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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 67 found.


Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution > Systems Biology

Ingalls, Brian. Mathematical Modeling in Systems Biology. Cambridge: MIT Press, 2020. A University of Waterloo, Ontario biomathematician provides a latest tutorial for all manner of nonlinear complex, network, dynamical phenomena at effect in this integrative field.

This book offers an introduction to mathematical concepts and methods needed for the construction and interpretation of models in molecular systems biology. The first four chapters cover the basics of mathematical modeling in molecular systems biology. The last four chapters address specific biological domains, treating modeling of metabolic networks, of signal transduction pathways, of gene regulatory networks, and of electrophysiology and neuronal action potentials.

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

Earth Life > Common Code

Radicchi, Filippo and Ginestra Bianconi. Epidemic Plateau in Critical SIR Dynamics with Non-trivial Initial Conditions. arXiv:2007.15034. We cite this entry by Indiana University and Alan Turing Institute, London network theorists as an example amongst a flood of similar papers about how the active COVID-19 pandemic seems to exhibit and be moved by intrinsic mathematical patterns and dynamics. See also An Infection Process near Criticality by P. Krapivsky at 2009.08940. And we wonder if this international effort, aided global coordination, could come to a common synthesis, it would result a concerted focus going forward to mitigate and prevent any more –demics.

Containment measures implemented by some countries to suppress the spread of COVID-19 have resulted in a slowdown of the epidemic characterized by a time series of daily infections plateauing over extended periods of time. We prove that such a dynamical pattern is compatible with critical Susceptible-Infected-Removed (SIR) dynamics. In traditional analyses of the SIR model, the critical dynamical regime is started from a single infected node. We describe that such non-trivial starting conditions affect the outbreak size as an increasing function of the initial number of infected individuals, while the expected duration of the outbreak is a non-monotonic function of the initial number of infected individuals. (Abstract excerpt)

Earth Life > Common Code

Sinha, Saurabh, et al. Behavior-related Gene Regulatory Networks: A New Level of Organization in the Brain. Proceedings of the National Academy of Sciences. 117/23270, 2020. In this significant contribution, fifteen systems biologists from the University of Illinois, SUNY Buffalo, UT Austin (Hans Hofmann), UM Amherst, University of Toronto, and Cornell University trace these basic genetic functions all the way to their cerebral presence and effect. By so doing, a novel dimension can be added to neural operations and cognitive behaviors. In a further take, here is another example of a common interchange of this archetypal formative system.

Neuronal networks are the standard model today to describe brain activity associated with animal behavior. Recent studies now reveal an extensive role for a completely distinct layer of networked activities in the brain — the gene regulatory network (GRN) — that expresses thousands of genes in a behavior-related manner. We examine emerging insights into the relationships between these two types of networks and discuss their interplay in spatial and temporal dimensions across multiple scales of organization. We discuss properties expected of behavior-related GRNs by drawing upon the rich literature on GRNs related to animal development. (Abstract excerpt)

A rich body of genetic and, more recently, genomic studies have revealed that behavior is also associated with the coordinated activities of genes that operate in brain cells. Many studies have found significant, predictable, and specific changes in brain gene expression profiles associated with behavioral responses to particular environmental stimuli. These findings suggest that a second layer of network biology — that of gene regulatory networks — also underlies behavior. (23270)

Earth Life > Nest > Geological

Ferreira, Douglas, et al. Long-range Correlation Studies in Deep Earthquakes Global Series. Physica A. Online August 27, 2020. We highlight this entry by Instituto Federal do Rio de Janeiro seismologists because it not only considers a realm of internal quakes at depths of 50 miles, but proceeds to characterize them by way of multiplex network theories. As the second quote notes, the same dynamic scale-invariance found in every other realm is present in this basic geological domain. As alluded to here, a self-organized criticality can also be detected. And as I log in papers about neural and symbiotic phases, a 2020 perception of an independent mathematic source force which is in universal effect becomes strongly evident. For more see a 2016 book Methods of Statistical Physics Applied to Seismology from the Viewpoint of Complex Networks by this extended group, and earlier Self-Organized Criticality and Earthquakes at arXiv:0711.1750.

In the present paper we have conducted studies on seismological properties using worldwide data of deep earthquakes (70 km), considering events with magnitude greater than 4.5. We have addressed this new realm of seismic activity by a complex networks perspective which reveals scale-free and small-world features, strengthening the use of a time window model to construct epicenters. The results for deep events were further analyzed using Nonextensive Statistical Mechanics and corroborate with those found for the shallow quakes, since the connectivity distribution also follows a q-exponential distribution and the scaling behavior is present. Our findings thus reinforce correlations between earthquakes and the criticality of the seismological system. (Abstract)

Several phenomena in nature exhibit characteristics of complex systems such as nonlinear dynamics, fractal dimensions, power law distributions and long-range spatiotemporal memory, where the earthquakes being one example. Theories of complex systems have been applied to many different areas of knowledge for a long time, such aseconomics, computer science, mechanical engineering, biology and chemistry. In the last decades, works have used complex systems theories to perform studies on spatiotemporal properties of seismicity. In that sense, we can highlight the important approach of using complex networks concepts, which provides powerful procedures to analyse the interactions and correlations between elements of complex systems, giving efficient descriptions about the dynamics of such systems. (1)

Earth Life > Nest > Life Origin

Cardoso, Silvana, et al. Chemobrionics: From Self-Assembled Material Architectures to the Origin of Life. Artificial Life. 26/3, 2020. Eleven systems biochemists from the UK, Scotland, Spain, Czech Republic, Belgium, Portugal, Hungary, and Italy including Julyan Cartwright, Leroy Cronin, and Michael Russell (search each) contribute to ever-increasing realizations of an innately fertile, life-bearing ecosmic genesis due to such innate properties. As a result, a generative inherency and consequent vital development is being found at procreative effect wherever organically conducive.

Self-organizing precipitation processes, such as chemical gardens forming biomimetic micro- and nanotubular forms, offer much potential to help explore, quantify, and understand nonequilibrium physicochemical systems with regard to life's original emergence. Advances in this area require a combination of expertise in physics, chemistry, mathematical modeling, biology, and nanoengineering, as well as in nonlinear complex systems and materials sciences, giving rise to this new synergistic discipline of chemobrionics. (Abstract excerpt)

It is today commonly accepted that self-assembly is an excellent way to form complex structures in an evolving series of small steps. Indeed, it is the foundation for much of modern nanoscience. Yet nature applies not only self-assembly, but also self-organization, which allows the stepwise building of complex patterns ultimately from simple building blocks. (316)

Earth Life > Nest > Life Origin

Prosdocimi, Francisco, et al. The Theory of Chemical Symbiosis: A Margulian View for the Original Emergence of Biological Systems. Acta Biotheoretica. August, 2020. Universidade Federal do Rio de Janeiro, Universidad Nacional Autónoma de México, and Universidade Federal da Paraíba theoretical biologists proceed to expand the occurrence of mutually beneficial symbiotic unions, as long advocated by Lynn Margulis (1938-2011) and now well proven, deeply into life’s prior biochemical beginnings. So into 2020, along with self-organization and networking phenomena, still another innately procreative agency can be found at constant effect at each and every lively stage.

The theory of chemical symbiosis (TCS) suggests that biological systems started with the collaboration of two polymeric molecules existing in early Earth: nucleic acids and peptides. Chemical symbiosis emerged when RNA-like nucleic acid polymers happened to fold into 3D structures capable of binding amino acids together. TCS suggests that there is no chicken-and-egg problem into the emergence of biological systems as RNAs and peptides were of equal importance to the origin of life. Life has initially emerged when these two macromolecules started to interact in molecular symbiosis. Further, we suggest that life evolved into progenotes and cells due to new layers of symbiosis. Mutualism is the strongest force in biology, capable to create novelties by emergent principles; on which the whole is bigger than the sum of the parts. TCS aims to apply the Margulian view of biology into the origins of life field. (Abstract excerpt)

Current works and views about the origins of life can be understood under two great epistemological grounds: the top-down and the bottom-up approaches. In a biological driven top-down approach, researchers have been looking into living organisms in order to search for features that could be observed in Bacteria, Archaea and Eukarya cells. In a chemical driven bottom-up approach, researchers have been looking into simple molecules capable to bind together and form the main biological polymers, to wit: proteins, nucleic acids, carbohydrates and lipids. (2)

Selfishness and Altruism: In everyday life, altruism and egoism are commonly used terminologies suggesting intentionality of acts, whether of collaboration or self-preservation to the detriment of others. When taking this terminology to the molecular level, we must keep in mind not the intentionality but the effect of the action. Thus, molecular altruism must be understood as the symbiotic process of interaction between molecules, creating a self-referring process. In terms of evolutionary processes, cooperation often allows greater system stability, a selective force that facilitates continuity via replication before degradation. (6)

Earth Life > Nest > Life Origin

Stubbs, Trent, et al. A Plausible Metal-free Ancestral Analogue of the Krebs cycle Composed Entirely of Alpha-ketoacids. Nature Chemistry. October, 2020. NSF-NASA Center for Chemical Evolution (Google) researchers including Greg Springsteen (Furman University) delve deeper into early biochemical phases so to reconstruct endemic ways that life’s emergent course could have plausibly taken place. Our late observance and accomplishment again implies a phenomenal fertility of an organically procreative ecosmos.

Efforts to decipher the prebiotic roots of metabolic pathways have focused on recapitulating modern biological transformations, with metals serving in place of cofactors and enzymes. Here we show that the reaction of glyoxylate with pyruvate under mild aqueous conditions produces a series of α-ketoacid analogues of the reductive citric acid cycle without the need for metals or enzyme catalysts. The transformations proceed in the same sequence as the reverse Krebs cycle, resembling a protometabolic pathway, with glyoxylate acting as both the carbon source and reducing agent. (Abstract excerpt)

Earth Life > Nest > Homo Sapiens

Roberts, Patrick and Brian Stewart. Defining the “Generalist Specialist” Niche for Pleistocene Homo Sapiens.. Nature Human Behavior. 2.542, 2018. . MPI Science of Human History and University of Michigan paleo-anthropologists suggest ways that a reciprocal combination of mental attention to detail, along with a capacity for wider scene views could explain why our (genius) genus arose and won out from an array of other candidates.

Definitions of our species as unique within the hominin clade have cited capacities for symbolism, language, social networking, technological competence and cognitive development. Recent thought has been turned towards humans’ unique ecological plasticity. Here, we review the growing archaeological and palaeo-environmental datasets relating to the Middle–Late Pleistocene (300–12 thousand years ago) dispersal of our species within and beyond Africa. We argue, in comparison with other members of the genus Homo, that our species developed a new ecological niche, that of a ‘generalist specialist’. Not only could a diversity of environments be occupied and utilized, but this mentality aided adaptations to some environmental extremes. (Abstract)

Earth Life > Sentience > Brain Anatomy

Roumazeilles, Lea, et al. Longitudinal Connections and the Organization of the Temporal Cortex in Macaques, Great Apes, and Humans. PLOS Biology. July, 2020. By way of advanced brain scan techniques, sixteen researchers based at Oxford University, Wellcome Centre for Integrative Neuroimaging and Radboud University, Donders Institute for Brain, Cognition and Behavior, are now able to compare neural architectures across the range of our primate forebears. Our philoSophia vista then wonders what kind of Ecosmic to Earthosmic course arduously evolves and develops to an intelligent, collaborative species whom altogether can reconstruct how they came to be. What is the nature and purpose of this “accumulated knowledge repository” (geonome?) which could serve to begin a better genesis co-creation?

The temporal association cortex is considered a primate specialization and is involved in complex behaviors such as language, a particular characteristic of humans. The emergence of these behaviors has been linked to major differences in temporal lobe white matter in humans compared with monkeys. It is unknown, however, how the organization of the temporal lobe differs across anthropoid primates. We systematically compared the organization of the major temporal lobe white matter tracts in the human, gorilla, and chimpanzee great apes and in the macaque monkey. We show that humans and great apes exhibit an expanded and more complex occipital–temporal white matter system. (Abstract excerpt)

A hominid is a member of the family Hominidae, the great apes: orangutans, gorillas, chimpanzees and humans. ... A human is a member of the genus Homo, of which Homo sapiens is the only extant species, and within that Homo sapiens sapiens is the only surviving subspecies. (Wikipedia)

Earth Life > Sentience > Animal Intelligence

Birch, Jonathan, et al. Dimensions of Animal Consciousness. Trends in Cognitive Science. August, 2020. We cite this contribution by London School of Economics and Cambridge University researchers including Nicola Clayton as a current example of how this long denied capacity for aware, knowing sentience is now commonly accepted and attributed to all manner of creatures.

Self-consciousness, or selfhood, is an awareness as distinct from the world outside. It involves registering a difference between self and other: some experiences as representing internal bodily events and others as events in an external world. Any complex, actively mobile animal needs a way of disentangling changes to its sensory input that are due to its own movements from changes due to the outside environs. (9)

Earth Life > Sentience > Animal Intelligence

Nieder, Andreas, et al. A Neural Correlate of Sensory Consciousness in a Corvid Bird. Science. 369/1626, 2020. By way of the latest neuroimaging abilities, University of Tubingen animal psychologists add proof that our feathered friends have quite an aware intelligence and behavioral repertoire. See also a commentary Birds do have a Brain Cortex and Think by Suzana Herculano-Houzel in the same issue. Once more the real presence of thoughtful, appropriate cognizance becomes evident. But all I really have to do is look out my window and witness clever blue jays frolicking at the bird bath.

Subjective experiences that can be consciously accessed and reported are associated with the cerebral cortex. Whether sensory consciousness can arise from differently organized brains that lack a layered cerebral cortex, such as the bird brain, remains unknown. We show that single-neuron responses in the pallial endbrain of crows performing a visual detection task correlate with the birds’ perception about stimulus presence or absence and argue that this is an empirical marker of avian consciousness. These results suggest that the neural foundations of sensory consciousness arose either before the emergence of mammals or independently in at least the avian lineage and do not necessarily require a cerebral cortex. (Abstract)

Earth Life > Individuality

Militello, Guglielmo, et al. Functional Integration and Individuality in Prokaryotic Collective Organisations. Acta Biotheoretica. August, 2020. IAS-Research Centre for Life, Mind and Society, University of the Basque Country biotheorists GM, Leonardo Bich and Alvaro Moreno find evidence of a vital relative selfhood even in this primal realm. One could then notice that while bacteria subsist in collective groupings, they yet each retain a reciprocal degree and measure of personal, semi-autonomous identity.

Both physiological and evolutionary criteria of biological individuality are based on the idea that an individual is an integrated whole. However, a good account of functional integration has not been provided so far. To address this, we focus on the organization of two representative associations of prokaryotes: biofilms and the endosymbiosis between prokaryotes. This paper has three aims: first, to analyse the organisational conditions and the physiological mechanisms that enable integration in prokaryotic associations; second, to discuss the differences between biofilms and prokaryotic endosymbiosis and the types of integration they achieve; finally, to provide a more precise account of functional integration based on these case studies. (Abstract excerpt)

In sum, functional integration can be defined as the degree to which the different components of a biological dynamic regime of self maintenance depend on one another for their production, maintenance, activity and reproduction. If we take the eukaryotic cell as the example of new forms of full fledged biological individuality by way of association between prokaryotes, individuality can be understood by the degree, scale and precision of the control and coordination of the parts that collectively make the system a viable functional whole. A cohesive integration between functional tasks is achieved, then, when the differentiation of functions is coordinated at the system level by control and regulatory mechanisms that (1) act across the entities in the association, and (2) are exerted in such a way that the components can contribute through their activity to the maintenance of the system. (22)

WumanKinder: An Emergent Earthomo Transition in Individuality

wumanomics > Integral Persons > Cerebral Form

Betzel, Richard. Network Neuroscience and the Connectomics Revolution. arXiv:2010.01591. An Indiana University neuroscientist (search) provides a concise tutorial for the revolutionary 2010s advance that our cerebral endowment displays an epitome of the nature’s universal multiplex, webby, informative topologies and dynamics. Since this cerebral anatomy and physiology is based on and is akin to genetic systems, it has been given an –omics identity (search S. Seung).

Connectomics and network neuroscience offer quantitative scientific frameworks for modeling and analyzing networks of structurally and functionally interacting neurons, neuronal populations, and macroscopic brain areas. This shift in perspective and emphasis on distributed brain function has provided deep insight into the role played by the brain's network architecture in cognition, disease, development, and aging. In this chapter, we review the core concepts of human connectomics at the macroscale. From the construction of networks using functional and diffusion MRI data, to their analysis using network neuroscience methods, so as to highlight key findings, common procedures, and emerging frontiers. (Abstract)

wumanomics > Integral Persons > Cerebral Form

Ju, Harang and Danielle Bassett. Dynamic Representations in Networked Neural Systems. Nature Neuroscience. 23/8, 2020. Akin to Muhua Zheng, et al below, University of Pennsylvania neuroscientists delve deeper into our cerebral endowment to find more consistent, layered repositories of knowing inputs and response. Each paper cites dozens of prior references as our collective, 21st project of retrospective self-quantification proceeds to reveal a macro-uniVerse to micro-wumanVerse familial correspondence.

Recent studies in neuroscience have begun to independently address the two components of information processing: the representation of stimuli in neural activity and the transmission of information in networks that model neural interactions. Yet only recently are studies seeking to link these approaches. Here we review the two separate bodies of literature; we next note progress made to join them. We then discuss how patterns of activity evolve from one representation to another, forming dynamic content that unfolds on the underlying network. Our goal is to offer a holistic framework for understanding and describing neural information representation and transmission along with exciting frontiers for future research. (Abstract excerpt)

wumanomics > Integral Persons > Cerebral Form

Lofti, Nastaran, et al. Statistical Complexity is Maximized Close to Criticality in Cortical Dynamics. arXiv:2010.040123. Nine Brazilian neuroscientists contribute to a growing notice that cerebral activity tends and prefers to reside in this optimum balance. See also Quasicritical Brain Dynamics by Leandro Fosque, et al at 2010.02938 and Testing the Critical Brain Hypothesis using a Phenomenological Renormalization Group by Giorgio Nicoletti, et al at 2001.04353 for further work.

Complex systems are typically characterized as an intermediate situation between a complete regular structure and a random system. Brain signals can be studied as a striking example of such systems: cortical states can range from highly synchronous and ordered neuronal activity to desynchronized and disordered regimes. It has been recently shown, by testing independent signatures of criticality, that a phase transition occurs in a cortical state of intermediate spiking variability. Here, we use a symbolic information approach to show that we can determine an intermediate state of maximum complexity based on the Jensen disequilibrium measure. We show that statistical complexity is maximized close to criticality for cortical spiking data, as well as for a network model of excitable elements at a critical point of a non-equilibrium phase transition. (Abstract excerpt)

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