IV. Ecosmomics: Independent, UniVersal, Complex Network Systems and a Genetic Code-Script Source

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.

Renken, Elena. Turing Patterns Turn Up in a Tiny Crystal. Quanta. August 10,, 2021.

Rosas, Fernando, et al. An Information-Theoretic Approach to Self-Organization. arXiv:1808.05602.

Sanchez-Puig, Fernanda, et al. Heterogeneity Extends Criticality. arXiv.2208.06439.

Strogatz, Steven, et al. Fifty Years of “More is Different.” Nature Reviews Physics. April, 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.

Thurner, Stefan, et al. Introduction to the Theory of Complex Systems. Oxford: Oxford University Press, 2018.

Wolfram, Stephen. The Physicalization of Metamathematics and Its Implications for the Foundations of Mathematics. arXiv:2204.05123.

Zhang, Mengsen, et al. Topological Portraits of Multiscale Coordination Dynamics. Journal of Neuroscience Methods. Vol. 339, 2020.

View the 202 Bibliographic Entries

A. 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.

2023:

View the 173 Bibliographic Entries

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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B. 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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