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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 61 through 75 of 94 found.


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

Earth Life > Nest > Geological

Biswas, Soumyajyoti, et al. Statistical Physics of Fracture and Earthquakes. Philosophical Transactions of the Royal Society A. Vol.377/Iss.2136, 2018. An introduction to an issue with this title which is a good example, for this section and throughout, how the presence and study of complex network systems has now expanded to and gained theoretical roots in this substantial domain. See also, for example, New Trends in Statistical Physics of Complex Systems by Antonio Scarfone in Entropy (20/12, 2018).

Manifestations of emergent properties in stressed disordered materials are often the result of an interplay between strong perturbations in the stress field around defects. The collective response of a long-ranged correlated multi-component system is an ideal playing field for statistical physics. Hence, many aspects of such collective responses in widely spread length and energy scales can be addressed by the tools of statistical physics. In this theme issue, some of these aspects are treated from various angles of experiments, simulations and analytical methods, and connected together by their common base of complex-system dynamics. (Abstract)

Earth Life > Nest > Life Origin

Bray, Marcus, et al. Multiple Prebiotic Metals Mediate Translation. Proceedings of the National Academy of Sciences. Online November 9, 2018. By way of a “bioinorganic chemistry” which studies the role of metals in biology, Georgia Tech biochemists including Nicholas Hud and Jennifer Glass explain the importance of ferrous elements during life’s animating origin and early evolution.

Ribosomes are found in every living organism, where they are responsible for the translation of messenger RNA into protein. The ribosome’s centrality to cell function is underscored by its evolutionary conservation; the core structure has changed little since its inception ∼4 billion years ago when ecosystems were anoxic and metal-rich. The ribosome is a model system for the study of bioinorganic chemistry, owing to the many highly coordinated divalent metal cations that are essential to its function. We studied the structure, function, and cation content of the ribosome under early Earth conditions. Our results expand the roles of Fe2+ and Mn2+ in ancient and extant biochemistry as cofactors for ribosomal structure and function. (Abstract)

Earth Life > Nest > Life Origin

Menor-Salvan, Cesar. ed. Prebiotic Chemistry and Chemical Evolution of Nucleic Acids. International: Springer, 2018. A Universidad de Alcala, Spain astrobiologist assembles ten authoritative chapters which provide strong evidence for an innate natural occasion and forward progress of living, evolving complex entities. We note Mineral-Organic Interactions in Prebiotic Synthesis by Stephen Benner, et al, Nucleobases on the Primitive Earth by James Cleaves, and Self-Assembly Hypothesis for the Origin of Proto-RNA by Brian Cafferty, et al. Of especial import is Network Theory in Prebiotic Evolution by Sara Imari Walker and Cole Mathis which is reviewed below for its inclusion of this essential feature.

Chemical evolution encompasses the processes and interactions conducive to self-assembly and supramolecular organization, leading to an increase of complexity and the emergence of life. The book starts with the pioneering work of Stanley Miller and Jeffrey Bada on the Chemistry of Origins of Life and how the development of organic chemistry beginning in the 19th century led to the emergence of the field of prebiotic chemistry, situated between organic, geo- and biochemistry. It continues with current central topics regarding the organization of nucleic acids: the origin of nucleobases and nucleosides, their phosphorylation and polymerization and ultimately, their self-assembly and supramolecular organization at the inception of life. (Publisher)

Earth Life > Nest > Life Origin

Nowak, Martin and Hisashi Ohtsuki. Prevolutionary Dynamics and the Origin of Evolution. Proceedings of the National Academy of Sciences. 105/14924, 2008. We enter a paper by Harvard biologists referenced in Walker and Mathis 2018 as an example of how a much decade of global collaboration can advance scientific studies from patchy rudiments to a robust integral finding.

Life is that which replicates and evolves. A fundamental question is when do chemical kinetics become evolutionary dynamics? Here we formulate a general mathematical theory for the origin of evolution. All known life on earth is based on biological polymers, which act as information carriers and catalysts. We describe prelife as an alphabet of active monomers that form random polymers. Prelife is a generative system that can produce information. Prevolutionary dynamics have selection and mutation, but no replication. Life marches in with the ability of replication as polymers act as templates for their own reproduction. Prelife is a scaffold that builds life. (Abstract)

Earth Life > Nest > Life Origin

Walker, Sara Imari and Cole Mathis. Network Theory in Prebiotic Evolution. Menor-Salvan, Cesar, ed. Prebiotic Chemistry and Chemical Evolution of Nucleic Acids. International: Springer, 2018. In a final chapter, Arizona State University astrobiology theorists expand the theoretical basis of this aboriginal advent with an intrinsic interconnective quality that joins discrete biochemicals and nucleotides into a whole dynamic living system. These node/link lineaments are also seen to foster and carry generative information. As many other fields, the “universal properties” of multiplex nets provides a formative physiology as a natural fertile materiality came to life and evolution. A further section extends the composite system onto Planetary Biospheres by way of a “network theory of biogeochemistry.”

A most challenging aspect of origins of life research is that we do not know precisely what life is. In recent years, the use of network theory has revolutionized our understanding of living systems by permitting a mathematical framework for understanding life as an emergent, collective property of many interacting entities. So far, complex systems science has seen little direct application to the origins of life, particularly in laboratory science. Yet, networks are important mathematical descriptors where the structure of interactions matters more than individual component parts – which is what we envision happens as matter transitions to life. We review notable examples of the use of network theory in prebiotic evolution, and discuss the promise of systems approaches to life’s origin. Our end goal is to develop a statistical mechanics that deals with interactions of system components (rather than parts alone) and is thus equipped to model life as an emergent phenomena. (Abstract)

Earth Life > Nest > Microbial

Allen, Rosalind and Bartlomiej Waclaw. Bacterial Growth: A Statistical Physicist’s Guide. Reports on Progress in Physics. 82/1, 2018. University of Edinburgh researchers post a joint tutorial for microbiologists and physicists so as to illustrate new findings of persistent cross-affinities such as modularity and self-propelled activity.

Bacterial growth presents many beautiful phenomena that pose new theoretical challenges to statistical physicists, and are also amenable to laboratory experimentation. This review provides some of the essential biological background, discusses recent applications of statistical physics in this field, and highlights the potential for future research. (Abstract) In this review we argue that the dynamics of growing bacterial populations provides another class of systems to which the methods of statistical physics can naturally be applied. To briefly illustrate this, we notice that the above example of the growth of an antibiotic resistant infection involves stochastic phenomena on scale ranging from macroscopic to molecular. (1)

Earth Life > Nest > Multicellular

Mietke, Alexander, et al. Self-Organized Shape Dynamics of Active Surfaces. Proceedings of the National Academy of Sciences. 116/1, 2019. We recall a decade ago when self-organization as a formative force in cellular development was rarely mentioned or factored in. Here MPI Physics of Complex Systems and Technical University of Dresden theorists add to its inherent contribution to physiological function and somatic vitality. May it also be said that some 65 years after WW II, a global human phenomenon can rise Phoenix-like to learn about cosmic life’s self-verification, and to so offset a looming WW III, achieve our common Earthwise understanding and affirmation.

Morphogenesis, the emergence of shape and form in biological systems, is a process that is fundamentally mechanochemical: Shape changes of material are driven by active mechanical forces that are generated by chemical processes, which in turn can be affected by the deformations and flows that occur. We provide a framework that integrates these interactions between the geometry of deforming materials and active processes in them by introducing the shape dynamics of self-organized active surfaces. We show that the tight coupling between surface mechanics and active processes gives rise to the spontaneous formation of nontrivial shapes, shape oscillations, and directed peristaltic motion. Our simple yet general description lays the foundation to explore the regulatory role of shape in morphogenetic processes. (Significance)

Earth Life > Nest > Homo Sapiens

Wynn, Thomas and Frederick Coolidge, eds. Cognitive Models in Palaeolithic Archaeology. Oxford: Oxford University Press, 2016. A University of Colorado anthropologist and a psychologist gather chapters such as The Origins of Visual Artistic Behavior, Material engagement and the Embodied Mind, and Bootstrapping Ordinal Thinking to scope out a field dubbed Evolutionary Cognitive Archaeology, which is the title of the first chapter.

Cognitive Models in Palaeolithic Archaeology explores hominin cognitive development by applying formal cognitive models to analyze prehistoric remains from the entire range of the Palaeolithic, from the earliest stone tools 3.3 million years ago to artistic developments that emerged 50,000 years ago. Several different cognitive models are presented, including expert cognition, information processing, material engagement theory, embodied/extended cognition, neuroaesthetics, visual resonance theory, theory of mind, and neuronal recycling. By examining archaeological remains, and thereby past activities and behavior, through the grounded lenses of these models, a mosaic pattern of human cognitive evolution emerges.

Earth Life > Sentience > Animal Intelligence

Wirthin, Morgan, et al. Parrot Genomes and the Evolution of Heightened Longevity and Cognition. Current Biology. 28/1, 2018. As the abstract details, a 21 person team from the USA, Brazil, and Argentina including Claudio Mello achieved a novel genomic-based explanation of why this Psittacine order is more effectively intelligent than any other avian species. The findings merited a New York Times item The Genes That Make Parrots into the Humans of the Bird World by JoAnna Klein (Dec. 7, 2018).

Parrots are one of the most distinct and intriguing groups of birds, with highly expanded brains, well developed cognitive and vocal communication skills, and a long lifespan compared to other similar-sized birds. To address this question, we have generated a high-coverage, annotated assembly of the genome of the blue-fronted Amazona aestiva and carried out extensive comparative analyses with 30 other avian species, including 4 additional parrots. We identified several genomic features unique to parrots which support a range of cellular functions, including telomerase activity; DNA damage repair; control of cell proliferation, cancer, and immunity. Intriguingly, parrot-specific changes in conserved regulatory sequences were associated with genes that are linked to cognitive abilities and have undergone similar selection in the human lineage, suggesting convergent evolution. (Abstract)

Earth Life > Sentience > Evolution Language

Tomlinson, Gary. A Million Years of Music. New York: Zone Books, 2015. The Yale University professor of music and the humanities retraces how primates and hominids came to and communicated by rhythmic compositions, broadly conceived, before all manner of linguistic utterances began. Once again an original propensity for prosodic, communicative intonations is identified to have arisen first.

What is the origin of music? In the last few decades this question has been reinvigorated by new archaeological evidence and the fields of cognitive science, linguistics, and evolutionary theory. Starting at a period of human prehistory before Homo sapiens or music, Tomlinson describes the incremental attainments that led to musical gestures and soundings. He traces in Neandertals and early sapiens the accumulation and development of these capacities, and their coalescence into modern musical behavior across the last hundred millennia. Tomlinson builds a model of human evolution that revises our understanding of the interaction of biology and culture across evolutionary time-scales, enriching current models of our deep history. He draws in other emerging human traits: language, symbolism, a metaphysical imagination and complex social structure, and the use of advanced technologies.

Earth Life > Genetic Info > DNA word

Zolyan, Suren and Renad Zhdanov. Genome as (hyper)Text: From Metaphor to Theory. Semiotica. 225/1, 2018. Immanuel Kant Baltic Federal University, Kalingrad and Moscow State Pedagogical University senior scholars present a strongest claim to date of a natural identity between these preeminent generative codes. With a past reference to I. Kant and Johann Goethe, in our age of global communication a true “isomorphism” is evident for these informative processes. A common trait is their code script (Schrodinger) and sign system (semiotic) quality. A conclusion can then be stated. They are two prime manifest exemplars of an inherently literate cosmos. If we might fully appreciate, in closing a novel beneficial phase of “social genomics” is proposed.

The similarity between language and genetic information transmission has been recognized since molecular genetics was founded. Numerous attempts have been made to use linguistics techniques to decipher protein genes. However, this approach cannot describe a language nor the semantic and textual structures that are decisive for communication. A text should be regarded as an artifact of the creation, conservation and conveyance of information. A general theory should be capable of describing linguistic writings and the process of their structuring, functioning and transformation. A (hyper) text can be considered as a quasi-organism that possesses memory, creative-cognitive characteristics and communicative force, and a cell as a quasi-intelligence capable of manipulating semiotic entities. (Abstract excerpt)

Earth Life > Integral Persons > Cerebral Form

Saxe, Andrew, et al. A Mathematical Theory of Semantic Development in Deep Neural Networks. arXiv:1810.10531. In a highly technical article, AS, Oxford University, James McClelland, Stanford University (original developer with David Rumelhart of Parallel Distributed Processing in the 1980s), and Surya Ganguli, Google Brain, CA advance this machine to brain revolution so as to better organize and encode knowledge by means of typicality and category coherence, optimal learning, invariant similarities and more. See a concurrent post Evolution of Scientific Networks in Biomedical Texts at 1810.10534.

An extensive body of empirical research has revealed remarkable regularities in the acquisition, organization, deployment, and neural representation of human semantic knowledge. These results raise a fundamental question: what are the principles governing the ability of neural networks to acquire, organize, and deploy abstract knowledge? We address this by analyzing the nonlinear dynamics of learning in deep linear networks. We find solutions to these learning dynamics that explain disparate phenomena in semantic cognition such as the hierarchical differentiation of concepts through developmental transitions, the ubiquity of semantic illusions between transitions, the emergence of category coherence which controls the speed of semantic processing, and the conservation of semantic similarity in neural representations across species. Our simple neural model can thus recapitulate diverse regularities underlying semantic development, while providing insight into how the statistical structure of an environment can interact with nonlinear deep learning dynamics results in these regularities. (Abstract edits)

Earth Life > Integral Persons > Complementary Brain

Davis, Simon, et al. Complementary Topology of Maintenance and Manipulation Brain Networks in Working Memory. Nature Scientific Reports. 8/17827, 2018. As the Abstract describes, by way of sophisticated MRI imaging studies, thirteen Duke University neurologists and cognitive psychologists achieve even more evidence that our brains require and avail a best balance of iconic conservative and creative modes of behavior.

Working memory (WM) is assumed to consist of a process that sustains memory representations in an active state (maintenance) and a process that operates on these activated representations (manipulation). We examined evidence for two distinct, concurrent cognitive functions supporting maintenance and manipulation abilities by testing brain activity as participants performed a WM alphabetization task. Maintenance was investigated by varying the number of letters held in WM and manipulation by varying the number of moves required to sort the list alphabetically. We found that both maintenance and manipulation demand had significant effects on behavior that were associated with different cortical regions: maintenance was associated with bilateral prefrontal and left parietal cortex, and manipulation with right parietal activity, a link that is consistent with the role of parietal cortex in symbolic computations. Both structural and functional architecture of these systems suggested that these cognitive functions are supported by two dissociable brain networks. (Abstract)

Earth Life > Integral Persons > Conscious Knowledge

Lombardi, Olimpia and Cristian Lopez. What Does “Information” Mean in Integrated Information Theory? Entropy. 201/12, 2018. As a current example of how this ITT model is gaining wide avail, University of Buenos Aires and University of Lausanne quantum physicists (search each) propose ways to finesse and include this vital instructional complement of aware knowing consciousness.

Integrated Information Theory (IIT) intends to provide a principled theoretical approach able to characterize consciousness both quantitatively and qualitatively. By starting off with the fundamental properties of experience itself, IIT develops a framework that relates those properties to the physical substratum of consciousness. One of the central features is the role that information plays. In this paper, we will conceptually analyze the notion of information underlying ITT. We argue that information should be understood in the light of a causal-manipulabilist view, such that information must be involved in causal links in order to be precisely defined. (Abstract edits)

Earth Life > Integral Persons > Conscious Knowledge

Nizato, Takayuki, et al. Finding Continuity and Discontinuity in Fish Schools via Integrated Information Theory. arXiv:1812.00718. University of Tsukuba and University of Tokyo neurobiologists first explain the generic ITT model whereby relative awareness occurs in tandem with knowledge content, and then show how it can well apply to collective creaturely behaviors such as marine pod assemblies.

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