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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 31 through 45 of 63 found.


Ecosmomics: A Survey of Nonlinear Complex Network Sciences

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 > 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

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 > 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)

Quickening Evolution > Systems Biology

DiFrisco, James and Johannes Jaeger. Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective. BioEssays. 42/6, 2020. A biological studies advance, KU Leuven philosopher and a Complexity Science Hub, Vienna systems biologist seek to add a relational network vista which can inform the historic turn from discrete nucleotides to whole entities, be it genomes or organisms.

The logic of genetic discovery remains in place, but the focus of biology is shifting from genotype–phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the reductionist view of genes as privileged causes is re‐examined. The scope of genetic effects in complex regulatory systems, in which dynamics are driven by feedback and hierarchical interactions across levels, are considered. This review argues that genes can be treated as specific difference‐makers for the molecular regulation of their expression. However, they are not stable, proportional or specific as causes of the behavior of regulatory networks. Proper dynamical models can illuminate cause‐and‐effect in complex biological systems so to gain an integrative understanding of underlying complex phenotypes. (Abstract edit)

Quickening Evolution > Intel Ev

Brun-Usan, Miguel, et al.. How to Fit In: The Learning Principles of Cell Differentiation. PLoS Computational Biology.. April, 2020. University of Southampton, UK, computer scientists including Richard Watson continue their revisionary studies of biological metabolisms by viewing them through a learning lens. A cerebral perspective, as this section reports, can provide better insights into cellular processes because both evolution and learning are explorations in search of solutions. A further step is to integrate this view with gene regulatory networks so these common models can reinforce each other. Altogether this approach implies that life’s oriented emergence is trying to achieve some manner of its own self-description and comprehension.

Cell differentiation in multicellular organisms requires cells to respond to complex combinations of extracellular cues, such as morphogen concentrations. But a general theory describing how cells integrate multi-dimensional signals is still lacking. In this work, we propose a framework from learning theory to understand the relationships between environmental cues (inputs) and phenotypic responses (outputs) underlying cell plasticity.. Altogether, these results illustrate the functional parallelisms between learning in neural networks and the action of natural selection on environmentally sensitive gene regulatory networks. This offers a theoretical framework for responses that integrate information from multiple cues, a phenomenon that underpins the evolution of multicellularity and developmental robustness. (Abstract excerpt)

Earth Life Emergence: Development of Body, Brain, Selves and Societies

Earth Life > Nest > Microbial

Menon, Shakti, et al. Information Integration and Collective Motility in Phototactic Cyanobacteria. PLoS Computational Biology. April, 2020. Institute of Mathematical Sciences, Tamil Nadu, India researchers describe how bacterial groupings can be seen to exhibit and be modeled by active matter phenomena. In regard, quorum sensing is interpreted to proceed by way of integrating relevant information. Altogether another manifestation of universal principles and formations.

Microbial colonies in the wild often consist of large groups of heterogeneous cells that coordinate and integrate information across multiple spatio-temporal scales. We describe a computational model for the collective behavior of phototaxis in the cyanobacterium Synechocystis that move in response to light. The results suggest that tracking individual cyanobacteria may provide a way to determine their mode of information integration. Our model allows us to address the emergent nature of this class of collective bacterial motion, linking individual cell response to the large scale dynamics of the colony. (Summary)

Earth Life > Nest > Symbiotic

, Pfannschmidt. Thomas, et al. Philosophical Transactions of the Royal Society B.. May, 2020. We cite this introduction to a special collection as a good example of how much these mutualistic processes are now being found to pervade and serve the formation and activity of eukaryotic cells, a feature not considered at all a few years ago.

Earth Life > Nest > Symbiotic

Varahan, Sriram, et al. Metabolic Constraints Drive Self-Organization of Specialized Cell Groups. eLife. June 26, 2019. Five Indian systems cell biologists contribute novel understandings of the many ways that cellular activities have a vitality of their own as they innately organize themselves into preferred states and solutions.

How phenotypically distinct states in isogenic cell populations appear and stably co-exist remains unresolved. We find that within a mature, clonal yeast colony in low glucose, cells arrange into metabolically disparate cell groups. Using this system, we model and experimentally identify metabolic constraints which drive such self-assembly. Our work suggests simple physico-chemical principles that determine how isogenic cells spontaneously self-organize into structured assemblies in complimentary, specialized states. (Abstract excerpt)

Earth Life > Nest > Multicellular

Naranjo-Ortiz, Miguel and Toni Gabaldon. Fungal Evolution: Cellular, Genomic and Metabolic Complexity. Biological Reviews. April, 2020. As the life sciences proceed apace to record the anatomic presence of networks everywhere, here Barcelona Institute of Science and Technology geneticists explore in detail how these prolific microorganisms can be an exemplary way to study this interlinked and communicative phenomena. Within a sense of a transitional emergence from nucleotides and prokaryotes to mobile, varigated organisms, the fungi family do indeed provide an iconic, valuable model.

The question of how phenotypic and genomic complexity are related and shaped through evolution is a central to animal and plant biology. Recently, fungi have emerged as an alternative system of much value because they present a broad and diverse range of phenotypic traits and many different shapes. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout their evolution. Similarly, fungal genomes have a diverse architecture with rapid changes in genome organization. We explore how the interplay of cellular, genomic and metabolic traits mediates the emergence of complex phenotypes. (Abstract)

Fungus compose a group of spore-producing organisms feeding on organic matter, including molds, yeast, mushrooms, and toadstools.

Earth Life > Nest > Societies

Brask, Josefine, et al. Animal Social Networks: An Introduction for Complex Systems Scientists. arXiv:2005.09598. University of Exeter animal behaviorists including Darren Croft show how equally real interactive relations between group members can reveal and achieve new insights and explanations. In regard, these topologies are not fixed or static in nature but provide a dynamic, beneficial matrix.

Many animals live in societies where individuals frequently interact socially with each other. Animal social network research, however, seems to not be well known by scientists outside of the animal behaviour field. Here we provide an introduction for complex systems researchers. In this paper, we describe what animal social networks are and how they are scientifically important; we give an overview of common methods; and highlight challenges where interaction between animal social network and general complex systems research could be valuable. We hope that this will help to facilitate future interdisciplinary collaborations and lead to better integration of these networks into the field of complex systems. (Abstract excerpt)

Earth Life > Nest > Societies

Grueter, Cyril, et al. Multilevel Organization of Animal Society. Trends in Ecology and Evolution. May, 2020. Sixteen researchers posted in Australia, China, Germany, the USA, Switzerland, and India including Larissa Swedell describe how animal groupings typically array into multiple nested networked units. And we note that a diagram display of this threading out appears as another epitome of life’s iterative evolutionary emergence whether bodies, brains or organisms.

Multilevel societies (MLSs), stable nuclear social units within a larger collective with multiple nested social levels, occur in several mammalian lineages. Their architectural complexity and size impose require their members to find adaptive solutions in disparate domains. Here, we propose a unifying terminology and operational definition of MLS. To identify new avenues for integrative research, we synthesise current literature on the selective pressures underlying the evolution of MLSs and their implications for cognition, intersexual conflict, and sexual selection. Mapping the drivers and consequences of MLS provides a reference point for the social evolution of many taxa, including our own species. (Abstract)

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