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Displaying entries 31 through 45 of 61 found.

Ecosmomics: Independent, UniVersal, Complex Network Systems and a Genetic Code-Script Source

Zhang, Yang, et al. Computational methods for analysing multiscale 3D genome organization.. Nature Reviews Genetics. 25/3, 2024. We note this report by Carnegie Mellon, NIH, and UCLA geneticists including Tom Misteli at the frontier of this amenable intersection of AI neural net methods with complex genomic forms and functions. Altogether it seems that a common nonlinear narrative, an original literacy from cerebral to ecosmic connectomes, is deftly being deciphered and translated.

Recent progress in whole-genome mapping and imaging technologies has illuminated the spatial organization and folding in of the nucleus. In parallel, advanced computations have revealed multiscale (3D) transcription features. Here, we discuss how machine-learning methods and integrative frameworks, have led to a systematic delineation of genomic and epigenomic features, nuclear components and connective function. However, approaches to scan a wide variety of genomic and imaging datasets are still needed to define cellular phenotypes in health and disease. (Excerpt)

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

Conway Morris, Simon. From Extraterrestrials to Animal Minds: Six Myths of Evolution.. Conshohocken, PA: Templeton Press, 2022. The Cambridge University emeritus paleontologist continues his strong views by which to set aside vested tenets of the neoDarwinian corpus. To wit, there are indeed constrained limits to anatomy and physiology, evolution does proceed along a defined course rather than exhibit blind randomness. Here is the deep difference. SCM long had running debate with Stephen Jay Gould whence each would read the same phenomena as either orderly or random by way of personal persuasion. With regard to the sixth issue of microbial to advanced life in the galactic cosmos, it is concluded the stellar environs are so harsh that most probably we Earthlings, albeit fantastic beings, are most likely uniquely alone.

In this learned romp of science writing, Simon Conway Morris challenges old assumptions that pass as truths amongst the evolutionary orthodox. Life’s onward course is not aimless but highly circumscribed and “seeded with inevitabilities.” Turning from fossils to minds, Conway Morris questions whether the intelligence of humans and animals is similar by a difference of degree. Finally, the existence of other habitable worlds is faced whence the size and scale of the universe suggest that alien beings must exist somewhere. But the author Conway Morris cites the Fermi Paradox (“Where are they?”) to conclude that we alone and unique in the cosmos.

Couce, Alejandro, et al. Changing fitness effects of mutations through long-term bacterial evolution.. Science. January, 2024. Michigan State University, Harvard Medica School and University of Paris biologists including Richard Lenski post a summary report for some years of laboratory test runs of computational organisms and their genetics code. As the Abstract says, and team interviews affirm, a general reliability does become evident.

The distribution of fitness effects of new mutations shapes evolution, but it is a challenge to observe how it changes as organisms adapt. Using Escherichia coli lineages spanning 50,000 evolutionary generations, we quantify the fitness effects of insertion mutations in every gene. Microscopically, changes in individual gene essentiality and deleterious effects often occurred in parallel. The identity and effect sizes of beneficial mutations changed rapidly over time, but many targets of selection remained predictable because of loss-of-function mutations. Taken together, these results reveal the dynamic—but statistically predictable—nature of mutational fitness effects.

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.

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)

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)

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)

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)

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)

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)

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)

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)

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

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)

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.

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