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Displaying entries 31 through 45 of 46 found.

Ecosmomics: Independent Complex Network Systems, Computational Programs, Genetic Ecode Scripts

Duan, Qihao, et al. JanusDNA: A Powerful Bi-directional Hybrid DNA Foundation Model.. arXiv:2505.17257. We cite this entry by Berlin Institute of Health, Shenzhen Technology University, Carnegie Mellon University and MPI Heart and Lung Research system scientists including Benjamin Wild as another example of how easily a cross-translation of AI textual algorithms and genetic code-scripts can be made, as a Rosetta ecosmos becomes increasingly legible.

Large language models (LLMs) have joined with natural language processing and are now being applied to genetic sequences. However, adapting to complex genomic interactions requires modeling long-range dependencies within DNA sequences, but DNA is inherently bidirectional, which regulates transcription. Here we introduce JanusDNA, the first foundation model built upon a pretraining paradigm that combines the optimization efficiency of autoregression as it faces in both directions. (Excerpt)

Liang, Wang. Human Genome Book: Words, Sentences and Paragraphs. arXiv:2501.16982. In these mid 2020s when an AI Large Language publicity fills the cyberair, a Huazhong University of Science and Technology, China physicist lays out a whole scale translation of life’s hereditary endowment in full literary and textual terms. See also Find Central Dogma Again by LW at arXiv:2502.06253 whereby these AI methods are able to “rediscover” basic genetic principles and DNA and Human Language: Epigenetic Memory and Redundancy in Linear Sequence by Li Yang and Dongbo Wang at arXiv:2503.23494 for a similar review.

A consideration of the genome as a book with equivalents of words, sentences, and paragraphs has been often proposed. Recently, large language models have provided a novel approach, whereby we can train a foundational model capable of transferring from English to DNA sequences. We were then able to translate a human genome by segments and tokens into a "book" comprised of genomic "words," "sentences," and "paragraphs."

Zhang, Fan, et al. CellVerse: Do Large Language Models Really Understand Cell Biology?. arXiv:2505.07865. As AI capabilities become adapted to genetic studies, CUHK-Shenzhen, Yale University, Peking University, Tsinghua University, UCLA and Westlake University, China researchers specify a more advanced, viable version. Altogether, one can observe a growing sense of nature’s universal ecosmome to geonome textuality and familementarity.

Recent studies have shown ways to model single-cell data as natural languages by leveraging large language models (LLMs) for understanding cell biology. Here we introduce CellVerse, a unified language-centric question-answering method that integrates single-cell multi-omics data to analyze annotation (cell-level), drug prediction (drug-level), and perturbations (gene-level). CellVerse offers the first large-scale empirical demonstration that challenges still remain in applying LLMs to cell biology. (Excerpt)

Recent advances in LLMs have applied them to scientific domains, including mathematics, chemistry, and biology. Galactica strives to unify knowledge representation, whereas AlphaCode expands into protein synthesis. Our work contributes to this emerging field by connecting LLMs with biological data to evaluate and improve LLM capabilities in real-world biological contexts. (3)

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

Hudnall, Kevin and Raissa D’Souza. What does the tree of life look like as it grows? Evolution and the multifractality of time.. Journal of Theoretical Biology. 607/112121, 2025. UC Davis bioscholars propose an innovative perception of life’s long creaturely, branching development after Darwin’s archetypal elm as an instantiation of an iterative self-similar fractal geometry. The article comes with an Animation video to depict such an arboreal growth on its mathematic way toward mammals and peoples. Our philoSophic interest continues on to evident implications in our Earthwinian era whereby life’s episodic emergence appears to have a phenomenal,
independent, orthogenetic essence. (See also Dragon kings in self-organized criticality systems at arXiv:2308.02658 for earlier work by Raissa D'Souza.)

By unifying foundational principles of modern biology, we develop a mathematical basis for growing tree of life. Contrary to the static phylogenetic tree, our model shows that life’s track is more like a Cantor dust where each stage is a fractal form. As a result, this variegated course is nested, dualistic and stochastic. Altogether, its shape appears as a random iterated function that generates convexly related sequences of Metazoan species. The multifractal nature implies that, for any two living entities, the time interval from their last common ancestor to the present moment is a fractal curve. (Excerpts)

Our anatomical view is obtained from three prime features. The first is a nested scale which follows from descent-with-modification. The second is duality as biological sets transition between singularities and populations. The third aspect is a random facet whereby phylogeny is a stochastic process. Hence the natural tree of life as a whole is multifractal in that it consists of many distinct monofractals. (11)

Raissa D'Souza is Associate Dean for Research of the College of Engineering and a Professor of Computer Science at the University of California, Davis and on the Science Board at the Santa Fe Institute. See her Wikipedia page for much more. Kevin Hudnall is in Biological Systems Engineering Graduate Group at UC Davis.

Attwater, James, et al. Trinucleotide substrates under pH–freeze–thaw cycles enable open-ended exponential RNA replication by a polymerase ribozyme. Nature Chemistry. May, 2025. Seven MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, UK add further explanations as to how early RNA nucleotides got themselves untangled, sorted out and on their long journey to Oxford and our vital retrospect.

RNA replication is considered a key process in the origins of life. However, both enzymatic RNA replication cycles are impeded by strand separation issues arising from the stability of RNA duplexes. Here we show that RNA trinucleotide triphosphates can overcome this by binding to RNA strands for replication by a polymerase ribozyme. Partial ribozyme self-replication alongside generation of new RNA sequences occurred, which then drifted towards primordial codons. (Excerpt)

Bunn, Hayley, et al. Laboratory Rotational Spectroscopy Leads to the First Interstellar Detection of Deuterated Methyl Mercaptan. Astrophysical Journal Letters. 980/L13, 2025. This entry by MPI Extraterrestrial Physics, Université Paris-Saclay, University of Saskatchewan and University of Copenhagen astroscientists is an example of mid-decade sophisticated instrumentation and techniques which are able to quantify critical precursors on the evident course to viable rudiments and replicant evolution.

We report an extensive rotational spectroscopic analysis of singly deuterated methyl mercaptan (CH2DSH) using both millimeter and far-infrared synchrotron spectra to achieve a global torsional analysis of the three lowest torsional substates of this species. This is the first interstellar detection of a deuterated sulfur-bearing complex organic molecule and an important step toward understanding the chemical origin of sulfur-based prebiotics.

Kosc, Thomas, et al. Thermodynamic consistency of autocatalytic cycles. PNAS. 122/18, 2025. Laboratoire de Biométrie & Biologie Evolutive, Université Lyon and École Normale Supérieure Lyon, CNRS bioresearchers enter a strong, quantified, endorsement of how profligate these innate, spontaneous, precursor self-making reactions are as living systems complexified itself on the way to an emergent evolution,

Autocatalysis is seen as a potential key player in the origin of life, and more generally in the emergence of Darwinian dynamics. Here we tackle the computational task of detecting minimal autocatalytic cycles in reaction networks. Overall, by better characterizing the conditions of autocatalysis in biochemical reactions, this work brings us closer to appreciating the collective behavior on the path to the emergence of natural selection. (Abstract excerpt)

Sole, Ricard and Manlio De Domenico. Bifurcations and Phase Transitions in the Origins of Life. arXiv:2504.08492.. Universitat Pompeu Fabra, Barcelona and University of Padua veteran system thinkers make a strongest case to date for life’s innate occasion and emergence based on the latest theoretical reaches and empirical explorations which here are drawn from and exemplify physical sources. Once again, autocatalytic processes are essential for this original onset as it complexifies, scales and heads toward evolution and people. By April this year, a critical veracity and realization may occur in our midst which as our Earthuman may achieve a phenomenal, revolutionary discovery.

The path toward the emergence of life in our biosphere involved several key events allowing for the persistence, reproduction and evolution of molecular systems. All these processes took place in a certain environment and required diverse, non-equilibrium conditions which favor complex self-sustaining networks. Here, we review case studies associated with the early origins of life in terms of phase transitions and bifurcations, along with symmetry breaking and percolation. We discuss vital steps such as molecular chirality, the first replicators and cooperators, and potential "order for free." (Excerpts)

Conceptually, autocatalytic sets illustrate how order and function can emerge spontaneously by simple rules, versus the idea that life required improbable events. Kauffman’s work emphasizes the importance of network interactions over components, providing insights into possible pathways to the first living systems. (15) By framing the origin of life within the context of phase transitions and emergent behaviours, our work establishes a robust foundation for abiogenesis and early life evolution. The forms and forces that govern nonlinear dynamical systems provide critical insights into the universal laws underlying the emergence of life. (16)

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

Rogers, Lesley and Giorgio Vallortigara, eds. Lateralized Brain Functions: Methods in Human and Non-Human Species.. Switzerland: Springer,, 2025. The University of New England, Australia and University of Trento, Italy editors are senior definers (search) of this 21st century project to realize and thoroughly quantify the evolutionary occurrence and emergent ramification of complementary hemispheres and their common archetypes. This volume adds the latest methods and evidence such as Lateralization in Invertebrates by Davide Liga and Elisa Frasnelli and Reversals of Bodies, Brains, and Behavior: Quantitative Analysis of Laterality by Douglas Blackiston and Michael Levin.

The chapters in this book cover topics such as measuring lateralization in a range of species by scoring behavior elicited by inputs to one of both brain hemispheres; behavioral studies of motor preferences; neurological methods to reveal lateralization; imaging and new genetic approaches to studying humans and zebrafish.

, . Girard-Buttoz, Cedric, et al. Versatile use of chimpanzee call combinations promotes meaning expansion. Science Advances. 11/19, 2025.. Science Advances. 11/19, 2025. Leibniz Primate Research and MPI Human Cognitive Sciences paleopsychologists including Angela Friederici can now parse these proto-language occurrences of content filled utterances which are then seen to portend our recursive,loquacious linguistics.

Language is a combinatorial communication system able to generate an infinite number of meanings. Nonhuman animals use similar modes to expand content, which suggests an evolutionary precursor to our human capabilities. We tested whether wild chimpanzees used these procedures and found four combinatorial cases whereby bigram meanings were or were not derived from their parts. Such a system in nonhuman animals has never been documented and may be transitional between rudimentary systems and open-ended systems like our own. (Abstract)

Gontier, Nathalie, et al. Introduction to Evolving (Proto)Language/s. Lingua. 305/103740, 2024. In this premier journal, University of Lisbon, Nicolaus Copernicus University, Poland, Dalarne University, Sweden and Rutgers University, USA system linguists describe wider and deeper sources now being found of informative creaturely conveyance, broadly conceived, based on interdisciplinary studies. A typical entry is Emergence and evolution of language in multi-agent systems by Dorota Lipowska and Adam Lipowski.

Long considered uniquely human, today scholars argue for evolutionary continuity between human language and animal communication systems. While it is recognized that language is an evolving communication system, it is not well known from which species language evolved, and what behavioral and cognitive features are precursors. This special issue on Evolving (Proto)Language/s bundles several current protolanguage theories to provide overviews from (paleo)anthropology, genetics, physiology, developmental, evolutionary, ecological, and pragmatic research lines. (Excerpt)

Our Earthuman Ascent: A Major Evolutionary Transition in Twindividuality

Liang, Xinyu, et al. Functional divergence between the two cerebral hemispheres contributes to human fluid intelligence. Communications Biology. May 17, 2025. Cognitive Neuroscience and Learning, Beijing Normal University, Institute for Brain-inspired Intelligence, Fudan University and University of York (Elizabeth Jefferies) neuroscientists describe their latest sophisticated imaging studies which further affirm the significance of our double duty cerebral faculty and archetypical hemispheric complements.

Hemispheric lateralization is considered a driving force behind the generation of human intelligence. In this study, we utilize the functional aligned multidimensional representation space derived from functional gradients to compute between-hemisphere distances within this space. We found that both global divergence between the cerebral hemispheres and regional divergence within the multiple demand network. Together, these findings deepen our understanding of bicamerality as a fundamental organizational principle of the human brain. (Excerpt)

Our results reveal an increasing functional lateralization which transitions from unimodal functions (visual, auditory, sensorimotor) to higher-level cognition (social cognition, decision-making). This aligns with established theories linking the left side to language processes and long-term memory and the right to the facial images and visual attention. (7)

Gontier, Nathalie, et al. Gontier, Nathalie, et al. Combinatoriality and Compositionality in Communication, Skills, Tool Use, and Language. International Journal of Primatology.. 45/473, 2024. University of Lisbon, Heinrich Heine University, Nicolaus Copernicus University, Poland and University Institute of Psychological, Social and Life Sciences, Lisbon scholars continue to reconstruct life’s long experience to better survive and benefit by way of salient gestures, lyric prosody, fluent articulations and natural narrative. We propose our Earthuman version as Her/History which serves to welcome fiterate ourselves. Altogether, one could suppose that a natural ecosmic genesis is trying to express its own voice, vision and self-recognition.

Combinatorial behavior involves joining elements into larger aggregates with meaning. It is contrasted with compositionality, which involves larger constituents whose content is derived from its component parts. Combinatoriality is found in primates and animals, whereas compositionality is considered uniquely human. In regard,, this special Combinatoriality and Compositionality in Apes, Hominins, Humans, and Birds issue unites papers that study these aspects in primate and bird communication systems, tool use, skills, and human language. (Abstract)

Bouchard, Jean-Philippe. The Self-Organized Criticality Paradigm in Economics & Finance. arXiv:2407.10284. We came to this entry from Markus Aschwanden’s Power Laws Associated with Self-Organized Criticality paper (2505.00748) wherein his astronomic SOC findings can be seen to extend in kind from coronae to metabolisms to informatics. Herein a senior European theorist describes how this optimum natural phenomenon appears equally evident in hyperactive monetary commerce. See also Critical fragility socio-technical systems by Jose Moran, et al at arXiv:2307.03546 for another J-P B paper.

Self-Organized Criticality (SOC) is the mechanism by which complex systems spontaneously settle close to a critical edge between stability and chaos. In this short review, we discuss how SOC could offer a plausible solution to the excess volatility puzzle in financial markets. We argue that in general the quest for efficiency and the necessity of *resilience* may be mutually incompatible and thus require specific policy considerations.

Jean-Philippe Bouchaud is a French physicist, co-founder chairman of Capital Fund Management, adjunct professor at École Normale Supérieure and held the Bettencourt Innovation Chair at Collège de France in 2020.

Earth Earns: An Open CoCreative Earthropocene to Astropocene PediaVerse

Wunderling, Nico. et al. Wunderling, Nico, et al. Climate tipping point interactions and cascades. Earth System Dynamics. 15/1, 2024. Thirty-two Potsdam Institute for Climate Research and European environmentalists including Jonathan Donges provide an extensive study of what might happen if major local weather zones tipped over to a new phase and in some cascade fashion proceeded to impact each other. See also Tipping in an adaptive climate network model by Tom Bdolach, et al at arXiv:2505.04533 for a latest update.

Climate tipping elements are large-scale subsystems of the Earth that may transgress critical thresholds (tipping points) under global warming pressures, with substantial impacts on the biosphere and human societies. Frequently studied examples include the Greenland Ice Sheet, the Atlantic Meridional Overturning Circulation (AMOC), permafrost, monsoon systems, and the Amazon rainforest. Here, we survey the literature on climate tipping forces and find that many of them are destabilizing. We conclude that tipping points should be studied both in isolation, but also with regard cross-interactions. (Excerpt)

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