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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 31 through 45 of 56 found.

Life's Corporeal Evolution Develops, Encodes and Organizes Itself: An EarthWinian Genesis Synthesis

Quickening Evolution

Noble, Denis and Raymond Noble.. Understanding Living Systems.. Cambridge: Cambridge University Press, 2023. The esteemed octogenarian British brothers continue on message that a fixation on genes and mutation only is quite misguided, out of date and should be replaced such as Philip Ball does in his 2023 work How Life Works: A User’s Guide to the New Biology (herein).

Life is definitively purposive and creative. This book presents a paradigm shift in understanding living systems where the genome is not a code, blueprint or set of instructions. The authors show that gene-centrism misrepresents what genes are and how they are used by living systems. In fact, organisms make choices, influence their behaviour, development and evolution, and act as agents of natural selection. Reading this book will make you see life in a new light as a marvellous phenomenon.

Denis Noble is a British physiologist and biologist who held the Burdon Sanderson Chair of Cardiovascular Physiology at the University of Oxford from 1984 to 2004. Noble established The Third Way of Evolution project with James Shapiro which predicts that the entire modern synthesis will be replaced. Raymond Noble is Honorary Associate Professor at University College London.

Quickening Evolution > Systems Biology

Daryakenari, Nazanin, et al.. AI-Aristotle: A physics-informed framework for systems biology gray-box identification.. PLoS Computational Biology. February, 2024. We cite this work by Brown University mathematicians for its leading edge use of computational methods with a physical basis for improved quantifications of active natural phenomena. Into the 2020s, a spiral synthesis like this can define a global integrative phase of scientific endeavors.

Discovering mathematical equations that govern physical and biological systems is a fundamental challenge in scientific research. We present a new physics-informed framework for parameter estimation in the field of Systems Biology. The proposed framework—named AI-Aristotle—combines the eXtreme Theory of Functional Connections (X-TFC) domain-decomposition and Physics-Informed Neural Networks (PINNs) with symbolic regression (SR).. To test the performance of AI-Aristotle, we use sparse synthetic data perturbed by uniformly distributed noise. More broadly, our work provides insights into the accuracy, cost, scalability, and robustness of integrating neural networks with symbolic regressors, offering a comprehensive guide for researchers tackling gray-box identification challenges in complex dynamical systems in biomedicine and beyond. (Excerpt)

Quickening Evolution > Nest > Life Origin

Fairchild, Jaspar, et al. Prebiotically plausible chemoselective pantetheine synthesis in water. Science. 383/911, 2024. In a paper that made science news, University College London biochemists including Matthew Powner report that they were able to explain how this unique intermediary compound came into existence on cue so as to complement a vital biochemical regimen so that protocellular metabolisms could proceed on their lively way.

Coenzyme A (CoA) is essential to life and its functional subunit, pantetheine, is vital to origin-of-life scenarios, but how pantetheine (a cysteamine amide analog of pantothenic acid = vitamin B5) emerged on the early Earth remains a mystery. In this work, we report high-yielding and selective prebiotic syntheses of pantetheine in water. Chemoselective multicomponent aldol, iminolactone, and aminonitrile reactions delivered spontaneous differentiation of pantoic acid and proteinogenic amino acid syntheses. Our results are consistent with a role for canonical pantetheine at the outset of life on Earth. (Excerpt)

Quickening Evolution > Nest > Life Origin

Papastavrou, Nikolaos, et al.. RNA-catalyzed evolution of catalytic RNA. PNAS. 121/11, 2024. Salk Institute of Biological Studies geneticists including its director Gerald Joyce are now able to discern a pathway by which this crucial nucleotide molecule could shape up, have the necessary capacities so as to propel living systems going on their evolutionary way. See also Prebiotic Astrochemistry from Astronomical Observations and Laboratory Spectroscopy by Lucy Ziurys in the Annual Review of Physical Chemistry (Volume 75, 2024.)

An RNA polymerase ribozyme obtained by directed evolution can propagate a functional RNA through repeated rounds of replication and selection. Earlier versions did not have sufficient copying fidelity, but an improved variant can now replicate the hammerhead ribozyme through a reciprocal synthesis. Two evolutionary lineages were carried out using either the prior low-fidelity or the newer high-fidelity polymerase. Deep sequencing followed the course of evolution, revealing variants that diverged from as fitness increased. This study demonstrates the critical importance of replication fidelity for maintaining heritable information in an RNA-based evolving system, such as is thought to have existed during the early history of life on Earth. (Abstract)

Quickening Evolution > Nest > Life Origin

Purvis, Graham, et al. Generation of long-chain fatty acids by hydrogen-driven bicarbonate reduction in ancient alkaline hydrothermal vents. Communications Earth & Environment. 5/30, 2024. Newcastle University paleobiochemists quantify how another vital complexity stage came to readily occur. Once again our Earthuman retrospective scenario from prebiotic sources onto replicative protocells indeed takes on a robust guise of a natural endemic fertility.

The origin of life at some point required membrane-bound compartments to foster the separation and concentration of internal biochemistry from the external environment. Long-chain amphiphilic molecules, such as fatty acids, appear good candidates to have formed the first cell membranes. Here we show that the reaction of dissolved hydrogen and bicarbonate with the iron-rich mineral magnetite under conditions of continuous flow, alkaline pH and simple low temperatures (90 °C) generate a range of long-chain aliphatic compounds. Readily generated membrane-forming amphiphilic organic molecules in the first cellular vesicles may have been driven by similar chemistry generated from the mixing of bicarbonate-rich water with alkaline hydrogen-rich fluids. (Abstract)

Quickening Evolution > Nest > Life Origin

Walton, Craig, et al. Cosmic dust fertilization of glacial prebiotic chemistry on early Earth. arXiv:2402.12310. ETH Zurich. Cambridge University, Oxford University, University of Bergen and Open University, UK including Oliver Shorttle make a latest case that an interstellar medium suffused with biomaterials shed from exoplanets may well have showered our own planet with vital missing reagents,

Earth's surface lacks many elements considered necessary for prebiotic chemistry. In contrast, extraterrestrial rocky objects are rich in these ingredients and may have delivered them as exogenous material. Today, the flux of extraterrestrial matter to Earth is made up of fine-grained cosmic dust deposits due to the action of sedimentary processes. We study dust formation and planetary accretion to show that localized deposits could have accumulated in arid environments on early Earth. Our results challenge the widely held assumption that cosmic dust is incapable of fertilizing prebiotic chemistry. (Abstract)

Quickening Evolution > Nest > Microbial

Bridges, Alice, et al.. Bumblebees socially learn behaviour too complex to innovate alone. Nature. March, 2024. Seven social biologists mainly at Queen Mary University of London including Lars Chittka demonstrate ways to extend life’s prevalent impetus for collaborative, informed societies all the way to invertebrate insects.

Culture refers to behaviours that are commonly learned and persist within a population over time. It has been found that animal culture can also be cumulative. Here we show that even bumblebees can learn from trained demonstrator bees to obtain food rewards, even though they fail to do so on their own. This suggests that social learning might permit the acquisition of behaviours too complex to ‘re-innovate’ through individual learning. (Excerpt)

Quickening Evolution > Nest > Societies

Gorbonos, Dan, et al. Geometrical Structure of Bifurcations during Spatial Decision-Making. PRX Life. 2/1, 2024. In this new Physical Review journal, DG and Iain Cousin, MPI Animal Behavior, and Nir Gur, Weizmann Institute of Science add a further technical finesse about how creaturely movements keep their assemblage and perform so well. Rapid internal responses are seen to imply a statistical physics spin model along with an active particle coherence.

Animals must constantly make decisions on the move among multiple options. Here we model this process to explore how its dynamics accounts for branching trajectories exhibited by animals during spatial decision-making, and to provide new insights into spatiotemporal computation. Our analysis reveals the nature of the spontaneous symmetry breaking bifurcations in trajectory space and new geometric principles for spatiotemporal decision-making. This suggests that a non-Euclidean neural representation of space may be expected to have evolved across species in order to facilitate spatial decision-making. (Excerpt)

These results highlight the richness of this spin model, where movement through space is determined by spin-spin interactions, which are in turn dependent on the position of the animal or group with respect to the targets. The model has a broader theoretical physics perspective due to its coupling of equilibrium spin dynamics and propulsion of active-matter particles, as well as its connection to general research on decision-making in moving agents. (10)

Quickening Evolution > Nest > Societies

Herbrich, Maxime, et al. Network nestedness in primates: a structural constraint or a biological advantage of social complexity?. arXiv:2402.13658. Université de Strasbourg, Utrecht University, University of Agder, Norway, University of Greenwich, UK, Leibniz Institute for Primate Research, Göttingen, University of Konstanz, Smithsonian Tropical Research Institute, Kyoto University, University of Lausanne, and Inkawu Vervet Project, South Africa animal behaviorists join field work with theoretic studies to conclude that external environs have a larger role than somatic or neural aspects.

This study investigates the prevalence of nestedness within primate social networks by its relationship with cognitive and structural factors. We studied 51 primate groups across 21 species to evaluate nestedness, modularity, neocortex ratio, and group size. We found a significant occurrence of this multiplex feature exceeding chance expectations. Our analysis showed little correlation with neocortex ratio or group size, which suggests a greater role for ecological factors in cognitive evolution. Overall, our research provides new insights into primate social network structures by way of complex interplays between network geometries. (Excerpt)

Quickening Evolution > Nest > Ecosystems

Enquist, Brian, et al. Scaling approaches and macroecology provide a foundation for assessing ecological resilience in the Anthropocene. Philosophical Transactions B. April, 2024. Senior environmental theorists BE, University of Arizona, Doug Erwin, National Museum of Natural History and Van Savage and Pablo Marquet, Santa Fe Institute make a case for wider perspectives as a better way to study, analyze and manage flora and fauna biotas because of their multiple complexities.

In the Anthropocene, intensifying ecological disturbances challenge our predictive capabilities for ecosystem responses. A macroecology of emergent statistical patterns in ecological systems can find consistent regularities in biodiversity and ecosystems by way of abundance, body size, geographical range, species interaction networks, or the flux of matter and energy. We suggest a conceptual and theoretical basis for ecological resilience that integrates macroecology with a stochastic diffusion approximation constrained by principles of biological symmetry. We show how our framework can quantify major disturbances and their extensive ecological ramifications. (Excerpt)

Life’s Cerebral Cognizance Becomes More Complex, Smarter, Informed, Proactive, Self-Aware

Earth Life > Intelligence

Reber, Arthur, et al. The CBC theory and its entailments: Why current models of the origin of consciousness fail.. EMBO Reports. 25/1, 2023. AR, University of British Columbia, William B. Miller, physician philosopher, Predrag Slijepcevic, University of Brunel, London and František Baluška, University of Bonn post their latest version of the CBC (Cellular Basis of Consciousness) which contends that sentient awareness is necessarily so pervasive and essential that its presence is evident at this basic metabolic level. See also All biology is cognitive information processing by WBM, et al in Progress in Biophysics and Molecular Biology. (182, September 2023) and The Sentient Cell: The Cellular Foundations of Consciousness by Arthur Reber, et al ( Oxford Press, 2023).

Accumulating scientific discoveries support the need for a revised Central Dogma to revise evolutionary biology's fixation on a Neodarwinian canon. Our reformulated version is that all biology is cognitive information processing based on the recognition that life is the self-referential state instantiated within the cellular form. Self-referential cells act to sustain themselves and to do so must be in harmony with their environment. Consequently, effective cellular problem-solving is information processing and management. As the internal measurement by cells of information is self-referential by definition, self-reference is biological self-organization, underpinning 21st century Cognition-Based Biology. (Excerpt)

Earth Life > Brain Anatomy > Bicameral Brain

Quin-Conroy, Josephine, et al.. Patterns of language and visuospatial functional lateralization and cognitive ability. Laterality. September, 2023. University of Western Australia linguists contribute a latest quantified affirmation of nature’s archetypal hemispheric preferences. Once again we wonder however these verse and vision complements could be known well enough such that they might apply to political parties.

For most individuals, language is predominately localized to the left hemisphere of the brain and visuospatial processing to the right. Evolutionary theories of lateralization suggest that this typical pattern is most common as it delivers a cognitive advantage. In contrast, deviations from the typical pattern may lead to poorer cognitive abilities. The aim of this systematic review was to assess the evidence for an association between patterns of language and visuospatial lateralization and measures of cognitive ability. (Excerpt).

University of Western Australia Just 10 minutes from Perth city, UWA is located on the banks of the Swan River on the land of the Whadjuk Nation. We have the privilege of being on sacred soil where Western Australian kaartdijin, or knowledge, began. It has been a place to gather and learn for tens of thousands of years by the world’s oldest continuous culture.

Earth Life > Individuality

Mitchell, Kevin. Free Agents: How Evolution Gave Us Free Will. Princeton: Princeton University Press, 2023. The author, a neuro-geneticist at Trinity College Dublin, studies the many relationships between genes, brains, and minds on both individual and evolutionary levels. Into these 2020s he has prepared the first whole book length treatment for the leading edge content of this Life’s Cerebral Cognizance Becomes More Complex, Smarter, Informed, Proactive, Self-Aware chapter. In so doing, the work describes an oriented encephalization from sensory stirrings to scales of ramified neural complexities all the way to our mosaic neocortex. A central track becomes evident as an increasing adaptive behavior with regard to one’s own life, group and environs. In retrospect, life’s cerebral/cognitive evolutionary course can then be seen to assert a liberated agency of personal choice. The vital message (my take) from brains instead of bones could be that we peoples can rise from sinners to winners, avoid nuclear war, and proceed to select ourselves as a unified Earthropocene success.

Scientists are finding how brain activity controls behavior and neural circuits effect actions. But many still conclude that agency—or free will—is an illusion. Free Agents presents a wealth of evidence to the contrary, arguing that we are not mere machines but distinct selves empowered with purpose. Across Earth’s long evolution, Mitchell describes how living beings capable of choice arose from physical origins. As nervous systems came to be, they gave sentient animals the capacity to model, predict, and simulate. These faculties have reached their peak with our human abilities to imagine, introspect, reason and view possible futures. {Publisher)

A purely reductionist, mechanistic approach to life misses the point. On the contrary, basic laws of physics that deal only with energy and matter and forces cannot explain what life is or its defining property – living organisms do things for reasons, as causal agents, in their own right. They are driven by information whose meaning is embedded in the structure of the system itself, based on its history. In short, there are distinct types of causation at play in living organisms by virtue of their organization. (x-xi)

As we will see in later chapters, meaning and value are the internal currency and action selection that emerged as life continued to evolve. From the rocks and sea of our early world, life arose as organisms that maintained theor internal states and sustain a degree of causal autonomy from the world around them. The next step in the evolution of agency is the ability of these autonomous organisms to back upon the world, to become causes in their own right. (43)

In humans, the expansion of our neural resources and recursive architecture of our cognitive systems gave us the ability to think about thoughts. Our minds were set free. We are capable of open-ended truly creative imaginations and hypothetical futures, of creating art, music, science, abstract reasoning that has revealed the deepest laws and principles of the universe. (294)

And we do not do this alone: the true power of human thought comes through collective interactions and cumulative culture. We have as individuals and as a species the power to transcend the immediacies of our own biology. And, though the prospects seem gloomy, we have within our reach the possibility of wisdom, of making optimal decisions for the long-term survival of our planet if we choose to exercise it. (294)

Earth Life > Individuality > Evolution Language

Youngblood, Mason. Language-like efficiency and structure in house finch song. Proceedings of the Royal Society B. April, 2024. As his bio below says, by way of the latest computational abilities, it is now possible to find generic similarities between avian twittering and the social network Twitter. The same mathematical formats thus seem to repeat themselves in kind across each and every conversational mode.

Communication needs to be complex enough to be functional while minimizing learning and production costs. Recent work suggests that the vocalizations and gestures of some songbirds, cetaceans and great apes may conform to linguistic laws that reflect this trade-off between efficiency and complexity. In these studies, clustering signals into types cannot be done a priori, and an analysis may affect statistical signals in the data. Here we assess the language-like efficiency and structure in house finch song across three levels of granularity in syllable clustering. The results show strong evidence for Zipf's rank–frequency law, Zipf's law of abbreviation and Menzerath's law. These statistical patterns are robust and exhibit a degree of scale invariance. (Excerpt)

My name is Mason Youngblood, and I am a postdoctoral fellow in the Institute for Advanced Computational Science at Stony Brook University. In my research, I apply methods from cognitive science, computational social science, and cultural evolution to questions about human and non-human animal behavior. Specifically, I’m interested in understanding how cognitive biases and population structure shape the cultural evolution of behaviors and beliefs (e.g. music, extremist ideology, birdsong, conspiracy theories).

Our Earthuman Ascent: A Major Evolutionary Transition in Individuality

wumanomics > Integral Persons > Somatic

Pierre-Yves Oudeyer. www.pyoudeyer.com.. . The French computational psychologist (search) is the director of the Flowers project-team at the Inria Center of University of Bordeaux. Current (March 2024) projects are now much involved with chatty AI features guided by insights gained from studies with children. A recent talk is Developmental AI: machines that learn like children and help children learn better. As the quotes say, another senior scholar finds evidence that both youngsters and large language modes use trail/error iterate methods in similar ways. See also Open-ended learning and development in machines and humans on the flowers.inria.fr. site.

Together with a great team, I study lifelong autonomous learning, and the self-organization of behavioural, cognitive and language structures at the frontiers of artificial intelligence and cognitive sciences. I use machines as tools to understand better how children learn and develop, and I study how one can build machines that learn autonomously like children, as well as integrate within human cultures, within the new field of developmental artificial intelligence. (P-Y O)

The Flowers project-team, at the University of Bordeaux and at Ensta ParisTech, studies versions of hoistic individual development. These models can help us better understand how children learn, as well as to build machines that gain knowledge as children do, aka developmental artificial intelligence, with applications in educational technologies, automated discovery, robotics and human-computer interaction.

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