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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 46 through 60 of 98 found.


Cosmomics: A Genomic Source Code is in Procreative Effect

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

Manca, Vincenzo. The Principles of Informational Genomics. Theoretical Computer Science. 701/190, 2017. The University of Verona computer scientist complements his chapter Decoding Genetic Information with G. Franco in Computational Matter (S. Stepney, 2017) about novel perspectives of genetic activity in terms of their algorithmic, semantic, linguistic qualities.

The present paper investigates the properties of genomes directly related with their long linear structure. A systematic approach is introduced that is based on an integration of string analysis and information theory, applied and verified on real genomes. New concepts and results are given in connection with genome empirical entropies (and related indexes), genome dictionaries and distributions, word elongations, informational divergences, genome assemblies, and genome segmentations.

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

Horstmeyer, Leonhard, et al. Network Topology near Criticality in Adaptive Epidemics. arXiv:1805.09358. Just as every other area from quantum to neural has become defined by the universally prevalent self-organized complex network systems, here LH and Stefan Thurner, Medical University of Vienna and Christian Kuehn, Technical University of Munich theorists describe how even human disease vectors among variegated populations similarly hold, as they mathematically must,Just as every other area from quantum to neural has become defined by the universally prevalent self-organized complex network systems, here LH and Stefan Thurner, Medical University of Vienna and Christian Kuehn, Technical University of Munich theorists describe how even human disease vectors among variegated populations similarly hold and exhibit, as they mathematically must, to predictable, critical principles.

We study structural changes of adaptive networks in the co-evolutionary susceptible-infected-susceptible (SIS) network model along its phase transition. We clarify to what extent these changes can be used as early-warning signs for the transition at the critical infection rate λc at which the network collapses and the system disintegrates. We analyze the interplay between topology and node-state dynamics near criticality. Several network measures exhibit clear maxima or minima close to the critical threshold that could potentially serve as early-warning signs. For the SI link density and triplet densities the maximum is found to originate from the co-existence of two power laws. (Abstract)

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)

Cosmic Code > 2015 universal

Tkacik, Gasper, et al. Thermodynamics and Signatures of Criticality in a Network of Neurons. Proceedings of the National Academy of Sciences. 112/11508, 2015. Seven theorists posted in Austria, France and the USA (Princeton) including Thierry Mora and William Bialek describe deep commonalities between far removed realms of condensed matter and cerebral matters by way of their energetic activities.

The activity of a brain—or even a small region of a brain devoted to a particular task—cannot be just the summed activity of many independent neurons. Here we use methods from statistical physics to describe the collective activity in the retina as it responds to complex inputs such as those encountered in the natural environment. We find that the distribution of messages that the retina sends to the brain is very special, mathematically equivalent to the behavior of a material near a critical point in its phase diagram. (Significance)

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Minelli, Alessandro. An Evo-Devo Perspective on Analogy in Biology. Philosophies. 4/1, 2019. In a special collection from the Second World Congress on Analogy at Adam Mickiewicz University, Poland in May 2017, the University of Padova senior biologist and author (search) describes new appreciations of life’s tendency to draw upon and repeat patterns and processes (aka homology, homoplasy, convergence, etc.) in creaturely kind across life’s evolution. As a result, this long, episodic emergence is increasingly becoming seen as a developmental gestation.

To explain the amazing morphological and biomechanical analogy between two distantly related vertebrates as a dolphin and a shark, framed only in terms of adaptation (i.e., Darwinian survival of the fittest) is far from satisfactory. The same is true of any other structurally similar, but phylogenetically unrelated organisms. An evolutionary argument does not say how the developmental processes of their ancestors could evolve so as to produce these phenotypes (the arrival of the fittest). To address the evolution of possible forms, we cannot ignore that these are products of development. This invites an integrated perspective, currently known as evolutionary developmental biology, or evo-devo. Paths through living forms are not satisfactorily explained in terms of geometrical transformations or the adaptive value of the phenotypes. The emergence of form is dependent on the intrinsic evolvability of developmental processes that translate the genotype into phenotypes. As a consequence, development makes analogous structures more likely to evolve than a purely adaptationist view would ever suggest. (Abstract)

This Special Issue follows the intention of the congress to promote interdisciplinary research, philosophical reflection, and discourse across multiple methodological perspectives about analogy. There are many definitions and conceptions of analogy, but it is always considered as a universal tool that enables us to discover, explore, compare, analyze, understand and illustrate similarities and differences. Formally speaking, analogy can be defined as a relation between relations; it is connected with proportions and remains pervasive in science, art and religion. If we agree that inter-cultural, inter-ideological and inter-religious dialogue is a crucial issue, the humanistic approach to analogy seems to be of the greatest importance. (Summary)

Quickening Evolution > Systems Biology

Ceska, Milan and David Safranek, eds. Computational Methods in Systems Biology. International: Springer, 2018. The Proceedings of the 16th International Conference on this title subject (CMSB) held in Brno, Czech Republic, in September. Some entries are Deep Abstractions of Chemical Reactions Networks, Synthesis for Vesicle Traffic Systems, and Experimental Biological Protocols with formal Semantics. May one then wonder, what grand phenomena, of we are as yet unawares, is our worldwise sapiensphere coming upon, trying to learn, provide a cosmic self-describe? What is going on, what language is natural genesis written in? Who are we phenomenal human beings to be able to do this, for what purpose? Does a universal procreation want us to intentionally take from here?

The 15 full and 7 short papers presented together with 5 invited talks were selected from 46 submissions. Topics of interest include formalisms for modeling biological processes; models and their biological applications; frameworks for model verification, validation, analysis, and simulation of biological systems; high-performance computational systems biology; parameter and model inference from experimental data; automated parameter and model synthesis; model integration and biological databases; multi-scale modeling and analysis methods; design, analysis, and verification methods for synthetic biology; methods for biomolecular computing and engineered molecular devices.

Quickening Evolution > Intel Ev

Pinero, Jordi and Ricard Sole. Statistical Physics of Liquid Brains. bioRxiv. November 26, 2018. Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona theorists post their paper from a December 2017 Santa Fe Institute seminar entitled Liquid Brains, Solid Brains, which was organized by Sole, Melanie Moses and Stephanie Forrest. (see fourth quote). A year later, an answer to its mission can be broached. A universal recurrence in kind across natural and social domains of the same generic complex network system does actually appear to be the case. While akin to genomes and ecosystems, an apt model is cerebral cognition, broadly conceived, by way of agental neurons and synaptic links in multiplex arrays. A definitive attribute is a cross-conveyance of viable intelligence and information, aka biological computation. This is how animal groupings from invertebrates to mammals to people achieve a collective decision-making. As 2020 nears, after centuries of intimation, decades of glimpses, a worldwide flow of convergent findings (a global brain learning on her/his own), augur for a realization and discovery forming in our midst.

Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona theorists post their paper from a December 2017 Santa Fe Institute seminar entitled Liquid Brains, Solid Brains, which was organized by Sole, Melanie Moses and Stephanie Forrest. (see fourth quote). A year later, an answer to its mission can be broached. A universal recurrence in kind across natural and social domains of the same generic complex network system does actually appear to be the case. While akin to genomes and ecosystems, an apt model is cerebral cognition, broadly conceived, by way of agental neurons and synaptic links in multiplex arrays. A definitive attribute is a cross-conveyance of viable intelligence and information, aka biological computation. This is how animal groupings from invertebrates to mammals to people achieve a collective decision-making. As 2020 nears, after centuries of intimation, decades of glimpses, a worldwide flow of convergent findings (a global brain learning on her/his own), augur for a realization and discovery forming in our midst.

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