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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 59 found.


Ecosmomics: A Survey of Animate Complex Network Systems

Cosmic Code > nonlinear > 2015 universal

Hidalgo, Jorge, et al. Information-based Fitness and the Emergence of Criticality in Living Systems. Proceedings of the National Academy of Sciences. 111/10095, 2014. We cite this entry by senior system theorists JH, Jacopo Grilli, Samir Suweis, Miguel Munoz, Jayanth Banavar and Amos Maritan (search each) as an early perception of life’s universal propensity to seek and reside at an optimum self-organized criticality. By 2020, a few years later, this section can now document its robust worldwide affirmation. In this time of great need, if we might mindfully allow and witness, here is a vital finding that a phenomenal nature prefers an active reciprocity of conserve/create, person/group and ever so on. Rather than totalitarian or anarchic extremes, me individual vs. We together politics, a salutary resolve going forward would be a middle way complementarity.

Recently, evidence has been mounting that biological systems might operate at the borderline between order and disorder, i.e., near a critical point. A general mathematical framework for understanding this common pattern, explaining the possible origin and role of criticality in living adaptive and evolutionary systems, is still missing. We rationalize this apparently ubiquitous criticality in terms of adaptive and evolutionary functional advantages. We provide an analytical framework, which demonstrates that the optimal response to broadly different changing environments occurs in systems organizing spontaneously—through adaptation or evolution—to the vicinity of a critical point. Furthermore, criticality turns out to be the evolutionary stable outcome of a community of individuals aimed at communicating with each other to create a collective entity. (Significance)

Cosmic Code > Genetic Info > Paleo/Cosmo

Frantz, Laurent, et al. Animal Domestication in the Era of Ancient Genomics. Nature Reviews Genetics. 21/8, 2020. Queen Mary University of London, Trinity College, Dublin, Oxford University, and University of Toulouse (Ludovic Orlando) paleogeneticists apply the latest advances in nucleotide recovery and sequencing ability to reconstruct, in this instance, the historic occasions by which many feral, native creatures were enjoined as beneficial hominid and human co-inhabitants. This long process, as readers know, led to much evolutionary modification, as cited and described in this paper.

The domestication of animals led to a major shift in human subsistence patterns from hunter–gatherers to a sedentary agricultural lifestyle. Over the past 15,000 years, the phenotype and genotype of multiple animal species, such as dogs, pigs, sheep, goats, cattle and horses, have been substantially altered during their adaptation to the human niche. Recent innovations such as improved ancient DNA extraction methods and next-generation sequencing, have enabled whole ancient genomes to be read. These genomes have helped reconstruct how animals entered into domestic relationships with humans and were subjected to selection pressures. Here, we discuss and update key concepts in animal domestication in light of these novel contributions. (Abstract)

Cosmic Code > Genetic Info > DNA word

Lackova, Ludmilla. Folding of a Peptide Continuum: Semiotic Approach to Protein Folding. Semiotica. 233/77, 2020. The Palacky University, Olomouc, CR linguist continues her studies of innate affinities across genetic, metabolic and onto communicative codes, which each seem to have a common textual nature. What then might be their phenomenal message as we first grade readers try to interpret, translate and understand?

In this paper I attempt to study the notion of “folding of a semiotic continuum” in a direction of a possible application to the biological processes (protein folding). The process of obtaining protein structures is compared to the folding of a semiotic continuum. Consequently, peptide chain is presented as a continuous line potential to be formed (folded) in order to create functional units. The functional units are protein structures having a certain usage in the cell or organism (semiotic agents). Moreover, protein folding is analyzed in terms of tension between syntax and semantics. (Abstract)

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Cohen, Irun and Assaf Marron. The Evolution of Universal Adaptations of Life is Driven by Universal Properties of Matter: Energy, Entropy and Interaction. F1000Research. July 30, 2020. While the olden neoDarwinian version of selection alone persists, Weizmann Institute of Science, Israel biomathematicans (search IC) contribute to a revolutionary genesis synthesis by viewing life’s oriented emergence as a complex dynamical process which involves not only objects, be they genes or animals, but equally real cooperative relations between them. I log this in along with a brain research paper (Harang Ju) which emphasizes a similar emphasis of neural interactions, and a symbiosis report (F. Prosdocimi) as another example of this pervasive entity/group mutuality. As a result, in each and all cases a whole, composite genome, connectome and regnant organism in community is thus achieved.

The evolution of multicellular eukaryotes expresses two sorts of adaptations: local aspects like fur or feathers, which serve species in bioregions, and universal adaptations like microbiomes or sexual reproduction, which distinguish multicellularity in any environment. We reason that the mechanisms which drive them should be universal, and based on properties of matter and systems: energy, entropy, and interaction. Energy from the sun creates complex arrangements while metabolic networks channel it to form cooperative interactions. Entropy, a term for disorder, acts as a selective force.

Dynamic Interactions restrain entropy and enable survival and propagation of integrated living systems. The “unit” of evolution is not a discrete entity what evolves are related interactions at multiple scales. Our “survival-of-the-fitted” can explain universal adaptations, including microbiomes, reproduction, diversification, altruism, environmental niches and more. We propose ways to test our theories, and implications for the wellbeing of humans and the biosphere. (Abstract excerpts)

Cooperative interactions are pervasive and central to life: We define an interaction as a relationship between two or more entities involving a transfer or exchange of matter, information and/or energy. Interactions include both struggle and cooperation: in a struggle, the participants each strive to win and dominate the others – who become the losers. In a cooperative interaction, there are no losers; the participants each gain some benefit, or at the least suffer no loss. (5)

Quickening Evolution

Schwartzman, David. Biological Evolution is Coarsely Deterministic. Journal of Big History. 4/2, 2020. This paper was presented by the veteran Howard University biologist at the Life in the Universe: Big History, SETI and the Future conference in Milan in July 2019. In essence, it continues his insightful views that “playing the tape over again” would necessarily lead to life’s development into human-like beings and cognitive capabilities because biochemical and thermal properties of the geobiosphere would again impel and channel it that way.

Starting with the origin of life, I argue that the general pattern of the tightly coupled evolution of biota and climate on Earth has been the very probable outcome from a relatively small number of possible histories at the macroscale, given the same initial conditions. Thus, the evolution of the biosphere self-selects a pattern of biotic evolution that is coarsely deterministic, with critical constraints likely including surface temperature as well as oxygen and carbon dioxide levels in the atmosphere. Environmental physics and chemistry drive the major events in biotic evolution, including photosynthesis and oxygenic photosynthesis, the emergence of new cell types (eucaryotes) from the merging of complementary metabolisms, multicellularity and even encephalization. (Abstract)

Quickening Evolution > Systems Biology

Gilpin, William, et al. Learning Dynamics from Large Biological Data Sets: Machine Learning Meets Systems Biology. Current Opinion in Systems Biology. July 30, 2020. As is the current case for many scientific fields, Harvard and Dartmouth researchers scope out ways by which a suitable apply of AI deep neural net techniques can effectively interface with life studies so to enhance research methods and results.

In the past few decades, mathematical models based on dynamical systems theory have provided new insight into diverse biological systems. In this review, we ask whether the recent success of machine learning techniques for large-scale biological data analysis can provide a complementary, beneficial approach to traditional modeling. Recent applications of machine learning have been used to study biological dynamics in diverse systems from neuroscience to animal behavior. We propose several avenues for bridging dynamical systems theory with large-scale analysis enabled by machine learning. (Abstract excerpt)

Taken together, these results introduce the question of whether universal mathematical constraints determine certain aspects of large biological systems whose interacting units spontaneously collapse onto a low-dimensional manifold. Has evolution driven complex biological networks toward these emergent motifs, and do they confer adaptive benefits such as stabilizing an ecosystem against an invasive predator, or suppressing unwanted fluctuations in a genetic circuit? We hope that further development of models at the intersection of machine learning and dynamical theory will provide unified insight into these questions. (6)

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

Earth Life > Common Code

Oborny, Beata. The Plant Body as a Network of Semi-Autonomous Agents. Philosophical Transactions of the Royal Society B. April, 2019. A Lorand Eotvos University, Budapest systems botanist shows how even life’s flora phase is distinguished and enabled by agent/link network modularities as they sense, process and convey vital information. See also Percolation Theory Suggests Some General Features Across Environmental Gradients by BO and Robert Juhasz at arXiv:1909.00585.

Plants can solve many difficult tasks while adjusting their growth and development to the environment. They can explore and exploit several resources, even when their distributions vary in space and time. Current research has found that the functional use of modular features enables the plant to adjust a flow of information and resources to ever changing conditions. Experiments have yielded many results about these processes but a theoretical model to encompass the high number of components and interactions has lagged behind. In this paper, I propose a framework on the basis of network theory, viewing the plant as a group of connected, semi-autonomous agents. I review some characteristic plant responses to the environment through changing the states of agents and/or links. (Abstract excerpt)

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

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 > Societies

Couzin, Iain. Collective Animal Migration. Current Biology. 28/17, 2018. The MPI Animal Behavior pioneer systems behavior researcher provides a good summary to date of this 21st century discovery of common dynamic phenomena across all manner of active, mobile organisms and their groupings from embryonic forms to aquatic, avian, herding and onto people on the move. See his lab website for a stream of collegial papers.

Migratory movement is a strategy employed by a broad range of taxa as a response to temporally and spatially varying environments. Migrating animals can often be seen to move together, sometimes in vast numbers. Despite this, the social aspects of migration have, to date, received very limited attention. Synchronisation of migratory behaviour among organisms, itself, does not imply that migrants utilize social information. However, as will be outlined here, there is there is growing evidence that many migratory animals do utilize social cues, and that collective factors could shape migration in a variety of important ways. (Abstract excerpt)

Earth Life > Nest > Societies

Deutsch, Andreas, et al. Multi-scale Analysis and Modelling of Collective Migration in Biological Systems. Philosophical Transactions of the Royal Society B. July, 2020. Senior complexity scientists AD, Technical University Dresden, Peter Friedl, Radboud University, Luigi Preziosi, Polytechnic University of Torino, and Guy Theraulaz, University of Toulouse introduce a special issue with this title. A full page graphic (second quote) depicts ten examples from neural maturation to cellular, insect, fish, bird and mammalian activities whence the same patterns and processes occur across this wide expanse. Some papers herein are An Agent-based Approach for Modelling Collective Dynamics in Animal Groups, Collective Migration during Early Development of Zebrafish, Collective Migration from the Wildebeest to the Neural Crest (search Shellard), Dynamic Heterogenity during Epithelial Wound Closure, and Collective Information Processing in Human Phase Separation (Jayles). As its 125 references span the 21st century, this 2020 synopsis can report the presence of an independent, mathematical source code program which universally iterates and exemplifies in vital kind everywhere. In regard, as a pandemic and other perils rage, we would do well to realize that an actual ecosmos uniVerse in our cognitive midst that is just being discovered by our worldwise EarthKinder.

Collective migration has become a paradigm for emergent, coherent behaviour in systems of moving and interacting individual units. Collective cell migration is important in embryonic tissue and organ development, as well as pathological processes, such as cancer invasion and metastasis. Animal group movements enhance individuals' decisions and aid navigation through environments. The articles in this theme issue on compile a range of mathematical models and multi-scale methods for the analysis of collective migration which uncover new unifying organization principles of collective behavior from individual to collective forms. As a common theme, self-organized collective migration is the result of ecological and evolutionary constraints both at the cell and organismic levels. (Abstract excerpt)

Figure 1, Collective migration in biological systems. (a) Collectively migrating neural crest cells in Xenopus embryos; (b) E-cadherin negative MMT cells invading three-dimensional fibrillar collagen; (c) collective migration of cancer cells in vitro (d) electronmicrograph showing the aggregate formed by seven sperm cells of the dear moue; (e) collective migration and aggregation by chemotaxis in the social amoeba;(f) a colony of termites on a march; (g) a migratory swarm of locusts; (h) a school of bigeye trevally Caranx sexfasciatus; (i) a flock of greater snow goose; (j) the great wildebeest migration in the Serengeti National Park.

Earth Life > Nest > Societies

Jayles, Bertrand, et al. Collective Information Processing in Human Phase Separation. Philosophical Transactions of the Royal Society B. July, 2020. In this same Collective Migration in Biological Systems issue, nine University of Toulouse researchers proceed to trace commonly recurrent people behavioral patterns all the way to deep physical phenomena. Our review issue introduction review (A. Deutsch herein) thus makes a proposal that in mid 2020, if of a mind to view and allow, a revolutionary genesis universe with its own genetic-like source code program has been well documented and explained.

In our digital societies, individuals interact through interfaces whose impact on collective dynamics can be important. In some contexts, segregation processes of human groups have been shown to share similarities with phase separation phenomena in physics. Here, we study the effect of information filtering on collective segregation behaviour of human groups. We introduce a model that describes the random motion of a group of pedestrians in a confined space, and which faithfully reproduces and allows interpretation of the results. (Abstract)

Earth Life > Nest > Societies

Shellard, Adam and Roberto Mayor. Rules of Collective Migration from the Wildebeest to the Neural Crest. Philosophical Transactions of the Royal Society B. July, 2020. In this Collective Migration in Biological Systems issue, University College London biologists go on to report, explain and depict life’s constant active groupings from self-propelled particles to bacteria, cancer and every Metazoan phylum. An especial point is the common affinity between early developmental processes and large herds on the move.

Collective migration, the movement of groups in which individuals affect the behaviour of one another, occurs at every scale from bacteria up to whole species' populations. Universal principles of collective movement can be applied at all levels. In this review, we describe the rules governing collective motility, with a specific focus on the neural crest, an embryonic stem cell population that undergoes extensive migration during development. We will discuss how the underlying principles of individual cell behaviour, and those that emerge from a supracellular scale, can explain collective migration. (Abstract)

Three rules of collective migration: Attraction: a behaviour that causes individuals to steer towards the centre of mass, which is the average position of individuals within a certain radius. Repulsion: a factor that causes individuals to steer away from all its neighbours. Alignment: a behaviour whence individuals line up with others close by, such that it moves with the averaged heading of the nearby individuals.

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 Computational 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, can compare neural architectures across the range of our primate forebears. Our philoSophia vista then wonders what kind of Ecosmic to Earthosmic course proceeds to arduously evolve an intelligent, collaborative species whom altogether can reconstruct how they came to be. What is the nature of this “accumulated knowledge repository” (geonome?) which could serve to begin a second genesis cocreation?

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 > 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)

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