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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 31 through 45 of 94 found.

An Organic, Conducive, Habitable MultiUniVerse

Animate Cosmos > Astrobiology

Yamamoto, Satoshi. Introduction to Astrochemistry: Chemical Evolution from Interstellar Clouds to Star and Planet Formation.. International: Springer, 2017. A University of Tokyo biophysicist provides a later 2010s comprehensive technical survey from Molecular Abundances and Diffuse Clouds to Star and Planet Forming Regions.

This important book describes the basic principles of astrochemistry — an interdisciplinary field combining astronomy, physics, and chemistry — with particular emphasis on its physical and chemical background. Chemical processes in diffuse clouds, dense quiescent molecular clouds, star-forming regions, and protoplanetary disks are discussed, along with molecular spectroscopy and observational techniques. These contents provide astronomers with a comprehensive understanding of how interstellar matter is evolved and brought into stars and planets, which is ultimately related to the origin of the solar system.

Cosmomics: A Genomic Source Code is in Procreative Effect

Cosmic Code

Brauns, Fridtjof, et al. Phase-Space Geometry of Reaction-Diffusion Dynamics. arXiv:1812.08684. In a densely technical, tightly composed 55 page paper, Ludwig-Maximilians University system physicists FB, Jacob Halatek and Erwin Frey (search) continue their decadal project to explain by way of nonequilibrium thermodynamics, structural formations, Turing-like morphogenesis, self-organized critical complexities, computational biology, and more how life proceeds to develop and maintain its physiological vitality. With 158 references, in these later 2010s a collaborative sense of a realistic model is evident. It is proposed in closing that such cellular coherence is an generalization which could apply to other natural systems. See also Rethinking Pattern Formation in Reaction-Diffusion Systems by Halatek and Frey in Nature Physics (14/5, 2018) and for example Guiding Self-Organized Pattern Formation in Cell Polarity Establishment by Peter Gross, et al (NP December 2018)

Experimental studies of protein pattern formation have stimulated new interest in the dynamics of reaction--diffusion systems. However, a comprehensive theoretical understanding of the dynamics of such highly nonlinear, spatially extended systems is still missing. Here we show how a description in phase space, which has proven invaluable in shaping our intuition about the dynamics of nonlinear ordinary differential equations, can be generalized to mass-conserving reaction--diffusion (McRD) systems. We present a comprehensive theory for two-component McRD systems, which serve as paradigmatic minimal systems. The fundamental elements of the theory presented suggest ways of experimentally characterizing pattern-forming systems on a mesoscopic level and are generalizable to a broad class of spatially extended non-equilibrium systems, and thereby pave the way toward an overarching theoretical framework. (Abstract excerpt)

Cosmic Code

Dingle, Kamaludin, et al. Input-Output Maps are Strongly Biased Towards Simple Outputs. Nature Communications. 9/761, 2018. By way of algorithmic information theory and system cartographic methods, Oxford University mathematicians KD, Chico Camargo and Ard Louis perceive an inherent tendency in complex network behavior to simplify and generalize themselves. The work merited notice as A Natural Bias for Simplicity by Mark Buchanan in Nature Physics (December 2018). See also by this group Deep Learning Generalizes because the Parameter-Function Map is Biased Towards Simple Functions at arXiv: 1805.08522.

Many systems in nature can be described using discrete input–output maps. Without knowing details about a map, there may seem to be no a priori reason to expect that a randomly chosen input would be more likely to generate one output over another. Here, by extending fundamental results from algorithmic information theory, we show instead that for many real-world maps, the a priori probability P(x) that randomly sampled inputs generate a particular output x decays exponentially with the approximate Kolmogorov complexity K~(x) of that output. We explore this strong bias towards simple outputs in systems ranging from the folding of RNA secondary structures to systems of coupled ordinary differential equations to a stochastic financial trading model. (Abstract)

Cosmic Code

Yao, Nan, et al. Self-Adaptation of Chimera States. arxiv:1812.06336. (Chimera states are self-organized spatiotemporal patterns of coexisting coherence and incoherence.) A global team based in China, Scotland, and the USA begin with the standard statement that such critical dynamics are now known to commonly occur across all chemical to cerebral domains. A further aspect of these orderly or chaotic conditions is that this active phenomena seems to exhibit a certain sensory ability by which to guide its responses. All these happen as if the chimera was “intelligent” (5).

(Chimera states are self-organized spatiotemporal patterns of coexisting coherence and incoherence.) A global team based in China, Scotland, and the USA begin with the standard statement that such critical dynamics are now known to commonly occur across all chemical to cerebral domains. A further aspect of these orderly or chaotic conditions is that this active phenomena seems to exhibit a certain sensory ability by which to guide its responses. All these happen as if the chimera was “intelligent” (5).

Cosmic Code > Algorithms

Stepney, Susan and Andrew Adamatzky, eds. Inspired by Nature. International: Springer, 2018. A 60th birthday tribute to Julian Miller, the University of York, UK computer applications pioneer with works such as Cartesian Genetic Programming (Springer, 2011, search). Seven years later, a further sense of universal computations occurs in chapters Evolution in Nanomaterio by Hajo Broersma, Code Evolution with Genetic Programming by Wolfgang Banzhaf, and Chemical Computing through Simulated Evolution by Larry Bull, et al, and others. This concurrent edition adds to the similar content of Computational Matter, (herein) also edited by S. Stepney. A tacit theme is a Big Code in pervasive effect beyond and before Big Data. As the sample quote conveys, within this scenario, it seems that natural cosmic genesis may intend to pass off its procreative to our human intention for all futures, if we might altogether appreciate this.

Evolution has done a great job for many living organisms, and it has done so through a conceptually rather easy but smart, albeit very slow bottom up process of natural Darwinian evolution. There seems to be no design involved in this process: the computational instructions that underlie living creatures have not been designed but rather have (been) evolved. Two questions come to mind: Can we use something similar as evolution on ‘dead’ matter in order to get something useful? Can we do it quickly, via a rapidly converging evolutionary process? (H. Broersma, University of Twente, 95)

Cosmic Code > Algorithms

Stepney, Susan, et al, eds. Computational Matter. International: Springer, 2018. With coeditors Steen Rasmussen and Martyn Amos, the volume is a broad survey of endeavors with an umbrella Unconventional Computing UCOMP name, drawn originally from Stanislaw Ulam, which considers every manifest phase from quantum to social realms to arise in an exemplary way from a mathematical source code. Some entries are Cellular Computing and Synthetic Biology (M. Amos, et al), Decoding Genetic Information (G. Franco and V. Manca), BIOMICS: A Theory of Interaction Computing (P. Dini, et al), and Nanoscale Molecular Automata (R. Rinaldi, et al). An inference is a natural “digitalization” process as a double reality via a software-like informative program and an overt material, creaturely result. And it would seem to readily infer “genotype and phenotype,” see also The Principles of Informational Genomics by V. Manca (search) in Theoretical computer Science (701/190, 2017).

This book is concerned with computing in materio: that is, unconventional computing performed by directly harnessing the physical properties of materials. It offers an overview of the field, covering four main areas: theory, practice, applications and implications. Each chapter synthesizes current understanding by bringing together researchers across a collection of related research projects. The book is useful for graduate students, researchers in the field, and the general scientific reader who is interested in inherently interdisciplinary research at the intersections of computer science, biology, chemistry, physics, engineering and mathematics. (Springer)

Cosmic Code > 2015 universal

Ananthaswamy, Anil. Through Two Doors at Once The Elegant Experiment That Captures the Enigma of Our Quantum Reality. New York: Dutton, 2018. The international science journalist chronicles this iconic situation which harks back to Thomas Young in 1801 whence dual aspects of position and momentum seem to co-exist at the same time. It has been a quandary for quantum studies, often due to personal opinion. Niels Bohr cited it in 1927 as an example of particle/wave complementarity. By way of many interviews such as Alain Aspect, David Mermin, Tim Maudlin, the well told story arrives at a similar point as Philip Ball’s Beyond Weird does. A century of speculation may gain some resolution by Bayesian probabilities and J. A. Wheeler’s observer participation.

The story of the “double-slit" experiment which splits a light beam into two paths first challenged our understanding of natural reality. Thomas Young devised it in the early 1800s to show that light behaves like a wave, and thus opposed Isaac Newton. In to the 20th century the issue led to a long debate between Albert Einstein and Niels Bohr. Richard Feynman held that the double slit embodies the central quantum mystery. Is there a place where the quantum world ends and the familiar classical world of our daily lives begins, and if so, can we find it? And if there's no such place, then does the universe split into two each time a particle goes through the double slit? (Publisher edits)

Cosmic Code > 2015 universal

Bala, Arun. Complementarity Beyond Physics. Basingstoke, UK: Palgrave Macmillan, 2017. The National University of Singapore senior research fellow is the author of significant works such as The Dialogue of Civilizations in the Birth of Modern Science (2006). This novel edition covers a cultural history of intuitions that this encompassing existence wherein we find ourselves is distinctly composed of opposite but reciprocal gender-like archetypes. Its premier modern view is by Niels Bohr in the 1920s, aka the Copenhagen interpretation, which he enhanced by referrals to yin/yang Asian wisdom. As the quote says, while subject to debate, a quantum essence of dual particle and wave states or modes has since grown in veracity and scope. The timely volume proceeds with further evidence from biological, anthropological, behavioral and philosophical domains. For a 2018 regard, see The Consciousness Instinct by Michael Gazzaniga which makes a strong claim via Bohr along with Howard Pattee (search) that this prime principle does reveal and exemplify a cosmic to cognitive complementarity.

In this study Arun Bala examines the implications that Niels Bohr’s principle of complementarity holds for fields beyond physics. Bohr, one of the founding figures of modern quantum physics, argued that the principle of complementarity he proposed for understanding atomic processes has parallels in psychology, biology, and social science, as well as in Buddhist and Taoist thought. But Bohr failed to offer any explanation for why complementarity might extend beyond physics, and his claims have been widely rejected by scientists as speculation. Arun Bala offers a detailed defense of Bohr’s claim that complementarity has far-reaching implications for the biological and social sciences, as well as for comparative philosophies of science, by explaining Bohr’s parallels as responses to the omnipresence of grown properties in nature.

(Robert) Oppenheimer suggest that not only does quantum theory seem to violate the rules of classical logic but also that there are traditions of Eastern thought which have come to recognize, long before that to comprehensively understand phenomena in the universe often requires the use of mutually exclusive but complementary notions. (3)

Cosmic Code > 2015 universal

Castellani, Elena and Sebastian De Haro. Duality, Fundamentality, and Emergence. arXiv:1803.09443. University of Florence and University of Amsterdam philosophers of science work toward a clarified resolve and integration of these conceptual qualities, which as usual requires a better definition of terms.

We argue that dualities offer new possibilities for relating fundamentality, levels, and emergence. Namely, dualities often relate two theories whose hierarchies of levels are inverted relative to each other, and so allow for new fundamentality relations, as well as for epistemic emergence. We find that the direction of emergence typically found in these cases is opposite to the direction followed in the standard accounts. Namely, the standard emergence is that of decreasing fundamentality. But in cases of duality, a more fundamental entity can emerge out of a less fundamental one. This possibility can be traced back to the existence of different classical limits in quantum field theories and string theories. (Abstract)

Cosmic Code > 2015 universal

Castellini, Elena and Dean Rickles. Introduction to Special Issue on Dualities. Studies in History and Philosophy of Modern Physics. 59/1, 2017. University of Florence and University of Sydney philosophers of science survey some dozen papers about nature’s apparent propensity to array into double phases and their altogether trinity. We note Complementarity, Wave-Particle Duality and Applicability by Peter Bokulich, Dualities and Emergent Gravity by Sebastian de Haro, and Duality as a Category-Theoretic Concept by David Corfield. The entry opens with a Yin/Yang Tao image, the ancient icon for this native quality. It is said herein the twoness is a general “elemental/composite” correspondence which forms a third whole. See also a later entry Duality, Fundamentality and Emergence by E. Castellini and S. de Haro above and at arXiv:1803.09443.

Cosmic Code > 2015 universal

Kolodrubetz, Michael. Quenching Our Thirst for Universality. Nature. 563/191, 2018. A UT Dallas systems physicist introduces three papers in this issue: Observation of Universal Dynamics in a Spinor Bose Gas Far from Equilibrium (Prufer, 217), Universal Prethermal Dynamics of Bose Gases Quenched to Unitarity (Eiger, 221) and Universal Dynamics in an Isolated One-Dimensional Bose Gas Far from Equilibrium (Erne, 225), that verify in different places and ways the natural presence of ubiquitous, infinitely iterated, formative patterns and active processes.

Although we live in a world of constant motion, physicists have focused largely on systems in or near equilibrium. In the past few decades, interest in non-equilibrium systems has increased, spurred by developments that are taking quantum mechanics from fundamental science to practical technology. Physicists are therefore tasked with an important question: what organizing principles do non-equilibrium quantum systems obey? Herein Prüfer et al, Eigen et al, and Erne et al report experiments that provide a partial answer to this question. The studies show, for the first time, that ultracold atomic systems far from equilibrium exhibit universality, in which measurable experimental properties become independent of microscopic details. (MK)
While the evolution of a many-body system is in general intractable in all its details, relevant observables can become insensitive to microscopic system parameters and initial conditions. This is the basis of the phenomenon of universality. Far from equilibrium universality is identified through the scaling of the spatio-temporal evolution of the system. This has been studied in the reheating process in inflationary cosmology, the dynamics of nuclear collision described by quantum chromodynamics, and the post-quench dynamics in dilute quantum gases in non-relativistic field theory. Here we observe the emergence of universal dynamics by spatially resolved spin correlations in a quasi-one-dimensional spinor Bose–Einstein condensate. (Prufer)

Understanding the behaviour of isolated quantum systems far from equilibrium and their equilibration is one of the most pressing problems in quantum many-body physics. There is strong theoretical evidence that sufficiently far from equilibrium a wide variety of systems — including the early Universe after inflation, quark–gluon matter generated in heavy-ion collisions, and cold quantum gases — exhibit universal scaling in time and space during their evolution, independent of their initial state or microscale properties. (Erne)

Cosmic Code > 2015 universal

Kossio, Felipe, et al. Growing Critical: Self-Organized Criticality in a Developing Neural System. arXiv:1811.02861. As it becomes well known that brains seek and best perform in a state of mutual balance between more or less orderly complements, University of Bonn, Radboud University and King Juan Carlos University, Madrid neuroinformatic researchers describe experimental evidence that developmental brain maturations likewise proceed toward this optimum condition.

Experiments in various neural systems found avalanches: bursts of activity with characteristics typical for critical dynamics. A possible explanation for their occurrence is an underlying network that self-organizes into a critical state. We propose a simple spiking model for developing neural networks, showing how these may "grow into" criticality. Avalanches generated by our model correspond to clusters of widely applied Hawkes processes. We analytically derive the cluster size and duration distributions and find that they agree with those of experimentally observed neuronal avalanches. (Abstract)

Cosmic Code > 2015 universal

Persi, Erez, et al. Criticality in Tumor Evolution and Clinical Outcome. Proceedings of the National Academy of Sciences. 115/E11101, 2018. University of Maryland and National Center for Biotechnology Information researchers including Yuri Wolf and Eugene Koonin report findings across a wide range of cancer cases that a complex generative dynamics is in effect which arrays as a critically poised state. It is said that appreciations of this common tendency could well aid diagnostics and treatment.

How mutation and selection determine the fitness landscape of tumors and hence clinical outcome is an open fundamental question in cancer biology, crucial for the assessment of therapeutic strategies and resistance to treatment. Here we explore the mutation-selection phase diagram of 6,721 tumors representing 23 cancer types by quantifying the overall somatic point mutation load (ML) and selection (dN/dS) in the entire proteome of each tumor. We show that ML strongly correlates with patient survival, revealing two opposing regimes around a critical point. In low-ML cancers, a high number of mutations indicates poor prognosis, whereas high-ML cancers show the opposite trend, presumably due to mutational meltdown. (Abstract excerpt)

Cosmic Code > 2015 universal

Qian, Xiao-Feng, et al. Bohr’s Complementarity: Completed with Entanglement. arXiv:1803.04611. University of Rochester physicists X-F Qian, A. Vamivakas, and Joseph Eberly arrive at a current mathematical resolve by way of a triune synthesis of mutual exclusivity and an integral composite. Octogenarian Eberly has been a lifetime theorist for optical quantum phenomena. See also Shifting the Quantum-Classical Boundary by this team in Optica (2/7, 2015).

Ninety years ago in 1927 at an international congress in Como, Italy, Niels Bohr gave an address which is recognized as the first instance in which the term "complementarity" was spoken publicly. Bohr had accepted duality as a principle of physics: close observation of any quantum object will reveal either wave-like or particle-like behavior, one or the other of two fundamental and complementary features. Some confusion followed his talk and complementarity has seen much discussion since but the concept retains a central place in quantum mechanics. Scholarly examinations provide speculations about the relevance of complementarity in fields as different from physics as biology, psychology and social anthropology. In regard, recent approaches by our group and others seem to show that entanglement is the ingredient needed to complete Bohr's formulation. (Abstract edits)

Cosmic Code > 2015 universal

Sorbaro, Martino, et al. Statistical Models of Neural Activity, Criticality, and Zipf’s Law. arXiv:1612.09123. We note this contribution by University of Edinburgh, School of Informatics researchers MS, Michael Herrmann and Matthias Hennig because it draws parallel between cerebral dynamics, their critical attractor state, and G. K. Zipf’s (second quote) linguistic origin. See also Statistical Criticality Arises in Maximally Informative Samples by Ryan Cubero, et al (1808.0249) for another take upon this synthesis.

In this overview, we discuss the connections between the observations of critical dynamics in neuronal networks and maximum entropy models that are often used as models of neural activity, focusing on the relation between "statistical" and "dynamical" criticality. We then discuss the emergence of Zipf’s law in neural activity, verifying their presence in retinal activity under a number of conditions. In the second part we review statistical criticality and the structure of the parameter space, as described by Fisher information. (Abstract excerpt)

Zipf's law is an empirical law formulated using mathematical statistics named after the linguist George Kingsley Zipf, who first proposed it in 1932. It states that given a large sample of words used, the occurrence of any word is inversely proportional to its rank in the frequency table. The most common word will occur about twice as often as the second most frequent word, etc. The relationship occurs in many other rankings, unrelated to language, such as the population ranks of cities in various countries, corporation sizes, income rankings, etc. (Wikipedia)

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