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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
Recent Additions

Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 16 through 30 of 43 found.

Ecosmomics: A Survey of Genomic Complex Network System Sources

Cosmic Code > nonlinear > 2015 universal

Ayyad, Marouane and Saliya Coulibaly. The Cellular Automata Inside Optical Chimera States. Chaos, Solitons and Fractals. December, 2021. We note this entry by University of Lille, CNRS researchers as one example of how any natural phenomena seems to spontaneously seek and reside at optimum dynamic poise between more or less order.

Cellular automata are conceptual discrete dynamical systems useful in the theory of information. The spatiotemporal patterns that they produce are intimately related to computational mechanics in distributed complex systems. Here, we investigate their physical implementation in the framework of chimera states in which coherent and incoherent behavior coexist. Hence, chimera states were subject to quantitative and qualitative analyzes borrowing the same tools used to characterize cellular automata. Our results reveal the existence of cellular automata-type dynamics submerged in the dynamics exhibited by our optical chimera states. Thus, they share a panoply of attributes in terms of computational abilities.

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

Earth Life > Common Code

Ambika, G. and Jurgen Kurths. Tipping in Complex Systems. European Physical Journal Special Topics. 230/3177, 2021. Indian Institute of Science Education and Research and Potsdam Institute for Climate Research scholars introduce a topical issue with this subject title. A typical entry is Critical Transition Influenced by Dynamic Quorum Sensing in Nonlinear Oscillators by Paul Asir, et al. (search) From late 2021, one ought to note the worldwise extent to which such hyper-active nonlinear phenomena has become well quantified, yet an organic genesis reality that it implies has not been considered or brought into full benefit.

Many real-world complex systems are observed to undergo sudden transitions in their dynamical states or pattern of behavior and then they are said to tip from one emergent state to another. A few such transitions that can affect humanity in many ways are global changes in climate, earthquakes, hurricanes, abrupt shifts in ecosystems, blackouts in power systems, crashing of financial markets, psychological breakdowns, and surge of epidemics. They happen mostly due to small perturbations in the critical values of the system’s parameters or variables leading to large qualitative changes. (Abstract)

Earth Life > Nest > Microbial

Astacioa, Luis, et al. Closed Microbial Communities Self-Organize to Persistently Cycle Carbon. Proceedings of the National Academy of Sciences. 118/45, 2021. University of Illinois, Center for the Physics of Living Cells and University of Chicago, Center for the Physics of Evolving Systems researchers describe a robust tendency to spontaneously form a conserved set of metabolic processes. In regard, as the late Eshel Ben Jacob foresaw years ago, bacterial colonies can well serve as archetypal ecosystem exemplars.

Life on Earth depends on ecologically driven nutrient cycles to regenerate resources. Understanding how nutrient cycles emerge from a complex web of ecological processes is a central challenge in ecology. However, we lack model ecosystems that can be replicated, manipulated, and quantified in the laboratory, making it hard to quantify how changes in composition and the environment impact cycling. Enabled by a new high-precision method, we show that microbial ecosystems (CES) with only light self-organize can robustly cycle carbon. Our study helps establish CES as model biospheres for studying how ecosystems persistently cycle nutrients. (Significance)

Earth Life > Nest > Societies

Daniels, Byron, et al. Introduction to the Special Issue: Quantifying Collectivity. Theory in Biosciences. November, 2021. BD and Manfred Laubichler, ASU and Jessica Flack, SFI collect and survey past papers such as Informational Architecture across Non-living and Living Collectives by Hyunju Kim, et al and Tempos and Modes of Collectivity in the History of Life by Douglas Erwin.

Biological systems are diverse, ranging from tightly packed, highly integrated, many-body systems like eukaryotic cells to decentralized microbial biofilms, to relatively small primate groups with on the order of 100 behaviorally flexible individuals all the way to large, complex societies (both insects and human) and ecosystems. This range suggests there is variation in both how collective a system is as well as how it is collective.

Earth Life > Nest > Societies

Sinhuber, Raphael, et al. Self-organization in Natural Swarms od Synchronous Fireflies. Science Advances. 7/28, 2021. Biofrontiers Institute, University of Colorado biobehavior researchers including Orit Peleg provide a further sophisticated analysis via 3D perceptions of this coordinated phenomena which natural mathematic interactive rules organize. See also An Equation of State for Insect Swarms by Michael Sinhuber, et al in Nature Scientific Reports (11/3773, 2021.)

Fireflies flashing is a sure sign of animal collective behavior and biological synchrony. To elucidate synchronization mechanisms and inform theoretical models, we recorded the collective display of thousands of Photinus carolinus fireflies in natural swarms. At low firefly density, flashes appear uncorrelated. At high density, the swarm produces synchronous flashes within periodic bursts. Our results suggest that fireflies interact through a dynamic network of visual connections defined by terrain and vegetation. This model illuminates how a certain environment shapes self-organization and collective behavior. (Sarfati abstract excerpt)

Collective behaviour in flocks, crowds, and swarms occurs throughout the biological world. Animal groups are generally assumed to be adapted by evolution to achieve vital functions, so there is much interest for bio-inspired usages. Here we show that collective groups can be described by a thermodynamic framework and define a set of state variables and an equation of state for midge swarms. Our findings provide a new way of quantifying collective groups so to serve future bio-engineering design. (Sinhuber abstract excerpt)

Earth Life > Sentience

Cisek, Paul. Evolution of Behavioral Control from Chordates to Primates. Philosophical Transactions of the Royal Society B. December, 2021. In this special issue about rooting brain studies within life’s long oriented developmental stirrings from whence they arose, a University of Montreal neuro-researcher provides a comprehensive reconstruction from invertebrates to our emergent homo and anthropo (236 references) sapiens. All told, this paper, and the whole content, ought to be appreciated as an historic understanding of how our own cerebral and cognitive acumen naturally came to be. In regard, a full page graphic shows some 22 continuous stages from sponges and jellyfish to reptiles, birds, mammals to ourselves which complexifies, learns and quickens, and learns from earliest stirrings all the Metazoan way to such a global retrospective.

This article outlines a sequence of evolutionary innovations along the lineage that produced humans by which an extended behavioural control from simple feedback loops to diverse species-typical actions occurred. I begin with response mechanisms of ancient mobile animals and follow the major niche transitions from aquatic to terrestrial mammals, onto nocturnality, arboreal life and to diurnality. Along the way, I propose an elaboration and diversification of behavioural repertoires and their neuroanatomical substrates. (Abstract excerpt)

Figure 2. Phylogenetic tree of animals expanded along the lineage that produced humans. Branch points represent some of the key divergences between different lineages, with timing estimates based on the fossil record and molecular clock analyses. Thick lines indicate the presence of relevant fossil data (paleobiodb.org), and small rectangles indicate the latest estimated timing of the innovations listed in the boxes.

Earth Life > Sentience

Cisek, Paul and Ben Hayden. Neuroscience Needs Evolution. Philosophical Transactions of the Royal Society B. December, 2021. University of Montreal and University of Minnesota editors introduce 15 papers in a special Systems Neuroscience through the Lens of Evolutionary Theory issue, in advance of a March 2022 London meeting. But it opens by reminding that Evolution has no goal, no metric aside from the general problem of differential survival. Yet as the content review proceeds, this latest reconstruction of sensory neural capacities back to invertebrate origins well conveys an oriented advance of homologous “elaborations” which fill in, trace and reveal life’s oriented cerebral and cognitive development all the way to our Earthuman retrospect. Into these fraught, terminal 2020s, it is an imperative intent of this Natural Genesis site to help identify and resolve this ecosmic contradiction.

We note these typical entries: Scaffolding Layered Control Architectures through Constraint Closure by Stuart Wilson and Tony Prescott, Evolution of Behavioral Control from Chordates to Primates by Paul Cisek (see review and pg. 4 graphic), An Evolutionary Perspective on Chordate Brain Organization and Function by Thurston Lacalli (herein), Self-Tuition as an Essential Design Feature of the Brain by David Leopold and Bruno Averbeck, The Neuroecology of the Water to Land Transition and the Evolution of the Vertebrate Brain by Malcolm Maclver and Barbara Finlay, and The Evolution of Quantitative Sensitivity by Margaret Bryer, et al.

The nervous system is a product of evolution. As a result, the organization and functions of the brain must be shaped by its history. While not well assimilated into systems neuroscience, this vista can help resolve many mysteries. In this introduction, we survey specific ways that evolutionary theory can enhance cerebral studies. The rest of the theme issue will consider the conservative effect of evolution’s transitional course.

Earth Life > Sentience

Fitch, W. Tecumseh. Information and the Single Cell. Current Opinion in Neurobiology. Vol. 71, 2021. In a special Evolution of Brains and Computation issue, the University of Vienna linguist discusses Bacterial Chemotaxis, Attractant Gradients, Paramecium Associative Learning, and more whence life began to stir to its senses on the long course to our collaborative reconstruction. By this widest scan, our current advance toward global self-discovery could be the potential achievement that Earthuman, and Ecosmic life needs to achieve on her/his own.

Understanding the evolution of cognition involves the costs and benefits of cerebral computation. Thus we need to know neuronal circuitry in terms of information-processing efficiency. In regard, along with synaptic weights and electrochemical dynamics, neurons have multiple mechanisms including ‘wetware’ and cell morphology. Insights into non-synaptic information-processing can be gained by examining the quite complex abilities of single-celled organisms (‘cellular cognition’) which neurons also share. Cells provide the basic level at which information processing interfaces with gene expression. Understanding cellular computation should be a central goal of research on cognitive evolution. (Abstract excerpt)

Information and the single cell: Evaluating the costs and benefits of cellular computation requires approximate answers to a seemingly simple question: what is the information contained in a single neuron, and by what mechanisms is it stored and processed? There are at least five major information storage and processing systems within a cell: synaptic weights, electrochemical dynamics, protein phosphorylation, gene transcription, and cell morphology. Some are quite well-understood in computational terms, but others are relatively neglected, and available data allow only very rough estimates of information capacity. The following estimates are intended as order-of-magnitude values to give some relative sense of their potential relevance in evolution and not as precise quantitative estimates. (154)

This special issue of Current Opinion in Neurobiology addresses issues at the intersection of brain design, evolution and computation. With today’s considerable interest in the structure and function of neural circuits, it struck us that a shot of comparative perspectives might be timely and useful. The papers assembled in this issue thus address old and fundamental
questions, but in light of recent data in dominant and non-dominant experimental model systems, modern techniques (genomic, transcriptomic, computational, connectomics, etc.), and theoretical neuroscience. (Editors)

Earth Life > Sentience

Hulse, Brad, et al. A connectome of the Drosophila central complex reveals network motifs suitable for flexible navigation and context-dependent action selection. eLife. October, 2021. A nine person team at the Janelia Research Campus, Howard Hughes Medical Institute, Virginia, report and discuss novel abilities to sequence the neural architecture of such a minimal insect entity. Thus our collaborative neuroscience is able to reconstruct ever deeper origins from whence this worldwise Earthuman acumen arose. Once more a true genesis uniVerse reveals itself as a grand learning process, which seems potentially on the way to its own vital acknowledge.

Flexible behaviors over long timescales are thought to engage neural networks in deep brain regions, which are often difficult to study. In insects, recurrent circuit dynamics in a brain region called the central complex enable directed locomotion, sleep, and context- and experience-dependent spatial navigation. We describe the first complete electron-microscopy-based connectome of the Drosophila CX. We also identified numerous pathways that may facilitate the selection of CX-driven behavioral patterns by their internal state. Our results provide a comprehensive brainscape mapping by which to understand network dynamics underlying sleep, flexible navigation, and state-dependent action selection. (Abstract excerpt)

Earth Life > Sentience

Leopold, David and Bruno Averbeck. Self-tuition as an Essential Design Feature of the Brain. Philosophical Transactions of the Royal Society B. December, 2021. National Institute of Health, Bethesda neuro-researchers provide a novel vista whereby cerebral faculties, as they form, arise, evolve in both ontogeny and phylogeny, have a primary impetus and need to gain relevant knowledge. In regard, life’s long ascent can thus appear as a processive, cumulative learning and educative advance.

We are curious by nature, particularly when young. Evolution has endowed our brain with an innate obligation to educate itself. In this review, we posit that self-tuition is an evolved principle of basic brain architecture and its normal development. We consider hypothalamic and telencephalic structures along with their anatomic segmentation architecture of forebrain circuits. We discuss educative behaviours, stimulus biases, and mechanisms by which telencephalic areas gradually accumulate knowledge. We argue that this aspect of brain function is of paramount importance for systems neuroscience, as it confers neural specialization and allows animals to attain more sophisticated behaviours than genetic mechanisms alone. (Abstract excerpt)

We posit that the vertebrate forebrain has evolved to support an interplay between brain areas that drives its own education based on a curiosity-driven exploration of the environment. We refer to this process as self-tuition. (1)

Earth Life > Sentience

Whiten, Andrew, et al. The Emergence of Collective Knowledge and Cumulative Culture in Animals, Humans, and Machines. Philosophical Transactions of the Royal Society B. December, 2021. University of St. Andrews, Oxford, Sorbonne, and Edinburgh editors introduce a special issue of 18 papers in advance of a Royal Society meeting in March 2022. The event (Google) is being held because these two subject fields now appear to be converging into a common, reinforcing synthesis. Typical entries are Human Cumulative Culture and the Exploitation of Natural Phenomena, When does Cultural Evolution become Cumulative Culture, Paradox of Diversity in the Collective Brain and The Origins of Human Cumulative Culture: From Foraging Niche to Collective Intelligence, by notables such as Ida Momennejad, Michael Tomasello and Simon Kirby (search each). St. Andrews was founded in 1413. Some six centuries later, may a worldwise sapiensphere at last close on itself so to reach a grand discovery of wuman and uniVerse?

The goal of this themed issue and meeting is to review and join the title topics whose research fields which have coalesced in recent years. One aspect is concerned with collective action, intelligence and knowledge among groupings which is much more is than any one alone. Some prior notations are consensus decision-making, quorum sensing, wisdom of the crowd, collective brain, group cognition and extended mind. The second interest covers the evolutionary emergence and evolution of their cultural content - the creation and spread of social traditions through communal learning processes. Culture has long been seen as a defining feature of humans. Yet, recent research has have revealed that intergroup culture plays a significant role for many vertebrate taxa and onto invertebrate insects. (Introduction excerpt)

Earth Life > Sentience > Evolution Language

Kirby, Simon and Monica Tamariz. Cumulative cultural evolution, population structure and the origin of combinatoriality in human language. Philosophical Transactions of the Royal Society B. December, 2021. In this special Emergence of Collective Knowledge and Cumuulative Culture issue, University of Edinburgh and Heriot-Watt University, Edinburgh linguists post their latest views on how effective communication arose by way of an increasing ability of speakers to join utterances and their content in more complex, meaningful ways.

Language is the primary repository and mediator of human collective knowledge. A central question for evolutionary linguistics is the origin of the combinatorial design structure of language. We consider that combinatoriality is the inevitable result of learning biases in cultural transmission, and that population structure explains differences across languages. We employ Bayesian learning agents with a prior preference for compressible languages which communicate in pairs to reduce ambiguity. Results suggest that (1) combinatoriality emerges during iterated cultural transmission under concurrent pressures for simplicity and expressivity and (2) population dynamics affect the rate of evolution, which is faster when agents learn from other learners. (Abstract excerpt)

Earth Life > Individuality

Jaeger, Johannes. The Fourth Perspective: Evolution and Organismal Agency. Mossio, M. ed. Organization in Biology. Berlin: Springer, 2022. A Complexity Science Hub, Vienna bioscholar and 2021 co-author herein with A. Roli and S. Kauffman contributes to growing perceptions that one’s own life, and indeed evolution’s long course, can be defined and tracked by an increasing degree of proactive, self-made individuality. (As P. Teilhard wrote long ago Someone is in Gestation). As these findings flow together, they reveal a true ecosmic genesis which brings personal beings and becomings in community into manifest reality.

This chapter examines the deep connections between biological organization, agency, and evolution by natural selection. But I contend here that the basic unit of evolution is not a genetic replicator, rather it is a complex hierarchical life cycle. Understanding the self-maintaining and self-proliferating properties of evolvable reproducers thus requires an organizational account of ontogenesis and reproduction. This leads us to an extended set of minimal conditions such as new principles of heredity, variation, and ontogenesis. An important result is that all evolvable systems are active agents. Novel appreciations of an agential evolutionary perspective on evolution can then complement and succeeding existing structural, functional, and processual approaches. (Abstract excerpt)

Earth Life > Individuality

Roli, Andrea, et al. How Organisms Come to Know the World: Fundamental Limits on Artificial General Intelligence. OSF Preprints. November 4, 2021. AR, University of Bologna, Johannes Jaeger, Complexity Science Hub, Vienna and Stuart Kauffman, Institute of Systems Biology, Seattle polyscholars (search each) claim that while advances in AGI continue to be made, it will be unable to match human intelligence due to its algorithmic machine basis. In contrast, biological beings possess an individual agency which conceive active “affordances” in response to variable situations and environments. As Stuart K. advises, our lives move forward into an “adjacent possible.” These behaviors are beyond any AGI, and their evolutionary occasion can track an emergent personal autonomy. That is to say, organic entities have far more engagement with their own life course. As other current works such as The Evolution of Agency by Michael Tomasello (MIT, 2022) attest, a wider, ontogenetic passage from UniVerse to WumanVerse can well be seen as a proactive, self-making individuation. (See also The Third Transition in Science: A Statistical Mechanics of Emergence by Kauffman and Roli at arXiv:2106.15271).

Artificial intelligence AI has made tremendous advances since its inception in the 1950s. However, there are now significant obstacles on this path. General intelligence involves situational reasoning, taking perspectives, choosing goals, and dealing with ambiguous information. Here we note that such characteristics involve an ability to identify and engage new affordances or opportunities as an agent seeks to live forward, which cannot be treated algorithmically. Thus only organisms can do this. Our inferential view also has important consequences for evolutionary theory.. We argue that organismic agency is required for open-ended evolution through radical emergence. (Abstract excerpt)

These insights limit what mechanistic science and engineering can understand and achieve when it comes to agency and evolutionary innovation. This affects the study of any kind of agential system in computer science, biology, the social sciences and onto ecosystems or the economy. In these areas, any formal approach will remain incomplete. This has repercussions for the philosophy of science with respect to learning about the world. If it is divided into a finite set of categories, it is difficult to see altogether and beyond. The evolution of scientific knowledge is then not entailed by no law. (19)

In regard, what would a “meta-mechanistic” science look like? Its concepts and methods are only now being elaborated. But for it will be moved to take agency seriously. It will allow a teleological behavior that is rooted in the self-referential closure of organization in living systems. It is naturalistic but not reductive. Goals, actions, and affordances are emergent properties of organismal agents and their relations to the world of meaning they live in. This radical ascendancy will go beyond predetermined ontologies as it moves into the adjacent possible. This novel worldview could then be seen as a 2020s semblance of r Alfred North Whitehead's philosophy of organism (1929). It sees the world less as a clockwork, and more like an evolving ecosystem, whence open creativities are centered around beneficial affordances. (20)

OSF Preprints is a free, open source web application that connects and supports an active research workflow so to help scientists to increase the efficiency and effectiveness of their research. Researchers use OSF to collaborate, document, archive, share, and register research projects, materials, and data.

Our Earthuman Moment: A Major Evolutionary Transition in Individuality

wumanomics > Integral Persons > Cerebral Form

Lynn, Christopher, et al. Broken Detailed Balance and Entropy Production in the Human Brain. PNAS. 118/47, 2021. We cite this technical exercise by CCNY, Princeton, and University of Pennsylvania researchers including Danieile Bassett because it is able to connect our cerebral functions all the way to a complex physical basis. With this in place, a wider creative presence is noted across natural and societal phenomena.

To perform biological functions, living systems must break detailed balance by consuming energy and producing entropy. At microscopic scales, broken detailed balance enables a suite of molecular and cellular functions, including computations, kinetic proofreading, sensing, adaptation, and transportation. But do macroscopic violations of detailed balance enable higher-order biological functions, such as cognition and movement? To answer this question, we adapt tools from nonequilibrium statistical mechanics to quantify broken detailed balance in complex living systems. (Significance)

More generally, we remark that the methods not only apply to the brain, but can be broadly used to investigate broken detailed balance in other living systems, including emergent behavior in human and animal populations, correlated patterns of neuronal firing, and collective activity in molecular and cellular networks. (5)

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