond discrete nucleotides. As the presence of complex gene regulatory networks was becoming known as they served to join the biomolecular components. A notice of “epigenetic” influences beyond the genome added a further interactive dimension. A whole scale approach dubbed “genome wide association studies” viewed genetic influences, broadly conceived, all the way to natural and social environs. By this year, TV documentaries such as The Gene by Ken Burns based on Siddhartha Mukherjee’ book, The Gene Doctors about medical applications, and CRISPR: The Realities of Gene Editing (as now readily doable) were being aired. A popular interest arose to fill in one’s family tree ancestry by low cost sequence studies. But the prime 21st century advance is a public awareness of how pervasively our lives, broadly conceived, are the ordained result of this generative source.

Barabasi, Daniel and Albert-Laszlo Barabasi. A Genetic Model of the Connectome. Neuron . 105/1, 2020. Cowen, Lenore, et al. Network Propagation: A Universal Amplifier of Genetic Associations. Nature Review Genetics 18/551, 2020. Eraslan, Gokcen, et al. Deep Learning: New Computational Modelling Techniques for Genomics. Nature Reviews Genetics. 20/7, 2019. Kaye, Alice and Wyeth Wasserman. The Genome Atlas: Navigating a New Era of Reference Genomes. Trends in Genetics. January, 2021 Koonin, Eugene. CRISPR: A New Principle of Genome Engineering Linked to Conceptual Shifts in Evolutionary Biology. Biology & Philosophy. 34/9, 2019. McGillivray, Patrick, et al. Network Analysis as a Grand Unifier in Biomedical Data Science. Annual Review of Biomedical Data Science. Vol. 1, 2018. Misteli, Tom. The Self-Organizing Genome: Principles of Genome Architecture and Function. Cell. 183/1, 2020. Mukherjee, Siddhartha. The Gene: An Intimate History. New York: Scribner, 2016. Nussimov, Ruth, et al. Protein Ensembles Link Genotype to Phenotype. PLoS Computational Biology. June, 2019. Sherman, Rachel and Steven Salzberg. Pan-Genomics in the Human Genome Era. Nature Reviews Genetics. 21/243, 2020. Snyder, Michale, et al. Perspectives on ENCODE. Nature. 583/693, 2020. Stenseth, Nils, et al.. Gregor Johann Mendel and the Development of Modern Evolutionary Biology. PNAS. 119/30, 2022. Warrell, Jonathan and Mark Gerstein. Cyclical and Multilevel Causation in Evolutionary Processes. Biology & Philosophy. 35/Art.50, 2020. Zimmer, Carl. She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity. New York: Dutton, 2018. 2023:

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1. Paleogenomics, Archaeogenomics: Natural Ancestry

This circa 2015 section is added to gather historic expansions of genetic research techniques so as to begin to recover and reconstruct all manner of prior entities, migrations, timelines and more. By this vista, a temporal “paleo” evolutionary retrospect across a span biospheric creatures from insects to sapiens can be perceived. As the entries describe, incipient attempts began in the 1980s and 1990s to recreate the DNA genomes of hominids and primates. After the 2001 Human Genome project, aided by sophisticated instruments and computer informatics, it became increasingly possible to sequence any present or past entity from Neanderthals and hominids to dinosaurs and onto invertebrates.

A companion effort is the ENCODE: Encyclopedia of DNA Elements project, which began in 2003 and proceeds apace with advanced genome sequencing. In February 2015 a similar discernment of the multifaceted Human Epigenome was announced. Together with the molecular nucleotide substrate, this much expanded appreciation of genetic phenomena promises many benefits. If we might reflect upon and extrapolate these abilities, collaborative human beings over round Earth might well seem to be the universe’s way, billions of years on, to achieve a whole-scale self-sequence of its own natural genetic code.

2020: As a result of steady advances in DNA sequence techniques. Into the 2010s it has become possible for our Earthhomic sapience to recover and recreate the hominid and primate lineages from when we came. In addition, all manner of prior migrations, ethnic mixings, ancient settlements, animal domestications, and even linguistic, artifactual and cultural mores can be genetically revealed. Frontier projects are proceeding to fill in past creaturely evolutions for canine and equine species even onto invertebrates. See Multiple Ancestries of Homo Sapiens above for more.


Allaga, Benoit, et al. Universality of the DNA Methylation Codes in Eucaryotes Nature Scientific Reports. 9/173, 2019.
Benitez-Burraco, Antonio and Dan Dediu. Ancient DNA and Language. Journal of Language Evolution. 3/1, 2018.
Frantz, Laurent, et al. Animal Domestication in the Era of Ancient Genomics. Nature Reviews Genetics. 21/8, 2020.
Krause, Johannes and Thomas Trappe. A Short History of Humanity: A New History of Old Europe. New York: Random House, 2021.
Racimo, Fernando, et al. Beyond Broad Strokes: Sociocultural Insights from the Study of Ancient Genomes. Nature Reviews Genetics. June 2020.
Reich, David. Ancient DNA and the New Science of the Human Past. New York: Pantheon, 2018.
Skoglund, Pontus and Iain Mathieson. Ancient Human Genomics: The First Decade. Annual Review of Genomics and Human Genetics. Vol. 19, 2018.

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2. The Innate Affinity of Genomes, Proteomes and Language

Around 1970, the linguist Roman Jakobson and the biopsychologist Jean Piaget opined that these prime informational domains ought to have common similarities. The familiar phrase Book of Life, along with analogous usage of language terms in genetics was popular at the time. Over subsequent decades, as gathered herein, parallels between the two code scripts grew in veracity and value, often as an insightful cross-comparison. We post this 2016 section because recent contributions strongly confirm an innate, natural continuity. A March 2016 issue of the Philosophical Transactions of the Royal Society A on “DNA as Information” (Julyan Cartwright) supports this view by novel rootings of genome phenomena in mathematics, physics and chemistry.

2020: As our worldwise personsphere proceeds to learn and know on her/his own, an ecosmic correlation and cross-translation between these archetypal generative codes is strongly evident. Both phases take on a commonly manifest textual, informative scriptome guise. A novel indicative sign, as entries convey, is an on-going transfer and avail of common sequencing and parsing techniques in both realms.

Bepler, Tristan and Bonnie Berger. Learning the Protein Language: Evolution, Structure, and Function. Cell Systems 12/6, 2021
Faltynek, Dan, et al. On the Analogy between the Genetic Code and Natural Language by Sequence Analysis. Biosemiotics. April, 2019.
Ferruz, Noelia, et al. ProtGPT2 is a Deep Unsupervised Language Model for Protein Design. Nature Communications. 13/4348, 2022.
Lackova, Ludmilla. Folding of a Peptide Continuum: Semiotic Approach to Protein Folding. Semiotica. 233/77, 2020.
Ros, Enric, et al. Learn from Nature to Expand the Genetic Code. Trends in Biotechnology. 19/5, 2021.
Wang, Li-Min, et al. Mechanism of Evolution Shared by Genes and Language. arXiv:2012.14309.
Zolyan, Suren. From Matter to Form: The Evolution of the Genetic Code as Semio-poiesis. Semiotica. March 2022.

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3. Whole Genome Regulatory Systems: DNA + AND = ANN/DAN

As our emergent sapiensphere proceeds to learn on her/his own, we add a 2015 section akin to other natural Systems units because genetic phenomena, with the internal components now identified and sequenced, are being seen and treated by the same informational, self-organized, complex modular network criticalities as everywhere else. In this Omics era whole genomes appear as a prime exemplar of this independent mathematical source. Nodal DNA nucleotides + connective AND networks array across dynamic scales to inform and guide life’s evolutionary gestation, each myriad creature, ourselves, and a celestial ovoGenesis. Gene regulatory networks (GRNs) which connect nucleotides and biomolecules are receiving concerted notice, as references attest.

2023: As international genetics research advanced the 2010s, an approach called ‘genome-wide association studies” or GWAS arose so as to view, represent and treat entire genomes. Further expansions involved “epigenetic” influences beyond a nucleotide basis, along with community, ethnic, regional, and environmental aspects. By so doing integral genomes became understood as self-organized, networked, critically poised composite entities. As a result, genomes, along with neural connectomes, become akin to other natural and social phases within a nascent ecosmos Omicsphere. The references below are meant convey how a spiral shift is to apply AI large language neural net learning methods to this premier informative phase

Angelin-Bonnet, Olivia, et al. Gene Regulatory Networks. arXiv:1805.01098.
Aguirre, Jacobo, et al. On the Networked Architecture of Genotype Spaces and Its Critical Effects on Molecular Evolution. arXiv:1804.06835.
Cowen, Lenore, et al. Network Propagation: A Universal Amplifier of Genetic Associations. Nature Reviews Genetics. 18/9, 2017.
Daban, Joan-Ramon. Soft-Matter Properties of Multilayer Chromosomes. Physical Biology. 18/5, 2021.
Daniels, Bryan, et al. Logic and Connectivity Jointly Determine Criticality in Biological Gene Regulatory Networks. arXiv:1805.01447.
Gourab, Ghosh Roy, et al. Bow-Tie Architecture of Gene Regulatory Networks in Species of Varying Complexity. Journal of the Royal Society Interface. June, 2021.
Misteli, Tom. The Self-Organizing Genome: Principles of Genome Architecture and Function. Cell. 183/1, 2020.
Roman-Vicharra, Cristhian and James Cai. Quantum Gene Regulatory Networks. arXiv:2206.15362.
Verd, Berta, et al. Modularity, Criticality, and Evolvability of a Developmental Gene Regulatory Network. eLife. 8/e43832, 2019.

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