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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 31 through 45 of 74 found.


Ecosmomics: A Survey of Nonlinear Complex Network Sciences

Cosmic Code > nonlinear > Algorithms

Kaznatcheev, Artem. Evolution is Exponentially More Powerful with Frequency-Dependent Selection. . An Oxford University computer scientist posts a latest appreciation of how living systems appear to evolve and develop as stochastic explore and educate optimization processes. In any event, the insight admits a deep mathematical presence of operative programs, which are modified along the way. See also Computational Complexity as an Ultimate Constraint on Evolution by AK in Genetics (212/245, 2019).

In 2009 (Leslie) Valiant (search) proposed to treat Darwinian evolution as a special kind of computational learning by way of statistical queries which represent a genotype’s fitness over a distribution of challenges. His model noted various environments that are “adaptable-to” from those that are not, but omits vital ecological interactions between different evolving agents. Here I extend an algorithmic Darwinism to include the ecological exigiences of frequency-dependent selection as a population-dependent bias and develop a game landscape view of evolution so to generalize the popular fitness landscape. The evolutionary game dynamics of finite populations are essential for finding a short adaptive path to the global fitness peak during the second stage of the adaptation process. This highlights the rich interface between computational learning theory, evolutionary games, and long-term evolution. (Abstract excerpt)

Artem K. website Prior to Oxford, I was at the Department of Integrated Mathematical Oncology at Moffitt Cancer, and at McGill University where I developed my interest in evolutionary dynamics, computer science, mathematical oncology and computational learning theory. In regard, I marvel at the world through algorithmic lenses. My theoretical work aims to ground the extended evolutionary synthesis in algorithmic game theory, computational learning theory, and combinatorial optimization.

Cosmic Code > nonlinear > Rosetta Cosmos

Chen, Hongjia, et al. Scaling Laws and Dynamics of Hashtags on Twitter. arXiv:2004.12707. University of Sydney systems linguists including Eduardo Altmann discern yet another case of nature’s universal mathematic patterns and dynamics at formative presence even is these hyper-active Internet communications.

In this paper we quantify the statistical properties and dynamics of the frequency of hashtag use on Twitter. Hashtags are special words used in social media to attract attention and to organize content. Looking at the collection of hashtags used in a period of time, we identify the scaling laws for their frequency distribution (Zipf's law), the number of unique hashtags as a function of sample size (Heaps' law), and the fluctuations around expected values (Taylor's law). While these scaling laws appear to be universal, their volume and nature depends strongly on time, with bursts at the minute scale, fat-tailed noise, and long-range correlations. Here we view hashtags as memes and quantify emerging properties of their collective interaction including scaling laws and time scales. (Excerpt)

Cosmic Code > nonlinear > Rosetta Cosmos

Gromov, Vasilii and Anastasia Migrina. A Language as a Self-Organized Critical System. Complexity. November, 2017. Oles Honchar National University, Ukraine mathematicians lay out a theoretical basis by which even this human cultural communicative quality appears to express nature’s universal middle way propensity.

A natural language (herewith texts generated by native speakers) is considered as a complex system. Namely, the authors hypothesize that such dynamic languages are self-organized critical systems and that their texts are “avalanches” flowing through word cooccurrence graphs. The respective statistical distributions of the number of words in English and Russian languages are calculated from a corpora of literary texts and sets of social media messages. The analysis found that the number of words in the texts obeys power-law distribution. (Abstract excerpt)

Cosmic Code > nonlinear > 2015 universal

Buendia, Victor, et al. Feedback Mechanisms for Self-Organization to the Edge of a Phase Transition. arXiv:2006.03020. University of Granada, Columbia University, and Rutgers University bioscientists including Migeul Munoz continue to explore and finesse the various ways that nature’s newly found propensity to seek and attain an optimum dynamic balance between reciprocal modes or stages can be seen to take and express.

Scale-free outbursts of activity are commonly observed in physical, geological, and biological systems. The idea of self-organized criticality (SOC) suggests that natural systems can self-tune to a critical state with its concomitant power-laws and scaling. Theoretical progress now explains SOC by relating its critical properties to those of a non-equilibrium phase transition that separates an active state in which dynamical activity reverberates indefinitely, from an absorbing or quiescent state where activity eventually ceases. Here, we consider a related concept: self-organized bistability (SOB). We review similarities and differences between SOC and SOB under a common theoretical framework, and discuss "self-organized quasi-criticality" and "self-organized collective oscillations", with the aim of providing feedback mechanisms for self-organization to the edge of a phase transition. (Abstract excerpt)

In summary, we have reviewed within a common and unified framework different types of mechanisms for the self-organization to the vicinity of phase transitions. We hope that this work help clarify the literature on the subject, and contribute to new and exciting developments in physics and other disciplines. This could be especially important in biology, where the idea that living systems can obtain important functional advantages by operating at the edge of two alternative/complementary types of phases/state has attracted a great deal of attention and excitement. (21)

Cosmic Code > nonlinear > 2015 universal

Nosonovsky, Michael and Prosun Roy. Scaling in Collodial and Biological Networks. Entropy. 22/6, 2020. We cite this contribution by University of Wisconsin bioengineers as another good example of how worldwide collaborations are finding a consistency of active topologies which form into similar nested recurrences across material, biochemical, cellular, metabolic to neural and communicative domains. By a philoSophia 2020 vision, a revolutionary organic genesis ecosmos seems well underway to being quantified.

Scaling and dimensional analysis is applied to networks that describe various physical systems. Some of these networks possess fractal, scale-free, and small-world properties. First, we consider networks arising from granular and colloidal systems due to pairwise interaction between the particles. Many networks found in colloidal science possess self-organizing properties and/or self-organized criticality. Then, we discuss the allometric laws in branching vascular networks, artificial neural networks, cortical neural networks, as well as immune networks. Scaling relationships in complex networks of neurons, which are organized in the neocortex in a hierarchical manner, suggest that the characteristic time constant is independent of brain size when interspecies comparison is conducted. The information content, scaling, dimensional, and topological properties of these networks are discussed. (Abstract excerpt)

The brain networks possess many characteristics typical to other networks, including over‐frequency and power‐law activities, avalanches, small‐world, scale‐free, and fractal topography. It is particularly interesting to look for the correlation between the spatial distribution (for example, hubs) and temporal organization (frequency spectrum) of human brain cognitive activities. Such research is being conducted by many groups, for example, the study of the DMN during such activities as the comprehension of a text in a natural language versus contemplating it (the “language of thought”). The information content of the neural networks can be studied using the standard characteristics of the information theory, such as the Shannon entropy. It may provide ways to distinguish between DNA‐encoded information and information generated during the embryonal and post‐embryonal development, which may be driven by the self‐organizing process. (22)

Cosmic Code > nonlinear > 2015 universal

Pavithran, Induja, et al. Universality in Spectral Condensation. arXiv:2004.10585. A 9 person team from IIT Madrus, UC San Diego, and the Potsdam Institute for Climate Change Research (Jurgen Kurths) provide a further instance of natural, self-organization in ubiquitous, imperative effect across a wide range of non-equilibrium phenomena.

Self-organization is the spontaneous formation of spatial, temporal, or spatiotemporal patterns in complex systems far from equilibrium. During such self-organization, energy distributed in a broadband of frequencies gets condensed into a dominant mode, analogous to a condensation phenomena. We call this phenomenon spectral condensation and study its occurrence in fluid mechanical, optical and electronic systems. We define a set of spectral measures to quantify this condensation spanning several dynamical systems. (Abstract excerpt)

Cosmic Code > nonlinear > 2015 universal

Satz, Helmut. Self-Organized Criticality. arXiv:2003.08130. This is an invited talk at the 40th Max-Born-Symposium, Wroclaw/Poland in October 2019 by the University of Bielefeld, Germany physicist. Its brief summary is We apply the concept of self-organized criticality in statistical physics to the study of multihadron production in high energy collisions. As its first paragraph below says, the posting is another notice of nature’s preferential occasion and resolve at this optimum balance at every such instantiation.

(Per) Bak went on to ask: How can the universe start with a few types of elementary particles at the big bang, and end up with life, history, economics and literature? Why did the big bang not form a simple gas of particles or condense into one big crystal? In other words, the issue was to understand how the structured complexity of the world around us could arise. Thus, new concepts of the past twenty years are emergence, complexity, fractality, chaos; non-equilibrium behavior, self-organization. In physics, this has led to intensive studies of emergent phenomena in non-equilibrium processes, and in mathematics to fractal structures. It has also led to a general framework applicable to swarm formation in biology and to financial market patterns. In this talk, I want to show how it can provide a new view of multihadron production in high energy collisions. (1-2)

Cosmic Code > nonlinear > 2015 universal

vandermeer, John, et al. New Forms of Structure in Ecosystems Revealed with the Kuramoto Model. arXiv:2006.16006. Reviewed more in Dynamic Ecosystems, we make note here as an example of how chimeric effects can even be apparent in these natural environs.

Cosmic Code > nonlinear > 2015 universal

zakharaova, Anna. Chimera Patterns in Networks. International: Springer, 2020. In a chimera state, a network spontaneously splits into two parts with different dynamics separated in space: one demonstrating coherent behavior and the other exhibiting incoherent behavior.<.i> (2) After some years of collegial papers (Google), a Technical University of Berlin theoretical physicist has written the first book length treatment of this newly recognized natural systemic propensity to reside at a dynamic poise of more or less relative order or stability. Typical subjects are Coherence-Incoherence Patterns with Topologies, Power-Law Coupling, Fractal Connectivities, and Multiplex Networks. Such synchronization phenomena is lately being detected in kind across quantum, chemical, and biologic areas onto neural and socio-economic domains, in a way as akin to self-organizing criticalities.

For main prior references the author recommends, Scholl, Eckehard. Synchronization Patterns and Chimera States in Complex Networks by Eckehard Scholl in European Physical Journal Special Topics (225/891, 2016) and Chimera States: Coexistence of Coherence and Incoherence in Networks by Mark Panaggio and Daniel Abrams in Nonlinearity (28/R67, 2015).

This is the first book devoted to chimera states - peculiar partial synchronization patterns in networks. Providing an overview of the state of the art in research on this topic, it explores how these hybrid states, which are composed of spatially separated domains of synchronized and desynchronized behavior, arise surprisingly in networks of identical units and symmetric coupling topologies. The book not only describes various types of chimeras, but also discusses the role of time delay, stochasticity, and network topology for these synchronization-desynchronization patterns. Moreover, it addresses the question of robustness and control of chimera states, which have various applications in physics, biology, chemistry, and engineering.

Cosmic Code > Genetic Info

Moghadam, S. Arbabi, et al. A Search for the Physical Basis of the Genetic Code. Biosystems. May, 2020. We cite because this entry by University of Alberta biophysicists including Jack Tuszynski discuss several ways that life’s genomic endowment can be rooted in and given a deeper substantial, innately fertile basis.

DNA contains the genetic code, which provides complete information about the synthesis of proteins in every living cell. Each gene encodes for a corresponding protein but most of the DNA sequence is non-coding. In addition to this non-coding part of the DNA, there is another redundancy, namely a multiplicity of DNA triplets (codons) corresponding to code for a given amino acid. In this paper we investigate possible physical reasons for the coding redundancy, by exploring free energy considerations and abundance probabilities as potential insights. (Abstract)

Cosmic Code > Genetic Info > Paleo/Cosmo

Racimo, Fernando, et al. Beyond Broad Strokes: Sociocultural Insights from the Study of Ancient Genomes. Nature Reviews Genetics. June, 2020. With prior hominids, migrations, primates, animal creatures and more now sequenced, and as techniques ever improve, University of Copenhagen and Universitat Pompeu Fabra, Barcelona researchers discuss a new phase which can reconstruct intangible behavioral, artifactual, and tribal features. So we wonder, what kind of temporal reality is this whereof a global species finally appears and becomes capable to recover, learn about and convert to knowledge all of whom and what went before. Why can we peoples do this, what is the great revelation and purpose?

In the field of human history, ancient DNA has provided answers to long-standing debates about major movements of people and has begun to inform on other important facets of the human experience. The field is now moving from large-scale supraregional studies to local perspectives of socioeconomic processes, inheritance rules, marriage practices and technological diffusion. In this Review, we summarize recent studies, insights and methods to infer sociocultural aspects of human behaviour. This approach often involves working across disciplines — such as anthropology, archaeology, linguistics and genetics — that have until recently evolved in separation. (Abstract)

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Bapteste, Eric and Philippe Huneman. Towards a Dynamic Interaction Network of Life to Unify and Expand the Evolutionary Theory. BMC Biology. 16/56, 2018. In a unique contribution to a genesis synthesis, Sorbonne University philosophers of biology describe the pervasive, innate presence of network topologies as they serve to link altogether prior organismic parts across biomolecular, cellular, and organism phases. This late addition is seen to bolster the holobiont symbiosis model, and accord with scaffolded, process, and chimeric gene aspects. Once again, if by a philosophia mind to allow and view, life’s homologous developmental course takes on a webwork anatomy, physiology and neural appearance. With this in place, a shift toward network thinking, as everywhere else, would advance and unify evolutionary theory. See also Testing the “(Neo-) Darwinian” Principles against Reticulate Evolution by Nathalie Gontier in Information (11/7, 2020).

The classic Darwinian theory and the Synthetic evolutionary theory and their linear models, while invaluable to study the origins and evolution of species, are not primarily designed to model the evolution of organisations, typically that of ecosystems, nor that of processes. How could evolutionary theory better explain the evolution of biological complexity and diversity? Inclusive network-based analyses of dynamic systems could retrace interactions between (related or unrelated) components. This theoretical shift from a Tree of Life to a Dynamic Interaction Network of Life, which is supported by diverse molecular, cellular, microbiological, organismal, ecological and evolutionary studies, would further unify evolutionary biology. (Abstract)

Quickening Evolution

Fields, Chris and Michael Levin. Scale-Free Biology: Integrating Evolutionary and Developmental Thinking. BioEssays. June, 2020. As a 2020 integrative phase goes forward, a veteran philosopher of biology now based in France and a Tufts University, Allen Discovery Center developmental biologist propose and scope out an array of unifying perspectives which are guided by an insight that life’s oriented emergence repeats in similar ways and means across the nested phases it engenders.

When the history of life on Earth is viewed as a history of cell division, all of life becomes a single cell lineage. The growth and differentiation of this lineage in reciprocal interaction with its environment can be viewed as a developmental process; hence the evolution of life can also be seen as the development of life. Here some fruitful research directions suggested by this perspective are highlighted. Variation and selection become bidirectional information flows between scales, while “cooperation” and “competition” become scale relative. The language of communication, inference, and information processing are more useful than the language of causation to describe homogeneous and heterogeneous living systems. Emerging scale‐free theories such as predictive coding and active inference can provide conceptual tools for the study of a unified, multiscale dynamical system. (Abstract)

Quickening Evolution

Gontier, Nathalie. Testing the “(Neo-) Darwinian” Principles against Reticulate Evolution. Information. 11/7, 2020. The University of Lisbon evolutionary epistemologist has been at the conceptual forefront (search) of a 2010s revision of life’s developmental emergence. This paper continues her 2015 edited Reticulate Evolution volume by noting exemplary network topologies in symbiosis, lateral gene transfer, adaptive fitness, infective (viral) heredity, organismic mobility, species affordances, hybridization and more. A distinct approach of reticulate studies is proposed as an overdue phase of interconnective linkages between all the prior parts. In regard, an inclusion and endorsement of symbiotic mutual unions in their role as a prime evolutionary property is achieved. A history of symbiogenesis from the 1900s to the work of Lynn Margulis to current holobiont models braces the claim. See also Towards a Dynamic Interaction Network of Life to Unify and Expand the Evolutionary Theory by Eric Bapteste and Philip Huneman in BMC Biology (16/56, 2018) for another confirmation.

Variation, adaptation, heredity and fitness, constraints and affordances, speciation, and extinction form the building blocks of the (Neo-)Darwinian research program. Several of these aspects have been called “Darwinian principles.” However, we will here describe the important role played by reticulate evolutionary mechanisms and processes in also bringing about these phenomena. Reticulate mechanisms and processes include symbiosis, symbiogenesis, lateral gene transfer, infective heredity mediated by genetic and organismal mobility, and hybridization. Because “Darwinian principles” are brought about by both vertical and reticulate processes, they should contribute to a more pluralistic theory of evolution, one that surpasses the Modern and Neo-Darwinian Synthesis. Instead, these general principles of evolution need to be understood as common goods that come about through interactions between different units and levels of evolutionary hierarchies, and they are exherent rather than inherent properties of individuals. (Abstract excerpt)

Reticulate: the formation of a net or web- work topology, or the presence of net structures such as veins of a leaf, or a nervous system.

Nathalie Gontier: I’m a philosopher of evolutionary sciences, with special interest in the nature and scope of evolutionary explanations, how they evolved within the overall genealogy of thought; how they are applied within the biological, sociocultural and linguistic sciences; and how they are depicted in hierarchical diagrams such as cycles, timelines, trees and networks.

Quickening Evolution > major

Sandora, McCullen and Joseph Silk. Biosignature Surveys to Exoplanet Yields and Beyond. arXiv:2005.04005. University of Pennsylvania and Johns Hopkins University cosmologists propose a more comprehensive guide for future search phases as they proceed to quantify the presence and stage of evolutionary life. As per the second quote, the major transitions scale finds service since each level from microbes to a metropolis will have a characteristic atmospheric signature, along with other indicators. In regard we want to record the wide acceptance and application of this episodic emergence, which is a major structural feature of a genesis synthesis.University of Pennsylvania and Johns Hopkins University cosmologists propose a more comprehensive guide for future search phases as they proceed to quantify the presence and stage of evolutionary life. As per the second quote, the major transitions scale finds service since each level from microbes to a metropolis will have a characteristic atmospheric signature, along with other indicators. In regard we want to record the wide acceptance and application of this episodic emergence, which is a major structural feature of a genesis synthesis.

Upcoming biosignature searches focus on indirect indicators to infer the presence of life on other worlds. Aside from just signaling the presence of life, however, some biosignatures can contain information about the state that a planet's biosphere has achieved. This additional information can be used to measure what fractions of planets achieve certain key stages of the advent of life, photosynthesis, multicellularity and technological civilization. Our approach is probabilistic and relies on large numbers of candidates rather than detailed examination of individual exoplanet spectra. The dependence on survey size, likeliness of the transition, and degrees of confidence are discussed. (Abstract excerpt)

The life history of our own planet can be seen as a sequence of transitions wrought by evolutionary innovations, from biogenesis to the evolution of photosynthesis, multicellularity, and technological civilization. As far as these transitions can be expected to be generic, they can each be sought for independently through their characteristic atmospheric imprints. The question we address here is, what fraction of planets undergoes each transition, and more importantly, which can be measured with upcoming surveys? By quantifying the uncertainty in measurements of each of these quantities, we provide a framework for understanding how they depend on proposed mission designs as well as on atmospheric modeling. (1)

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