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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 16 through 30 of 46 found.


Ecosmomics: A Survey of Animate Complex Network Systems

Cosmic Code > Genetic Info > Genome CS

Misteli, Tom. The Self-Organizing Genome: Principles of Genome Architecture and Function. Cell. 183/1, 2020. The veteran Swiss-American systems biologist (search) is director of the NIH Center for Cancer Research. This paper describes a confirmation of his collegial 21st century project to reconceive life’s genetic and cellular phases by way of a primary self-organization. As the quotes say, this intrinsic developmental process is not random happenstance but a guided process which results in a reliable array of forms, units and features. A further significant finding is that even genetic phenomena can be seen to reach and take on a critical balance of conserved, stable states along with creative responses to external changes. We add several quotes for this consummate achievement.

Genomes have complex three-dimensional architectures. The recent convergence of genetic, biochemical, biophysical, and cell biological methods has uncovered several fundamental principles of genome organization. They highlight that genome function is a major driver of genome architecture and that structural features of chromatin act as modulators, rather than binary determinants, of genome activity. The interplay of these principles in the context of self-organization can account for the emergence of structural chromatin features, the diversity and single-cell heterogeneity of nuclear architecture in cell types and tissues, and explains evolutionarily conserved functional features of genomes, including plasticity and robustness. (Abstract)

An important realization from these studies has been that the organization of genomes is characterized by a high degree of order and non-randomness. An overt example is the physical segregation of transcriptionally active euchromatin from repressed heterochromatin into distinct regions in the cell nucleus of most eukaryotic cells. Other non-random features of genomes include the formation of chromatin domains and the positioning of genes to preferred locations within the nuclear space. In addition to the genetic material, many proteins are non-randomly distributed in the nucleus and are concentrated in sub-nuclear bodies. These observations highlight a considerable degree of order and non-randomness in genome organization. (28)

As outlined above, genomes are characterized by a high degree of order represented by ubiquitously conserved architectural features, such as chromatin loops, domains, and nuclear bodies, as well as by non-random patterns, such as the location of genes and chromosomes in 3D space. In addition, the transcriptional program of a given cell is stable and defines its overall state. (35)

At the same time, genome organization and gene expression are also highly dynamic, variable, and stochastic. How can these two apparently conflicting aspects of genome organization — steady-state stability and intrinsic variability — be reconciled? One hint comes from the realization that the major characteristics of genome organization, including a dynamic, stable steady state and a high degree of heterogeneity and variability, are hallmarks of a self-organizing system. The principle of self-organization is ubiquitous in nature and, when applied to the genome, provides a unifying mechanism to account for many of its structural and functional features. (35)

With the realization that genome architecture is an emergent property of a self-organizing system, the next phase of studying the genome is now upon us. (42)

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Aria, Cedric. Macroevolutionary Patterns of Body Plan Canalization in Euarthropods. Paleobiology. October, 2020. A University of Toronto biologist meticulously analyzes datasets for these diverse invertebrates as they appeared in the prolific Cambrian era (~540 my ago). He concludes that their swift rise was mostly due to the buildup of genetic regulatory networks. See also Early Fossil Record of Euarthropoda and the Cambrian Explosion by Allison Daley, et al in PNAS (115/5325, 2018.)

Quickening Evolution > major

Rafiqi, Matteen, et al. Origin and Elaboration of a Major Evolutionary Transition in Individuality. Nature. 585/239, 2020. As the abstract cites, McGill University, Montreal and Bezmialem Vakif University, Istanbul biologists discuss how the latest detailed studies of morphogenetic forms and processes are revealing the innate, persistent ways that a natural genesis proceeds toward further scalar levels of organismic complexities. An elaborate graphic display depicts a course for bacterial symbiotic integration.

Obligate endosymbiosis, in which distantly related species integrate to form a single replicating individual, represents a major evolutionary transition in individuality. Although such transitions are thought to increase biological complexity, the evolutionary and developmental steps that lead to integration remain poorly understood. Here, we show that obligate endosymbiosis between the bacteria Blochmannia and the hyperdiverse ant tribe Camponotini originated and elaborated through radical alterations in embryonic development, as compared to other insects. By this example and others, we find that the convergence of pre-existing molecular capacities and ecological interactions—as well as the rewiring of highly conserved gene networks—may be a general feature that facilitates the origin and elaboration of major transitions in individuality. (Abstract excerpts)

We therefore propose that other major transitions in individuality may originate and also elaborate through the rewiring of highly conserved gene regulatory networks, as well as by exploiting pre-existing molecular or developmental capacities and ecological interactions. (243)

Quickening Evolution > major

Warrell, Jonathan and Mark Gerstein. Cyclical and Multilevel Causation in Evolutionary Processes. Biology & Philosophy. 35/Art.50, 2020. Yale University computational biophysicists and geneticists (search MG) post a 36 page careful consideration of how novel machine learning techniques and models seem able to gain deeper insights about into life’s structured developmental advance, better ways to understand and mitigate diseases and a sense of identities.

We develop here a general theoretical framework for analyzing evolutionary processes drawing on recent approaches to causal modeling developed in the machine-learning literature, which have extended Pearls do-calculus to incorporate cyclic causal interactions and multilevel causation. We show how our causal framework helps to clarify conceptual issues in the contexts of complex trait analysis and cancer genetics, including assigning variation in an observed trait to genetic, epigenetic and environmental sources in the presence of epigenetic and environmental feedback processes, and variation in fitness to mutation processes in cancer using a multilevel causal model respectively. Finally, we consider the potential relevance of our framework to biology and evolution, including supervenience, multilevel selection and individuality. (Abstract excerpt)

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 > 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

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 > 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)

Earthomo Sapiens: An Emergent 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

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)

wumanomics > Integral Persons > Conscious Knowledge

Aru, Jaan, et al. Cellular Mechanisms of Conscious Processing. Trends in Cognitive Sciences. September, 2020. By virtue of the latest theories and techniques, Humboldt University of Berlin neurobiologists advance ways that human awareness can be associated with and seen to arise from intrinsic, complex neuronal properties and interactivities. Might one imagine a quickening ecosmos is stirring and awakening into its own perceptive sentience?

Recent breakthroughs in neurobiology can help us understand how cellular-level mechanisms are related to conscious experience. Here, we study the biophysical properties of pyramidal cells which allow them to act as gates that control the evolution of global activation patterns. In conscious states, this cellular mechanism enables complex sustained dynamics within the thalamocortical system, whereas during unconscious states, such signal propagation is prohibited. We then suggest that conscious processing is the flexible integration of bottom-up and top-down data streams at the cellular level. This cellular integration mechanism provides the foundation for Dendritic Information Theory, a novel neurobiological theory of consciousness. (Abstract)

Apical Compartment: part of the pyramidal cell toward the surface of the cortex. It integrates contextual information from the corticocortical and thalamocortical loops. Basal compartment: part of the pyramidal cell around the cell body including the basal dendrites that controls the spike output of the cell. The basal compartment mainly receives feature specific information. (Glossary, 2)

These two information streams could also be seen as the first-order representation in the basal compartment and the higher order representation in the apical compartment. Hence, this cellular mechanism within the L5p cells could lay the foundation for higher order theories of consciousness. In summary, the architecture and biophysical properties of the L5p cells enable flexible integration of segregated data streams. Here we point out that the segregation and integration of data streams within a pyramidal neuron are conceptually fundamental and render cognitive, high-level, or global descriptions. Dendritic integration of segregated data streams might be the defining characteristic of conscious processing. (9)

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