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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 98 found.


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

Earth Life > Nest > Life Origin

Ogata, Norichika. Quantitative Measurement of Heritability in the Pre-RNA World. arXiv:1901.07400. We cite this entry by a Nihon BioData Corp., Japan researcher, formerly at Kawasaki Medical University, as a 2019 example of how origin of life studies have moved beyond biomolecules (RNA) or metabolism alone to include the generative presence of nature’s universal independent generative propensities.

Before assembly with nucleotides, in the pre-RNA era, what system dominated heredity? Self-organized complex systems are hypothesized to be a primary factor of the origin of life and to dominate heritability, mediating the partitioning of an equal distribution of structures and molecules at cell division. The degree of strength of self-organization would correlate with heritability; self-organization is known to be a physical basis of hysteresis phenomena, and the degree of hysteresis is quantifiable. However, there is no argument corroborating the relationship between heritability and hysteresis. Here, we show that the degree of cellular hysteresis indicates its heritability and daughter equivalence at cell division. Our results demonstrate that self-organized complex systems contribute to heredity and are still important in mammalian cells. Discovering ancient and hidden heredity systems enables us to study our own origin, to predict cell features and to manage them in the bio-economy. (Abstract excerpt)

Earth Life > Nest > Multicellular

Chen, Zhanqi, et al. Prolonged Milk Provisioning in a Jumping Spider. Science. 362/1052, 2018. In a paper which received popular notice, ten zoologists and botanists in China report for the first time that even insect species possess and this prime maternal attribute of vertebrate mammals. In regard, evolutionary life seems to hold to a common physiology, anatomy and behavioral repertoire which is then availed and repeated in creaturely kind.

Lactation is a mammalian attribute, and the few known nonmammal examples have distinctly different modalities. We document here milk provisioning in a jumping spider, which compares functionally and behaviorally to lactation in mammals. The spiderlings ingest nutritious milk droplets secreted from the mother’s epigastric furrow until the subadult stage. Maternal care, as for some long-lived vertebrates, continues after the offspring reach maturity. These findings demonstrate that mammal-like milk provisioning and parental care for sexually mature offspring have also evolved in invertebrates, encouraging a reevaluation of their occurrence across the animal kingdom, especially in invertebrates. (Abstract)

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 > Ecosystems

Rocha, Juan, et al. Cascading Regime Shifts Within and Across Scales. Science. 362/1379, 2018. Stockholm Resilience Centre ecological scholars including Simon Levin provide a latest finesse of complex ecosystems as they interact and transition within local and planetary bioregions and climates. The work merited a review Seeing a Global Web of Connected Systems by Marten Scheffer and Egbert van Nes (362/1357), second quote.

The potential for regime shifts and critical transitions in ecological and Earth systems, particularly in a changing climate, has received considerable attention. However, the possibility of interactions between such shifts is poorly understood. Rocha et al. used network analysis to explore whether critical transitions in ecosystems can be coupled with each other, even when far apart (see the Perspective by Scheffer and van Nes). They report different types of potential cascading effects, including domino effects and hidden feedbacks, that can be prevalent in different systems. Such cascading effects can couple the dynamics of regime shifts in distant places, which suggests that the interactions between transitions should be borne in mind in future forecasts. (Rocha summary)

The Arab Spring, the invention of penicillin, and the recent mass bleaching of coral reefs are reminders that much of the change in nature and society happens in just a tiny portion of time. Understanding why and when such critical transitions happen remains notoriously difficult. In this issue, Rocha et al mine a database of shifts in social and ecological systems and conclude that about half of them may be causally linked on different scales. Their results highlight the importance of unraveling hidden connections in the web of ecological and social systems on which we depend. (Scheffer abstract)

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 > Genetic Info

Zou, James, et al. A Primer on Deep Learning in Genomics. Nature Genetics. 51/1, 2019. Stanford University, Karolinska Institute, Sweden, and Scripps Translational Research Institute, CA genoinformaticians introduce how these neural net methods can apply to and serve genetic studies. See also A Guide to Deep Learning in Healthcare in Nature Medicine by Andre Esteva, et al (25/1, 2019).

Deep learning methods are a class of machine learning techniques capable of identifying highly complex patterns in large datasets. Here, we provide a perspective and primer on deep learning applications for genome analysis. We discuss successful applications in the fields of regulatory genomics, variant calling and pathogenicity scores. We include general guidance for how to effectively use deep learning methods as well as a practical guide to tools and resources. This primer is accompanied by an interactive online tutorial.

Earth Life > Genetic Info > Paleo/Cosmo

Allaga, Benoit, et al. Universality of the DNA Methylation Codes in Eucaryotes. Nature Scientific Reports. 9/173, 2019. Five University of Montpelli biogeneticists make a strong case to date that “epigenetic” aspects, much a work in progress, have a major part to play along with the nucleotide contribution. A graphic representation of 147 species from insects to us illustrates how often this methylation feature occurs across life’s evolutionary scale. See also Epigenetics: A Way to Bridge the Gap between Biological Fields by Antoine Nicoglou and Francesca Merlin in Studies in History and Philosophy of Biological and Biomedical Sciences (66/73, 2017).

Genetics and epigenetics are tightly linked heritable information classes. Question arises if epigenetics provides just a set of environment dependent instructions, or whether it is integral part of an inheritance system. We argued that in the latter case the epigenetic code should share the universality quality of the genetic code. We focused on DNA methylation. Since availability of DNA methylation data is biased towards model organisms we developed a method that uses kernel density estimations of CpG observed/expected ratios to infer DNA methylation types in any genome. Our analysis indicates that there are only four gene body methylation types. We conclude that the gene body DNA methylation codes have universality similar to the universality of the genetic code and should consequently be considered as part of the inheritance system. (Abstract excerpt)

DNA methylation is an epigenetic mechanism that occurs by the addition of a methyl (CH3) group to DNA, thereby often modifying the function of the genes and affecting gene expression. The most widely characterized DNA methylation process is the covalent addition of the methyl group at the 5-carbon of the cytosine ring resulting in 5-methylcytosine (5-mC), also informally known as the “fifth base” of DNA. These methyl groups project into the major groove of DNA and inhibit transcription. (whatisepigenetics.com)

Earth Life > Genetic Info > Paleo/Cosmo

Henn, Brenna and Lluis Quintana-Murci. The History, Geography and Adaptation of Human Genes: A Tribute to Luca Cavalli-Sforza. Current Opinion in Genetics & Development. 53/iii, 2018. An introduction to this special issue by a UC Davis anthropologist and a Pasteur Institute, Paris evolutionary geneticist about the lifetime contributions (1922-2018) of the University of Parma, Pavia and Stanford population geneticist, who first realized and pursued historic parallels between genomes and languages. Among the 26 entries, e.g., are Admixture and Adaptation in Human Evolution by Michael Dannemann and Fernando Racimo, Insights from Epigenetic Studies on Human Health by Connie Mulligan, Clarify Distince Models of Modern Human Origins in Africa by B. Henn, et al, and Fine-Tuning of Approximate Bayesian Computation for Human Population Genomics by Niall Cooke and Shigeki Nakagome.

This special issue on the Genetics of Human Origins is dedicated to Luigi Luca Cavalli-Sforza who passed away last August 2018. Luca — “please, call me Luca” he always said whoever he was talking to — was the grandfather of the field of human population genetics , and influenced many of the perspectives we review here in foundational ways. His interests in human prehistory cut across several disciplines, as he worked to compare patterns from linguistic, cultural and archaeological data with emerging protein polymorphism, mitochondrial and Y-chromosomal data. His cross-disciplinary thinking opened new avenues of research, including that of how cultural evolution may impact biological evolution: “If there's any interaction between genes and languages, it is often languages that influence genes, since linguistic differences between populations lessen the chance of genetic exchange between them”.

Earth Life > Integral Persons > Cerebral Form

Fornito, Alex, et al. Bridging the Gap between Connectome and Transcriptome. Trends in Cognitive Sciences. 23/1, 2019. Into the year 2019, advances such as imaging techniques and computational graphics allow Monash University, Australia clinical neuroscientists to discern spatial and temporal relations from DNA nucleotides to protein interactions via innate network paths. The wide use of –omic suffixes implies how important the genetic factors are in neural activity. The article glossary contains a Hierarchical Modularity term as another example of how nature’s universal complexity is so manifest in our own cerebral raiment.

The recent construction of brain-wide gene expression atlases, which measure the transcriptional activity of thousands of genes in multiple anatomical locations, has made it possible to connect spatial variations in gene expression to distributed properties of connectome structure and function. These analyses have revealed that spatial patterning of gene expression and neuronal connectivity are closely linked, following broad spatial gradients that track regional variations in microcircuitry, inter-regional connectivity, and functional specialisation. Superimposed on these gradients are more specific associations between gene expression and connectome topology that appear conserved across diverse species and different resolution scales. (Abstract)

The transcriptome is the set of all RNA molecules in one cell or a population of cells. It broadly “transcribes” genome DNA to proteome proteins. A connectome is a comprehensive map of neural networks in the brain. In another view, it includes mappings of all neural connections within an organism’s nervous system. (Wikipedia)

Earth Life > Integral Persons > Cerebral Form

Majhi, Soumen, et al. Chimera States in Neuronal Networks. Physics of Life Reviews. September, 2018. As complex network studies proceed apace, Indian Statistical Institute, Kolkata, and University of Maribor, Slovenia (Matjaz Perc) join a growing notice of this attractor preference for an optimum cerebral coexistence between a more or less orderly, conserve/create condition.

Neuronal networks, similar to many other complex systems, self-organize into fascinating emergent states that are not only visually compelling, but also vital for the proper functioning of the brain. Recent research has shown that the coexistence of coherent and incoherent states, known as chimeras, is particularly important characteristic for neuronal systems. The emergence of this unique collective behavior is due to diverse factors that characterize neuronal dynamics and the functioning of the brain in general, including neural bumps and unihemispheric slow-wave sleep in some aquatic mammals. (Abstract excerpt)

Earth Life > Integral Persons > Cerebral Form

Voorhees, Burton, et al. Identity, Kinship, and the Evolution of Cooperation. Current Anthropology. Online September, 2018. Senior psychological anthropologists BV Athabasca University, Alberta, Dwight Read UCLA and Liane Gabora University of British Columbia trace near and further social affinities to a personal self-reflective awareness, within and supported by, extended familial relations.

Extensive cooperation among biologically unrelated individuals is uniquely human. This paper presents a theory of cooperation that draws on social, cultural, and psychological aspects of human uniqueness for which current theories have little or no explanation. We propose that the evolution of human cooperative behavior required (1) a capacity for self-sustained, self-referential thought manifested as an integrated worldview, including a sense of identity and point of view, and (2) the cultural formation of kinship-based social organizational systems within which social identities can be established and transmitted through enculturation. Human cooperative behavior arose, we argue, through the acquisition of a culturally grounded social identity that included the expectation of cooperation among kin. (Abstract excerpt)

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

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.

Earth Life > Integral Persons > Conscious Knowledge

Zanardi, Paolo, et al. Towards Quantum Integrated Information Theory. arXiv:1806.01421. As this IIT model gains veracity and broad acceptance, we note this certain entry because these USC physicists pursue its application to and synthesis with quantum phenomena as it lately becomes reconceived (see Quantum Organics) as a complex network system akin to all other “classical” phases.

Integrated Information Theory (IIT) has emerged as one of the leading research lines in computational neuroscience to provide a mechanistic and mathematically well-defined description of the neural correlates of consciousness. Integrated Information (Φ) quantifies how much the integrated cause/effect structure of the global neural network fails to be accounted for by any partitioned version of it. The holistic IIT approach is in principle applicable to any information-processing dynamical network regardless of its interpretation in the context of consciousness. In this paper we take the first steps towards a formulation of a general and consistent version of IIT for interacting networks of quantum systems. (Abstract)

The main goal of classical Integrated Information Theory (IIT) is to provide a mathematical and conceptual framework to study the neural correlates of consciousness. In this paper we took the first steps towards a possible quantum version of IIT. Our approach is a quantum information-theoretic one, in which neural networks are being replaced by networks of qudits, probability distributions by non-commutative density matrices, and markov processes by completely positive maps. The irreducible cause/effect structure of the global network is encoded by a so-called conceptual structure operator. We have studied quantum effects in small qubit networks and provided examples, analytical and numerical, of families of low integration networks. (11)

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