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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 46 through 60 of 74 found.

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

Earth Life > Genetic Info

Trieu, Tuan, et al. Hierarchical Reconstruction of High-Resolution 3D Models of Large Chromosomes. Nature Scientific Reports. 9/4971, 2019. University of Missouri bioinformatic scientists Tuan Trieu (Vietman), Oluwatosin Oluwadare (Nigeria), and Jianlin Cheng (China) come together in mid America where they are developing better ways to visualize whole genome structures, as the paper illustrates. An improved image quality is achieved by a novel algorithm which can fully reveal these complex nucleotide packages

Earth Life > Genetic Info > DNA word

Bolshoy, Alexander, et al. Genome Clustering: From Linguistic Models to Classification of Genetic Texts. Berlin: Springer, 2010. Israeli geneticists contribute to growing indications of a pervasive code system by which engender phrases such as DNA texts and DNA linguistics, along with implications that our language corpus is then in some ways genomic in nature.

Earth Life > Genetic Info > DNA word

Faltynek, Dan, et al. Bases are not Letters: On the Analogy between the Genetic Code and Natural Language by Sequence Analysis. Biosemiotics. Online April, 2019. Palacky University, Olomouc, Czech Republic system scholars DF, Vladimir Matlach, and Ludmila Lackova (search) continue their project to parse an endemic, natural affinity between the prime informative occasions of biochemical nucleotide genomes and human linguistic complexities.

The article deals with the notion of the genetic code and its metaphorical understanding as a “language”. In the traditional view of the language metaphor of the genetic code, combinations of nucleotides are signs of amino acids. Similarly, words combined from letters (speech sounds) represent certain meanings. The language metaphor of the genetic code assumes that the nucleotides stay in the analogy to letters, triples to words and genes to sentences. We propose an application of mathematical linguistic methods on the notion of the genetic code. We provide quantitative analysis (n-gram structure, Zipf’s law) of mRNA strings and natural language texts, along with a representative analysis of DNA, RNA and proteins. Our analysis of mRNA confirms an assumption that the design of the genetic code cannot analogize DNA bases and letters. The notion of the letter is much more appropriate if analogized with triplets or amino acids (Abstract excerpt)

Earth Life > Integral Persons > Somatic

Bartsch, Ronny, et al. Network Physiology: How Organ Systems Dynamically Interact. PLoS One. November 10, 2015. RB, Bar-Ilan University, Kang Liu and Plamen Ivanov, Boston University, and Amir Bashan, Harvard Medical School scope out initial realizations that along with everything else, our bodily well-being, or lack thereof is wholly graced by and dependent on active webwork geometries. Their relative robustness or breakdown can then be a good measure of health or sickness (similar models are being applied to neural and behavioral states). See Network Medicine in the Age of Biomedical Big Data by Abjijeet Soanwane, (search) et al at arXiv:1903.05449 for an example of its actual utility.

We study how diverse physiologic systems in the human organism dynamically interact and collectively behave to produce distinct physiologic states and functions. This is a fundamental question in the new interdisciplinary field of Network Physiology, and has not been previously explored. Introducing the novel concept of Time Delay Stability (TDS), we develop a computational approach to identify and quantify networks of physiologic interactions from long-term continuous, multi-channel physiological recordings. Applying a system-wide integrative approach, we identify distinct patterns in the network structure of organ interactions, as well as the frequency bands through which these interactions are mediated. Our findings demonstrate a direct association between network topology and physiologic function, and provide new insights into understanding how health and distinct physiologic states emerge from networked interactions among nonlinear multi-component complex systems. (Abstract excerpt)

Earth Life > Integral Persons > Somatic

Soanwane, Abjijeet, et al. Network Medicine in the Age of Biomedical Big Data. arXiv:1903.05449. Brigham and Women’s Hospital, Boston systems physicians provide a good example of a novel holistic, systemic approach which takes in not only parts and a whole but internal, vital interconnections as a major factor for diagnosis and treatment

Earth Life > Integral Persons > Complementary Brain

Grossberg, Stephen. A Half Century of Progress Towards a Unified Neural Theory of Mind and Brain. Kozma, Robert, et al, eds. Artificial Intelligence in the Age of Neural Networks and Brain Computing. Cambridge, MA: Academic Press, 2018. The veteran Boston University neuroscientist and original theorist of this whole BI and AI revolution reviews his 50 year project (search) to theoretically and conceptually explain how our bilaterally complex brains proceed to envision, quantify, consider, think, learn, and effectively act in dynamic social and natural environments. The invited chapter is fully available on the author’s publication page. See herein his major paper Towards Solving the Hard Problem of Consciousness a year earlier in Neural Networks (87/38, 2017), along with Iain McGilchrist 2019. We include 3 quotes to convey its essence and message.

This article surveys some of the main design principles, mechanisms, circuits, and architectures that have been discovered during a half century of systematic research aimed at developing a unified theory that links mind and brain, and shows how psychological functions arise as emergent properties of brain mechanisms. This project advanced in stages by way of revolutionary computational paradigms like Complementary Computing and Laminar Computing that constrain the kind of unified theory that can describe the autonomous adaptive intelligence that emerges from advanced brains. Adaptive Resonance Theory, or ART, is one of the core models that has been discovered in this way. ART is not, however, a “theory of everything” if only because, due to Complementary Computing, different matching and learning laws tend to support perception and cognition on the one hand, and spatial representation and action on the other. (Abstract excerpt)

Complementary Computing clarifies why there are multiple parallel processing streams in the brai to resolve computational uncertainties that cannot be overcome by just one processing stream or stage. Complementary Computing describes how the brain is organized into complementary parallel processing streams whose interactions generate biologically intelligent behaviors. A single cortical processing stream can individually compute some properties well, but cannot, by itself, process other computationally complementary properties. Pairs of complementary cortical processing streams interact to generate emergent properties that overcome their deficiencies to compute complete information with which to represent or control some faculty of intelligent behavior. (35)

The WHAT and WHERE cortical streams are complementary: The category learning, attention, recognition, and prediction circuits of the ventral, or What, cortical processing stream for perception and cognition are computationally complementary to those of the dorsal, or Where and How, cortical processing steam for spatial representation and action. One reason for this What - Where complementarity is that the What stream learns object recognition categories that are substantially invariant under changes in an object's view, size, and position. These invariant object categories enable our brains to recognize valued objects. They cannot, however, locate and act upon a desired object in space. Cortical Where stream spatial and motor representations can locate objects and trigger actions towards them, but cannot recognize them. By interacting together, the What and Where streams can recognize valued objects and direct appropriate goal-oriented actions towards them. (36-37)

Earth Life > Integral Persons > Complementary Brain

McGilchrist, Iain. The Master and His Emissary. New Haven: Yale University Press, 2019. This is a second edition of the magisterial 2009 volume by the Scottish psychiatrist because 10 years later it has become a best-selling, luminous exposition of the awesome bicameral brain that evolution has endowed us with. The first edition is extensively reviewed in Current Vistas and cited elsewhere. Today its deep analysis is well proven and its message even more imperative. Our human cerebral faculty is graced with asymmetric hemispheres that are distinguished by complementary archetypal attributes and purposes. The long litany of entity/empathy, particle/wave, dot/connect, fire/love and so ever on is familiar (see also Jonathan Rowson herein for a 2013 interview with Iain). His prime point is that through history and especially now the mechanistic, objects only, left side sans any right contextual meaning and guidance has reached a terminal planetary crisis. One may add in April 2019, this is why American politics polarize, Brexit is intractable, small and large gang wars rage (Sri Lanka), all the while that Antarctica melts.

Earth Life > Integral Persons > Complementary Brain

Rowson, Jonathan and Iain McGilchrist. Divided Brain, Divided World. iainmcgilchrist.com. The whole transcript is reachable from McGilchrist’s website under Events as an interview/ conversation by Rowson, a Scottish chess grand master who has a doctorate in wisdom philosophy from Bristol University, with the author of The Master and His Emissary (2009, search). As our review above of its 2019 edition says, his 600 page testimony about how much our dual hemispheres possess definitive part/object focus and field/context image options has gained wide acceptance. As Iain explains, the left emissary side has historically taken leave of any original right masterful guidance to such an extent that its mechanistic sterility is at the base of an aberrant, terminal world.

JR: Iain, let me begin by stating the argument as I have come to understand it, and you can tell me how you might express it differently or more fully. You seem to be saying that the left hemisphere of the brain is gradually colonising our experience. While the brain hemispheres are connected by the corpus callosum, and both are involved in everything we do, if we cease to ask what the hemispheres do such as language, reasoning, creativity, forecasting, and instead ask how they do it, we find very significant differences in the two hemispheres. For instance the left hemisphere tends to decontextualise issues while the right contextualises, the left tends to abstract while the right makes vivid and concrete, the left seeks instrumental feedback while the right prefers affectively nuanced responses, and the right hemisphere appears to be much more receptive to evidence that challenges its own position. (10)

IM: It’s like this. Suppose it could be shown – because it can – that our brains are so constructed as to enable us to bring into being and conceive the experiential world in two quite distinct, complementary, but ultimately incompatible, ways. Suppose each has its uses, and that – here’s why the brain view helps – these versions of the world, which have importantly different qualities, are generally so well combined or alternated from moment to moment in everyday experience that individuals are not aware of this being the case. (14) The left hemisphere is not, as is sometimes thought, unemotional and down to earth. Anger is one of the most clearly lateralised emotions and it lateralises to the left hemisphere. The left hemispheres is manifestly not in touch with reality, and when it does not understand something it simply makes up a story that makes sense in its own terms and tells it with conviction. (21)

Earth Life > Integral Persons > Conscious Knowledge

Ginsburg, Simona and Eva Jablonka. The Evolution of the Sensitive Soul: Learning and the Origins of Consciousness. Cambridge: MIT Press, 2019. Veteran scholars (search) Simona G., an Open University of Israel psychologist and Eva J., a Tel Aviv University geneticist and historian of science achieve a lucid exposition of the ascent of sentient knowing from its earliest flicker to our human integrated information. As worked out in prior papers, a continuum can be traced from limited rudiments to an unlimited learning process. EJ and Marion Lamb were the authors of Evolution in Four Dimensions (2005, 2014) whose stages are here joined with the major evolutionary transitions model (Maynard Smith & Szathmary) so as to fill in an oriented, sequential scale. By 2019 life’s long development can be well realized (as we try to report) as a deeply homologous, teleological, quickening by way of an epigenetic knowledge gain in social groupings from minimal microbes to our linguistic florescence. A “rational” soul is seen to rise in tandem, as if (though not formally put) a meaningful holistic complement to an analytic detail mode. Self-organizing, goal-directed systems are thus at work to engender an emergent, autopoietic self-making. Altogether again, a universal gestation which (whom) is trying to come to her/his own senses, witness and discovery becomes evident.

What marked the evolutionary transition from organisms that lacked consciousness to those with minimal subjective experiencing, or, as Aristotle described it, “the sensitive soul”? In this book, Simona Ginsburg and Eva Jablonka propose a new theory that finds learning to be the driving force in the transition to basic consciousness. Using a method that helped identify the transition from non-life to life then allows biological, psychological, and philosophical aspects to be considered. Along with historical, neurobiological, and philosophical foundations, the authors propose an evolutionary marker of basic consciousness as a complex form of associative learning, which is then seen as the driver of the Cambrian explosion and its diversification of organisms. Finally, symbolic language as a similar type is proposed as a marker for the evolutionary transition to human rationality.

I read The Evolution of the Sensitive Soul with an immense interest. It is the best synthesis I know about consciousness. It includes a fascinating history of the concepts and discoveries about consciousness together with an outstanding presentation of the most recent scientific data, theories and philosophical speculations. The evolution of consciousness from the 'Cambrian explosion' up to the Golem predicament is one among the many original aspects of the book. A book that must be read and meditated on. (Jean-Pierre Changeux)

Earth Life > Integral Persons > Conscious Knowledge

Toker, Daniel and Friedrich Sommer. Information Integration in Large Brain Networks. PLoS Computational Biology. February, 2019. UC Berkeley neuroscientists proceed to tidy up some mathematical issues with this popular theoretic synthesis by Giulio Tononi and many colleagues that appears to quantify a parallel, tandem relation between an aware cerebral sentience and a sapient knowledge content.

An outstanding problem in neuroscience is to understand how information is integrated across the many modules of the brain. While classic information-theoretic measures have transformed our understanding of feedforward information processing in the brain’s sensory periphery, comparable measures for information flow in the massively recurrent networks of the rest of the brain have been lacking. To address this, recent work has produced a sound measure of network-wide “integrated information.” But, a computational hurdle has stymied attempts to measure large-scale information integration in real brains. Here, we show that spectral clustering, applied on the correlation matrix of time-series data, provides an approximate but robust solution. Finally, we use our solution to support of the hypothesis that information integration is maximized by networks with a high global efficiency, and that modular network structures promote the segregation of information. (Abstract excerpt)

Earth Life > Integral Persons > Gender

Tadic, Bosiljka, et al. Functional Geometry of Human Connectome and Robustness of Gender Differences. arXiv:1904.03399. Jozef Stefan Institute, Lujbljana, Slovenia (search), University of Belgrade and Wilfrid Laurier University, Waterloo, Canada system mathematicians achieve a new phase of sophistication with regard to network cerebral relative to female and male genders. As the quotes say, a woman’s brain appears to have a more intricate, better connected, multiplex form than a man’s faculty.

Mapping the brain imaging data to networks, where each node represents a specific area of the brain, has enabled an objective graph-theoretic analysis of human connectome. However, the latent structure of higher-order connections remains unexplored, where many brain regions acting in synergy perform complex functions. Here we analyse this hidden domain using the simplicial complex parametrisation where the shared faces encode higher-order relationships between groups of nodes and an emerging hyperbolic geometry. By providing new insights into the internal organisation of anatomical brain modules as well as into the links between them that are essential to dynamics, these results also highlight the functional gender-related differences. (Abstract)

Our analysis has revealed that the human connectome possesses a hyperbolic geometry and a complex structure on the scale between the node’s edges and the mesoscopic anatomical communities within the cerebral hemispheres. This structure, composed of simplicial complexes of different sizes and cycles describes the higher-order connectivity among different regions of the brain, divided into anatomical modules. Therefore, it can provide a reliable basis for understanding the functional complexity of the brain. Moreover, the female connectome appears to have a structure different from the common F & M connectome, not only in the number of edges but also in its organization expressed by these higher-order connections. It might be conjectured that these excess connections imply additional functionality of the female connectome, which can have evolutionary, biological, biochemical, and even social origins. (11)

Earth Life > Phenomenon > Cultural Code

Oudeyer, Pierre-Yves, et al. Computational and Robotic Models of Early Language Development. arXiv:1903.10246. Ensta Paris Tech University (see below, search) and Stanford University systems psychologists continue to finesse how self-organizing processes are inherently at work so as to bring about and advance communicative abilities by which a child can negotiate an expanding, variable world of experiences.

We review computational and robotics models of early language learning and development. We first explain why and how these models are used to understand better how children learn language. We argue that they provide concrete theories of language learning as a complex dynamic system, complementing traditional methods in psychology and linguistics. We review different modeling formalisms, grounded in techniques from machine learning and artificial intelligence such as Bayesian and neural network approaches. We then discuss their role in understanding several key mechanisms of language development: cross-situational statistical learning, embodiment, situated social interaction, intrinsically motivated learning, and cultural evolution. (Abstract)

I (Pierre-Yves Oudeyer) have been studying lifelong autonomous learning, and the self-organization of behavioural, cognitive and cultural structures, at the frontiers of artificial intelligence, machine learning, cognitive sciences and educational technologies.
I employ a special focus on mechanisms enabling agents to set their own goals, and how this can self-organize curriculum learning. I consider cognitive development as a complex dynamical system which needs to be understood through systemic thinking, leveraging tools and concepts from computational sciences, neuroscience and psychology. (www.pyoudeyer.com website)

Earth Life > Phenomenon > Human Societies

Cliff, Oliver, et al. Network Properties of Salmonella Epidemics. Nature Scientific Reports. 9/6159, 2019. University of Sydney and Westmead Hospital, Sydney complexity theorists including Mikhail Prokopenko apply the latest nonlinear theories to the seasonal spread of this common disease. By clever technique and analysis, once again even such vicarious public inflictions can be seen to take on similar mathematical forms just as everywhere else. Here then is ever more evidence of a universal, independent genetic-like source at generative, exemplary effect.

We examine non-typhoidal Salmonella (S. Typhimurium or STM) epidemics as complex systems, driven by evolution and interactions of diverse microbial strains, and focus on emergence of successful strains. Our findings challenge the established view that seasonal epidemics are associated with random sets of co-circulating STM genotypes. We use high-resolution molecular genotyping data comprising 17,107 STM isolates representing nine consecutive seasonal epidemics in Australia, genotyped by multiple-locus variable-number tandem-repeats analysis (MLVA). From these data, we infer weighted undirected networks based on distances between the MLVA profiles, depicting epidemics as networks of individual bacterial strains. (Abstract excerpt)

Earth Life > Phenomenon > Human Societies

Lee, Edward D., et al. Emergent Regularities and Scaling in Armed Conflict Data. arXiv:1903.07762. I have been tracking the scientific quest for a natural, commonly recurrent, formative principle since general systems in the 1960s. When I visited the Santa Fe Institute in 1987, this endeavor was an incentive and Grail goal. Into Spring 2019, computational theorists EDL and Christopher Myers, Cornell University along with Jessica Flack, David Krakauer and Bryan Daniels, SFI, post a good example whence “dynamic self-similarities and large-scale symmetries” can be discerned even for violently chaotic human behaviors. As the quotes allude, an independent, universally exemplified, mathematical code indeed seems in effect across cosmic to social phases. As long intimated, a second immaterial source is now being found which moves and constrains our travails and micro-social mayhem. See also Universal Scaling Across Biochemical Networks on Earth by this collaborative team in Science Advances (5/1, 2019).

Large-scale armed conflict is a characteristic feature of modern civilization. The statistics of conflict show remarkable regularities like power law distributions of fatalities and durations, but these properties have remained disparate, albeit prominent, features of conflict. We explore a large, detailed data set of 105 armed conflict reports spanning 20 years across nearly 104 kilometers. By clustering proximate events into conflict avalanches, we show that the number of conflict reports, fatalities, duration, and geographic extent satisfy consistent scaling relations. The temporal evolution measured by these scaling variables display emergent symmetry, reflecting self-similarity in the trajectories of conflict avalanches. A natural interpretation of our findings is a criticality state, suggesting that armed conflicts are dominated by a low-dimensional process that scales with physical dimensions in a unified and predictable way. (Abstract)

Taken all together, these features furnish quantitative constraints for the prediction of armed conflict. In kind, universal features and scaling laws have now been found in a variety of large-scale social systems demonstrating that ideas from statistical physics can structure our understanding of social phenomena. In this wider context, our findings hint at the intriguing possibility that these emergent regularities reflect underlying physical principles that shape the evolution of armed conflicts. (4)

Earth Life > Phenomenon > Human Societies

Mesoudi, Alex. Pursuing Darwin’s Curious Parallel: Prospects for a Science of Cultural Evolution. Proceedings of the National Academy of Sciences. 114/7853, 2017. As the extended Abstract says, the University of Exeter cultural psychologist (search) continues his project, as David S. Wilson and others, to reconcile and join life’s biological phase with our human linguistic societies. A working answer is in sight as better finesses of field, experimental, and conceptual domains come aboard. See also by AM and collaborators Shared Group Membership Facilitates the Persistence of Cultural Transmitted Behavior (PsyArXiv 2018)

In the past decades, scholars have pursued the curious parallel noted by Darwin between the genetic evolution of species and the cultural evolution of beliefs, skills, knowledge, languages, institutions, and socially transmitted information. Here, I review current progress in the pursuit of an evolutionary science of culture that is grounded in both biological and evolutionary theory, but also treats culture as more than a proximate mechanism that is directly controlled by genes. Both genetic and cultural evolution can be described as systems of inherited variation that change over time in response to processes such as selection, migration, and drift. The foundation of cultural evolution was laid in the late 20th century with population-genetic style models of cultural microevolution, and by phylogenetic methods. Since then, there have been major efforts to understand the sociocognitive mechanisms underlying cumulative cultural evolution, the consequences of demography along with social learning biases, transformative and selective processes, and quantitative phylogenetic and multilevel selection models. (Abstract excerpts)

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