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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 46 through 60 of 82 found.


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

Cosmic Code > Genetic Info > Genome CS

Wall, Brydon, et al. Machine and deep learning methods for predicting 3D genome organization. arXiv:2403.03231. We cite this entry by Virginia Commonwealth University computational physicians as an example of how current neural net Ai methods, which have already taken over protein research, can similarly apply to and enhance complex genetic studies. Altogether life’s whole organismic realm continues to gain a deeply common textual essence.


Three-Dimensional (3D) chromatin interactions, such as enhancer-promoter interactions (EPIs), loops, Topologically Associating Domains (TADs), and A/B compartments play vital roles in cellular processes by regulating gene expression. However, current catalogs of 3D structures remain incomplete due to low data resolution. Machine learning methods can be an alternative to obtain more interactions and improve resolution. In this review, we discuss computational tools for predicting three types of 3D interactions (EPIs, chromatin interactions, TAD boundaries) and suggest future research directions.

Cosmic Code > Genetic Info > Genome CS

Zhang, Yang, et al. 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

Quickening Evolution

Adami, Christoph. The Evolution of Biological Information: How Evolution Creates Complexity, from Viruses to Brains. Princeton: Princeton University Press, 2024. A senior authority in computational biology for over 20 years based at Michigan State University contributes his unique, 600 page opus. Its comprehensive chapters flow from the subject theory to biotic precursors, its genetic prescription, digital lab experiments, physiologic robustness, RNA origins, all the way to ascendant intelligence and social cooperation. As these aspects unfold in thorough turn they are braced by many equations.

An overall course becomes evident from the earliest replicants to metabolic biomolecules, cellular animals and relative linguistic knowledge. Although not a theme, it does trace a central trend that winds up with our sentient, observant selves. While Caleb Scharf and Yavul Harari write of algorithms that pass on from the human phase, for Adami the plot thickens and quickens as life’s genomic heredity proceeds from simple cells to neural cognizance. By 2024, a temporal progression may come into view of a procreative ecosmos were trying to decipher and read its own hereditary endowment.

In this final chapter I discussed three prime scales of life: how information is the key element that distinguishes life from nonlife, how the communication of information is the main factor that makes cooperation possible from cells to societies and how information is used to predict the future state of the world. Just as I wrote in the chapter introduction, once we look at biology in the light of information, it is hard not to see the fundamental importance of this concept. (519)

In this book, Christoph Adami adds a 21st century perspective to Darwinian evolution through the lens of an informational quality. This novel theoretical stance sheds light on how cells evolve to communicate, intelligence arises and viruses evolve drug resistance, By this account, information emerges as the central unifying principle which allows us to think about the origin of life on Earth and elsewhere. A leader in the field of computational biology, Adami especially considers the information theory of biomolecules and its content in genetic sequences and proteins. After viewing bacteria and digital organisms, he goes onto explain cooperation among cells, animals, and people. (MIT)

Christoph Adami is professor of microbiology and molecular genetics at Michigan State University. A pioneer in the application of methods from information theory to the study of evolution, he designed the Avida system that launched the use of digital life as a tool for investigating basic questions in evolutionary biology.

Quickening Evolution

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.

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 > Recapitulation > Life Origin

Douglas, Jordan, et al. Douglas, Jordan, et al. Enzymic recognition of amino acids drove the evolution of primordial genetic codes. Nucleic Acids Research. 52/2, 2024. Into this late year, University of Auckland and University of North Carolina paleobiologists including Peter Wills and Charles Carter (search each) are able todelve deeper to reach better quantified reasons of how and why prebiotic precursors and reactions formed biomolecular systems that could replicate themselves. And as one reads along, an impression grows that our Earthuman retrospective has indeed come upon a preordained ecosmic fertility as it proceeds to complexify, reproduce, develop and evolve.

How genetic information gained its control over chemical processes which build living cells remains to be understood. Today, the aminoacyl-tRNA synthetases (AARS) are known to foster the genetic codes in all living systems. A phylogenetic reconstruction of extant AARS genes, enhanced by modular acquisitions, reveals six AARS with distinct bacterial, archaeal, eukaryotic, or organellar clades. The resulting model shows a tendency for less elaborate enzymes, with simpler catalytic domains, to activate amino acids that did not appear until later. A probable evolutionary route for an amino acid type to find a place in the code was by recruiting older, less specific AARS. (excerpt)

Quickening Evolution > Recapitulation > 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 > Recapitulation > 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 > Recapitulation > 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 > Recapitulation > Life Origin

Yu, Jinhan, et al. Prebiotic access to enantioenriched amino acids via peptide-mediated transamination reactions.. PNAS. 121/7, 2024. As life origin retro-studies continue to gain a finer focus, Scripps Research, La Jolla, CA biochemists including Donna Blackmond report how these appropriate metabolic biomaterials played their vital role early on. And once again, the whole animate process seems to be unfolding by its own innate merits.

The kinetic resolution of racemic amino acids mediated by dipeptides and pyridoxal provides a prebiotically plausible route to enantioenriched proteinogenic amino acids. The enzymatic transamination cycles that are key to modern biochemical formation of enantiopure amino acids may have evolved from this half of the reversible reaction couple. Kinetic resolution of racemic precursors emerges as a general route to enantioenrichment under prebiotic conditions. (Abstract)

Transamination is the process by which amino groups are removed from amino acids and transferred to acceptor keto-acids to generate the amino acid version of the keto-acid and the keto-acid version of the original amino acid.

Quickening Evolution > Recapitulation > 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 > Recapitulation > Multicellular

Bingham, Emma and William Ratcliff. A nonadaptive explanation for macroevolutionary patterns in the evolution of complex multicellularity. PNAS. 121/7, 2024. Georgia Tech biologists (search WR) contribute additional insights into the many insistent occasions when all manner of animalia came together into reciprocal groupings as life arose on its way.

Complex multicellular organisms have evolved five times independently in eukaryotes, but never within prokaryotes. Here, we propose an alternative for this broad macroevolutionary pattern. By binning cells into groups with finite genetic bottlenecks between generations, multicellularity reduces the effective size of cellular populations, increasing the role of genetic drift in evolutionary change. While both prokaryotes and eukaryotes experience this phenomenon, they have opposite responses to drift: eukaryotes tend to undergo genomic expansion, while prokaryotes face genomic erosion. (Abstract)

Multiicellularity has evolved over 50 times independently, arising at least 3 billion years ago in cyanobacteria. Most of these lineages have remained relatively simple, with “complex multicellularity” arising only five times (animals, plants, fungi, brown, and red algae). Complex multicellularity is a term of art used to capture an important axis of multicellular organismality: the evolution of large, often relatively long-lived, multicellular organisms composed of many cell types (2).

Quickening Evolution > Recapitulation > 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 > Recapitulation > 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 > Recapitulation > Societies

Ma, Yin-Jie, et al.. Social norms and cooperation in higher-order networks. arXiv:2401.14905. Complexity theorists with postings in China, Korea, Italy, Slovenia and Austria including Matjaz Perc and Stefano Boccaletti provide a latest review and preview of 21st century studies which have by now quantified and proven that organisms have as much and more of a beneficial tendency to group together and get along then to engage in divisive competition. (While our own human phase is rife with violent conflict, this may be due to its total male patriarchy, with no feminine mediation.) See also Quantitative assessment can stabilize indirect reciprocity under imperfect information by Laura Schmid, et al in Nature Communications. (14/2086, 2023).


Recent research has studied how cooperation is fostered through various mechanisms in cognitive settings, mostly through pairwise interactions. However, the real-world involves multiple cliques with higher-order interactions. We introduce a model that explores collective strategies and social norms within a diverse environment. We show that prosocial norms lead to increased cooperation across an array of social situations. Our research thus offers insights into the evolution of cooperation through the lens of social norm diffusion in higher-order networks.

Cooperation, where individuals bear costs to benefit others, is a common occasion across biological and social spheres. In-depth investigations into ecological factors such as memory, repeated interaction and network structure have shown that cooperation to be more beneficial than selfish behavior. Building on the work of Martin Nowak, kin selection, direct reciprocity, indirect reciprocity, group selection, and network reciprocity have been found as explanations. Recent research efforts have refined these mechanisms such as indirect reciprocity, along with cognitive processes and reciprocal actions within various social norms. (1)

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