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Displaying entries 31 through 45 of 62 found.

Ecosmomics: An Independent, UniVersal, Source Code-Script of Generative Complex Network Systems

Nefdt, Ryan. Biolinguistics and Biological Systems: A Complex Systems Analysis of Language. Biology & Philosophy. March, 2023. A University of the Cape Town, RSA (search RN website) enters a latest synthesis of life’s communicative essence, as biosemiotic now articulates (see Ch. V), with a wide array of animate nonlinear features as they have likewise become recently identified. With some 140 references across 21st century studies from Chomsky to Pattee, Deacon, De Boer and many more, it is asserted that typical modular, robust, nested structures, adaptive, recursion, qualities are also strongly present in speech and script. See also A Note on Retrodiction and Machine Evolution by Gustavo Caetano-Anolles at arXiv:2303.14590 for a companion view.

In their recent book, Ladyman and Wiesner (What is a Complex System?, Yale UP, 2020) offer an exemplary synopsis of the interdisciplinary field of complexity science to date. Here, I extend their feature survey to include the formal study of natural language, i.e. linguistics. Indeed, I argue that language exhibits many of the hallmarks of a complex biological system. In regard, I will advocate the ‘Minimalist Program’ (Chomsky, MIT, 1995), which cites basic underlying mechanisms that, in their idealizations, such a novel biolinguistics should embrace a ‘Maximalist Program’ in which multiple subfields contribute component explanations to an emerging whole. (Excerpt)

Sherman, Nicholas, et al. Universality of Critical Dynamics with Finite Entanglement. 2301.09681. An example of 2023 integrative frontiers as UC Berkeley physicists find a 21st century quantum organics to be robustly distinguished by critically poised states for optimum performance across a wide array of occasions and applications. At the same while, we post Fish Shoals Resemble a Stochastic Excitable System (Gomez-Nava) about similar criticalities which grace and serve animal groups. So in this discovery year, our Earthwise pedia sapience is indeed finding proof of nature’s innate preference everywhere.

When a system is swept through a quantum critical point, the quantum Kibble-Zurek mechanism makes universal predictions for the number and energy of excitations produced. In this work, we study how low-energy dynamics of quantum systems near criticality are modified by finite entanglement, using invariant critical points. Our result establishes the precise role played by entanglement in time-dependent critical phenomena and has direct implications for quantum state preparation and classical simulation of quantum states. (Excerpt for essence)

Talaga, Szymon and Andrzej Nowak. Structural Measure of Similarity and Complementarity in Complex Networks. Nature Scientific Reports. 12/16580, 2022. We note this current entry by University of Warsaw and Florida Atlantic University complexity scholars (search AN), while densely theoretic, as an example to natural tendencies to commonly avail these creative reciprocities. See also Budel, Gabriel, et al. Topological Properties and Organizing Principles of Semantic Networks by Gabriel Budel, et al (2023) herein.

The principle of similarity, or homophily, is often used to explain patterns observed in complex networks such as transitivity and the abundance of triangles (3 cycles). However, many phenomena from division of labor to protein-protein interactions (PPI) are driven by complementarities and synergies. Here we show that the first principle is linked to the abundance of quadrangles (4-cycles) and dense bipartite subgraphs. Using multiple social and biological networks, we demonstrate that our similarity coefficients capture structural properties related to domain-specific phenomena. (Excerpt)

In summary, we showed that both similarity and complementarity are important organizational principles shaping the structure of social and biological networks and can be linked to interpretable, domain-specific phenomena. (14)

Mattick, John. RNA Out of the Mist. Trends in Genetics. 19/3, 2023. Looking back 50 years, the veteran University of New South Wales geneticist reviews some 50 years of research studies as twists, turns and progress, in which he participated, toward current appreciations of the vital functions played by this major nucleotide.

RNA has long been regarded as the intermediate between genes and proteins. It was a surprise then to discover that eukaryotic genes are mosaics of mRNA sequences with by large tracts of transcribed but untranslated sequences, and that multicellular organisms express long ‘intergenic’ and antisense noncoding RNAs (lncRNAs). The emerging picture is that most lncRNAs are the products of genetic loci termed ‘enhancers’, which marshal generic effector proteins to their sites of action to control cell fate decisions during development. (Excerpt)

Lee, Juhyeon, et al.. Genetic Population Structure of the Xiognu Empire at Imperial and Local Scales.. Science Advances. 9/15, 2023. We cite this entry by Seoul National University, MPI Science of Human History, University of Michigan, and MPI Evolutionary Anthropology members as a latest instance by our major Earthropo sapiens transition now proceeding, by way of novel DNA insights, to revive and enhance in fine detail these historic occasions. (A thousand name reference list well documents.) In respect, how curious is it that an emergent cognizance can turn and reconstruct of how we all came to this moment. Whatever kind of self re-presentation might be going on in a procreative genesis uniVerse which seems to require such an internal realization?

The Xiongnu established the first nomadic imperial power over the Eastern Eurasian steppe from ca. 200 BCE to 100 CE. Recent archaeogenetic studies have identified extreme levels of genetic diversity across the populace which agree with prior multiethnic records. However, it is still unknown how this diversity occurred at the local community level or by sociopolitical level. Here we investigate elite and local graves at the western border. Genetic heterogeneity was highest among the lowest-status individuals, while higher-status individuals were more akin, which suggests that higher status occurred within specific subsets of the Xiongnu peoples. (Abstract)

Vignieri, Sacha, ed.. The Zoonomia Project. Science. 380/356, 2023. This issue collects a papers on novel abilities to recover and sequence the past genetic basis of a diverse array of mammalian species. We note, e.g., Seeing Humans Through an Evolutionary Lens, Relating Enhancer Genetic variation Across Mammals to Complex Phenotypes, A Genetic Timescale for Placental Evolution, and Integrating Gene Annotation with Orthology Inference at Scale. These contributions were of such merit that two articles, What Cheetahs, Armadillos and Whales Revealed About Human DNA by Carl Zimmer and From Alpacas to Yaks, Mammal DNA Yields its Secrets by Emily Anthes, appeared in the New York Times on April 27, 2023. The international program itself can be reached at zoonomiaproject.org. So it seems that just as recent paleogenomic research, as noted herein, has been able to reconstruct many past histories, its compass can similarly include all manner a creaturely ancestors with a new heritage.

Mammals are diverse classes of animals, ranging in size across many orders of magnitude, and every possible shape. Understanding when, how, and under what selective pressures this variation has developed has long been of interest. But into the 21st century and 2020s, a robust science of paleogenomics can provide novel insights into the evolution of important genetic variation and morphological traits. Further, because we humans are also mammals, these understandings can help illume our own evolutionary history and health. Genes that are conserved across many species may indicate those that are essential for normal function and may lead to disease when altered. Here the genomes of 240 mammals inform studies to identify adaptive traits, morphologies and innovations all the way to homo sapiens. The Zoonomia project thus heralds a new era in which genomes recovered from hundreds of species will explain much about mammals, and ourselves. (VS, Issue Introduction)

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

Babajanyan, Sanasar, et al. Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes. PNAS. 12/14, 2023. An international team posted at the National Library of Medicine, NIH, the Yerevan Physics Institute, and CNRS, University of Paris including Eugene Koonin offers this latest proposal, reviewed by Eors Szathmary, of a 2023 convergent synthesis across the full span of life’s cellular and organism emergence within an evidently conducive ecosmic universe. By this integral vista, an oriented developmental process seems to unfold along a scalar sequence from biochemical precursors through some manner of hereditaries all the way to our Earthuman retrospective sapience.

The origin of life, which is equivalent to the origin of cells, is arguably the greatest enigma in biology. The intricate complexity of the simplest extant cells could only evolve from simpler, prebiological entities, but how to reconstruct. Here we present an evolutionary scenario in which cells evolved via symbiosis between protocells composed of protometabolic reaction networks could divide and become subject to selection, but as yet without primordial genetic elements (GE). Mathematical models can describe conditions for the survival of such symbionts and the origin of modern-type genomes, in particular, coordination of the rates of protocell division and replication. (Significance)

Salazar-Ciudad, Isaac, and Hugo Cano-Fernandez. Evo-Devo Beyond Development: Generalizing Evo-Devo to All Levels of Phenotypic Evolution. BioEssays. March, 2023. Into this year, Universitat Autònoma de Barcelona system biologists propose an expanded unifed cross-synthesis between life’s embryonic, physiological and historic phases. In regard, their contribution is further suggestive of an embryonic gestation (all the way to our latest transition in pediawise individuality.

A foundational idea of evo-devo is that morphological variation is not isotropic in all directions. Instead, some directions are more likely than others from DNA variations which depend on development. We argue that this evo-devo perspective should apply not only to morphology but to evolution across its phenotypic phases. To do this, two types of arguments need be combined: generative about which phenotypic mode arises in each instance and selective issues about which passes to the offspring. (Excerpt)

Egbert, Matthew, et al. Behavior and the Origin of Organisms. Origins of Life and Evolution of Biospheres. May, 2023. A nine person international effort by ME and Emily Parke, University of Auckland, Martin Hanczyc, University of Trento, Inman Harvey, University of Sussex, Nathaniel Virgo, Earth-Life Science Institute, Tokyo, Hiroki Sayama, SUNY Binghamton, Tom Froese, Okinawa Institute of Science and Technology, Alexandera Penn, University of Surrey, and Stuart Bartlett, Cal Tech (search each) draw on years of empirical and theoretic research, a good part their own, to quantify how prebiotic environs are suffused by an innately conducive viability. Typical sections include Behavior that Responds to Viability: A Common Structure Underlying the Self-Perserving Behaviors of Ante-Organisms; A Platform of Opportunity for Organismic Functional Diversity. Just as the JWST can hark back to the earliest galaxies, so a deeply rooted fertility can be found long before. Here is a prime 2023 advance as biology and physics come together within a phenomenal natural genesis.

It is common in origins of life research to view the first stages of life as the passive result of particular environmental conditions. This paper considers the alternative possibility: that the antecedents of life were already actively regulating their environment to maintain the conditions necessary for their own persistence. In support of this proposal, we describe ‘viability-based behaviour’: a way that simple entities can adaptively regulate their environment in response to their health, and in so doing, increase the likelihood of their survival. Drawing on empirical investigations of simple self-preserving abiological systems, we argue that these viability-based behaviours are simple enough to precede neo-Darwinian evolution. We also explain how their operation can reduce the demanding requirements that mainstream theories place upon the environment(s) in which life emerged. (Abstract)
Along the way, four ante-organism (ancestor) modes are reaction-diffusion spots, motile oil droplets, charge transportation networks, and Bénard convection cells which share a basic essential form: their activities occur in response to a systemic liveliness. To explain, each is a far-from-equilibrium dissipative structure (Nicolis and Prigogine 1989) whose ‘metabolism’ (i.e., energy-dissipating, structure-producing processes of self-construction) is distributed spatially. (10)

Frolov, Nikita\, et al. Self-Organization of Microtubules: Complexity Analysis of Emergent Patterns. arXiv:2305.00539. KU Leuven, Belgium cell biologists describe a realistic method into the 2020s to well integrate life’s physiological cellular phenomena with a deep formative substrate from which they evidentially arise. In addition, phase transitional scales can be seen to express dynamic critical states. See also Order from Chaos: How Mechanics Shape Epithelia and Promote Self-Organization by Filipe Vicente and Alba Diz-Munoz in Current Opinion in Systems Biology ( Vol. 32-33, March 2023).

Microtubules self-organize to form the cellular cytoskeleton, give cells their shape and play a crucial role in division and intracellular transport. A question remains if there is a good way to quantify these structures and gain new knowledge about the active physical principles of self-organization they exhibit. Here we introduce a entropy-based method to evaluate the formal complexity of spatial patterns emerging in an agent-based computational model of microtubule-motor interaction. We find that the proposed quantifier can discriminate between ordered, disordered, and intermediate states. Moreover, our study indicates that transitions in such a system are likely to exhibit properties of self-organized criticality. (Abstract)

Nature exploits fascinating self-organization principles to provide the mechanisms of life on different scales. Just as the maintenance of an ecosystem depends on populations of species cooperating or competing for shared resources, life at the cellular level is determined by the arrangement and interaction between its constituents, such as proteins, polymers, and organelles. (1)

Merle, Melody, et al. Precise and Scalable Self-Organization in Mammalian Pseudo-Embryos. arXiv:2303.17522. Pasteur Institute, Paris cell biologists report still another advanced way to quantify just how these natural intrinsic propensities are in vivifying effect for every aspect of a cellular and organismic evolutionary genesis.

During multi-cellular development, reproducible gene expression patterns determine cellular fates which are crucial when the body plan and the asymmetric axes emerge at gastrulation. In some species, such as flies and worms, these early processes achieve micro-spatial precision. However, we know little about such accuracy in mammalian development. Using an in vitro model for gastruloids, we find that gene expressions neatly reproduce protein concentration variabilities. Our results reveal developmental precision, reproducibility, and size scaling for mammalian systems, which notably arise spontaneously in self-organizing cell aggregates as fundamental features of multicellularity. (Excerpt)

Roughgarden, Joan. Holobiont Evolution: Population Theory for the Hologenome. American Naturalist. April, 2023. The University of Hawaii wise-wuman bioecologist posts a latest, thorough appreciation of the actual presence of life’s integrative cell and organism reciprocities. A detailed Abstract lists the many ways that this integral quality manifests and vivifies itself.

Vicente, Filipe and Alba Diz-Munoz. Order from Chaos: How Mechanics Shape Epithelia and Promote Self-Organization. Current Opinion in Systems Biology. March, 2023. European Molecular Biology Laboratory, Heidelberg biophysicists describe more innate reasons how and why life’s actual orthogenesis proceeds to organize itself across many animal species and scales.

Collective cell behaviors are essential for the shape and function of tissues. Much recent work has provided experimental evidence that tissue mechanics are key drivers of morphogenesis. In regard, the spatiotemporal coordination of cellular contractility, adhesion and volume regulation can drive development. At the same time, the epithelial sheets have strong mechanical properties so to distribute stress throughout the physical deformations necessary for their function. In this review, we address recent findings on epithelia morphogenesis and mechanical resistance and highlight the importance of quantitative new approaches for achieving novel understanding.

Bozdag, Ozan, et al. De Novo Evolution of Macroscopic Multicellularity. Nature. May 10, 2023. Nine Georgia Tech systems biologists including William Ratcliff continue their Institute project as conveyed in The Evolution of Multicellularity edition (Herron herein) by citing further instances of life’s emergent persistence to attain more complex, viable, integrative organismic forms.

While early lineages started as simple cells, much less is known about how they became Darwinian entities capable of sustained evolution. Here we investigate these precursors within a long-term experiment so as to select for larger group sizes. Our model is the snowflake yeast model system, which after many runs, in an anaerobic mode evolved to macroscopic complexities which are more biophysically tough. Altogether, this research provides unique insights into life’s ongoing evolutionary transitions in individuality, whence simpler phases overcome biophysical limitations through multicellular advances.

Herron, Matthew, et al, eds. The Evolution of Multicellularity. Boca Raton, FL: CRC Press, 2022. As this major evolutionary transitions model from 1995 steadily gains credible acceptance, Georgia Tech biologists MH, William Ratcliff and Peter Conlin edit a first comprehensive volume about life’s prime cell to organism emergent ramification. An initial Theory and Philosophy section has papers by Margaret O’Malley, Corina Tarnita, Richard Michod; see next Aggregative Multicellularity (David Queller); then Clonal Multicellularity; onto Life Cycles and Complex Multicellularity (Eric Libby); finally Syntheses and Conclusions (see quote). Certain chapters are Life Cycles as a Central Organizing Theme, Group Transformation, Life History, Division of Labor, and Individuality Transitions aand Single-Celled Ancestors of Animals. See

Among the most important innovations in the history of life is the transition from single-celled organisms to more complex, multicellular organisms. Multicellularity has evolved repeatedly across the tree of life, resulting in the evolution of new kinds of organisms that collectively constitute a significant portion of Earth’s biodiversity and have transformed the biosphere. This volume examines the origins and subsequent evolution of multicellularity, reviewing the types of multicellular groups that exist, their evolutionary relationships, the processes that led to their evolution, and the conceptual frameworks in which their evolution is understood. (Publisher)

The goal of this book is to provide an overview of the evolution of multicellularity by way of the types of groups that exist, their evolutionary relationships, processes that led to their origins and advance, and the conceptual frameworks in which they can be understood. In four main sections, veteran contributors review the philosophical issues and theoretical approaches as life arose and came altogether as myriad organisms by way of the evolution of aggregations, clonal assemblies, and developmental unities. (Editors Introduction)

In this chapter, we view future research on the evolution of multicellularity from a range of philosophy, natural history, phylogenetics, biophysics and astrobiology perspectives. We consider further issues such as multicellular life cycles, organismal size and complexity, the origin of development, environmental drivers and niche construction over geological timescales. So there has not been a better time to learn all we can about life’s florescent collective emergence. (Editors: Syntheses and Conclusions)

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