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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
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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 1 through 15 of 112 found.

The Natural Genesis Vision

The Genesis Vision > Historic Precedents

Johnson, George. Murray Gell-Mann, Who Peered at Particles and Saw the Universe. New York Times. May 25, 2019. This is an obituary by a science writer for the Nobel laureate polymath physicist (search) who has passed at age 89. Beyond finding and naming quarks, he is known for contributions from archaeology and linguistics to complex system theories at Santa Fe Institute. His 1994 work The Quark and the Jaguar helped establish the field of complex adaptive system studies. We quote a line as a capsule of 20th and 21st century science in which Murray avers the real presence of independent, generative principles. Murray Gell-Mann was a true iconic genius who merited a May 29 essay The Physicist Who Made Sense of the Universe in NY Times by the cosmologist Sean Carroll. But his books such as The Big Picture (2016) tout a quite opposite view that no intrinsic laws exist on their own. Here is the dichotomy - to be or not to be - that so troubles and daunts us today. In regard, Natural Genesis seeks to document humanity’s project in search of a mathematical source that is wholly repetitive at each and every realm. Could our late 2019 year begin to be the “someday” to come? After 8,000 annotated entries cited herein, this achievement may at last be evident.

In a talk (SFI) in 2007, Dr. Gell-Mann compared the last century of physics to pulling back the skins of an onion, finding at every layer that the same mathematics applies – and hinting that an objective reality can conceivably be explained someday by a universal set of laws.

The Genesis Vision > Historic Precedents

Nolte, David. Galileo Unbound: A Path Across Life, the Universe and Everything. Oxford: Oxford University Press, 2018. A Purdue University physicist and astronomer complements his course text Introduction to Modern Dynamics: Chaos, Networks, Space and Time (2015) with a 400 year trajectory of the scientific method so well initiated by Galileo Galilei (1564-1642) all the way from his moon to our multiverse.

Galileo Unbound traces the history of dynamics that brought us from Galileo's law of free fall to geneticists measuring evolutionary drift, entangled quantum particles moving among many worlds, and our lives as trajectories through a multidimensional phase space. Remarkably, common themes persist that predict the evolution of species as readily as the orbits of planets or the collapse of stars into black holes. This book tells the history of expanding dimensions and more complex systems since Galileo’s early 1600s.

The Genesis Vision > Current Vistas

Wilson, David Sloan. This View of Life: Completing the Darwinian Revolution. New York: Pantheon, 2019. In his latest work, the SUNY Binghamton University biological anthropologist seeks a 21st century fulfillment of what Charles Darwin began by extending and applying life’s evolutionary development to the societies and cultures of homo sapiens. A Prologue advises that the endeavor also embodies Pierre Teilhard’s vision of a phenomenal cognitive noosphere. In regard, the author is a rarest professor trying to move scholarship beyond academe so to avail a better way to live on Earth. D. S. Wilson has long been an advocate of group selection (see also E. O. Wilson) whence animal communities can take on organism-like features. While aware of old Social Darwinisms, the tendency of all manner of creatures to form viably assemblies, if properly understood, could provide guiding principles for an equitable human “superorganic” phase. A practical solution, which we desperately need, is proposed as sustainable ecovillages. A case example is Dancing Rabbit in Missouri with many reciprocal member-community benefits. (Teilhard’s phrase was Creative Union whence a person becomes liberated within a supportive group).

It is widely understood that Charles Darwin’s theory of evolution completely revolutionized the study of biology. Yet, according to David Sloan Wilson, the Darwinian revolution won’t be truly complete until it is applied more broadly—to everything associated with the words “human,” “culture,” and “policy.” In a series of engaging and insightful examples—from the breeding of hens to the timing of cataract surgeries to the organization of an automobile plant—Wilson shows how an evolutionary worldview provides a practical tool kit for understanding not only genetic evolution but also the fast-paced changes that are having an impact on our world and ourselves. What emerges is an incredibly empowering argument: If we can become wise managers of evolutionary processes, we can solve the problems of our age at all scales—from the efficacy of our groups to our well-being as individuals to our stewardship of the planet Earth.

The Genesis Vision > Current Vistas

Wilson, Edward O.. Genesis: The Deep Origin of Societies. New York: Liveright Norton, 2018. The newly nonagenarian (June 10) Harvard behavioral biologist and prolific author provides a latest view upon life’s proclivity to form viable groupings from invertebrates to homo sapiens. I heard him speak in Cambridge in 1975 about his then contentious work Sociobiology. E. O. Wilson has long been an advocate of such group selection whence each stage may take on the guise of a whole subject organism, and has coauthored papers with David Sloan Wilson, another proponent. Some 44 years later, the presence of multi-level social assemblies from bacterial and insect colonies to aquatic pods and avian starling flocks is well evident. Their occasion is set within a “major transitions in evolution” model due to John Maynard Smith and Eors Szathmary (section VI. H. 8) as members (genes, cells, humans) join into communal forms. Within this nested scale, a new emphasis is placed on salutary cooperative altruism rather than competitive, selfish individuals.

But the contribution can also illustrate a deep conceptual quandary that besets current science and philosophy. Up front E. O. Wilson states that while evolution is a proven fact, the sole motive agency is environmental post-selection of random gene mutations. All life, including human beings, can thus be reduced to chemistry and physics, as his 1998 Consilience contends. The result is a strong materialist view which denies any inherent creativity or purpose, especially divine influence, akin to Steven Pinker, Yuval Harari, Richard Dawkins and others. Yet do they realize that denunciations of an extant natural genesis only drives peoples back to “delusional” religious beliefs. With climate change, nuclear arsenals and barbaric warlords all the rage, it is so imperative, as this site tries to report and document, that a revolutionary, palliative resolve is soon achieved.

As a twenty-first-century statement on Darwinian evolution, Genesis shows that the only way for us to fully understand human behavior is to study the evolutionary histories of nonhuman species. Of these, Wilson demonstrates that at least seventeen―among them the African naked mole rat and the sponge-dwelling shrimp―have been found to have advanced societies based on altruism and cooperation. Whether writing about midges who “dance about like acrobats” or schools of anchovies who huddle “to appear like a gigantic fish,” Genesis is an insightful advance which braids scientific theory with biological and humanistic observations. (Publisher edits)

Among the millions of species around us are survivors, evolutionary products that one way or another reveal the six major steps of evolution leading from single-celled bacteria and other single organisms to humanity’s advanced capacity for language, empathy, and cooperation. (37) In each major transition in evolution, altruism at a lower level of biological organization is needed to reach the one above, as in cell to organism and organism to society. The dilemma, which at first seems paradoxical is in fact susceptible to explanation by evolution through natural selection. (47)

Planetary Prodigy: A Global Sapiensphere Learns by Her/His Self

A Learning Planet > Original Wisdom > Rosetta Cosmos

Markovic, Rene, et al. Applying Network Theory to Fables: Complexity in Slovene Belles-Lettres. Journal of Complex Networks. 7/1, 2019. University of Maribor, Slovenia theorists including Matjaz Perc show how nature’s common nonlinear geometry and dynamics can even be applied to any corpora of textual literature. And by turns if our conversant and written language are parsable by the same complex network systems as every other realm, it could strongly impart a narrative character to this universe to human procreation. That is to say, an organic doubleness of genomic script and score for this phenotypic genesis becomes increasingly evident.

Words are the building blocks of human communication. They are arranged in sentences in a non-trivial and universal way, which implies the existence of fundamental organizational principles that have shaped language development. One example is Zipf’s law which says that the frequency of word occurrence is generally an inverse power-law function of its rank. In our article, we study the structure and complexity of texts in Slovene belles-lettres, with an emphasis on differences across age groups. We show that the co-occurrence connectivity of words forms a complex and heterogeneous network characterized by an efficient transfer of information. We show that with the increasing age of readers, the length of texts and of words, along with complex social interactions between literary characters, all increase. Taken together, we demonstrate that network theory enables an in-depth theoretical exploration of Slovene belles-lettres, with clear distinctions in statistical properties between age groups, thus bridging art and exact sciences in a mutually rewarding way. (Abstract excerpt)

A Learning Planet > The Spiral of Science

Astro2020: Decadal Survey on Astronomy and Astrophysics. sites.nationalacademies.org/SSB/CurrentProjects/SSB_185159. his is the main website for the National Academies of Sciences, Engineering and Medicine, Space Studies Board request for wide-ranging cosmological projects across the next 10 years. In regard, from January to May 2019 over 300 proposals were posted on the arXiv e-print site, just search Astro2020. As a small sample, we note The Next Decade of Astroinformatics, Toward Finding Earth 2.0, The Super Earth Opportunity, Stellar Characterization for Holistic Planetary Habitability, Tracing the Origin of Seed Black Holes, Quantum Chemistry for Exoplanetary Science, Cosmic Dawn and Reionization, Mapping Galactic Clusters, and every other astro-aspect as humankinder begins to carry out a genesis universe’s way of necessarily quantifying itself. The entries are often from a nominal group of 10 to 50 co-authors. Altogether a good example of nascent global science going on via its own many agent self-organization.

A Learning Planet > The Spiral of Science

Bauer, Amanda, et al. Petabytes to Science. arXiv:190505116. We cite this 80 page, 27 author posting including Alexander Szalay as an example going forward of a worldwide, collaboration necessary to handle data inputs at this 1 million gigabyte scale. Akin to the USA Astro2020 project (herein) its cosmic vista surveys planetary systems, stellar evolution, messenger astrophysics, galactic clusters, fundamental physics and about every aspect as our yet unknown and unnamed person/sapiensphere begins to carry out the universal self-quantification that a genesis procreation seems to require. The quotes describes a meeting held in regard.

A Kavli foundation sponsored workshop on the theme Petabytes to Science was held in February 2019 in Las Vegas. The aim of this workshop was to discuss important trends and technologies which may support astronomy. We also tackled how to better shape the workforce for the new trends and how we should approach education and public outreach. This document was coauthored during the workshop and edited in the weeks after. It comprises the discussions and highlights many recommendations which came out of the workshop. We shall distill parts of this document and formulate potential white papers for the decadal survey.

A Learning Planet > The Spiral of Science > deep

Das Sarma, Sankar, et al. Machine Learning Meets Quantum Physics. Physics Today. March, 2019. In a “most read” journal paper, University of Maryland and Tsinghua University, Beijing computational theorists show how these disparate fields actually have common qualities, which can serve to inform, meld and advance each endeavor. The graphic article goes on to compare affine neural network and quantum states so as to join “classical and quantum” phases, especially for communicative and computational purposes.

A Learning Planet > The Spiral of Science > deep

Kozma, Robert, et al. Artificial Intelligence in the Age of Neural Networks and Brain Computing. Cambridge, MA: Academic Press, 2018. A large international edition with 15 authoritative chapters from The New AI: Basic Concepts and Urgent Risks to Evolving Deep Neural Networks. See especially A Half Century of Progress toward a Unified Neural Theory of Mind and Brain by Stephen Grossberg (search).

A Learning Planet > The Spiral of Science > deep

Palazzi, Maria, et al. Online Division of Labour: Emergent Structures in Open Source Software. arXiv:1903.03375. Internet Interdisciplinary Institute, Open University of Catalonia computer theorists report that even group-wide developments of computational codes can be seen to take on and follow a common course as all other organic assemblies. A further implication, we add, would be another perception that cosmic evolutionary nature draws upon and repeat this same complex adaptive systems generative program at each and every instance. See also a cited reference Multi-scale Structure and Geographic Drivers of Cross-infection within Marine Bacteria and Phages in the ISME Journal (7/520, 2013) which describes a similar pattern for microbes.

The development Open Source Software fundamentally depends on the participation and commitment of volunteer developers to progress. Several works have presented strategies to increase the on-boarding and engagement of new contributors, but little is known on how these diverse groups of developers self-organise to work together. To understand this, one must consider that, on one hand, platforms like GitHub provide a virtually unlimited development framework: any number of actors can potentially join to contribute in a decentralised, distributed, remote, and asynchronous manner. On the other, however, it seems reasonable that some sort of hierarchy and division of labour must be in place to meet human biological and cognitive limits, and also to achieve some level of efficiency.

These latter features (hierarchy and division of labour) should translate into recognisable structural arrangements when projects are represented as developer-file bipartite networks. In this paper we analyse a set of popular open source projects from GitHub, placing the accent on three key properties: nestedness, modularity and in-block nestedness -which typify the emergence of heterogeneities among contributors, the emergence of subgroups of developers working on specific subgroups of files, and a mixture of the two previous, respectively. These analyses show that indeed projects evolve into internally organised blocks. (Abstract excerpts)

To answer these questions, we will look at three structural arrangements which have been identified as signatures of self-organisation in both natural and artificial systems: nestedness (i.e. do projects evolve in a way such that the emergence of generalists and specialists is favoured?); modularity (i.e. do OSS projects split in identifiable compartments, thus avoiding Brook’s law despite the addition of contributors? Are these compartments bounded?); and in-block nestedness (i.e. if bio-cognitive limits and division of labour are in place, do the resulting specialised modules self-organise internally?) (2)

A Learning Planet > The Spiral of Science > deep

Schuchardt, Jan, et al.. Learning to Evolve. arXiv:1905.03389. Technical University of Munich informatics researchers advance ways to employ evolution-based algorithms which in turn shows how life’s long development can appear as a computational process. From our late vantage, it may seem that a cosmic genesis needs to pass on this genetic-like agency to our own continuance.

Evolution and learning are two of the fundamental mechanisms by which life adapts in order to survive and to transcend limitations. These biological phenomena inspired successful computational methods such as evolutionary algorithms and deep learning. Evolution relies on random mutations and on random genetic recombination. Here we show that learning to evolve, i.e. learning to mutate and recombine better than at random, improves the result of evolution in terms of fitness increase per generation and even in terms of attainable fitness. We use deep reinforcement learning to learn to dynamically adjust the strategy of evolutionary algorithms to varying circumstances. (Abstract)

A Learning Planet > The Spiral of Science > deep

Taylor, P., et al. The Global Landscape of Cognition: Hierarchical Aggregation as an Organizational Principle of Human Cortical Networks and Functions. Nature Scientific Reports. 5/18112, 2019. As the deep neural network revolution began via theory and neuroimaging, UM Amherst neuroscientists including Hava Siegelmann attest to a nested connectome architecture which then serves cognitive achievements. On page 15, a graphic pyramid rises from a somatosensory, prosodic base through five stages to reason, language, visual concepts. Might one now imagine this scale as a personal ontogeny recap of life’s evolutionary sapient awakening? See Deep Neural Networks Abstract like Humans by Alex Gain and Hava Siegelmann at arXiv:1905.11515 for a 2019 version.

A Learning Planet > Mindkind Knowledge > News

Evolution: Genetic Novelty – Genomic Variations by RNA Networks and Viruses. www.rna-networks.at. A July 2018 conference in Salzburg, Austria organized by Guenther Witzany and Luis Villarreal (search each) to reconceive how life began, evolved, and developed by better appreciations of its genetic, biomolecular and viral agencies. From this home page, full slide presentations of authorities such as James Shapiro, Karin Moelling, Eugene Koonin, and Sabine Muller can be viewed. One might note this group is more a nucleotide node school, while a lively regulatory system complement also flourishes, as in the Origin of Life section. In his presentation, Gustavo Caetano Anolles (abstract below) does include a network/modular aspect in his accretion model.

This symposium assembles approximately 60 experts from different fields to discuss a new paradigmatic understanding of genetic novelty, code-generating, genome-formatting factors and the current knowledge of regulatory control in all steps und sub-steps of transcription, translation, repair, immunity, epigenetic marking and heredity.

The evolution of structure in biology is driven by accretion and change. Accretion brings together disparate parts to form bigger wholes. Change provides opportunities for growth and innovation. Networks can describe how parts associate in wholes. Here I review patterns and processes that are responsible for a ‘double tale’ of evolutionary accretion in the structure of biological networks. Parts are at first weakly linked and associate variously. As they diversify, they compete with each other and are selected for performance. The emerging interactions constrain their structure and associations. This causes parts to self-organize into modules with tight linkage. In a second phase, variants of the modules evolve and become new parts for a new generative cycle of higher-level organization. Evolutionary genomics and network biology support the ‘double tale’ of structural module creation and validate an evolutionary principle of maximum abundance that drives the gain and loss of modules. Gustavo Caetano-Annolles (search)

Evolutionary outcomes are difficult, if not impossible, to predict, largely because the effect of any possible mutation is unknown. In other words, understanding evolution requires detailed knowledge of the relationship between sequence and activity, or the fitness landscape. Inspired by theRNA World of early life, in which RNA carried information and also performed catalytic functions, we study the emergence and evolution of functional RNAs. I will describe our experimental efforts to map complete fitness landscapes for ribozymes and the implications for optimizing ribozyme activity and replaying the ‘tape of life’. (Irene Chen)

An Organic, Conducive, Habitable MultiUniVerse

Animate Cosmos > Quantum Cosmology

Kiukas, Jukka, et al. Complementary Observables in Quantum Mechanics. Foundations of Physics. Online April, 2019. Aberystwyth University, UK and University of Turku, Finland mathematicians contribute to a special issue about the esteemed University of York physicist Paul Busch (1955-2018) with whom they collaborated with for years. They advance Busch’s insights and expressions that natural phenomena tends to ever seek and reside in a dynamic duality, rather than a single state. Albeit by way unfamiliar terms and mathematical depth, a salient conclusion can be broached. This fantastic spacescape whence we find ourselves, which is yet amenable to our inquiry, is indeed distinguished by reciprocal archetypes at each and every instance. The authors open with a quote (see below) from his 1997 paper which suggests an “unsharp” milieu that is in some critical poise between complements, rather than a one thing theory. His Quantum Research Page is still online (paulbusch.wixsite.com/research-page) where an array of papers and conferences can be accessed. A special journal issue about Paul Busch is forthcoming, to which this belongs. See also Quantum Reality, Perspectivalism and Covariance by Dennis Dieks at arXiv:1905.05097 for another entry.

We review the notion of complementarity of observables in quantum mechanics, as formulated and studied by Paul Busch and his colleagues over the years. In addition, we provide further clarification on the operational meaning of the concept, and present several characterisations of complementarity—some of which new—in a unified manner, as a consequence of a basic factorisation lemma for quantum effects. We work out several applications, including the canonical cases of position–momentum, position–energy, number–phase, as well as periodic observables relevant to spatial interferometry. We close the paper with some considerations of complementarity in a noisy setting, focusing especially on the case of convolutions of position and momentum, which was a recurring topic in Paul’s work on operational formulation of quantum measurements and central to his philosophy of unsharp reality. (Abstract)

We hope to have demonstrated that one can safely open a pair of complementary ‘eyes’ simultaneously. He who does so may even ‘see more’ than with one eye only. The means of observation being part of the physical world, Nature Herself protects him from seeing too much and at the same time protects Herself from being questioned too closely: quantum reality, as it emerges under physical observation, is intrinsically unsharp. It can be forced to assume sharp contours – real properties – by performing repeatable measurements. But sometimes unsharp measurements will be both, less invasive and more informative. (Operational Quantum Physics Paul Busch 1997)

Animate Cosmos > Quantum Cosmology

Smolin, Lee. Einstein’s Unfinished Revolution: the Search for What Lies Beyond the Quantum. New York: Penguin, 2019. Another insightful volume by the Perimeter Institute for Theoretical Physics natural philosopher as he continues to sort out and clarify a past century of entangled quantum theories. Smolin presses on because the field seems to have reached an impasse that only a novel, missing dimension can resolve. In regard, a first part, An Orthodoxy of the Unreal, recites personal opinions, aspects and arguments since the early 1900s that have mostly wound up with ephemeral, anti-realist schemes. A survey of Leibniz, Mach, Einstein, Bohr, de Broglie, Schrodinger, Hugh Everett, and many others is covered to prepare for further glimpses such as by David Bohm and John Bell. A Realism Reborn section then avers that an independent reality outside our human conjectures must be seen to exist on its distinct own. By so doing, Smolin lays out the contrast between giving in to unintelligible quandaries or allowing that clouds can clear and a resolve be found.

True to his cause, a third part, Beyond the Quantum, offers approaches and proposals. A unifying synthesis will be based on principles such as background independence, a relational spacetime, an interactive reciprocity amongst objects (entities), and so on. Akin to Philip Ball’s Beyond Weird (a writer’s phrase for what Lee is trying to do), a prime informational quality need be factored in, pervasive network topologies, and John A. Wheeler’s “bit to it” participatory universe. But as my take, the (male) quest seems (cognitively) unable to face whether there is an actual cosmic elephant. That is to say, does an overall, intrinsic, evident (natural genesis) identity prevail of which human peoples who are able to find gravity waves and black holes, are a central phenomenon? This historic task is quite current since other 2019 books such as Totally Random by Jeffrey Bub and Quantum Strangeness by George Greenstein persist in the olden school.

Quantum physics is the basis of our understanding of atoms, radiation, and so much else. But it has been plagued by intense disagreements between its inventors, strange paradoxes, and implications that seem like fantasy. In Einstein's Unfinished Revolution, theoretical physicist Lee Smolin argues that the problems which have bedeviled quantum physics since its inception are unsolved for the simple reason that the theory is incomplete. Our task - if we are to have simple answers to our simple questions about the universe we live in - must be to go beyond quantum mechanics to a description of the world on an atomic scale that makes sense. (Publisher excerpts)

There is no purer model of a system of relations than a graph or network. Interestingly enough, networks are ubiquitous in those approaches to quantum gravity which are in accord with the principle of background independence. These include loop quantum gravity, causal sets, and causal dynamical relations. This suggests two exciting deepenings of our hypothesis : First, space emerges from the fundamental network. Second, quantum physics arises from nonlocal interactions left over when space emerges. (240)

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