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Displaying entries 46 through 60 of 77 found.

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

Camps, Jean-Baptiste, et al. Camps, Jean-Baptiste, et al. On the transmission of texts: written cultures as complex systems.. arXiv:2505.19246. Ecole nationale des chartes Paris, University Paris-Saclay and Ben Guerir, Morocco computational philologists provide a 2020s expansion and deepening of this academic pursuit by recasting literature as an exemplary manifestation of nonlinear, creative phenomena. By turns, our human literary corpora can actually be appreciated and parsed as a natural narrative.

Our knowledge of past cultures relies on recovering and parsing written material. While philologists like us reconstruct text phylogenies, the sources of prior genealogies is an open issue. Here we rethink literary transmission through a complexity science approach which integrates stochastic modelling, computer simulations, and data analysis, akin to statistical physics and evolutionary biology. Thus, we design general models that can account for diachrony and other aspects such as the extinction of branches or trees. (Excerpt)

Finally, the commonality of our models makes it applicable not only to medieval texts, but to any type of cultural transmission. Further investigations should include Western Medieval literature along with other time periods and geographical areas. In this sense, our work calls for the emergence of a new research endeavor dedicated to evolutionary modelling of cultural transmission. (15)

Gong, Wen. A New Exploration into Chinese Characters: From Simplification to Deeper Understanding. arXiv:2502.19428. A City University of Macau scholar posts a unique synthesis across millennia of oriental wisdom, mathematics and geometry and our 2025 intelligent cybersphere frontiers. The achievement is a luminous preview of a Earthuman (East/west, South/north) spatial and temporal textual universality.

This paper presents a novel approach to Chinese characters through the lens of physics, networks, and natural systems. Computational analysis of over 6,000 characters served to identify 422 elemental logographs which exhibit properties of emergent complexity, self-organization, and adaptive resilience. By viewing Chinese characters as a living system, this research can reveal how human cognition organizes and transmits knowledge. This perspective, combined with AI approaches, promises to transform language education from knowledge gain to meaning discovery.

This paper represents a collaborative effort between the author, and a team of AI assistants including Claude 3.3 from Anthropic, Gemini 2 from Google and Qwen2.5-Max from Alibaba. The fusion of human knowledge and software development, physics, and Chinese language with AI capabilities enables the novel perspectives and methodologies presented in this work.

Natural Growth Patterns in Character Evolution Just as natural systems evolve from simple to complex through predictable patterns, Chinese characters follow a similar organic development. The Fibonacci sequence provides an elegant metaphor for how complexity emerges from simplicity in systematic ways. The accompanying images of Fibonacci patterns in nature - from sunflowers to nautilus shells and fern fronds to spiral galaxies - reveal this universal principle of growth and organization. (22)

Dedication This work is dedicated to the late Professor T.D. Lee whose efforts opened doors for many Chinese students to pursue studies in the United States as a bridge between Eastern and Western traditions. His vision and support have enabled countless scholars like myself to contribute to global discourse.

Aschwanden, Markus and Felix Scholkmann. Power Laws Associated with Self-Organized Criticality. arXiv:2505.00748. In this latest posting, Lockheed Martin, Palo Alto and ETH Zurich mathematicians extend and apply some two decades of celestial findings (search MA) of nature’s dynamic proclivity onto an emergent Earthly array from life’s animations to cerebral knowledge. By so doing, another salient proof this year of an universe to humanverse is established.

We investigate the relevance of self-organized criticality (SOC) models in empirical datasets drawn from statistical observations in astrophysics, geophysics, biophysics, sociophysics and informatics. We study 25 interdisciplinary phenomena with event detection and power law methods. We find that the phenomena of solar flares, earthquakes, and forest fires are consistent with the theoretical predictions, while the size distributions of other phenomena are not as conclusive. (Abstract)

What is common to all SOC processes is the fractality, physical scaling laws, power law-like size distributions, and the evolution from an exponential-growth phase to a diffusive-decay phase. In the following we discuss SOC properties grouped by science disciplines (astrophysics, geophysics, biophysics, sociophysics, informatics), as enumerated in Table 1. (6)

SOC processes in biophysics have been proposed such as protein-interaction yeast networks, the metabolism bacterium Escherichia coli and the number of species per genus of mammals. The scale-free topology of protein interaction and metabolic networks and their balance between robustness and fragility are characteristics of SOC. In terms of species, ecological systems could exhibit SOC due to the dynamics of interactions (competition, cooperation) between them and their environment. (7)

Sociophysics is a novel discipline that uses mathematical tools or physical models to understand human groups which can be defined by citizenship, power customers, soldiers in wars, religions, financial net worth and so on. The evolution of a SOC process can be associated with an event which displays an instability or exponential-growth phase and a diffusive decay process. Differences in the power law slope size have been noticed for countries, genocides, famines, epidemics, and climates. (7)

Informatics SOC phenomena have been discovered in literature as well as in global networks by way of computer software. Such studies have found that vocabularies, book sales, family names, citation of papers and more exhibit SO criticalities. The last group of SOC in the discipline of informatics deals with global networks such as telephone calls, internet usage, HTTP size, emails sent and hyperlinks to websites. (8)

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)

Arnold, Carrie. How a Biofilm’s Strange Shape Emerges from Cellular Geometry. Quanta. April 21, 2025. A science writer reports on the latest research which is on the way to uncovering the physical forces and lineaments that serve as a deep source and drive for biological forms and functions. A lead example is the work of Peter Yunger at Georgia Tech, along with others such as Omaya Dudin and Lars Dietrich. In regard, a theme persists through these achievements that these various microbes and eukaryotes are always moving on their ordained evolutionary way toward more complex multicellular organisms. In regard, these papers are referred to The Biophysical Basis of Bacterial Colony Growth, Aawaz Pokhrel, et al in Nature Physics (20/1509, 2024), Morphological Entanglement in Living Systems by Thomas Day, et al in Physical Review X (14/011008, 2024) and A multicellular developmental program in a close animal relative by Marine Olivetta, et al in Nature. (635/382, 2024, search).

Olivetta, Marine, et al. A multicellular developmental program in a close animal relative. Nature. 635/382, 2025. Five Swiss Federal Institute of Technology, Lausanne microbiologists including Omaya Dudin contribute another mid 2020s instance of sophisticated, intricate empirical findings to an extent that life’s common, cellular gestational process can be well defined and described. As an implied generalization, a universal, ovular “embryogenesis” increasingly seems in (re)productive effect at each and every stage and instance. See also Charting the landscape of cytoskeletal diversity in microbial eukaryotes in BioRxiv (October 18, 2024) by this group.

All animals develop from a single-celled zygote into a complex multicellular organism through a series of orchestrated processes. Despite the conservation of early embryogenesis across animals, the evolutionary origins of how and when this process emerged remain elusive. By combining imaging and transcriptomic profiling, we show that single cells of C. perkinsii, which diverged about 1 billion years ago, undergo symmetry breaking and develop cleavage divisions to produce a multicellular colony. Our findings about this autonomous and palintomic developmental program hint that such multicellular development either is much older than thought or evolved convergently in ichthyosporeans. (Excerpt)

Rados, Theopi, et al. Tissue-like multicellular development triggered by mechanical compression in archaea. Science. April 3, 2025. Brandeis University, MPI Biology and MRC Laboratory of Molecular Biology, Cambridge, UK microbioogists have achieved the first quantified detection of an inherent transit to a higher cellular ordered phase in this category (see below). Thus life’s three eukaryote, microbial and now archeal domains are all found to exhibit an innate tendency to combine into integral unions.

Multicellularity has evolved multiple times in eukaryotes and is observed in bacteria. Rados et al. explored haloarchea, demonstrating that many archaea species can also form multicellular tissue–like structures when compressive forces are applied. These results establish multicellularity as a feature of all three domains of life and highlight the role of mechanical forces in shaping archaeal tissues. (Editor)

The advent of clonal multicellularity is a critical evolutionary milestone, seen often in eukaryotes, rarely in bacteria. We show that uniaxial compression induces clonal multicellularity in haloarchaea, forming tissue-like structures. Archaeal tissues undergo a multinucleate stage followed by tubulin-independent cellularization. Our findings highlight the potential convergent evolution of a biophysical mechanism in the emergence of multicellular systems across domains of life. (Excerpt)

Archaea and bacteria, while both prokaryotes, differ significantly in their cell structure, biochemistry, and genetics. Key distinctions includ membrane lipids (ether-linked in archaea, ester-linked in bacteria), and unique genetic elements like introns in archaeal DNA.

Brose, Ulrich. et al. Embedding information flows within ecological networks. Nature Ecology & Evolution. 9/547, 2025. Friedrich Schiller University, Cornell University, Imperial College London and Université de Montpellier including Sonia Kefi ecotheorists state a major case for including the heretofore unnoticed but significant social-scale contacts and relations between all manner of resident animals.

Natural communities form networks of species linked by interactions. Understanding their structure and dynamics is vital to predict species extinction risks, group stability and ecosystem functioning under global change. Here we argue that this information network of nature is a crucial aspect of community organization. We show that synthesizing information and matter flow interactions in multilayer networks can lead to shorter pathways connecting species and a denser aggregation of species in fewer modules. (Excerpt)

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