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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 31 through 45 of 70 found.


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

Earth Life > Common Code

Boldini, Alain, et al. Application of Symbolic Recurrence to Experimental Data from Firearm Prevalence to Fish Swimming. Chaos. 29/113128, 2019. NYU and Technical University of Cartagena, Spain bioengineers finesse mathematical techniques in search of better ways to parse and compare complex interactive phenomena across wide scales and instances. And coincidently we log in on the December 14 date of the 2012 Newton school shooting, which is mentioned in the paper. However then might a breadth and depth of credible, sufficient, phenomenal proof be achieved so we peoples could realize and implement an independent, universal naturome code? See also Symbolic Recurrence Plots to Analyze Dynamical Systems by Victoria Caballero-Pintado, et al in Chaos (28/063112, 2018).

Recurrence plots and recurrence quantification analysis are powerful tools to study the behavior of nonlinear dynamical systems. Previous usages, however, have led to arbitrary definitions of recurrence. Here we describe a symbolic recurrence to overcome this issue, and to better book-keep recurrent portions of the phase space and real time series. We illustrate by examining a wide range of experimental datasets from firearm prevalence and media coverage to the sexual interaction of swimming fish. These results demonstrate the potential of symbolic recurrence in real-world applications across research fields. (Abstract excerpt)

Earth Life > Common Code

Garcia-Ruiz, Ronald and Adam Vernon. Emergence of Simple Patterns in Many-Body Systems from Macroscopic Objects to the Atomic Nucleus. arXiv:1911.04819. . R. Garcia Ruiz is posted at CERN Geneva and MIT, while A. Vernon is with KU Leuven, Belgium and the University of Manchester. Among an increasing number of reports, this entry with 175 references is a good example to date of a global scientific endeavor now able to quantify a substantial nature that everywhere gives rise to common forms and flows by its own propensities. With a root basis in nuclear shell clusters, a recurrent regularity spreads in kind across micro-physical and macro-biological realms. As the second quote cites, iconic mathematical shapes can found throughout, aka “magic numbers.” See also Underlying Structure of Collective Bands and Self-Organization in Quantum Systems by Takaharu Otsuka, et al at arXiv:1907.10759, and Magic Number Colloidal Clusters as Minimum Free Energy Structures by Junwei Wang, et al in Nature Communications (9/5259, 2018.)

Strongly correlated many-body systems often display the emergence of simple patterns and regular behavior of their global properties. Phenomena such as clusterization, collective motion and shell structures are commonly observed across different size, time, and energy scales in our universe. Although at the microscopic level their individual parts are described by complex interactions, the collective behavior of these systems can exhibit strikingly regular patterns. This contribution provides an overview of the experimental signatures that are used to identify the emergence of structures and collective phenomena in distinct physical systems, along with macroscopic examples. (Abstract)

Throughout nature, driving forces give rise to the arrangement of constituents in many-body systems at almost every size. On biological scales, this manifests in collective phenomena and pattern formation such as the phyllotaxis of plants, where growth patterns appear in the leaves or flowers around a plant stem. A striking example is observed in the seeds in a sunflower head, which follows the Fibonacci sequence. Complex many-body systems often form clusters to minimise their energy by interactions between neighbours and their mean field. This can form “magic” numbers, as in the atomic nucleus, where certain integer numbers of constituents of a given system result in greater stability of its collective whole. Another instance is the abundance distribution of isotopes in the universe following nucleosynthesis. (2, edits)

In nuclear physics, a magic number is a number of nucleons (either protons or neutrons, separately) such that they are arranged into complete shells within the atomic nucleus. The seven most widely recognized magic numbers as of 2019 are 2, 8, 20, 28, 50, 82, and 126. For protons, this corresponds to the elements helium, oxygen, calcium, nickel, tin, and lead. (Wikipedia)

Earth Life > Nest > Geological

Terui, Akira, et al. Metapopulation Stability in Branching River Networks. Proceedings of the National Academy of Sciences. 115/E5963, 2018. University of Minnesota and Hokkaido University system environmentalists provide a sophisticated analysis of the pervasive presence of self-similar network topologies even in these ever variable fluid flow geoscape regimes.

Intraspecific population diversity is an essential component of metapopulation stability and persistence in nature. However, current theories developed in simplified landscapes may be inadequate to predict emergent properties of branching ecosystems, a prime feature of habitat geometry. Here, we analyze a long-term dataset to show that a scale-invariant characteristic of fractal river networks, branching complexity stabilizes watershed metapopulations. In riverine systems, each branch (tributary) exhibits distinctive ecological dynamics, and confluences serve as “merging” points of those branches. We theoretically revealed that the stabilizing effect of branching complexity is due to probabilistic processes in natural conditions, where within-branch synchrony exceeds among-branch synchrony. (Abstract excerpt)

Earth Life > Nest > Life Origin

Cornish-Bowden, Athel and Maria Luz Cardenas. Contrasting Theories of Life: Historical Context, Current Theories. Biosystems. November, 2019. CRNS, University of Marseilles biochemists post a 64 page synoptic review of prior conceptions about how life came to be, evolve and develop. The integral (all male) survey runs from Aristotle to Stuart Kauffman and Karl Friston, with extra time given to Manfred Eigen, Robert Rosen, and Francisco Varela. A steady implication is that some manner of autocatalytic, self-making optimization process is going on.

Most attempts to define life have been individual opinions, but here we compare all of the major current theories. We begin by asking how we know that an entity is alive, and continue by way of the contributions of La Mettrie, Burke, Leduc, Herrera, Bahadur, D’Arcy Thompson and, especially Schrödinger, whose book What is Life? is a vital starting point. All of these incorporate the idea of circularity, but fail to take account of metabolic regulation. In a final section we study the extent to which each of the current theories can aid the search for a more complete theory of life, and explain the characteristics of metabolic control analysis essential for an adequate understanding of organisms. (Abstract)

Earth Life > Nest > Life Origin

Szostak, Jack. The Narrow Road to the Deep Past: In Search of the Chemistry of the Origin of Life. Angewandte Chemie International. 56/37, 2017. The Nobel chemist (2009) at the Howard Hughes Medical Institute, Center for Computational and Integrative Biology, Boston writes a popular update on his own work and on the long project to recover and quantify how living, evolving systems came to be. A salient aspect is the appearance of membrane-bounded protocell vesicles, which then play a role in forming vital RNA polymerase replicators. Once life got going, other catalytic biochemicals could complexify toward enzymes, metabolisms all the way to we curious curators.

The sequence of events that gave rise to the first life on our planet took place in the Earth's deep past, seemingly beyond our reach. Understanding the processes that led to the chemical building blocks of biology and how these molecules self‐assembled into cells that could grow, divide and evolve, nurtured by a rich and complex environment, seems insurmountably difficult. And yet, to my own surprise, simple experiments have revealed robust processes that could have driven the growth and division of primitive cell membranes. Even our efforts to combine replicating compartments and genetic materials into a full protocell model have moved forward in unexpected ways. Fortunately, many challenges remain, so the future in this field is brighter than ever! (Abstract)

Earth Life > Nest > Symbiotic

Collens, Adena, et al. The Concept of the Hologenome, an Epigenetic Phenomenon, Challenges Aspects of the Modern Evolutionary Synthesis. Journal of Experimental Zoology B. Online November, 2019. In this issue of responses to John Bonner’s call to re‐evaluate evolutionary theory in light of major transitions scale, Smith College biologists including Laura Katz advocate a factoring in and appreciation of epigenesis, symbiosis, microbiome and their manifest holobiont unity. These novel, significant insights are then seen to imply a radically expanded, 21st century evolutionary synthesis.

Earth Life > Nest > Symbiotic

West-Eberhard, Mary Anne. Modularity as a Universal Emergent Property of Biological Traits. Journal of Experimental Zoology B. Online November, 2019. In another response to John Bonner’s call to revise evolutionary theory due to major transitions, the senior Smithsonian Tropical Research Institute, University of Costa Rica field and theoretical biologist extols the formative importance of nature’s structural preference for a scale of self-contained whole units nested within larger, bounded entities. This deep propensity is then seen to serve all manner of biological features and viabilities.

Earth Life > Nest > Societies

Jolles, Jolle, et al. The Role of Individual Heterogeneity in Collective Animal Behavior. Trends in Ecology and Evolution. Online December, 2019. Jolle J, MPI Animal Behavior, Andrew King, Swansea University, UK, and Shuan Killen, University of Glasgow scope out ways that an array of diverse member behaviors can actually foster their overall group cohesion and viability.

Social grouping is omnipresent in the animal kingdom. Considerable research has focused on understanding how animal groups form and function, including how collective behaviour emerges via self-organising mechanisms and how phenotypic variation drives the behaviour and functioning of animal groups. Here we present a common framework to quantify heterogeneity in the literature so as to explain and predict its role in collective behaviour across species, contexts, and traits. We show that member diversity provides a key intermediary factor with regard to group structure, functioning, response to environmental change, and evolution. (Abstract)

Earth Life > Nest > Societies

Whitehead, Hal, et al. The Reach of Gene-Culture Coevolution in Animals. Nature Communications. 10/2405, 2019. A premier team of bioecologists - HW, Kevin Laland, Luke Rendell, Rose Thorogood and Andrew Whiten – describe the creative interplay between genetic source codes and the common presence of behavioral groupings across aquatic, avian and mammalian species. See also Animal Learning as a Source of Developmental Bias by K. Laland, et al in Evolution & Development (e12311, 2019).

Culture (behaviour based on socially transmitted information) is present in diverse animal species, yet how it interacts with genetic evolution remains largely unexplored. Here, we review the evidence for gene–culture coevolution in animals, especially birds, cetaceans and primates. We describe how culture can relax or intensify selection under different circumstances, create new selection pressures by changing ecology or behaviour, and favour adaptations, including in other species. Finally, we illustrate how, through culturally mediated migration and assortative mating, culture can shape population genetic structure and diversity. This evidence suggests that animal culture plays an important coevolutionary role, in nature. (Abstract)

Earth Life > Sentience > Brain Anatomy

Thiebaut de Schotten, Michel and Karl Zilles, eds. The Evolution of the Mind and Brain. Cortex. 118/1, 2019. An introduction to this special issue with some 20 entries such as The Biological Bases of Color Categorization from Goldfish to the Human Brain, The Left Cradling Bias, Large Scale Comparative Neuroimaging, and The Hippocampus of Birds in a View of Evolutionary Connectomics.

Earth Life > Sentience > Bicameral Brain

Vallortigara, Giorgio and Lesley Rogers. A Function for the Bicameral Mind. Cortex. Online December, 2019. The University of Trento, Italy and University of New England, Australia senior scholars continue to advance understandings of the pervasive presence and advantages across all phyla of dual brain hemispheres with opposite but complementary discrete particle (seed, me) or whole image (relations, We) attributes. This deep evolutionary benefit is most manifest in human cerebral activity, but we seem to work against this reciprocity as evident by local and global political conflicts. (Here is an example of a worldwide scientific discovery about a vital neural anatomy across animal kingdoms which a male (dots only) academia is unable to comprehend.)

A lateralized brain, in which each hemisphere processes sensory inputs and carries them out in different ways, is common in vertebrates, and it now reported for invertebrates too. As shown in many animal species, having a lateralized brain can enhance the capacity to perform two tasks at the same time. Why is this the case? Not only humans, but also most non-human animals, show a similar pattern of directional asymmetry. For instance, from fish to mammals most individuals react faster when a predator approaches from their left side. Using mathematical theory of games, it has been argued that the population structure of lateralization may result from the type of interactions asymmetric organisms face with each other. (Abstract excerpt)

Earth Life > Sentience > Evolution Language

Mehr, Samuel, et al. University and Diversity in Human Song. Science. 366/eaao868, 2019. Some 19 researchers posted in the USA, Germany, and Canada including Stephen Pinker report upon a comprehensive, cross-cultural study of the past and present occasion of melodious communication, with and without words, which well confirms its personal and societal significance. See also a commentary The World in a Song by Tecumseh Fitch and Tudor Popescu in the same issue.

What is universal about music, and what varies? We built a corpus of ethnographic text on musical behavior from a representative sample of the world’s societies, as well as a discography of audio recordings. The ethnographic corpus reveals that music varies along three formality, arousal, and religiosity aspects, more within societies than across them; and that music is associated with behavioral contexts such as infant care, healing, dance, and love. In addition, acoustic features of tonality are almost universal; music varies in rhythmic and melodic complexity; and elements of melodies and rhythms found worldwide follow power laws. (Abstract excerpt)

Earth Life > Sentience > Evolution Language

Townsend, Simon, et al. Compositionality in Animals and Humans. PLOS Biology. 16/8, 2018. As this long title word gains currency (search) to describe how our language “composes” itself, University of Zurich, Warwick, UK, and of Neuchatel, Switzerland comparative linguists including Sabrina Engesser and Nalthasar Bickel elucidate how this quality can likewise be seen in formative effect across multi-faceted creaturely communications. See also Call Combinations in Birds and the Evolution of Compositional Syntax by Toshitaka Suzuki, et al, in this journal and date.

origins of language’s syntactic structure. One approach seeks to reduce the core of syntax in humans to a single principle of recursive combination for which there is no evidence in other species. We argue for an alternative approach. We review evidence that beneath the complexity of human syntax, there is an extensive layer of nonproductive, nonhierarchical syntax that can well be compared to animal call combinations. This is the essential groundwork that must be in place before we can elucidate, with sufficient precision, what made it possible for human language to explode its syntactic capacity from simple nonproductive combinations. (Abstract edits)

Earth Life > Genetic Info

Barabasi, Daniel and Albert-Laszlo Barabasi. A Genetic Model of the Connectome. Neuron. 105/1, 2020. A son and father team a few miles apart at Harvard University (doctoral candidate) and Northeastern University (professor, group leader, founding theorist, search) apply mathematic scale-free network topologies such as biclique graphs (see below) to better trace and join regulatory genomes with cerebral multiplex intricacies. As A-L S’s 2016 Network Science conveys, from its 1998 advent, an ever wider anatomy/physiology-like webwork has been cast and quantified which now spreads from galactic clusters to literary works, and every node/link entity phase in between.

The connectomes of organisms of the same species show architectural and often local wiring similarities, which raises the question: where and how is neuronal connectivity encoded? Our premise is that the genetic identity of neurons should guide synapse and gap-junction formation and show that genetically driven wiring predicts the existence of specific biclique (see below) motifs in the connectome. We identify significant biclique subgraphs in the connectomes of three species and show that the neurons share expression patterns and morphological characteristics. Our proposed model thus offers a self-consistent framework to link the genetics of an organism to the reproducible architecture of its connectome. (Abstract excerpt)

Biclique: A special kind of bipartite graph where every vertex of the first set is connected to every vertex of the second set.

Earth Life > Genetic Info

Mozziconacci, Julien, et al. The 3D Genome Shapes the Regulatory Code of Developmental Genes. arXiv:1911.04779. Drawing upon the latest research results, Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensé theoretical geneticists JM, Melody Merle and Annick Lesne contribute a deeper conceptual appreciation of nature’s pervasive, semantic, prescriptive source program.

We revisit the notion of gene regulatory code in embryonic development in the light of new findings about genome spatial organisation. By analogy with the genetic code, we posit that the concept of code can only be used if the corresponding adaptor can clearly be identified. An adaptor is here defined as an intermediary physical entity mediating the correspondence between codewords and objects. In our context, the encoded objects are gene expression levels, while specific transcription factors in the cell nucleus provide the codewords. We propose that an adaptor for this code is the gene domain, that is, the genome segment comprising the gene and its enhancer regulatory sequences. (Abstract excerpt)

Our starting point is the definition of a code that will be used in the present text. Different meanings of this word are encountered in science, from the secret codes in cryptography, the source codes in computer science, to the neural codes and the genetic code. The latter is the emblematic example of a semantic code, in a biological context. The definition of a semantic code relies on three ingredients, namely codewords, objects, and adaptors: codewords are inputs to be interpreted; a single object is associated to each codeword; adaptors are physical entities that implement the association of each codeword with a unique object. (3)

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