
IV. Ecosmomics: Independent, UniVersal, Complex Network Systems and a Genetic CodeScript Source4. Universality Affirmations: A Critical Complementarity D’Amico, Guido, et al. A Theory of Taxonomy. arXiv:1611.03890. Physicists Guido, CERN Geneva, and Raul Rabadan, NYU, with biologist Matthew Kleban, Columbia University apply this method of species assortment to detect an invariant pattern across a wide range of natural and social phenomena. Search Didier FraixBurnet for a similar array for distributions of galaxies. Whatever does all this mean – might there be a cosmic anatomy and physiology? A taxonomy is a standardized framework to classify and organize items into categories. Hierarchical taxonomies are ubiquitous, ranging from the classification of organisms to the file system on a computer. Characterizing the typical distribution of items within taxonomic categories is an important question with applications in many disciplines. Ecologists have long sought to account for the patterns observed in speciesabundance distributions and computer scientists study the distribution of files per directory. Is there a universal statistical distribution describing how many items are typically found in each category in large taxonomies? Here, we analyze a wide array of large, realworld datasets  including items lost and found on the New York City transit system, library books, and a bacterial microbiome  and discover such an underlying commonality. A simple, nonparametric branching model that randomly categorizes items and takes as input only the total number of items and the total number of categories successfully reproduces the abundance distributions in these datasets. (Abstract) Daniels, Bryan, et al. Criticality Distinguishes the Ensemble of Biological Regulatory Networks. Physical Review Letters. 121/138102, 2018. An ASU based collaboration of BD, Hyunju Kim, Doug Moore, Siyu Zhou, Harrison Smith, Brad Karas, and Sara Walker, along with Stuart Kauffman, achieve a strongest articulation to date of nature’s constant tendency to seek and reach a preferred, optimum poise and balance of archetypal conservative order and liberal creativity states. One is naturally led onto yin and yang, feminine and masculine principles, entity/empathy, fire/love, DNA/AND, brain hemispheres so on everywhere and forever. Each bigender harmony then forms and resides within a tripartite familial genome, quantum, atome, neurome, cosmome, atome and Taome. We gloss, but here and in concurrent 2018 entries is auspicious evidence for an historic, literate discovery of a once and future human uniVerse genesis code. An earlier version, Logic and Connectivity Jointly Determine Criticality in Biological Gene Regulatory Networks, is at arXiv:1805.01447. The hypothesis that many living systems should exhibit nearcritical behavior is well motivated theoretically, and an increasing number of cases have been demonstrated empirically. Here, we provide a first comprehensive survey of criticality across a diverse sample of biological networks, leveraging a database of 67 Boolean models of regulatory circuits, all of which are near critical. We show that criticality in biological networks is not predictable solely from macroscale properties. Instead, the ensemble of real biological circuits is jointly constrained by the local causal structure and logic of each node. In this way, biological regulatory networks are more distinguished from random networks by their criticality. (Abstract excerpt) Davis, Martin. Universality is Ubiquitous. Floyd, Juliet and Alisa Bokulich, eds. Philosophical Explorations of the Legacy of Alan Turing. International: Springer, 2017. In this Volume 324 of the Boston Studies in the Philosophy and History of Science series, the NYU Courant Institute emeritus mathematician advises that this computational revolution reveals and quantifies a natural code in operation which programs life’s Earthly and cosmic evolution. As the algorithmic source independently runs, it results in exemplary instantiations, a universal repetition, at each and every stage and instance. In our worldwide midst, if of a mind to reflect, an epochal magnum opus, great work fulfillment is just being achieved. 6.5 Universality in Nature: Stephen Wolfram has famously argued for the significance of the existence of tiny abstract structures that already exhibit universality. In particular he has argued that universality is important in biological evolution. I conjecture that he is correct about this, though perhaps not in the way he intends. My conjecture is that DNA participates in the execution of algorithms that act on germplasm and so effect, and I’m guessing, speed up evolution. Let us suppose that the DNA includes a record of past evolutionary development. Next suppose that as part of the reproductive process algorithms modify the germplasm based on this record. If the change is beneficial to survival, Darwinian natural selection will preserve it. If anything like this is correct, then evolutionary change will not have been entirely dependent on random mutations, but will also include a quasiteleological aspect. (157158 excerpts) De, A., et al. Nonequilibrium Critical Scaling and Universality in a Quantum Simulator.. arXiv:2309.10856. In a paper that could be seen as a thirty year review of these natural oscillatory dynamics from early inklings to our consummate global stage, University of Maryland, Michigan State University, Johns Hopkins University, Rice University, and Duke University computational theorists here describe their similar, default effectiveness even in these previously remote realm. And we record once again how the first paragraph cites this current fulfillment from universe to human. Universality and scaling laws are hallmarks of equilibrium phase transitions and critical phenomena. However, extending these concepts to nonequilibrium systems remains a challenge. Here we use a trappedion quantum simulator to investigate nonequilibrium critical fluctuations following a quantum quench to the critical point. We show that the amplitude and timescale of the postquench fluctuations scale with system size with distinct universal critical exponents. Our results demonstrate the ability of quantum simulators to explore universal scaling beyond the equilibrium paradigm. (Excerpt) Del Papa, Bruno, et al. Criticality Meets Learning: Criticality Signatures in a SelfOrganizing Recurrent Neural Network. PLoS One. May 26, 2017. Computational neuroscientists BDP and Jochen Triesch, Goethe University, Frankfurt, and Viola Priesemann, MPI Dynamics and SelfOrganization press on with studies of a neural propensity to seek and reside at a preferred, simultaneous poise of more or less orderly states. Many experiments suggest that the brain operates close to a critical state, based on signatures such as powerlaw distributed neuronal avalanches. In neural network models, criticality is a dynamical state that maximizes information processing capacities, e.g. sensitivity to input, dynamical range and storage capacity. Although models that selforganize towards a critical state have been proposed, the relation between criticality signatures and learning is still unclear. Here, we investigate criticality in a selforganizing recurrent neural network (SORN). We show that, after a transient, the SORN spontaneously selforganizes into a dynamical state that shows criticality signatures comparable to those found in experiments. Overall, our work shows that the biologically inspired plasticity and homeostasis mechanisms responsible for the SORN’s spatiotemporal learning abilities can give rise to criticality signatures in its activity. (Abstract excerpt) Dobrovolska, Olena. Interrelationship Between Fractal Ornament and Multilevel Selection Theory. Biosemiotics. Online May, 2018. A Kharkiv National University of Radioelectronics, Ukraine philosopher achieves a unique synthesis across the sciences and the cultural ages. From an ancient land beset by internecine conflict, a woman scholar is able to cast an intellectual survey to broach an animate natural iteration. If to allow and consider, it promises to fulfill perennial wisdom as it reveals a universally recurrent pattern and process. As our worldwide sapience finds a cosmic biosemiosis via an informational agency, such a selfsimilarity and reference in kind can be noticed at each and every scale and instance. See also a 2018 paper by O. Mryglod for more an Ukranian uniVerse. Interdisciplinarity is one of the features of modern science, defined as blurring the boundaries of disciplines and overcoming their limitations or excessive specialization by borrowing methods from one discipline into another, integrating different theoretical assumptions, and using the same concepts and terms. Biosemiotics, a field that arose at the crossroads of biology, semiotics, linguistics, and philosophy, enables scientists to borrow theoretical assumptions from semiotics and extend them to different biological theories. In the present research, the semiotic system of Ukrainian folk ornament is analyzed through the theory of fractals, key features of which are recursion and selfsimilarity. What follows is a discussion of how this assumption can contribute to the multilevel selection theory, one of the foundations of extended synthesis, which employs the concept of selfsimilarity at all levels of the biological hierarchy. (Abstract) DodigCrnkovic, Gordana. Information, Computation, Cognition: AgentBased Hierarchies of Levels. Muller, Vincent, ed. Fundamental Issues of Artificial Intelligence. Switzerland: Springer, 2016. In this select collection from a Philosophy and Theory of AI conference at Oxford University, the Chalmers University theorist, among her many writings (search) again offers a cogent recitation of life’s emergent, nested, repetitive iteration from atomic and biomolecular origins to our aware collective cognizance. This cosmic and Earthly evolution is seen to proceed by an interplay of agent entities in relational communication. As many concurrent papers herein attest, a fractal self similarity is thus said to repeat in kind from universe to humanity. In order to study within one framework cognition in living organisms (including humans) and machines (including cognitive software), this article is generalizing some common ideas, thus using extended concepts of Dunham, Christopher, et al. Nanoscale Neuromorphic Networks and Criticality. Journal of Physics: Complexity. 2/4 December, 2021. We record this entry by nine UCLA, University of Sydney, and UnLAB, Savannah, GA researchers as a latest example of many wide and deep areas where critical point behavior is being found. Its dynamic distinction is to become situated and balanced between more or less orderly or coherent phases. (As chimera theory notes, often in both states at once.) The paper reviews these phenomenal findings and goes on to describe how cerebral activity is seen as an archetypal instance. Numerous studies suggest critical dynamics may play a role in information processing and task performance in biological systems. However, studying these systems can be challenging due to many biological variables that limit access to underlying physical processes. Here we offer a perspective on the use of abiotic, neuromorphic nanowire networks as a means to investigate critical dynamics in complex adaptive systems. Neuromorphic nanowire networks are composed of metallic nanowires and metalinsulatormetal junctions. They selfassemble into interconnected, variabledensity forms and exhibit nonlinear electrical switching properties and information processing capabilities. We posit that such neuromorphic networks can function as abiotic physical systems for studying critical dynamics and computation. (Abstract excerpt) Ermann, Leonardo, et al. Google Matrix Analysis (GMA) of Directed Networks. Reviews of Modern Physics. 87/4, 2015. Theoretical physicists Ermann, CNEA Argentina, with Klaus Frahm and Dima Shepelyansky (search), University of Toulouse, write a lengthy tutorial on such scalefree mathematical and topological methods including Markov chains, which are found to similarly apply from genomes to economies. But searching the title phrases does not result in a simple definition. As a gloss, a meld of directed graphs with weighted, oriented edges and the PageRank algorithms, topics considered in initial pages. This generic pattern is seen to appear in software architecture, the worldwide web, Wikipedia, social media, global trade, scientific citations, neural nets, gene regulation, and more. An allusion is made to Jorge Borges’ The Library of Babel that such a common recurrence could begin to bring some organizational sense across nature and society. See also prior papers GMA of DNA Sequences (1301.1626), and GMA of C.elegans Neural Network (1311.2013), and GMA of the World Network of Economic Activities (1504.06773) by these authors and colleagues. A further surmise might be that the constant system is much akin to a genome, a semblance of a universe to human genetic code. In past ten years, modern societies developed enormous communication and social networks. Their classification and information retrieval processing become a formidable task for the society. Due to the rapid growth of World Wide Web, social and communication networks, new mathematical methods have been invented to characterize the properties of these networks on a more detailed and precise level. Various search engines are essentially using such methods. It is highly important to develop new tools to classify and rank enormous amount of network information in a way adapted to internal network structures and characteristics. This review describes the Google matrix analysis of directed complex networks demonstrating its efficiency on various examples including World Wide Web, Wikipedia, software architecture, world trade, social and citation networks, brain neural networks, DNA sequences and Ulam networks. The analytical and numerical matrix methods used in this analysis originate from the fields of Markov chains, quantum chaos and Random Matrix theory. (Article Abstract) Fan, Jingfang, et al. Universal Gap Scaling in Percolation. Nature Physics. April, 2020. We cite this technical entry by JF, Jun Meng, Yang Liu, Abbas Saberi, and Jurgen Kurths, Potsdam Institute for Climate Impact Research, along with Jan Nagler, Deep Dynamics Group, Frankfurt School of Finance as another current finding about the universal presence, so it seems, from physical networks to everywhere else such as cells, brains, hearts, genomes, and onto to linguistic information. Cosmic to cultural nature can now indeed be found to draw upon and express a single, infinitely recurrent, critical condition. Universality is a principle that underlies many critical phenomena from epidemic spreading to the emergence of connectivities in networks. Percolation, the transition to global connectedness on gradual addition of links, may exhibit substantial gaps in the size of the largest connected network component. We uncover that the largest gap statistics is governed by extremevalue theory. This allows us to unify continuous and discontinuous percolation by virtue of universal critical scaling functions. This links extremevalue statistics to universality and criticality in percolation. (Abstract) Filatov, Denis and Alexey Lyubushin. Stochastic Dynamical Systems Always Undergo Trending Mechanisms of Transition to Criticality. Physica A. Volume 521, 2019. Sceptica Science, UK and Russian Academy of Sciences physicists post a theoretical affirmation as to why and how nature’s active phenomena has an intrinsic attraction to reach a critically poised state. See also A Method for Identification of Critical States of Open Stochastic Dynamical Systems by D. Filatov in Journal of Statistical Physics (165/4, 2016). We study the transition of stochastic dynamical systems to critical states. We begin from employing two independent quantitative methods of time series analysis, firstorder detrended fluctuation analysis and multivariate canonical coherence analysis. We find out that there are two different mechanisms of the transition to criticality: the first mechanism is consistent with that observed in some biological dynamical systems and associated with a growth of the energies at low frequencies in the power spectrum, whereas the second mechanism is new and governed by a decay of the energies at high frequencies. Despite this difference, we show that both mechanisms lead to a loss of chaoticity in the system’s behavior and result in a more deterministic evolution of the system as a whole. The obtained results allow hypothesis that in stochastic dynamical systems of any nature the transition to a critical state is always realized through a trending nonlinear process. (Abstract) Frank, Steven A.. The Price Equation Program: Simple Invariances Unify Population Dynamics, Thermodynamics, Probability, Information and Inference. arXiv:1810.09262. The UC Irvine biologist continues his project (search SAF website) to finesse and expand evolutionary and selective theories by way of affinities with and rootings in physical, mathematical, energetic, and communicative domains. Into the 2010s by contributions as this, it is increasingly apparent that a universal recurrence in kind of a common iconic source code is in independent, procreative effect. See also Universal Expressions of Population Change by the Price Equation by SAF in Ecology and Evolution (7/3381, 2017). The fundamental equations of various disciplines often seem to share the same basic structure. Natural selection increases information in the same way that Bayesian updating does. Thermodynamics and probability distributions express maximum increase in entropy, which appears mathematically as loss of information. Physical mechanics follows paths of change that maximize Fisher information. This web of vague analogies hints at a deeper common mathematical structure. I suggest that the abstract Price equation expresses that underlying universal structure as it describes dynamics as the change between two sets. One component of dynamics expresses the change in the frequency of things, holding constant the values associated with things. The other component of dynamics expresses the change in the values of things, holding constant the frequency of things. From that perspective, interpretations such as selection, information, entropy, force, acceleration, and physical work arise from the same underlying geometry expressed by the Price equation. (Abstract excerpts)
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