Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 31 through 45 of 66 found.
Cosmic Code > nonlinear > networks
Berner, Rico, et al.
Adaptive Dynamical Networks.
This April entry by Humboldt University and University of Munich theorists including Thilo Gross and Jurgen Kurths can serve to gather and note current contributions which altogether presage for a robust 2023 synthesis of nature’s anatomical vitality. In the same while, see also On the Transient and Equilibrium Features of Growing Fractal Complex Networks by Alexandre Benatti and Luciano da Costa at arXiv:2034.12780, Dense Network Motifs Enhance Dynamical Stability by Bnaya Gross, et al (2304.12044) and Emergent Stability in Complex Network Dynamics by Chandrakala Meena, et al in Nature Physics (April 2023) among a growing number.
Adaptive dynamical networks (ADNs) represent a broad class of systems that can change their connectivity over time depending on a dynamical state. Here we provide a detailed description of ADNs, note applications in research fields, highlight their arising dynamical phenomena, and give an overview of workable mathematical methods. (Excerpt)
Cosmic Code > nonlinear > Rosetta Cosmos
Budel, Gabriel, et al.
Topological Properties and Organizing Principles of Semantic Networks.
Delft University of Technology complexity theorists including Maksim Kitsak post a deeply technical exercise to identify and describe the pervasive, nested, multiplex features of global languages. While certain classes take on their own guise, our most human realm of linguistic conveyance and repository is found to exemplify and be inherently arranged by the same genetic-like principles as everywhere else. See also Structural Measure of Similarity and Complementarity in Complex Networks byy Szymon Talaga and Andrzej Nowak for a companion contribution.
Natural Language Processing (NLP) applications rely on semantic networks for structured knowledge representation whose basic properties must be relied on when designing algorithms, yet they mostly remain to be investigated. We study the properties of semantic networks from ConceptNet (see below), defined by 7 semantic relations from 11 different languages. We find universal basic properties: they are sparse, highly clustered, and exhibit power-law, scale-free degree distributions. But in some networks the connections are self-similar, while in others they are more complementarity-based. (Excerpt)
Cosmic Code > nonlinear > Rosetta Cosmos
ConceptNet is a freely-available semantic network, designed to help computers understand the meanings of words that people use. ConceptNet originated from the crowdsourcing project Open Mind Common Sense, which was launched in 1999 at the MIT Media Lab. It has since grown to include knowledge from other crowdsourced resources, expert-created resources, and games with a purpose.
Biolinguistics and Biological Systems: A Complex Systems Analysis of Language.
Biology & Philosophy.
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)
Cosmic Code > nonlinear > 2015 universal
Sherman, Nicholas, et al.
Universality of Critical Dynamics with Finite Entanglement.
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)
Cosmic Code > nonlinear > Common Code
Talaga, Szymon and Andrzej Nowak.
Structural Measure of Similarity and Complementarity in Complex Networks.
Nature Scientific Reports.
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)
Cosmic Code > Genetic Info > Paleo/Cosmo
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)
Lee, Juhyeon, et al..
Genetic Population Structure of the Xiognu Empire at Imperial and Local Scales..
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)
Cosmic Code > Genetic Info > Paleo/Cosmo
Vignieri, Sacha, ed..
The Zoonomia Project.
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)
Cosmic Code > Genetic Info > DNA word
Romero-Romero, Sergio, et al.
Exploring the Protein Sequence Space with Global Generative Models.
We note this entry by University of Bayreuth, Heidelberg, and Barcelona researchers as an early example of efforts to integrate and enhance life’s new intentional phase by way of deep neural machine language resources.
Recent advancements in large-scale architectures for training images and languages have taken over the field of computer vision and natural language processing (NLP). The recent ChatGPT and GPT4 models have exceptional capabilities to process, translate, and generate textual scripts.. As a result these advances are also aiding protein research wby way of rapid development of new methods with unprecedented performance. Language models have been utilized to embed proteins, generate novel ones, and predict tertiary structures. In this book chapter, we discuss 1) language models for the design of novel artificial proteins, 2) works that use non-Transformer architectures, and 3) applications in directed evolution approaches. (Abstract)
The field of protein design is being transformed due to advances in the field of artificial intelligence. The use of architectures that excel in other areas, such as computer vision and natural language processing, is highly successful in generating sequences in previously inaccessible regions of the protein space. In this work, we provided an overview of these advances in sequence generation and their potential applications in directed evolution. This progress provides an optimistic outlook for designing à-la-carte protein functions with new-to-nature enzymes becoming realistic in the near future. (Conclusion, 17)
Babajanyan, Sanasar, et al.
Coevolution of reproducers and replicators at the origin of life and the conditions for the origin of genomes.
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)
Crocker, Justin, et al.
Interdisciplinary Approaches to Predicting Evolutionary Biology.
Royal Society Philosophical Transactions B.
JC and Joshua Payne, European Molecular Biology Laboratory, Aleksandra Walczak, Sorbonne University, and Patricia Wittkopp, University of Michigan system biologists introduce a special issue with this integral purposeful quest. As the quote says, topical discussions were about The Predictable Genome, Gene Regulation and Networks, Community Evolution, and more. Some entries are Global Epistasis on Fitness Landscapes (Juan Diaz-Colunga, et al), Mutation Bias and Predictability of Evolution (Alejandro Cano, et al) and. Evolutionary Repeatability of Emergent Properties of Ecological Communities (S. Venkataram and S. Kryazhimskiy). See also Evolution Towards Increasing Complexity through Functional Diversification in a Protocell Model of the RNA World by Suvam Roy and Supratim Sengupta in Royal Society Proceedings B. (October 2021).
In the light of theoretic and empirical advances, we hosted an EMBO workshop at the European Molecular Biology Laboratory in June 2021 called ‘Predicting Evolution’ to ensure that this growing body of evolutionary knowledge moves toward mechanistic and causal accounts of biological processes. The conference explored the evolution of biological systems at different levels: from genes and molecules to organism development and ecology. As such, we invited leaders across various scales of evolution: molecular, network, microbial, developmental and community. The meeting explored biology at the interface of evolution, quantitative genetics, development and systems biology. (Editors)
Predicting evolutionary outcomes is an important research goal in a diversity of contexts. The focus of evolutionary forecasting is usually on adaptive processes, and efforts to improve prediction typically focus on selection. However, adaptive processes often rely on new mutations, which can be strongly influenced by predictable biases in mutation. Here, we provide an overview of existing theory and evidence for such mutation-biased adaptation and consider the implications of these results for the problem of prediction, in regard to topics such as the evolution of infectious diseases, resistance to biochemical agents, as well as cancer and other kinds of somatic evolution. (A. Cano)
Feigin, Charles, et al.
The GRN Concept as a Guide for Evolutionary Developmental Biology.
Journal of Experimental Zoology B.
In a special Animal Gene Regulatory Network Evolution section, see intro by Mark Rebeiz and Thomas Williams, Princeton University and University of Melbourne biologists provide a latest survey of the formative importance that these interconnective anatomies serve. As the quote says their active presence as they join and arrange nucleotides as life grows and quickens.
Organismal phenotypes result from inherited developmental programs, carried out during embryonic and juvenile life stages. These programs are not blank slates onto which natural selection can draw arbitrary forms. Rather, the mechanisms of development play an integral role in shaping phenotypic diversity and the evolutionary trajectories of species. The gene regulatory network (GRN) concept represents a potent tool for achieving this goal whose utility has grown along with advances in “omic” techniques. In this Perspective, we go on to discuss how experiments and projects can be designed and enhanced in light of the vital GRN concept. Finally, we show how the major steps of GRN model construction and experimental validation suggest generalizable workflows that can serve as a scaffold for project design.
Properties of Life: Toward a Theory of Organismc Biology.
Cambridge: MIT Press,
The Institute of Evolutionary Biology and Morphology, Witten/Herdecke University, Germany biotheorist (search) contributes another prescient vista as a current 2023 genesis evolutionary synthesis becomes clearly evident. Due September 19, it joins current works by Philip Ball, Peter Corning, William B. Miller and a growing host who realize and convey its robust, credible occasion. A long book Abstract is posted on pubmed.ncbi.nlm.nih.gov/27485949/, along with a synopsis on the publisher’s site.
Quickening Evolution > > Life Origin
Egbert, Matthew, et al.
Behavior and the Origin of Organisms.
Origins of Life and Evolution of Biospheres.
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)
Quickening Evolution > > Symbiotic
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.
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)
Quickening Evolution > > Symbiotic
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.
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)