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

. Cosmo Sapiens: A 2004 - 2014 Decadal Review

The Two Infinities of a Particulate Multiverse
1.0 Infinite Cosmic Breadth
2.0 Infinitesimal Atomic Depth

A Third Infinity of Life, Code, Complexity, Mind, and Symbiotic Selves

1.0 A 21st Century Systems Synthesis

2.0 Ecosmos: A Fertile Spacescape

2.1 Physics and Biology Reunite
2.2 Astrochemistry and Astrobiology
2.3 Quantum-Classical Integration
2.4 Statistical Mechanics and Complexity Science
2.5 Active Matter
2.6 Systems Cosmology
2.7 Organism as Machine Metaphor
2.8 Cosmic Consciousness
2.9 Universal Darwinism

3.0 Habitable Heavens: A Proliferation of Planets

4.0 Cosmome: A Mathematic Materiality

4.1 An Information Milieu
4.2 Algorithmic Computation
4.3 Cellular Automata
4.4 Nonlinear Complex Self-Organization Sciences

5.0 A Genesis Evolutionary Synthesis
5.1 A Skeletal Scaffold
5.1.1 The Origins of Life
5.1.2 The Major Transitions Scale
5.1.3 A New Evolutionary Synthesis

5.2 A Natural Genotype

5.3 Embryogeny: Evolution and Development
5.3.1 Anatomy and Physiology
5.3.2 A Constant Convergence
5.3.3 Encephalization – A Neural, Cognitive, Learning Experience
5.3.4 The Prevalence and Primacy of Cooperation

5.4 Animal Consciousness, Intelligence, Personality, Behavior, Sociality, Culture

5.5 A Ubuntu Universe: Our Symbiotic Selves

6.0 A Human and Humankinder Epitome
6.1 Phenomenal Persons
6.1.1 Systems Physiology and Psychology
6.1.2 Systems Neuroscience: Our Mindful Microcosm
6.1.3 Our Conscious Knowledge

6.2 An Emergent Humankind
6.2.1 Cultural Code: Systems Linguistics
6.2.2 Complex Symbiotic Societies
6.2.3. A Planetary Physiosphere: Anatomics, Economics, Urbanomics
6.2.4 Systems History: Planetary Individuation

With an acquaintance with our resident planetary progeny in place, we move on to humankinder’s collaborative witness of an organic procreative uniVerse as an ecosmos Copernican revolution. For this vista, as the Human and UniVerse table conveyed, an overall theme and motif becomes evident. While the 20th century and earlier was a prior, necessary scientific phase of taking matter, life, earth, and nature apart for reductive, particulate analysis, dividing into many topical fields, today a subsequent global reunification of a cosmic genesis and phenomenal people is much underway.

At the outset it serves to contrast past and future models, paradigms or scenarios. To do so we draw upon a working “three infinities” view. An initial exploration and research sought to plumb large cosmic and small atomic dimensions. Presently, a “third infinity” or stage has been engaged to study life’s emergent complexity and consciousness. Presciently cited by Pierre Teilhard in the 1930s, this phrase is the title of a 2013 Max Planck Institute conference on the Physics of Biological and Complex Systems (search Domany). It is this latter turn that we are most trying to express and document.

We begin with a look at The Two Infinities of a Particulate Multiverse. Beyond this prior matrix, we survey A Third Infinity of Life, Code, Organization, Mind, and Symbiotic Selves. This waxing phase has general sections of Systems Shift, Organic Life and Substantial Cosmos, Earth and Heavens, Mathematics and Materiality, Genesis Evolutionary Synthesis, UniVerse and Human Epitome.

The Two Infinities of a Particulate Multiverse
Two days after the 2014 Nobel physics prize, Nigel Goldenfeld (search) spoke at the University of Massachusetts, Amherst where he announced “Biology is the physics of the 21st century.” We seem in the midst of an epochal traverse between an old and new universe, which Natural Genesis attempts to collate and document.

Surely readers are familiar with the legendary chronicle from the 17th century scientific revolution to explore and experiment. The project proceeded to this day to collect, identify, name, characterize, and sort all the parts and facets from quarks, bosons and quasars to elements, chemicals, fossils, creatures, continents, bubble cosmoses, every last thing. This initial, necessary stage of object emphasis sought all the “cosmic Legos” building blocks, per Max Tegmark (2014). But the pursuit has stopped there, unable to connect the dots, so concludes nature is pointless and signifies nothing. To a large degree, any systemic relations in between, or an implicate generative source, a systems physics, has remained outside its machine model. We next register Infinite and Infinitesimal aspects, which in the past two years have reached closure with findings of the Higgs Boson and signs of original gravitational waves.

1.0 Infinite Cosmic Breath What a fantastic journey human beings have been on from a home world once at the center of starry raiment to orbiting a sun, Milky Way galaxy, then myriad galaxies, a singular point of cosmic origin, and now a multitude of vicarious universes. Whoever are we altogether to be able to do and learn this, surely there must be a reason and discovery of cosmic significance.

As an entry we cite an arXiv:1402.0527 eprint entitled Inflationary Cosmology after Planck 2013 where the Russian-American physicist Andrei Linde posts his latest views of an initial expansive event. Linde, with Alan Guth, were prime conceivers of this theory in the 1980s. In September 1983 I attended Linde’s first public lecture in the United States at Harvard, where he spoke of bubbling fractal cosmoses. He remains on message decades later, as does Guth who I have also heard. But speculative versions still vie, often as opinions and/or metaphysics, with little or no reference to an independent mathematics or greater reality. Our human acumen that can quantify such reaches are rarely factored in or given a place and purpose.

And readers know, in March 2014 it was announced as front page news that the BICEP2 (Background Imaging of Cosmic Extragalactic Polarization) project at the South Pole seemed to detect gravity waves from the early universe that if real would prove an inflationary start, and the overall cosmological scenario. Its main posting is arXiv:1403.3985. In the meantime this report has come under much scrutiny, for example in Physics Review Letters Editorial: Signals from the Dawn of Time? (112/240001, 2014) – is it just dust or what.

For another angle, from a string theory school, whence physical particles are seen as one-dimensional objects called strings, (search Google) these latest quantum cosmology results are taken as confirmation of a numberless flickering universes, maybe parallel or serial, a multiverse milieu. (This evident scenario will be seen in the Part III posting to have a genesis essence.) But alas our habitable cosmos is then a rare, accidental concatenation. Quite up for grabs, for example The Singular Universe (December 2014) by physicist Lee Smolin and philosopher Roberto Unger contend they only occur one at a time but remain inane happenstance.

2.0 Infinitesimal Atomic Depth
At the other extreme, the ever deeper descent begun by Max Planck, Niels Bohr, a renowned cast, from opaque atoms to a proton/neutron center and orbital electrons onto a colorful zoo such as baryons, muons, gluons, leptons, charmed quarks in scalar or nested forms. We mention Nobel laureates Murray Gell-Mann, Sheldon Glashow (who I heard speak in October), Steven Weinberg, and Abdus Salam, amongst thousands of contributors. A grand triumph in 2012 was the detection in the ten billion dollar Large Hadron Collider built by the European Organization for Nuclear Research (CERN) of the subatomic Higgs boson, whose finding was crucial to the particle physics standard model. This finding confirmed a long period of theory and test, but is seen as bringing an end to that stage. Commentators have wondered what might it signify, if anything, and whatever to do next.

So this historic exploration of the opposite breadth and depth environments, with valiant earthlings in between has much run its course. But in some Ptolemaic way, as lately noted, some critical quality is missing to explain sentient peoples able to traverse such magnitudes. Into the 21st century, as if a parallel paradigm, by a worldwise science and scholarship, a network systems cosmology, physics, chemistry, and developmental evolution, along with every realm, a Copernican revolution is well along. Uniquely facilitated by the enveloping collaborative Internet, nature’s material substance is again becoming active, fertile, a conducive matheMatter spacescape. We next introduce a third infinity of life’s quickening complexity and consciousness. OK

A Third Infinity of Life, Code, Organization, Mind, and Symbiotic Selves
An overall theme can distinguish this occasion. By our humankinder vista, circa 2014, the many disparate domains from interstellar to social media are in the midst of a holistic reassembly and reunion unto one whole animate dynamic universe. What was first necessary to take apart as a machine, is now being put back together in an organic way. A measure is the complex network systems turn underway in every field from biology and genetics to quantum and cosmos. It is then apparent that an iterative repetition of the same pattern and process occurs in relative kind at each stage and instance. As a consequence, an independent, mathematical, recurrent universality, intimated through history, is at last proven. OK

In regard, as a ready name we offer “uniVerse” with a capital V to indicate its heretofore missing narrative script. Another term might be “Ecosmos” for an ecological spacescape. We next arrange this global unification into general sections: Systems Synthesis, Ecosmos: An Organic UniVerse, Earths and Heavens, Mathematics and Materiality, A Genesis Evolutionary Synthesis, UniVerse and Human Epitome.

1.0 A 21st Century Systems Synthesis A familiar entry would be the systems biology turn from a prior emphasis on biomolecular components to equally important relations, interactions, webworks and cross-communication in between. In 2001 leading human genome sequencers such as Francis Collins, Craig Venter, Leroy Hood, and others were quick to say that finding the discrete genes was only half the task. While the goal of one gene to one trait or disease has not worked out, much progress since has discerned interconnective modules and nested networks for nucleotides, proteomes, epigenomes, metabolomes, onto neural connectomes and more.

The Natural Genesis resource site tries to document this course correction and holistic completion, which now has an “–omics” interpretation from cosmos to cultures. It is reflected in the outline across Quantum, Astrobiology and Chemistry realms to Neuroscience, Psychology and History as well, and in cases as Systems Physics when not yet at the fore. A 2014 volume A Systems View of Life by Fritjof Capra and Pier Luigi Luisi is an excellent survey, which we cite next.

Such a new understanding of life is now emerging. At the forefront of contemporary science, we no longer see the universe as a machine composed of elementary building blocks. We have discovered that the material world, ultimately, is a network of inseparable patterns of relationships; that the planet as a whole is a living, self-regulating system. The view of the human body as a machine and of the mind as a separate entity is being replaced by one that sees not only the brain, but also the immune system, the bodily tissues, and even each cell as a living, cognitive system. (Capra and Luisi)

Within our humankind purview, to express the extent of this revolution we note its copious scope in scientific fields such as astrobiology and traditional chemistry which have seen fit to reinvent themselves as Systems studies.

What is Systems Chemistry? It’s the study of complex systems, or networks, of molecules. Tools for analyzing complex networks are being developed and employed in fields as diverse as computer science and sociology. By applying these tools to systems of interacting molecules – molecules that might link together into larger superstructures, or catalyse one another’s formation – chemists can investigate how interactions between members propagate through networks, allowing complex behaviour to emerge. (Jonathan Nitschke)

We have attempted to illustrate how systems astrobiology assumes a new role in the science of astrobiology. In our theory of life in the universe, we have underlined several stages that are analogous with the standard systems biology, namely: 1. The theory: the universe is treated as a complex system with evolutionary convergence. 2. The computational modelling: statistical correlations of astronomical data are needed from Kepler and subsequent missions and spectroscopic data from the HST and the next generation of space telescopes. 3. A testable hypothesis: the Earth-like exoplanets in HZs of MS stars will yield anomalous fractions of biogenic gases in the spectroscopic analyses of their atmospheres. 4. The complex system: the universe itself is interpreted as a complex system. (Julian Chela-Flores)

This radical, imperative shift across the sciences is evident by noting that social studies, psychology and linguistics, many other fields, have also strongly endorsed. While environmentalists perceived intricate eco-systems from the early days, economies and cities are now likewise viewed as animate organizations, as A Planetary Physiosphere reports. Another affirmation is expressed by Temple University psychologist Willis Overton, and colleagues, in the next quote. Similarly Clay Beckner, speaking for an extended team, applies the same “complex adaptive systems” model to language and dialogue.

This chapter argues that the Cartesian-split-mechanistic scientific paradigm that until recently functioned as the standard conceptual framework for subfields of developmental science (including inheritance, evolution, and organismic—prenatal, cognitive, emotional, motivational, sociocultural—development) has been progressively failing as a scientific research program. An alternative scientific paradigm composed of nested metatheories with relationism at the broadest level and relational developmental systems as a midrange metatheory is offered as a more progressive conceptual framework for developmental science. (Overton, 2013)

Language as a CAS involves the following key features: The system consists of multiple agents (the speakers in the speech community) interacting with one another. The system is adaptive, that is, speakers’ behavior is based on their past interactions, and current and past interactions together feed forward into future behavior. The structures of language emerge from interrelated patterns of experience, social interaction, and cognitive mechanisms. The CAS approach reveals commonalities in many areas of language research, including first and second language acquisition, historical linguistics, psycholinguistics, language evolution and computational modeling. (Beckner, 2008)

This Systems re-unification by a bicameral humanity, if to admit the very vista, is a main feature of our revolutionary reconception from a barren material mechanism to an quickening organic development, which we review next. OK

2.0 Ecosmos: A Fertile Spacescape
In our planetary purview, an independently innate organic, proactive presence is being encountered from several approaches. Among these are the vital reunion of physics and biology, astrochemistry and astrobiology, a quantum-classical synthesis, an “active matter” appreciation, “systems physics” as statistical mechanics joins complexity theory, and much more. OK

2.1 Physics and Biology Reunite As the Revolution Table shows, since the 17th century, an inane dichotomy has existed between an inhospitable physical cosmos and the presence of living, evolving, personal, sentient beings. This disconnect and impediment is at last being resolved, as it must be, by our global genius. The Systems Physics, Active Matter: The Reunion of Biology and Physics, Systems Cosmology sections, and elsewhere cite many contributions that quantify and approve. Among advocates and theorists are William Bialek, Sriram Ramaswamy, Cristina Marchetti, Andrea Cavagna, Irene Giardina, Nicholas Ouelette, Erwin Frey, and Nigel Goldenfeld, who we quote next.

With the growing recognition of the importance of collective phenomena in evolution, but also in ecology, immunology, microbiology and even global climate change, it is timely to assess the extent to which a condensed matter physics perspective—with its unifying principles of collective behavior arising from interactions—can be illuminating in biology. Equally fascinating is the notion that biology may extend the frontier of non-equilibrium physics, revealing principles of self-organization that seem absent in purely physical processes such as pattern formation. (Goldenfeld/Woese, 2011)

2.2 Astrochemistry and Astrobiology In a July 2011 TED talk “The Stuff of Life: Making Matter Come Alive,” Lee Cronin (search), a University of Glasgow professor of chemistry advised that cellular beings seem to be as encoded into the universe as the stellar galaxies. Over the past decade, an interdisciplinary cross-fertilization has led to an ever deeper rooting of living systems into an increasingly conducive cosmos. As reported throughout Organic Universe, an innate natural propensity is being found and quantified from elemental nucleosynthesis to an array of complex biochemicals across the interstellar medium. A gravid cosmic genesis is now known to form bioprecursors for evolving organisms and cognitive sapiens by its own quintessence.

But there's a problem, because up until maybe a decade ago, we were told that life was impossible and that we were the most incredible miracle in the universe. In fact, we were the only people in the universe. So as a chemist, I wanted to say, "Hold on. What is going on here? Is life that improbable?" And this is really the question. I think that perhaps the emergence of the first cells was as probable as the emergence of the stars. And in fact, let's take that one step further. Let's say that if the physics of fusion is encoded into the universe, maybe the physics of life is as well. (Lee Cronin)

2.3 Quantum-Classical Integration: Another untenable divide has persisted for a century between this infinitesimal, subatomic domain and overt macroscopic forms and phases. Technical terms such as entanglement, superposition, uncertainty, decoherence, nonlocality led to an arcane, off-putting strangeness, daunting efforts to unify and make sense of things. Around 2003 this began to change by realizations that quantum phenomena seems to be most characterized by information and its processing. With an incentive of quantum computers, these real properties are much researched and employed, as noted in the Information Computation section.

But since 2010, as every other natural and social strata, the complexity turn spread to these depths as it became clear that nonlinear complexities are just as prevalent there. Here is a good example of a mostly unnoticed advance that can be apparent by our humankind ken. One can now search arXiv e-prints for “quantum” self-organization, networks, modularity, and get a growing number of responses. A 2014 posting there by the Nobel laureate Gerard ‘t Hooft (search) is an emphatic statement not only of this merger but of the necessary existence of a greater intelligible reality from which all arises. A Quantum Complex Systems section has been added for this literature. International conferences such as Emergent Quantum Mechanics 2011 and 2013 (Google “EmQM” and search here), and the Heinz von Forester Self-Organization and Emergence Congress (2011) did much to establish their presence and basis. OK

We hope to inspire more physicists to do so, to consider seriously the possibility that quantum mechanics as we know it is not a fundamental, mysterious, impenetrable feature of our physical world, but rather an instrument to statistically describe a world where the physical laws, at their most basic roots, are not quantum mechanical at all. (‘t Hooft, 2014)

Another significant aspect then came to light. As the micro-macro rift is healed, it is being concluded this is where the turtles bottom out, no further material stage lies beneath. Rather both quantum and classical realms can be understood as arising from a deeper, non-material, mathematical source. In the other direction, as nonlinear quantum complexities are explored, the presence of quantum-like effects has become evident in regnant nature and society. Recent books such as Quantum Effects in Biology Decision by Masoud Mohseni and Yasser Omar discuss equivalent effects in biological, psychological, cognitive, and societal aspects.

In a historical train, it is worth notice that two prescient, sage scientists are often referred to. John Archibald Wheeler’s (1911-2008) famous “It from Bit” phrase whence “under and behind quantum mechanics lies some deep and wonderful principle yet to be discovered” (Tegmark 2014) is availed as an overall model. Similarly David Bohm (1917-1992) described a dual reality of an independent “implicate” order from which “explicate” manifest worlds spring and exemplify. And of course homage is paid to Galileo Galilei (1564-1642) who wrote that the book of nature must be read in terms of its mathematical language, which maybe we can at long last decipher. OK

2.4 Statistical Mechanics and Complexity Science Around 2007 the traditional fields of statistical, condensed matter, many-body physics began an assimilation and accommodation with nonlinear systems theories because it was realized they studied the same phenomena from different approaches. The endeavor presently comes under Interdisciplinary, Biological Physics, Econophysics, Soft Matter, and so on labels, not really suitable. The nascent synthesis can be seen in journals such as Annals of Physics, Physical Review, Reviews of Modern Physics, Europhysics Letters, Physics Reports wherein complex biological or social phenomena were rarely included. Today more than half of the articles pertain to this subject. For example, the August 15, 2014 contents of Physica A: Statistical Mechanics and its Applications is mostly listed as Dynamical processes, Biological, ecological and evolutionary systems, Econophysics, Other complex systems, Networks, and Systems biology.

2.5 Active Matter This phrase to denote a material spontaneity proceeding on its own was coined in a 2010 paper in the Annual Review of Condensed Matter Physics by Siram Ramaswamy of the Indian Institute of Science. Since it aptly described natural self-organizing phenomena that many researchers were studying, it has become widely used. For an example, Andrea Cavagna and Irene Giardina of the University of Rome (2014) see fit to interpret dynamic bird flocks in this way. A common implication is an independent, universally applicable source that serves to structure and guide nonequilibrium animation from sensitive colloids to creaturely colonies. The new Active Matter section contains current references.

Even more active is a colony of bacteria, each member of which can carry out sustained motion as well as complex signaling and coordination with others. Or think of a flock of birds or herd of migratory animals. Despite obvious differences, these systems all share a similar character as collectives of interacting and self-propelling elements with internal sources of energy. It’s natural to think of all of these as examples of a more general kind of “active” matter – a new frontier where ideas from physics on the principles of order and organization are proving very useful. (Mark Buchanan)

2.6 Systems Cosmology This is title phrase was added in 2012 to Fractal SpaceTimeMatter with the posting of paper on Network Cosmology by Dmitri Krioulov, et al. The concurrent work of Markus Aschwanden and colleagues on self-organized criticalities in astrophysics such as interstellar webs and solar flares, and similar citations, contributes to this novel sense of a celestial ecosystem. This section engages the two, far removed, infinities of quantum and cosmos to show how they are better understood in terms of the same nonlinear dynamical patterns as everywhere in between. Here you will find reports of self-similarity from subatomic charged pions and quantum fluids to particulate clouds and galactic clusters. If to collate these separate accounts within a humankind purview, in our midst a revolutionary systems spacescape akin to a living environment is just being realized.

2.7 The Organism as Machine Metaphor Since this is a natural philosophy endeavor, it is vital that a long-standing conflation with and description of living entities and activities in mechanical terms needs to be addressed. We began this Systems Synthesis with Fritjof Capra and Pier Luisi’s confrontation of the dichotomy. In biological, genetic, and even ecological articles and books, it is standard fare. We read of nucleotide or protein machinery, cells are factories, evolution as a thermodynamic engine. Books have titles such as The Mind’s Machine (psychology) and The Earth Machine (geosciences). Type machinery into the search box on the home page to get more examples. This is an unhelpful contradiction, a fundamental misnomer, yet little if any notice or correction is made.

In regard, we want to cite a recent effort by Daniel Nicholson, an Israeli-British philosopher now at the University of Exeter, who confronts this erroneous usage in evolutionary and developmental paradigms in Studies in History and Philosophy of Biological and Biomedical Sciences (search). A 2012 essay is entitled Organisms ≠ Machines, and in 2014 as The Machine Conception of the Organism in Development and Evolution.

The machine conception of the organism (MCO) is one of the most pervasive notions in modern biology. However, it has not yet received much attention by philosophers of biology. The MCO has its origins in Cartesian natural philosophy, and it is based on the metaphorical redescription of the organism as a machine. In this paper I argue that although organisms and machines resemble each other in some basic respects, they are actually very different kinds of systems. I submit that the most significant difference between organisms and machines is that the former are intrinsically purposive whereas the latter are extrinsically purposive. (Nicholson, 2012)

Although both organisms and machines operate towards the attainment of particular ends - that is, both are purposive systems - the former are intrinsically purposive whereas the latter are extrinsically purposive. A machine is extrinsically purposive in the sense that it works towards an end that is external to itself; that is, it does not serve its own interests but those of its maker or user. An organism, on the other hand, is intrinsically purposive in the sense that its activities are directed towards the maintenance of its own organization; that is, it acts on its own behalf. The intrinsic purposiveness of organisms is grounded on the fact that they are self-organizing, self-producing, self-maintaining, and self-regenerating. (Nicholson, 2014)

2.8 Cosmic Consciousness Still another animate quality comes from novel recognitions of an immanent mindfulness that both suffuses natural materiality and ascends with our evolutionary gestation. We revive this phrase from a century ago to evoke this reunion of matter and mind, rather than an incongruous separation. An admission that aware, informed, knowing sentience is not an “epiphenomenon” but a legitimate subject of science and philosophy is now established. Through sophisticated neuroimaging, international collaborations, better theories, wakeful cognizance is real and amenable to study. This cerebral faculty is seen to arise, as long intimated, by relative degrees through life’s creaturely sequence. While Conscious Knowledge reports on its validity in human persons, Intrinsic Consciousness and Intelligence attests to a natural universe graced with primordial, procreative mind from its original vitality.

Major affirmations were independently made in the 2010s. Mind and Nature by the philosopher Thomas Nagel makes states that by virtue of our own reflective awareness, a cosmic milieu and source must exist from which this acumen arose. A significant parallel has also been drawn between consciousness and a relative knowledge content. The integrated information and global workspace theories of Giulio Tononi, Christof Koch, Bernard Baars, Antonio Damasio, Todd Feinberg, and colleagues, are much along to a mature synthesis. An episodic tandem of and neural complexity and knowing sentience, as Pierre Teilhard once advised, does indeed track and distinguish life’s developmental embryogeny. These same authors, together with physicists Max Tegmark, Alwyn Scott, and Henry Stapp, philosophers Nagel, Francoise Tibika, Menas Kafatos, and Elizabeth Swan, linguists such as Yoshimi Kawade, and a growing chorus now affirm a mindful cosmos which then arises and awakens through nested individuations to ourselves.

We examine the hypothesis that consciousness can be understood as a state of matter, with distinctive information processing abilities. Our approach generalizes Giulio Tononi's integrated information framework for neural-network-based consciousness to arbitrary quantum systems, and we find interesting links to error-correcting codes, condensed matter criticality, and the Quantum Darwinism program, as well as an interesting connection between the emergence of consciousness and the emergence of time. (Tegmark, 2014)

2.9 Universal Darwinism This is a new section in Autumn 2014 for an array of concurrent research methods that are being employed to study a locally stochastic yet globally lawful nature. The working title comes from one view that an evolutionary self-organization and selective optimization may even apply across the celestial reaches. The citations are drawn from the site and convey various interpretations. By turns, Bayesian statistics or inference, genetic and algorithmic computations, Markov processes, neural connectionism, multiple variation and selective retention, iterative maximizations, and so on, are being sensed from quantum and biological phases to planetary, solar and galactic realms.

A 2004 – 2014 survey of an Ecosmos: A Fertile Spacescape can well verify a “Creative, Organic Universe” revolution that the website first set out to document. Before we get to its genetic code source, we enter the grandest discovery of the period, as readers know, of a conducive cosmos, a natural nursery, filled with as many planets as stars.

3.0 A Proliferation of Planets
Although anticipated by visionaries long ago, we had to wait until 1995 for the first actual detection of an orbiting planet in a solar system other than our own. By various methods, independent observatories, and international teams, the number grew into the hundreds in the 2000s. But since the 2009 NASA Kepler Planet Finder Satellite launch, thousands of orbital orrerys from gaseous giants to rocky Earth-analogs have been found everywhere. A radical profligate universe is revealed which by its own energetic and material propensities spawns a profusion of solar systems and bioworlds.
Circa 2012, astronomers have been homing in on a true earth-like neighbor. Solar system depictions in popular magazines and even textbooks come with an intermediate “habitable zone” of favorable thermal and environmental conditions for organic life to originate and evolve. With Nobel laureate Christian de Duve, a fertile raiment is “pregnant” with life, and now with planets, which is not an accident. With more license, a heavenly hatchery seems filled with “solar incubators” for a personal and communal intelligence to emerge and wonder in retrospect. And this epic revolution has hardly dawned upon us.

A major question is whether planets suitable for biochemistry are common or rare in the universe. Small rocky planets with liquid water enjoy key ingredients for biology. We used the National Aeronautics and Space Administration Kepler telescope to survey 42,000 Sun-like stars for periodic dimmings that occur when a planet crosses in front of its host star. We find that 22% of Sun-like stars harbor Earth-size planets orbiting in their habitable zones. The nearest such planet may be within 12 light-years. (Erik Petigura)

The known odds of something — or someone — living far, far away from Earth improved beyond astronomers’ boldest dreams on Monday. Astronomers reported that there could be as many as 40 billion habitable Earth-size planets in the galaxy, based on a new analysis of data from NASA’s Kepler spacecraft. One out of every five sunlike stars in the galaxy has a planet the size of Earth circling it in the Goldilocks zone — not too hot, not too cold — where surface temperatures should be compatible with liquid water. (Dennis Overbye)

This celestial community and neighborhood, often front page news, would imply a gravid genesis of starry galaxies with ovular bioplanets. But a major, explanatory aspect is missing to fulfill an organic familial procreation. The prior scientific project is mostly engaged with overt objects much as resultant “phenotypes.” But over past years, the presence of a natural “genotype” is being realized from many approaches which we review next. OK

4.0 Cosmome: A Mathematic Materiality
At the outset, the scientific perception of an intrinsic formative source is so significant that it ought to have an appropriate name. As a suggestion, “matheMatter” for a spontaneous substantial cosmos with its own informed organization and vitality. Another coinage, noted earlier, is “uniVerse” as an easy way to cite a once and future doubleness that adds to manifest entities and earths a heretofore absent narrative, genetic script.

After the large and small infinities, as if a transitional version and phase, a number of theorists contend that some kind of computational, generative process does seem to be in effect. We mentioned John A. Wheeler’s It from Bit, David Bohm’s implicate/explicate modes, and a quantum rising from a deeper, immaterial basis. We next tour some aspects and schools that presage a cosmic code - an Information Milieu, Algorithmic Computation, Cellular Automata, Nonlinear Complexity Self-Organization, Natural Networks, Complex Adaptive Systems, and a Universality they each infer.

As an entry, the Cosmic Code chapter opens with a 30 page history, topical glossary, and synthesis for the new sciences of complex living systems. Circa 2004, the field remained an eclectic array of facets, emphasis, techniques and approaches being worked through, with arcane terms and little consilience. Here is a list: Agent-Based Modeling, Autopoiesis, Biosemiotics, Cellular Automata, Chaos Theory, Complex Adaptive Systems, Computational Information, Developmental Systems Theory, Dissipative Structures, Dynamical Systems Theory, Econophysics, Ecosystems, 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, Symbiosis, Synergetics, Synergy, Universality. But by this 2014 a unification is underway which we now try to convey.

4.1 An Information Communicative Milieu: Into the 21st century, novel realizations have arisen that physical domains are suffused with a prescriptive content, a prime quality along with and prior to space, time, matter and energy. As James Gleick did for chaos theory in 1987, his 2011 opus The Information lucidly chronicles its occasion. A technical entry could be Information and the Nature of Reality (2010) edited by Paul Davies and Neils Gregersen, and other works in the subject section. To fill out, we note some certain facets such as quantum computation, biological communication, an algorithmic nature, as they form a consensus.

A reformation of Quantum Physicsis underway with information and conveyance as its distinctive feature. Vlatko Vedral, Christopher Timpson, Seth Lloyd, Jeffery Bub and others find it theoretically imperative to admit and include something deeply textual about ponderable things. The promise of super quantum computers is a large factor driving the effort.

Another engagement is concerned with internal and external biological messaging known as Biosemiotics. The term is due to Thomas Sebeok (1920-2001) from “semiotics” or science of signs to express constant communications in organic, animal, and human phases. A major advocate has been Marcello Barbieri, who is editor of a journal with this name, along with expositors such as Jesper Hoffmeyer, Claus Emmeche, Wendy Wheeler, and a prolific Danish-Estonian-Scandinavian nexus. A burst of books can be found at the International Society for Biosemiotic Studies website. Please see the new Life as Biosemiotics section for these many references.

4.2 Algorithmic Computation : A companion effort, often with an information rubric, treats natural, viable, evolving complexity as emerging from a necessary software-like program. This is a “digital universe” view whereof appropriate software-like equations calculate, iterate, and generate from cosmoses to cultures. With the Alan Turing centennial in 2012, many conferences and publications provided endorsements and explanations. A leading advocate is the Serbian-Swedish philosopher Gordana Dodig-Crnkovic, along with Mark Burgin, Barry Cooper, Gregory Chaitin, Hector Zenil, a host of others. A good start could be Turing’s Cathedral by George Dyson. For much more, we have just added a dedicated section, Natural Algorithms, to the main site.

4.3 Cellular Automata The contributions of polymath physicist Stephen Wolfram also merit notice. As his 2002 tome A New Kind of Science describes, this is a technical term for nonlinear programs which as they run produce emergent, animate complexities. On Wolfram’s Blog this approach is “computational knowledge, symbolic programming, dynamic interactivity, algorithm ontology and discovery, we must be on to Something Very Big.” But a greater independent reality, which Wolfram does aver, remains machine or hardware-like, not yet alive and well. To bracket our decade, a 2014 arXiv entry The Cellular Automaton Interpretation of Quantum Mechanics by Nobel laureate physicist Gerard ‘t Hooft, noted earlier, affirms a unified, coherent uniVerse made sensible by such insights.

Our models suggest that Einstein may still have been right, when he objected against the conclusions drawn by Bohr and Heisenberg. It may well be that, at its most basic level, there is no randomness in nature, no fundamentally statistical aspect to the laws of evolution. Everything, up to the most minute detail, is controlled by invariable laws. Every significant event in our universe takes place for a reason, it was caused by the action of physical law, not just by chance. This is the general picture conveyed by this report. (‘t Hooft)

With these various entries in place, we can introduce a huge transformative advance, namely the sciences of complex, self-organizing network systems, which quite exemplify an organic and genetic MatheMatter. OK

4.4 Nonlinear Complex Self-Organization Sciences: A suitable name for the scientific study of nature’s nonlinear dynamic network spontaneities, with many abstract terms, has not yet arisen, to its deficit. As noted, at the request of Yale University colleagues in 2010 I wrote an extended introduction to Part IV: Cosmic Code to arrange and introduce these multiple entries as they try to quantify and express a lively nature that is organizing, developing, becoming by itself. Apropos, Part VI: Universal Principles goes on to report findings of a similar, recurrent pattern and process at each scale and instance from cosmos to civilization.

Our decade neatly brackets a consolidation and maturity of this “theory of everywhere,” more true to life, alternative. While an incipient notice began in the 1980s and earlier, such as general systems theory, from the 1984 Santa Fe Institute to the early 2000s was a preparatory working through its myriad intricacies and facets. For example, ubiquitous scale-free networks only came to light with Albert-Laszlo Barabasi and Reka Albert in 1998.

The situation in 2005 might be conveyed by a book Self-Organization and Evolution of Social Systems, edited by Charlotte Hemelrijk. With e-books, or publisher’s sites, not yet online, one had to find a paper copy. As library catalogs were just on the web, I located one at Yale University. The volume (search CH) was one of the first collections to gather and realize that similar dynamics were in formative effect from microbial colonies to animal groups and even to linguistic discourse. Just nine years later, we mention Yale computational biophysicist Nicholas Ouellette (search) who advised in a talk it didn’t matter which critter or species he choose to study in his laboratory from midges (his choice) to starlings or wildebeests since they each exemplify the same phenomena.

This book contains a collection of studies of social behaviour that are mainly biologically oriented and are carried out from the perspective of emergent effects and self-organization…..the entire range of organisms (from single-celled organisms via slugs, insects, fish and primates to humans). The book treats the broadest range of organisms as regards self-organization and social behavior that has been treated so far in one book. (Hemelrijk, 2005)

As readers know, the whole scene and project has radically shifted into worldwide cyberspace. Printed books are on the wane, paper journals gone from shelves, a revolution dubbed “from Gutenberg to Google” by Peter Burke has overtaken us. With the University of Massachusetts at Amherst close by, at their libraries, or at home, one can log on, access, and print from many thousands of texts and periodicals. Along the way complexity departments or groups have formed across academia and institutes such as the Center for Complex Networks and Systems Research at Indiana University, Max Planck Institute for Dynamics and Self-Organization, and a Complexity Science Initiative at Nanyang Technological University in Singapore.

In the interim years, ubiquitous nonlinear phenomena have now been well researched, terms clarified, with every subject field from cosmology and chemistry to sociology and history redefined and better understood by way of these theories. Mostly independent of each other, planetary motions, river topologies, bacterial films, child psychology, human migrations, and so on are newly appreciated as dynamic complex network systems. The promise of universal, totally repetitive, natural principles has at last been fulfilled. This is an historic discovery which has not registered because it need be attributed to our composite worldwise humankind. With so many constant overt exemplifications in place, it is becoming increasingly evident that there must be an independent mathematical source in generative effect which they manifest.

Complexity science is the study of systems with many interdependent components, which, in turn, may interact through many different channels. Such systems – and the self-organization and emergent phenomena they manifest – lie at the heart of many challenges of global importance for the future of the Worldwide Knowledge Society. The development of this science is providing radical new ways of understanding many different mechanisms and processes from physical, social, engineering, information and biological sciences. (Boccaletti, et al, 2014)

From about 2012 on, papers usually have a lead paragraph saying that just as everywhere else from interstellar media to protein webs and social media, our certain area, say neural memory, evinces the same model. For examples we quote from Individual and Meta-Immune Networks by Sharron Bransburg-Zabary, et al (2013). Its Physical Biology journal is just ten years old. Another is Epidemic Processes in Complex Processes by Romualdo Pastor-Satorras, et al. at the e-print site arXiv:1408.2701.

Complex networks can be found everywhere, in man-made systems and in human social systems, in organic and non-organic matter, in natural and anthropogenic structures as well as in biological systems. Examples include linked molecular or cellular structures, climate networks, communication and infrastructure networks, social and economic networks, gene networks, neuron networks and immune networks. (S B-Z)

In recent years the research community has accumulated overwhelming evidence for the emergence of complex and heterogeneous connectivity patterns in a wide range of biological and socio-technical systems. Here we present a coherent and comprehensive review of the vast research activity concerning epidemic processes, detailing the successful theoretical approaches as well as making their limits and assumptions clear. (R P-S)

For another input, the physicist philosopher Geoffrey West testified in a talk (2011) that the same complex scale invariance recurs over 50 orders of magnitude from microbes to a metropolis. In our online 2014, one can access a conference summary, “25 Years of Self-Organized Criticality” by Markus Aschwanden, et al, that proclaims not only a “universality” of one creative dynamics everywhere, especially in astrophysics, but the strongly implied presence of an independent, mathematical origin.

In another view, Physica A: Statistical Mechanics and its Applications, whose lineage goes back to the 1930s, is now more filled with “Organics” with rubrics as soft condensed matter, dynamical processes, biological, ecological and evolutionary systems, econophysics. A July 2014, Volume 405, sample of papers attests to a global witness of the same something going on at every stage and instance from universe to us: An Introduction to the Physics of Active Matter, Fractals and Self-Organized Criticality in Proteins, Continuum Modelling of Pedestrian Flows, Evolutionary Model of Stock Markets, Evolutionary Model of Stock Markets, and Diffusion of Knowledge and Globalization in the Web of Twentieth Science.

From these divergent and convergent findings, the phrase “Complex Adaptive System” has come into most popular use. In general, it stands for many discrete agents or entities in interaction, guided by tacit rules, in response to variable environments, which altogether self-organize and emerge into a viable whole. Such components could be a prokaryotic bacterium or a financial investor, while communicative interconnections are chemical quorum sensing for microbes, or no insider trading for markets. An important quality to appreciate is that they abide a reciprocal mutuality by semi-autonomous components within a supportive, bounded grouping. And as noted in Systems Science (Yi Lin, et al, 2012) written be Chinese scientists, these dual modes of agent and community can be seen as a 21st century confirmation of Yang and Yin as they form an archetypal gender complementarity. OK

A good introduction would be Complexity: A Guided Tour by Melanie Mitchell which clearly explains nature’s propensities for scale-free networks, power laws, cellular automata, genetic algorithms, cross-conversation, evolvability, and so on, along with founders and researchers. For websites, one could visit the New England Complex Systems Institute, Complexity Digest, Santa Fe Institute, and others around the world.

Altogether as humankind learns by her/his self these decadal findings and reports are an epochal discovery in our midst. Instead of barren, accidental, blind matter and mechanism, a animate, quickening genesis with its own procreative code and phenomenal people to read and realize is just adawning. Such a conducive, expectant spacescape is a fertile ground or womb for life’s emergent development, which we review next.

5.0 A Genesis Evolutionary Synthesis
Within our cosmic revolution theme, older and newer versions of evolutionary theory are similarly in contention. The 1950s Modern Synthesis which joined Darwinian natural selection with Mendelian genetic mutation is seen in need of much updating and extension, if not replacement. But this has not yet occurred and a strident minority claims that chance and winnowing are all that is necessary, or going on. This textbook misinterpretation denies any teleological drive, direction or purpose, which is at the root of a religious or popular rejection. The problem is not so much evolutionary science but this elective distortion and misinterpretation.

Again the two options involve a prior emphasis on particulate objects or a novel sense of informed systemic interconnections. Naturalists first explored and collected the creaturely, cellular, and lately molecular components, the phenotype entities from skeletal fossils to living forms. The voyages and writings of Alexander von Humboldt, Charles Darwin, and Alfred Russel Wallace are legendary. But although the genomes of individual organisms have now been sequenced, evolutionary theory still proceeds without any equivalent natural genotype, much because life is situated in a mechanical, moribund cosmos. By our biological uniVerse or ecosmos coming into view and veracity, this missing concept and quality can be realized as an active matheMatter takes on a genetic essence.

The 21st century advent of a third infinity of animate complexity and consciousness (by literary license we might attribute to a Charles, and Mary EarthWin), is based upon confirmations across a wide array of disciplines and discoveries. Among these are the origin of life, intrinsic self-organization, algorithmic computation, epigenetics, evolution and development aka evo-devo, constant convergence, social cooperation, a major transitions scale, modules and networks everywhere, a deep homology, structural morphogenesis, neural anatomy and intelligence as encephalization, proactive autonomy and behavior, integral symbiotic selves, biosemiotic dialogue, and much more. These topics, as they come to life altogether, are noted here, supported by Part II references, and the whole sourcebook site. A grand achievement of our time can be to realize that life’s long nested maturation is truly an embryonic gestation.

As a general plan, our sapient reconstruction of how we came to be on earth as it is in heaven will be in four parts. An initial skeletal section looks at origins of life, major transitions, and an evolution revolution. Various receptions of an equivalent natural genotype are next. With this in place, the multi-faceted record of life’s developmental emergence via a deeply homologous and convergent morphogenetic anatomy, physiology, and neural system is entered. With body and brain in embryo, a quickening intelligence, personality, autonomy, knowledge, culture, and sociality follows. Finally, we note a 2010s symbiotic synthesis as an integral understanding of individual entities and ambient cooperative groupings.

5.1 A Skeletal Scaffold
5.1.1 The Origins of Life
As we saw in Ecosmos above, the occasion of rudimentary organisms has been traced ever deeper into biochemistry and biophysics. Before the 1960s an abysmal void separated living entities from a physical substrate. Through the 1970s and 1980s I heard researchers such as Cyril Ponnamperuma, Sidney Fox, Gunter Wachtershauser, and Harold Morowitz as they and colleagues methodically explored, filled in and articulated the ancient scenario. Into the 2000s a turn toward experimental and theoretical integration began.

Readers have seen attempts to define “life,” often with a long list of features. Around 2010, by philosophers Carol Cleland, Mark Bedau and others, three aspects came to the fore – physiological metabolism, a replicative, informational program, and membrane containment, a minimal vesicle or cell. Another issue settled was a priority and primacy of either RNA nucleotides or of metabolic functions. Actually both modes appear in some concerted way, see for example How did Metabolism and Genetic Replication Get Married by Vic Norris, et al (2013).

A viable explanation was then completed by factoring in the effect of implicate nonlinear self-organizing imperatives such as autocatalysis. For some examples, see Self-Organization at the Origin of Life as broached by Athol Cornish-Bowden and Maria Luz Cardenas (2008) and Theory, Modelling and Simulation in Origin of Life Studies by Peter Coveney, et al (2012).

5.1.2 The Major Transitions Scale
At the same time that scientific controversy goes on over whether life has an inherent drive or a teleological direction, evolutionary theory, as now pursued by a composite humanity, has actually entered a whole new phase of integral coherence. Instead of gradual, aimless drift, an organizational procession traces an emergent, nested succession or hierarchy of stages from biomolecules to animals to human sociality. Originally conceived by John Maynard Smith and Eors Szathmary in the 1990s over atomic, genetic, cellular, neuronal, organism, primate, and people phases, each with an information carrier from chemicals to language, it has lately come into much use and embellishment.

An overall evolutionary progression to replace aimless blind variation and selective retention is thus well in place. A recent volume is The Major Transitions in Evolution Revisited (2011) edited by Brett Calcott and Kim Sterelny. Another example among many would be Geometry Shapes Evolution of Early Multicellularity by Eric Libby, et al (PLoS Computational Biology 10/9, 2014) which opens with the sentence Organisms have increased in complexity through a series of evolutionary transitions, in which autonomous entities become parts of a novel higher-level entity.

A concurrent effort is contained in Evolution in Four Dimensions: Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life (2005/2014) by Eva Jablonka and Marion Lamb. Again for each stage, with some subdivisions, a code quality is seen to accompany and inform the ascent. So a sharp dichotomy, indicative of a Copernican revolution, is quite in our midst if we might attend, which seems to need a good push to make happen.

In an influential work, Maynard Smith and Szathmáry argued that the majority of the increase in complexity is not gradual, but it is associated with a few so-called major transitions along the way of the evolution of life. For each major transition, they identified specific mechanisms that could account for the change in complexity related to information transmission across generations. In this work, I propose that the sudden and unexpected improvement in the functionality of an organism that followed a major transition was enabled by a phase transition in the network structure associated with that function. (Bela Suki, 2012).

The theory of major transitions has the merit of defining evolutionary increases in complexity both at the phenotypic-organizational (the newly evolved super-units) and genotypic-informational (the new methods of transmitting biological information) levels. Major transitions and the rationale they present for evolutionary increases in complexity suggest that Darwin’s belief in evolutionary progress was not completely unjustified. (Lucio Vinicius, 2010).

5.1.3 A New Evolutionary Synthesis
As Part V: Systems Evolution documents with some 250 entries, research findings from many areas make a novel holistic theory of life’s oriented gestation increasingly imperative. But a vested paradigm and cadre claims that post selection upon passive organisms is the only force necessary or responsible. A mantra has been that “if the tape was played over again” since all is contingent happenstance, human-like beings would not appear a second time.

At the same while, if the wealth of these independent advances via humankind are gathered together, they attest to a quite different picture. An episodic tandem reiteration of bodily form, morphogenesis, cooperative behavior, recapitulations, cumulative cerebration and knowledge gain, and so on from the earliest rudiments now explain life’s evolutionary course much as an embryonic development. This is a huge, corrective achievement which has not yet registered.

A further addition, the crucial missing piece, is an innate formative agency for the myriad phenotypes. Researchers now increasingly assume some manner of intrinsic self-organizing, algorithmic dynamics at work across the systemic, modular and network topologies of the organic kingdoms. A pioneer theorist has been physician and biologist Stuart Kauffman who has long pressed a view that includes both self-organization and selection. In late 2014, an strong affirmation was entered by University of Zurich biologist Andreas Wagner in Arrival of the Fittest wherein nature’s pervasive network propensities serve to complete Darwin’s project by explaining how species appear in the first place. Another instance is a paper The Evolution of Phenotypic Correlations and “Developmental Memory” by Richard Watson, et al (2014) who propose life’s maturation as akin to how a brain forms and learns. Here are samples among a rising chorus. OK

We trace the history of the Modern Evolutionary Synthesis, and of genetic Darwinism generally, with a view to showing why, even in its current versions, it can no longer serve as a general framework for evolutionary theory. The main reason is empirical. Genetical Darwinism cannot accommodate the role of development (and of genes in development) in many evolutionary processes. We go on to discuss two conceptual issues: whether natural selection can be the “creative factor” in a new, more general framework for evolutionary theorizing; and whether in such a framework organisms must be conceived as self-organizing systems embedded in self-organizing ecological systems. (Depew and Weber, 2012)

Our basic claim is that biological thinking about heredity and evolution is undergoing a revolutionary change. What is emerging is a new synthesis, which challenges the gene-centered version of neo-Darwinism that has dominated biological thought for the last fifty years. (Eva Jablonka and Marion Lamb, 2005/2014)

Self-organization permeates the universe so completely that most of us don’t even notice it. Much older that life and natural selection, self-organization is how stars and solar systems form, how the earth accreted, how it acquires a moon, oceans, and an atmosphere, and how the continents started to shift. We shouldn’t be surprised to find self-organization in life’s precursors, because it is everywhere else too. (57) Genotype networks are yet another example of pervasive self-organization – the same phenomenon that pervades both the living and nonliving worlds, from the formation of galaxies to the assembly of membranes. They exist in the timeless eternal realm of nature’s libraries. But they certainly have a form of organization so complex that we are just beginning to understand it, and this organization arises all by itself. (Andreas Wagner, 2014)

That is, the direction of selective pressures on individual relational loci described above has the same relationship with a selective environment that the direction of changes to synaptic connections in a learning neural network has with a training pattern. In other words, gene networks evolve like neural networks learn. Bringing together these two observations with this new in-sight explains the memory behaviors we observe in an evolved network of recurrent nonlinear interactions. (Watson, 2014)

5.2 A Natural Genotype
Again, our premise is that as an evolutionary transition itself fledgling humankinder is proceeding to learn and discover on her/his collaborative own. By this worldwise perspective an animate generative agency prior to, and in concert with, selective effects is being identified and proven. Such an equivalent cosmic genetic code is the crucial missing explanatory element needed to integrate and inform life’s evolutionary gestation in an organic uniVerse.

Over the decade, studies have variously engaged its presence and effect through complex system, algorithmic venues and more. As Cosmome: A Mathematic Materiality above reports, this global project has taken a dual dimension. Across creaturely kingdoms from microbes to sapiens, their exemplary presence and activity is evident at each plane and instance. As a consequence, it has become obvious that some common, independent source must be at work. Generic complex adaptive systems via many agents or entities in communicative interaction appear as self-organized criticalities, gene regulatory networks, and neural connectomes, nested modular communities, and so on as they display a recurrent scale invariance. As prior sections note, these lineaments are further seen in accord with and to spring from with statistical physics phenomena, renormalization groups, algorithmic programs, whatever is their true translation.

One result is the spread and usage of biological –omics designations everywhere such as proteome, metabolome, transcriptome, cellular interactomes, cerebral connectomes, microbiome, organome, phenome, onto culturomics, scientomics, the list goes on. Might we muse a naturome, cosmome, human epitome?

A companion aspect, recorded in the main Cultural Code, is a confirmation, intimated since the 1970s, that genetics and linguistics are deeply alike, as if equivalent projections, and can be studied by similar techniques (Atkinson, 2013). By our purview, they could appear as earlier and later instantiations of life’s informative, genomic passage, might one suggest “languagome.” In a further guise, the nascent field of biosemiotics (see 4.1) is effectively articulating evolution and development as a pervasive array of “organic codes.”

As a contribution to the history of scientific investigations, we trace here a sequence of steps of conceptual and experimental approaches to understand microbial evolution at the molecular level. This shall allow us to extrapolate to generally valid laws of nature guiding biological evolution by self-organization. (Nobel laureate Werner Arber, 2013)

The shared insight from these different approaches is that biological processes are inclined to self-organize, in which a network of localized interactions yields an emergent structure that subsequently feeds back on and strengthens the original network. Our analysis demonstrates that the networks of coregulated gene expression and chromosomal association are indeed mutually related during differentiation, resulting in the self-organization of lineage-specific chromosomal topologies. (Tom Misteli, 2009)

The Neo-Darwinian concept of natural selection is plausible when one assumes a straightforward causation of phenotype by genotype. However, such simple 1:1 mapping must now give place to the modern concepts of gene regulatory networks and gene expression noise. Both can, in the absence of genetic mutations, jointly generate a diversity of inheritable randomly occupied phenotypic states that could also serve as a substrate for natural selection. This form of epigenetic dynamics challenges Neo-Darwinism. It needs to incorporate the non-linear, stochastic dynamics of gene networks. (Sui Huang, 2012)

The contemporary concept of life forms as self-modifying beings coincides with the shift in biology from a mechanistic to informatic view of living organisms. Paralleling the contemporaneous transformation from a largely mechanical-industrial society to a densely interconnected information-driven society, the life sciences have converged with other disciplines to focus on questions of acquiring, processing, and transmitting information to ensure the correct operation of complex vital systems. (James Shapiro, Evolution: A View from the 21st Century, 2011)

5.3 Embryogeny: Evolution and Development
A vital re-integration of evolutionary phylogeny with developmental ontogeny, aka Evo-Devo, has been underway since the 1990s. Along with a missing genome, this reunification of embryology and evolution resolves the separation which took place at the turn of the 20th century. Its robust verification is aided by sorting the endeavor into three phases, namely body, brain and behavior, which are noted next.

5.3.1 Anatomy and Physiology
As an entry, evolutionary biologists Sean Carroll, Neil Shubin and colleagues coined the phrase Deep Homology to convey how animal anatomies and physiologies can be seen to ramify in kind all the way from pre-Cambrian rudiments. For an example, tetrapod, reticulated limbs can be traced from ourselves to amphibians. One might say, along with Shubin’s book title, that people are fish on feet. After a century apart, it is becoming evident that a basic bodily structure as an archetypal Bauplan was in place from the onset. Life’s evolutionary gestation, as each individual embryo, as now filled in, appears as an expansive elaboration via mosaic modules and concerted continuity from the earliest eons to homo and anthropo sapiens.

Homology, as classically defined, refers to a historical continuity in which morphological features in related species are similar in pattern or form because they evolved from a corresponding structure in a common ancestor. Deep homology also implies a historical continuity, but in this case the continuity may not be so evident in particular morphologies; it lies in the complex regulatory circuitry inherited from a common ancestor. The deep homology of generative processes and cell-type specification mechanisms in animal development has provided the foundation for the independent evolution of a great variety of structures. (Shubin, et al, 2009)

The companion experimental and theoretical study of anatomical development and its evolutionary course known as Morphogenesis likewise describes an ancient heritage of form and function. Salient contributions would be Morphogenesis: Origins of Patterns and Shapes (2010) edited by Paul Bourgine and Annick Lesne, and Life Unfolding: How the Human Body Creates Itself (2014) by the Scottish embryologist Jamie Davies. These recent achievements trace our corporeal soma to chemical and physical origins, which is seen to confirm the 20th century prescience of D’Arcy Thompson and Alan Turing.

The way in which adaptive self-organization allows non-living molecules to produce a living cell, and allows cells with very limited individual abilities to produce a very able multicellular body, will form a theme that runs through all of this book because it is the core of development. (Davies)

Another benefit is an appreciation of nature’s essential correspondence between an organism’s developmental ontogeny and life’s maturation as an evolutionary phylogeny. While “universal gestation” was a guiding principle in Darwin’s 19th century day and before, this view was later rejected in its preliminary stage. But as the website section documents, real parallels and recapitulations are now apparent not only for anatomies, but also for language learning, behavioral repertoires, kinetic movement, and more. An especial paper is Von Baer’s Law for the Ages: Lost and Found Principles of Developmental Evolution by the Harvard University geneticist Arhat Abzhanov.

5.3.2 A Constant Convergence
Another relevant aspect of an oriented expression is the verification that life’s long development proceeds and converges from diverse, disparate occasions upon the same solution. Over and over, similar bodily forms and appendages, sensory capacities for sight, hearing, smell, neural network cerebral attributes, onto reciprocal groupings are reached. A foremost advocate, once under attack from deniers, is the Cambridge University paleontologist Simon Conway Morris, as for example in his edited volume The Deep Structure of Biology. A consummate work would be Convergent Evolution (2011) by George McGhee which cites cases in every kingdom of the same result occurring in relative kind again and again. Here is strong evidence at odds with the old vested version of nothing going on but vicarious, aimless selection. OK

In summary, convergent evolution occurs across the entire spectrum of molecules that make up life. We have studied examples of the convergent evolution of identical nucleotide substitutions in nuclear and mtDNA molecules of distantly related organisms, similar amino acid sequences in unrelated protein molecules, similar structural geometries in proteins with different amino acid sequences, and similar protein functions by gene sharing; the convergent evolution of the same enzyme function produced by the convergent evolution of the same protein producing that function;….and the convergent evolution of the same macromolecular structure in unrelated enzymes. The number of molecular evolutionary pathways available to life is not endless but is quite restricted, and convergent evolution is the direct result. (McGhee)

5.3.3 Encephalization - A Neural, Cognitive, Learning Experience
Again via retrospective humankind a similar elaboration has been found for central nervous systems and cerebral structures, as if a brain Bauplan. We will say more about a progressive intelligence and knowledge, as a starter one might consult the PNAS volume In the Light of Evolution VII: The Human Mental Machinery (Cela-Conde 2013), along with The Custom-Made Brain (Lledo 2014) which has a section entitled Behind Diversity in the Animal Kingdom, a Single Plan. For a specific paper try Evolution and Development of Brain Networks: From Caenorhabditis elegans to Homo Sapiens (2011) by Marcus Kaiser and Sreedevi Varier with this Abstract.

Neural networks show a progressive increase in complexity during the time course of evolution. From diffuse nerve nets in Cnidaria to modular, hierarchical systems in macaque and humans, there is a gradual shift from simple processes involving a limited amount of tasks and modalities to complex functional and behavioral processing integrating different kinds of information from highly specialized tissue. However, studies in a range of species suggest that fundamental similarities, in spatial and topological features as well as in developmental mechanisms for network formation, are retained across evolution. (143)

A prime aspect to be included is an occurrence and passage throughout the Metazoan kingdoms of similar bilateral, complementary brain hemispheres as our homo sapiens faculty. The 2013 volume Divided Brains: The Biology and Behavior of Brain Asymmetries gathers many findings not only for primates, but for mammalian, avian, aquatic, reptile, even arthropod crustaceans. In each case a common neural asymmetry is retained along with a left side penchant for fine detail and a right half for composite perceptions. Evolution found it best early on to separate these functions so as to both seek edible food and avoid predator at the same time. As every other age and culture knows, phenomenal people, life’s long procreation, and a dynamic genesis universe are one and the same, an iconic mirror and revelation.

Ultimately, we conclude that the neurobiological structure of the vertebrate central nervous system is evolutionarily ancient and highly conserved across species and that the basic neurophysiologic mechanisms supporting consciousness in humans are found at the earliest points of vertebrate brain evolution. (Mashour & Alkire, PNAS 2013)

As life’s emergence becomes increasingly appreciated as an embryonic maturation, and as this development is seen to involve brain and behavior more than body, researchers have begun to interpret it by way of neural net dynamics and consequent learning processes. Richard Watson and colleagues at the University of Southampton, UK, are pursuing this approach within a general “evolutionary connectionism.” A 2014 paper The Evolution and Phenotypic Correlations and “Developmental Memory” in the journal Evolution by Watson, with Gunter Wagner and others is a good summary wherein life proceeds similar to a brain by comparing new experience with prior representations. A companion entry by neuroscientists Jeremice Cabessa and Hava Siegelmann (2012) is also noted next.

In this article, we have demonstrated a formal equivalence between the direction of selection on phenotypic correlations and associative learning mechanisms. In the context of neural network research and connectionist models of memory and learning, simple associative learning with the ability to produce an associative memory, to store and recall multiple patterns, categorize patterns from partial or corrupted stimuli, and produce generalized patterns from a set of structurally similar training patterns has been well studied. The insight that the selective pressures on developmental correlations are equivalent to associative learning thus provides the opportunity to utilize well-established theoretical and conceptual frameworks from associative learning theory to identify organizational principles involved in the evolution of development. (Watson, et al)

Indeed, in the brain (or in organic life in general), information is processed in an interactive way, where previous experience must affect the perception of future inputs and older memories themselves may change with response to new inputs. Hence, neural networks should be conceived as performing sequential interactions or communications with their environments and be provided with memory that remains active throughout the whole computational process. Accordingly, we propose to study the computational power of recurrent neural networks from the rising perspective of interactive computation. (Cabessa & Siegelmann, 2012)

5.3.4 The Prevalence and Primacy of Cooperation
Ever since Darwin, and misunderstandings of his theories, survival of the fittest was seen to imply competition and conflict as the rule in nature. Again since circa 2000 studies across species, genera, and phyla have quantified that animals persistently tend to form salutary cooperative groupings. Reciprocal caring and sharing in fact increases both the chances of each member and of the relative colony, troop, flock, and community to get sustenance, avoid dangers, survive, reproduce, and thrive.

As Part II and the site documents, mutual, reciprocal aid occurs as a self-organized division of labor of benefit to all. Leading researchers and advocates are Martin Nowak of Harvard, Kenneth Weiss and Anne Buchanan of Penn State, and many colleagues. Salient works might be Collective Animal Behavior (2010) by David Sumpter, The Age of Empathy, (2009) Frans De Waal, Principles of Social Evolution (2011) by Andrew Bourke, and Cooperation and its Evolution (2103) edited by Kim Sterelny and Richard Joyce. Here is one more example of a radical revolution from entities ever at odds and war to an endemic propensity for the golden rule.

Last but not least – or should we say last but perhaps most – the principles of life we have described imply a variety of forms of cooperation. Cooperation, that is, literally co-operation, refers to different components working together successfully by some criterion, including that of evolutionary viability. The signals that produce branching, modular, and hierarchically nested organization inherently work cooperatively – indeed, signaling means the co-expression of all the sending and receiving factors. Cooperative communication enables sequestered parts to be coordinated so that the system can function as a whole. (Weiss and Buchanan, 2009)

5.4 Animal Consciousness, Intelligence, Personality, Behavior, Sociality, Culture
In addition, the study of these title attributes has moved from initial denials and doubts to a robust confirmation. As the Animal Intelligence section conveys, abilities of forethought, stored memory, improvisation, mimesis, clever, cooperative behavior, stretches through the Metazoan kingdoms to cephalopods, insects and earliest invertebrates. While human beings are uniquely graced by linguistic and societal intensities, who can reconstruct from whence they came, an anthropometric familiarity and relative continuity is quite evident.

Of course, we all know this as ever amazed by the sensitive affect and playfulness of our creaturely companions. An international conference, Consciousness in Human and Non-Human Animals, (2012) wrote a manifesto to affirm its real presence from an ancient awakening. A concurrent volume Animal Personalities (2013) averred a wide array of familiar behaviors amongst animal groupings of every kind, which would be their own cultural dimension. One could cite the TV series Meerkat Manor, dolphin pods, migratory herds, hunting parties, social insects, we are one family.

While textbook evolution views organisms as passive subjects impacted by capricious environments, it is now established that all manner of animals engage in proactive behaviors to improve their fitness and survival. As Kevin Laland, John Olding-Smee, and others have articulate, a constant process of “niche construction” of nests, bowers, caches, stashes, hives, beaver dams goes on.

With these novel perceptions, it has become necessary to factor such intentional activities of organisms and groups into revised evolutionary theories. A special 2014 issue of the Biological Journal of the Linnean Society (112/2) on The Role of Behavior in Evolution contains several papers such as New Thinking about Biological Evolution by Patrick Bateson, and Adaptive Evolution without Natural Selection by Kalevi Kull. OK

My sense is that the theories of biological evolution have been reinvigorated by the convergence of different disciplines. The combination of developmental and behavioral biology, ecology, evolutionary biology, and now microbiology has shown how important the active roles of the organism are in the evolution of its descendants. (Bateson)

5.5 A Ubuntu Universe: Our Symbiotic Selves
By our vista, in the past few years an historic understanding about personal organisms, social memberships, and a natural principles of autonomy and community, stability and change has occurred. Human beings, and organisms in general, are rightly appreciated as composite entities of microbiomes, organelles, and ones overall individuality. Since the 1970s, as perceived and championed by microbiologist Lynn Margulis (1938-2011), eukaryotic nucleated cells are known to have evolved by and made up of a beneficial symbiosis between disparate (mitochondria, undulipodia, cilia) components in a bounded compartment. After decades of research this arrangement is robustly proven not only for cells, but is being extended across emergent life to people and societies.

A synoptic volume might be The New Foundations of Evolution (2009) by the York University biologist Jan Sapp. A succinct paper is A Symbiotic View of Life: We Have Never Been Individuals by Scott Gilbert, Alfred Tauber, and Sapp in the Quarterly Review of Biology (2012). Gilbert, a Swarthmore College embryologist and author, has taken up Lynn Margulis’ mission to aver that an organism’s identity is actually a viable mutuality between myriad microbiota and an integral self, dubbed a symbiont or holobiont community. See also Gilbert’s luminous 2013 paper Wonder and the Necessary Alliances of Science and Religion.

Molecular analyses of symbiotic relationships are challenging our biological definitions of individuality and supplanting them with a new notion of normal part–whole relationships. This new notion is that of a ‘holobiont’, a consortium of organisms that becomes a functionally integrated ‘whole’. This holobiont includes the zoological organism (the ‘animal’) as well as its persistent microbial symbionts. This new individuality is seen on anatomical and physiological levels, where a diversity of symbionts form a new ‘organ system’ within the zoological organism and become integrated into its metabolism and development. Symbionts have also been found to constitute a second mode of genetic inheritance, providing selectable genetic variation for natural selection. We develop, grow and evolve as multi-genomic consortia/teams/ecosystems. (Scott Gilbert)

On a communal level, animal entities are found to survive and flourish by way of similar reciprocities between diverse members and relative groupings from bacterial to sapient creatures. For each nested evolutionary stage, the same symbiotic mutuality repeats in turn each time. One could mention biofilms, troops, clans, pods, herds, flocks, allegiances, teams, bands, sects, and so on. In each instance, a reciprocity of competition and cooperation, semi-autonomy and supportive whole, entity and empathy, of benefit both to both free beings and group sustenance and survival is nature’s preference.

From these many studies can be gleaned a recurrent principle, intimated over the ages, of indispensible value today. Pierre Teilhard de Chardin coined “creative union,” decades later the French biologist Vic Norris cites a “competitive coherence,” Elizabeth Hussa and Heidi Goodrich-Blair offer “multipartite interdependence.” There are many more versions throughout the site. As readers know, Asian wisdom teaches an integral Yin/Yang balance, akin to African ubuntu or MesoAmerican teotl traditions (search terms). A premier quality to then emphasize, often stressed by Teilhard, is that the more a person becomes part of a shared assembly, the more liberated and empowered they actually are. As noted in Organic Democracy above, a capsule might be: me + We = US. A budding social instance is entered in Sustainable Ecovillages.

Microbial symbioses, in which microbes have either positive (mutualistic) or negative (parasitic) impacts on host fitness, are integral to all aspects of biology, from ecology to human health. Even in relatively simple associations, symbiont-derived benefits can be context dependent and influenced by other host-associated or environmental microbes. Furthermore, naturally occurring symbioses are typically complex, in which multiple symbionts exhibit coordinated, competing, or independent influences on host physiology, or in which individual symbionts affect multiple interacting hosts. (Hussa and Goodrich-Blair, It Takes a Village)

Another penchant of nature’s dynamic balance which has lately gained veracity, drawn from specific instances and implied generalities, is for living systems to seek a maximum vitality poised between order and chaos, stability and flexibility. By various names, it is a self-organized criticality or metastable state. A well-studied case is the way our brains think via a reciprocal interplay between semi-autonomous neurons and their relative networks. The contributions of Stuart Kauffman, Scott Kelso, Stephen Grossberg, Vic Norris, Jorge Hildago and many colleagues over the years are a prime resource. A quote from Outline of a General Theory of Behavior and Brain Coordination by Scott Kelso, et al (2013) can give the gist.

According to the present theory, the normal brain realizes its complexity at all scales not in its most ordered form (integration qua synchronization) or disordered form (segregation qua desynchronization), but in a subtle blend of both tendencies. Dual tendencies for integration and segregation constitute a complementary pair very much along the lines proposed by Stephen Grossberg, one of the pioneers of the field of Neural Networks: the brain is organized to obey principles of complementarity. (Kelso)

And from our own microcosm, we can go far afield to Self-Organized Criticality in Astrophysics (2011) by Martin Aschwanden, Evolution and Selection of River Networks (2014) by Andrea Rinaldo, et al, Patterns in Our Planet (2010) Alison Ord, et al, and the synoptic Emergence of Criticality in Living Systems through Adaptation and Evolution by Jorge Hidalgo, et al (2013). An example of the scientific acceptance of a dynamic creativity could be Power Laws and Self-Organized Criticality in Theory and Nature by Dimitrije Markovic and Claudius Gros in Physics Reports (2014).

Empirical evidence has proliferated that living systems might operate at the vicinity of critical points with examples ranging from spontaneous brain activity to flock dynamics. Here we employ tools from statistical mechanics and information theory to prove that systems poised at criticality are much more efficient in ensuring that their internal maps are good proxies of reality. Analytical and computational evolutionary models vividly illustrate that a community of such systems dynamically self-tunes toward a critical state either as the complexity of the environment increases or even upon attempting to map with fidelity the other agents in the community. Our approach constitutes a general explanation for the emergence of critical-like behavior in complex adaptive systems. (Hidalgo)

We have now traced the Third Infinity from a lively Ecosmos, via formative Mathematter, through a quickening Genesis Evolutionary Synthesis. The grand achievement of this late hour, and our transition as free members of a personsphere progeny, is the long foreordained discovery of a true universal repetition of the same iconic gender archetype everywhere. We can now consider and report its notice and presence in our individual and social selves.

6.0 A Human and Humankinder Epitome
6.1 Phenomenal Persons
This first part, in accord with the site outline, will note complex system advances in body, brain, psyche, and knowing awareness.

6.1.1 Systems Physiology and Psychology
As citations in Part II, and this website section attest, from a later 1990s “dynamic systems theory” by Esther Thelen and Linda Smith of Indiana University every aspect of our lives from infants to seniors is now better understood by way of invariant self-organizing, network nonlinearities. In early childhood, progress in anatomic maturation, visual perception, kinetic agility, social behavior and sequential stages of cognition are each guided by these natural propensities. A major statement is Volume 44, Embodiment and Epigenesis, of Advances in Child Development and Behavior (Lerner, 2013) under the banner of a corrective “relational” turn for the field, as championed by Willis Overton, the veteran Temple University psychologist.

Anyone who has witnessed a newborn baby grow up into a toddler and then a schoolchild, an adolescent, and an adult has an intuitive appreciation of the fact that developmental processes are prime examples of nonlinear dynamical systems. (243) The course of human development over the life span is a prime example of a complex, nonlinear dynamical system. The process of development is recursive and self-organizing. It occurs simultaneously at many levels of organization – for example, the individual person and the person in interaction with others, institutions, and cultures to which the person relates. (271) (Paul Van Geert, 2009)

For our adult years, an international team of physicians and systems scientists reports in the article Network Physiology Reveals Relations between Network Topology and Physiological Function (Bashan, 2011) how along with homeostasis, a person’s condition most depends on being in a state of critical poise between order and disorder. Indeed ones true health can be accessed by how well one maintains this balance, often by degrees of fractalness. And onto senescence, by how much this vitality and form quite deteriorates.

The human organism is an integrated network where complex physiological systems, each with its own regulatory mechanisms, continuously interact, and where failure of one system can trigger a breakdown of the entire network. Here we develop a framework to probe interactions among diverse systems, and we identify a physiological network. We find that each physiological state is characterized by a specific network structure, demonstrating a robust interplay between network topology and function. The proposed system-wide integrative approach may facilitate the development of a new field, Network Physiology. (Bashan)

6.1.2 Systems Neuroscience: Our Mindful Microcosm
Certain vital realms of nature, evolution, and humanity have become especial subjects of research, and are exemplary portals upon a greater genesis. Microbial colonies and dynamic genomes are examples. Another prime focus of the complex systems revolution is its application to understand our own neural endowment and intelligence. A human brain, both in neural development and cogitation, is now seen as to epitomize a dynamic, self-organizing, critically poised, fractal, nested network, modular system, aka connectomes. For the whole brain/mind, a global workspace theory or working memory have gained acceptance to explain how we effectively remember and respond.

As an instance, both the United States and Europe have initiated mega scientific consortiums to totally analyze and map brain anatomies and faculties. In regard, a good entry is the edited volume The Future of the Brain (2014) with a chapter by George Church entitled Rosetta Brain. By still another take the same structure and message occur and repeat at every micro and macro phase. My we observe that these collaborative projects and achievements are due to an emergent global faculty whom seems retrospectively trying to map, describe, quantify and qualify the brave human brains that such a noosphere has arisen from.

In addition, as we saw for evolving animals, A Complementary Brain and Thought Process attests that for our own bicameral hemispheres the left side penchant for dot detail and right for contextual connections is now established. Or in another way, we have archetypal yang and yin genders in our very heads, if we could only abide. By our global vista, microcosmic human and macrocosmic universe become more of an iconic mirror to each other than ever imagined. In an especial work The Master and His Emissary (2009), the British psychologist Iain McGilchrist conveyed this so well, as we sample next.

My thesis is that for us as human beings there are two fundamentally opposed realities, two different modes of experience; that each is of ultimate importance in bringing about the recognisably human world; and that their difference is rooted in the bihemispheric structure of the brain. It follows that the hemispheres need to co-operate, but I believe they are in fact involved in a sort of power struggle, and that this explains many aspects of contemporary Western culture. (3)

In the opening pages of this book, I wrote that I believed it to be profoundly true that the inner structure of our intellect reflects the structure of the universe. By ‘profoundly’ I meant not just true by definition, as would be the case for those who believe that the universe is in any case a creation of our brains. I think it goes further than that. I believe our brains not only dictate the shape of the experience we have of the world, but are likely themselves to reflect, in their structure and functioning, the nature of the universe in which they have come about. (460)

6.1.3 Our Conscious Knowledge
While Cosmic Consciousness noted new admissions of its natural presence, here we record scientific affirmations of a true self awareness in ourselves, mind you. Although some who remain in the materialist paradigm still deny, actual this real phenomenon is accredited as a proper field for study. Our wakeful sentience is quite evident and real on its own. Advances in neural imaging can now attribute to specific cerebral cortex areas and even to neuron and network firings. A significant equation of perceptive consciousness with a relative information content, championed by Giulio Tononi, Christoph Koch (search) and others, has become a leading explanation. By these lights, an ancient evolutionary continuity, a long stirring, quickening, learning, knowing individual and social mindfulness, is lately revealed as a fact.

6.2 An Emergent Humankind
As we may convey, a pervasive achievement over the past years is a reconception of every field from cosmology and geology to genomes, brains, psyches and behaviors in terms of the nonlinear, self-organizing, complexity network sciences. In the previous section, we saw their avail for integral persons. As the site documents, this novel approach is of equal value for all manner of literacy, social, urban, economic, civilizational and even historic phases, which we note next.

6.2.1 A Cultural Code
As this site section reports, human language in both grammar and syntax linguistic and textual or conversational modes has also been amenable to this nascent interpretation. Rosetta Cosmos documents how our written literary corpus is being found to manifest and exemplify the universal complex network self-organization. A Chinese-Spanish nexus has made many contributions, often comparing the logogram and alphabetic scripts.
In Systems Linguistics we mean a waxing view of language that likewise exemplifies a dynamic fractal scale-invariance, so to speak. A breakthrough work might be Complex Systems and Applied Linguistics (2008) by Diane Larsen-Freeman and Lynne Cameron. Around 2009 going forward a team effort with a Santa Fe Institute – University of Michigan core, including John Holland, affirmed Language as a Complex System (search Clay Beckner).

Language as a CAS involves the following key features: The system consists of multiple agents (the speakers in the speech community) interacting with one another. The system is adaptive, that is, speakers’ behavior is based on their past interactions, and current and past interactions together feed forward into future behavior. A speaker’s behavior is the consequence of competing factors ranging from perceptual constraints to social motivations. The structures of language emerge from interrelated patterns of experience, social interaction, and cognitive mechanisms. The CAS approach reveals commonalities in many areas of language research, including first and second language acquisition, historical linguistics, psycholinguistics, language evolution and computational modeling.

The advantage of viewing language as a CAS is that it allows us to provide a unified account of seemingly unrelated linguistic phenomena. These phenomena include the following: variation at all levels of linguistic organization; the probabilistic nature of linguistic behavior; continuous change within agents and across speech communities; the emergence of grammatical regularities from the interaction of agents in language use; and stagelike transitions due to underlying nonlinear processes. We outline how the CAS approach reveals commonalities in many areas of language research, including cognitive linguistics, sociolinguistics, first and second language acquisition, psycholinguistics, historical linguistics, and language evolution. (Beckner, et al)

Other work traces a common continuity of our speech patterns with birdsong and throughout the talkative creatures. The biosemiotic approach is keen on this. And as we saw contributions work both ways – genomes are now parsed for linguistic features, while cultural discourse is being realized to have many genetic affinities. A 2011 paper Statistical Physics and Language Dynamics (Loreto) goes on to trace etiologies to these root realms. As this scenario fills in, a singular formative code seems to emerge and reiterate with evolutionary transitions from nucleotides to libraries. This is an auspicious discovery in the air by humanity’s knowsphere. OK

6.2.2 Complex Symbiotic Societies
As our daily lives become ever intricately intertwined, whether in local environs, or by global communications and breaking news, again their fabric equally imbues and is guided by the same mathematical source. Rather than one thing after another sans any deeper context, complex dynamic systems are similarly found to organize the form and activities of groups, neighborhoods, settlements, cities, nations, every human polity.

To give a sense, one aspect has been to quantify that human assemblies as they hold forth take on a character as a higher level, organism-like entity. The work of Robert Goldstone, Anita Woolley, Thomas Malone, David Sloan Wilson, and others, such as group selection and collective intelligence, augur for a further evolutionary iteration. With the burst of social media like Facebook and Twitter, along with mobile phones and tablets, vast amounts of data are available for their usage, which can be shown to exhibit modular network dynamics akin to neural architectures.

Just as neurons interconnect in networks that create structured thoughts beyond the ken of any individual neuron, so people spontaneously organize themselves into groups to create emergent organizations that no individual may intend, comprehend, or even perceive. (10) Social phenomena such as the spread of gossip, the World-Wide Web, the popularity of cultural icons, legal systems, and scientific establishments all take on a life of their owe, complete with their own self-organized divisions of labor and specialization, feedback loops, growth, and adaptations. (Goldstone, 2008)

Life forms are organized in nested clusters. Genes are bundled in chromosomes that occur in cells. Cells are joined together in multi-cellular organisms, and some multi-cellular organisms live in societies. This hierarchical organization strongly suggests that the amazing diversity of life forms is partly due to the grouping of biological units into higher-level units. The dynamic underlying the hierarchical organization of life forms has been called major transitions in evolution (which) occurs when individual organisms become so integrated that they transform into a higher-level organism in their own right. (Selin Kesebir, 2012)

6.2.3 Planetary Physiosphere: Anatomics, Economics, Urbanomics
This section weaves several aspects of potential emergent transitions to a more organically conceived and healthy viability of human societies. Neighborhoods, villages and towns onto cities, urban areas, bioregions and a physiological, neural anatomy of an anthroposphere (Baccini) are presently morphing, growing, coming into their own. Consequent commercial economies from financial markets to ethnic migrations are being realized understood as dynamical network phenomena with a fractal self-similarity, quite an animate in kind.

For human settlements, a pioneer of the complexity revolution has been the British systems geographer Michael Batty. A current work is The New Science of Cities (2013). Another advocate is the Israeli urban planner Juval Portugali, his latest book is Complexity Theories of Cities Have Come of Age (2012). Another nonlinear take is achieved by a team from the American Southwest, such as Geoffrey West, Luis Bettencourt, Jose Lobo, Deborah Strumsky, and colleagues, who extend a prior ecological invariance to over 50 orders of magnitude from microbes to a metropolis.

We have shown that power law scaling is a pervasive property of human social organization and dynamics in cities and holds across time and for different nations with very different levels of development, economic sector distribution, and with different cultural norms and geographic location. This is an extraordinary assertion indicating that, on average, different cities are scaled up versions of each other, particularly in terms of rhythms of social activity – such as the creation of wealth and ideas, infectious contacts and crime, and patterns of human behavior. (Bettencourt, et al, 2009)

On the basis of these structures we propose a new universal definition of a city as a network of linked centres at all scales set into a background network of residential space. We then show that this universal pattern comes about in tow interlinked but conceptually separable phases: a spatial process through which simple spatial laws govern the emergence of characteristically urban patterns of space from the aggregations of buildings; and a functional process through which equally simple spatio-functional laws govern the way in which aggregates of buildings become living cities. It is this dual process that is suggested can lead us in the direction of a ‘genetic’ code for cities. (Bill Hillier, 2012)

A companion aspect would be financial market economies, as engaged from a number of angles. A hybrid field dubbed econophysics uses statistical mechanics to better study industry and trade. A founder and prime theorist has been Eugene Stanley of Boston University. From the Santa Fe Institute, an endeavor initiated by Kenneth Arrow, Brian Arthur and others applies self-organizing complexity theories to sponsor a nonlinear economics. A veteran journal such as Physica A is now filled with sophisticated analyses of stock exchanges, business cycles, and so on which again exemplify universal principles. An especial entry is The Origin of Wealth (2006) by London economist Eric Beinhocker which draws both reinterprets evolutionary theory and commerce by way of complex adaptive systems.

Similar efforts have informed a broad field of societal studies. For example Agent-Based Models of Geographical Systems edited by Alison Heppenstall, et al (search) consider complex cellular topologies from land cover changes to demographics, epidemics, pedestrian and vehicular traffic, crime waves, migrations, even battlefields. These global sciences are of indispensible value to analyze, and control disease vectors. The Peking University information theorist Hai Zhuge, with whom I have had an email correspondence, was able to quantify the SARS epidemic this way.

As these efforts matured and merged into the 2010s, witnesses of a planetary, social and urban “anthropocene metabolism” have grown, as recent volumes herein express. This promise has inspired architecture from Frank Lloyd Wright and Christopher Alexander to Paul Downton and James Harris, with many local and urban practitioners. But an intentional integral ascent to a sustainable, organism-like Ecozoic era, the great work of our time advised by Thomas Berry, will not be accomplished without a radical breakthrough to a common planet-wise knowledge.

6.2.4 Systems History: Planetary Individuation
While the “individuation” aspect has not yet occurred, as these rarefied references attest the complex systems revolution is being extended even to the fraught, brutal course of perpetual, internecine war, nation building, fracture, conquest, migrations, diasporas, over the millennia. As The Phenomenon of Humankind, and this review attest, the universal complex dynamic network of agent entity, community relation, and whole system equally applies to the august temporal and spatial past and present of homo unto anthropo sapiens.

During this period, with the publication of David Christian’s Maps of Time: An Introduction to Big History (2005) an imperative, necessary joining of human millennia with cosmic evolutionary duration was achieved. This expansive integration has led to a spate of similar volumes and updates, an International Association, conferences, a Big History Project, (Google each) with ambitions to situate our earthly abide in its celestial context. As Christian observed, over this vista the prime vectors were an increasing complexity, and a proactive intelligence, now shifting to a global scale.

A parallel effort was initiated by the University of Connecticut historian Peter Turchin, the son of Russian-American systems philosopher Valentin Turchin, to explore ways to recast the course of civilizations by way of the complexity sciences. An online journal Cliodynamics: Journal of Theoretical and Mathematical History was posted in 2010 for articles that express such deeper forces and lineaments at work behind the crush of events, as long intimated. We note in a 2011 issue papers by Santa Fe Institute theorists David Krakauer and Geoffrey West, see Part II.

Of course this is a huge subject, we saw above, and on the website, how even the most tragic, seemingly chaotic events of our roiling human condition can yet reflect a common mathematics. A 2014 work Complexity Science and World Affairs by Boston University scholar Walter Clemens is a salient volume in this regard. We ought to cite that the eminent historian William McNeill broached this scenario in a 2001 article The Convergence of Evolutionary Science with Scientific History (search). A 2011 edition Deep History by Andrew Shryock and Daniel Smail is a good evocation of this vital rooting, as next.

The goal of this book is to offer a set of tools – patterns, frames, metaphors – for the telling of deep histories. These include kinshipping, fractal replication, exchange, hospitality, networks, trees, extensions, scalar integration, and the spiraling patterns of feedback intrinsic to all coevolutionary processes. Skillfully deployed, these frames and the narratives and evidence they create offer a dynamic of connectedness that can render deep time accessible to modern scholarship, thereby bringing the long ages of human history together in a single story. (Shryock and Smail)

As we did for Anthropo, here is a summary of 21st century scientific discoveries by Cosmo Sapiens. As our prior human stage sought to explore and examine, humanity is altogether revising every field to a systems synthesis of parts, relations and integral wholes. We note again physics and biology, quantum and classical, statistical mechanics and complexity theory, as active matter comes alive again. A dramatic accomplishment is surely a gravid cosmos filled with as many planets as stars. Suns appear as solar incubators for habitable zones. While large and small infinities have run their course, a missing mathematical, formative agency has been articulated that takes on a guise of a natural genetic code. In accord, a new evolutionary synthesis is in the air as life’s emergence becomes an embryonic gestation. We refer the reader on to Part II for select reference highlights over the period, and especially into the 2010s to document in support.