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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 76 through 90 of 130 found.


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

Earth Life > Genetic Info > DNA word

Searls, David. A Primer in Macromolecular Linguistics. Biopolymers. 99/3, 2013. The philosophical geneticist (bio below) has been a prescient observer (search) that nature’s dual domains of informational nucleotides and literary discourse are innately similar in kind. This entry describes via graphic, evidential visuals their parallel, self-similar essence. The import is that if the relation could move from metaphor to analogy to factual, both the genetics and linguistics endeavors could much benefit from cross-applications of methods and analytic techniques.

Polymeric macromolecules, when viewed abstractly as strings of symbols, can be treated in terms of formal language theory, providing a mathematical foundation for characterizing such strings both as collections and in terms of their individual structures. In addition this approach offers a framework for analysis of macromolecules by tools and conventions widely used in computational linguistics. This article introduces the ways that linguistics can be and has been applied to molecular biology, covering the relevant formal language theory at a relatively nontechnical level. Analogies between macromolecules and human natural language are used to provide intuitive insights into the relevance of grammars, parsing, and analysis of language complexity to biology. (Abstract)

David A. Searls received degrees in Philosophy and Life Sciences from MIT and a PhD in Biology from Johns Hopkins University. Following a postdoctoral fellowship at the Wistar Institute in Philadelphia he completed a Master's in Computer and Information Science at the University of Pennsylvania. He went on to co-found the Computational Biology and Informatics Laboratory at UP. He then spent 13 years at SmithKline Beecham and GlaxoSmithKline Pharmaceuticals, where he was Senior Vice-President of Bioinformatics. He left GSK in 2008 and is now an independent consultant.

Earth Life > Genetic Info > DNA word

Wu, Yanying and Quanlong Wang. A Categorical Compositional Distributional Modelling for the Language of Life. arXiv:1902.09303. Oxford University computer neuroscientists are able to treat and parse protein biology in a linguistic manner by use of this title computational insight achieved by the Oxford computer science group, search Bob Coecke. We log in amongst concurrent papers which establish this deep affinity between genetic and literary domains, broadly conceived, as a later evolutionary stage of one, same natural script.

The Categorical Compositional Distributional (DisCoCat) Model is a powerful mathematical method for composing the meaning of sentences in natural languages. Since we can think of biological sequences as the "language of life", here we apply this model to see if we can obtain new insights and a better understanding of life’s language. We choose to focus on proteins as their linguistic features are more prominent as compared with other macromolecules such as DNA or RNA. Thus, we treat each protein as a sentence and its constituent domains as words. The meaning of a word or the sentence is its biological function, and the arrangement of protein domains corresponds to the syntax. Putting all those into the DisCoCat frame, we can "compute" the function of a protein with grammar rules that combine them together. (Abstract excerpts)

Earth Life > Integral Persons > Somatic

Assmann, Birte, et al. Self-Organization in Spontaneous Movements of Neonates Generates Self-Specifying Sensory Experiences. arXiv:1902.10169. As their extensive reference list attests, four German child psychologists based at the Free University of Berlin post a 2019 affirmation of the dynamical systems theory approach initiated in the mid 1990s by Esther Thelen, Linda Smith, (search herein) and others. This insight that infants and children learn and develop by way of complex behavioral iterations, as so does the rest of evolutionary nature and culture, is now established and practiced. Once again human and universe, child and cosmos, become one and the same.

Movement experience and the coordination of perception and action are the basis of developing body awareness, emotion, motivation and cognition and the sense of self. The four limbs play a key role in the developing sense of body ownership, agency and peripersonal space. Neonatal limb movements were investigated by way of respective processes of self-organization and developing body awareness. With increasing age a shift from configurations with proximal to distal positions suggests a role of the proximal-distal dimension in movement development. We conclude that self-organization in spontaneous movements provides neonates with perceptual body- and self-specifying stimuli involved in developing body awareness and postulate the involvement of emotional and cognitive essences. (Abstract excerpt)

Earth Life > Integral Persons > Somatic

Bjorklund, David and Bruce Ellis. Children, Childhood, and Development in Evolutionary Perspective. Developmental Review. 34/3, 2014. We examine children, childhood, and development from an evolutionary perspective. We begin by reviewing major assumptions of evolutionary–developmental psychology, including the integration of “soft” developmental systems theory DST with ideas from mainstream evolutionary psychology. We then discuss the concept of adaptive developmental plasticity and describe the core evolutionary concept of developmental programming and some of its applications to human development, as instantiated in life history theory and environmental influence. We then discuss the concept of adaptation from an evolutionary–developmental perspective, including ontogenetic and deferred adaptations. We conclude that evolutionary theory can serve as a metatheory for developmental science. (Abstract)

At the core of developmental systems theoryis the concept of probabilistic epigenesis: “individual development is characterized by an increase in novelty and complexity of organization over time due to the sequential emergence of new structural and functional properties and competencies. In biology, epigenesis also refers to the complex biochemical system that regulates gene expression. A DST view describes ontogeny as a process of continuous, bidirectional interaction between components at all levels including the genetic, cellular, phenotypic, behavioral, ecological, and cultural. (227)

Earth Life > Integral Persons > Somatic

Guidolin, Diego, et al. The “Self-Similarity Logic” Applied to the Development of the Vascular System. Developmental Biology. 351/156, 2011. University of Padova, Udine, and Bari medical morphologists here apply this mathematical insight originally posted in 2009 by neuroscientists Luigi Agnati, et al (search) to physiological purposes. We add in 2019 that the presence of such an innately universal repetition in kind has been found and robustly proven from human to universe.

From a structural standpoint, living systems exhibit a hierarchical pattern of organization that is nested within one another. Recently, it has been suggested that some auto similarity prevails at each level or developmental stage and a principle of “self-similarity logic” has been proposed to convey the concept of a multi-level organization in which similar rules (logic) serve at each level. This study suggests that such a principle is likewise apparent in many morphological and developmental aspects of the vascular system. In fact, not only the morphology of the vascular system exhibits a high degree of geometrical self-similarity, but its remodelling processes also seem to be characterized by almost the same rules. (Abstract excerpt)

Earth Life > Integral Persons > Cerebral Form

Agnati, Luigi, et al. The Brain as a “Hyper-Network:” The Key Role of Neural Networks as Main Producers of the Integrated Brain Actions via the “Broadcasted” Neuroconnectomics. Journal of Neural Transmission. 125/6, 2018. As global studies of dynamic multiplex structures gain a robust credence, University of Modena, University of Genova, National Institute of Drug Abuse, USA, and University of Padova (Diego Guidolin) neuroscientists can describe an iconic micro-universe which distinguishes our cerebral endowment and human acumen.

Investigations of integrative cerebral activities involve neural networks, glial, extracellular molecular, and fluid channels networks. Here we propose that this phenomena can result in a brain hyper-network that has as fundamental components known as tetra-partite synapses. Global signalling via astrocyte networks and pervasive signals, such as electromagnetic fields (EMFs), allow the integration of various networks at crucial nodes level, the tetra-partite synapses. The concept of broadcasted neuroconnectomics is introduced to describe highly pervasive signals involved in the information handling of brain networks at miniaturisation levels. Thus, it is surmised that neuronal networks are the “core components” of the brain hyper-network. (Abstract excerpt)

Earth Life > Integral Persons > Cerebral Form

Agnati, Luigi, et al. Mosaic, Self-Similarity Logic and Biological Attraction Principles. Communicative & Integrative Biology. 2/6, 2009. Senior scientists LA, University of Modena, Frantisek Baluska, University of Bonn, Peter Barlow, University of Bristol, and Diego Guidolin, University of Padova presciently discern an array of inherent structural features which take on a fractal as they recur at each and every minute neuronal to whole cerebral domains. Search each author for more contributions.

From a structural standpoint, living organisms are organized like a nest of Russian matryoshka dolls, in which structures are buried within one another. From a temporal view, this organisation is due to a history comprised of a set of time backcloths which have accompanied the passage of living matter from its origins up to the present day. The aim of the present paper is to indicate a possible course through time and suggest how today’s complexity has been reached by living organisms. This investigation will employ three conceptual tools, namely Mosaic, Self-Similarity Logic, and Biological Attraction principles.

Self-Similarity Logic indicates the self-consistency by which elements of a living system interact, irrespective of the spatio-temporal level. The term Mosaic indicates how, from a same set of elements assembled according to different patterns, it is possible to arrive at various constructions: hence, each system becomes endowed with different emergent properties. The Biological Attraction principle states that there is an inherent drive for association and merging of compatible elements at all levels of biological complexity. By analogy with the gravitation law in physics, biological attraction means that each living organism creates an attractive ‘field’ around itself. (Abstract excerpt)

Earth Life > Integral Persons > Cerebral Form

Chang, Le and Doris Tsao. The Code for Facial Identity in the Primate Brain. Cell. 169/6, 2017. A main technical paper from Tsao’s CalTech lab about her collegial breakthrough decipherment of how pixelated neuronal architectures and mosaic areas are dynamically able to recognize whole faces. See also a commentary How Do We Recognize a Face? by Rodrigo Quiroga in this issue.

Primates recognize complex objects such as faces with remarkable speed and reliability. Here, we reveal the brain’s code for facial identity. Experiments in macaques demonstrate an extraordinarily simple transformation between faces and responses of cells in face patches. By formatting faces as points in a high-dimensional linear space, we discovered that each face cell’s firing rate is proportional to the projection of an incoming face stimulus onto a single axis in this space, allowing a face cell ensemble to encode the location of any face in the space. Using this code, we could precisely decode faces from neural population responses and predict neural firing rates to faces. Our work suggests that other objects could be encoded by analogous metric coordinate systems. (Abstract excerpt)

How individual faces are encoded by neurons in high-level visual areas has been a subject of active debate. An influential model is that neurons encode specific faces. However, Chang and Tsao conclusively show that, instead, these neurons encode features along specific axes, which explains why they were previously found to respond to apparently different faces. (R. Quiroga summary)

Earth Life > Integral Persons > Cerebral Form

Di Ieva, Antonio, ed.. The Fractal Geometry of the Brain. New York: Springer, 2016. A Macquarie University, Sydney neuroscientist (search) collects the latest research in a dedicated volume on how much cerebral dynamics are graced and facilitated by nested self-similar topologies, aka “fractalomics.” Typical chapters are Does a Self-Similarity Logic Shape the Organization of the Nervous System? by Diego Guidolin, et al and The Fractal Geometry of the Human Brain: An Evolutionary Perspective by Michel Hofman (both Abstracts next). We also want to record parallel efforts by Luigi Agnati (search) and colleagues.

From the morphological point of view, the nervous system exhibits a fractal, self-similar geometry at various levels of observations, from single cells up to cell networks. From the functional point of view, it is characterized by a hierarchic organization in which self-similar structures (networks) of different miniaturizations are nested within each other. On this basis, the term “self-similarity logic” was introduced to describe a nested organization where at the various levels almost the same rules (logic) to perform operations are used. Thus, they can represent key concepts to describe its complexity and its concerted, holistic behavior. (Abstract excerpt, Guidolin, et al)

The evolution of the brain in mammals is characterized by changes in size, architecture, and internal organization. Also the geometry of the brain, and the size and shape of the cerebral cortex, has changed notably during evolution. Comparative studies of the cerebral cortex suggest that there are general architectural principles governing its growth and development. In this chapter some design principles and operational modes that underlie the fractal geometry and information processing capacity of the cerebral cortex in primates, including humans, will be explored. (Abstract, M. Hofman)

Earth Life > Integral Persons > Cerebral Form

Di Ieva, Antonio, et al. Fractals in the Neurosciences. Part I: General Principles. The Neuroscientist. 20/4, 2014. Brain researchers with posts in Canada, Austria, Spain, Poland and Venezuela offer a good review to date of realizations that nature’s ubiquitous recurrence of the same forms everywhere indeed also braces and graces our cerebral faculty, as it facilitates our constant cognitive activities.

The natural complexity of the brain, its hierarchical structure, and the sophisticated topological architecture of the neurons organized in micro-networks and macro-networks are all factors that limit an Euclidean geometry and linear dynamics. The introduction of fractal geometry for the quantitative description of complex natural systems has been a major paradigm shift. Modern neurosciences admit the prevalence of fractal properties such as self-similarity in the brain at molecular, anatomic, functional, and pathological levels. Fractal geometry is a mathematical model that offers a universal language for neurons and glial cells as well as the whole brain with its physiopathological spectrums. For a holistic view of fractal geometry of the brain, we review here the basic concepts and main applications. (Abstract excerpts)

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

Kwisthout, Johna, et al. Special Issue on Perspectives on Human Probabilistic Inference and the Bayesian Brain. Brain and Cognition. 112/1, 2017. An issue editorial for a collection of papers broadly about the predictive brain theory of Karl Friston and many colleagues. See for example, The Infotropic Machine, A Social Bayesian Brain, and Explanatory Pluralism.

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 that brains seem to seek and reside at an optimum 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 > Phenomenon > Human Societies

Blanton, Richard and Lane Fargher. How Humans Cooperate: Confronting the Challenges of Collective Action. Boulder: University of Colorado Press, 2016. . In a broad retrospective, a Purdue University anthropologist and a National Polytechnic Institute, Mexico archaeologist join the rising consensus (our own cooperative synthesis) that communal groupings have an evolutionary precedence in fostering survival and prosperity. As individual members gain in return, a viable (democratic) collectivity best serves each and all. These findings are then braced by neurobiological, primatology, social intelligence, economic trading, and beyond.

. In a broad retrospective, a Purdue University anthropologist and a National Polytechnic Institute, Mexico archaeologist join the rising consensus (our own cooperative synthesis) that communal groupings have an evolutionary precedence in fostering survival and prosperity. As individual members gain in return, a viable (democratic) collectivity best serves each and all. These findings are then braced by neurobiological, primatology, social intelligence, economic trading, and beyond.

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