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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 16 through 30 of 39 found.


Ecosmomics: A Survey of Genomic Complex Network System Sources

Cosmic Code > nonlinear > Rosetta Cosmos

Semple, Stuart, et al. Linguistic Laws in Biology.. Trends in Ecology and Evolution. October, 2021. SS, University of Roehampton, London, Ramon Ferrer-i-Cancho, Quantitative Linguistics, Relational Algorithmics, Learning Research Group, Polytechnic University of Catalunya, Barcelona and Morgan Gustison, Integrative Biology, UT Austin propose that recent advances so to interpret (parse) written script and oral conversation by way of self-organizing complex network theories has reached a maturity so that they can be compared with and integrated into biological phenomena. And we note how well this synthesis accords with our 2020s theme of a natural genesis narrative. A broad array of 118 references are posted in support.

Linguistic laws, the common statistical patterns of human language, have been investigated by quantitative linguists for some decades. Recently, biologists have started to note and study the prevalence of these laws beyond this field to find patterns consistent with linguistic laws across multiple levels of biological organisation from molecular (genomes, genes, and proteins) to organismal (animal behaviour) to ecological (populations and ecosystems). We propose a new conceptual framework for the study of linguistic laws in biology, comprising and integrating distinct levels from description and prediction to novel theories. Adopting this framework will provide critical new insights into the fundamental rules of organisation underpinning natural systems, unifying linguistic laws and core theory in biology. (Abstract)

Cosmic Code > nonlinear > 2015 universal

Notarmuzi, Daniele, et al. Universality, Criticality and Complexity of Information Propagation in Social Media. arXiv:2109.00116. Indiana University systems theorists including Filippo Radicchi post a strong exposition to date of how all manner of dynamic self-organizing systems can be seen to spring from and express an iconic array of similar forms and behaviors. As a result, it is noted that all this disparate phenomena quite implies an independent generative source which seems to be in eternal effect. Into these 2020s, a natural propensity to seek and reside at an active bilateral poise from galaxies to Google becomes evident.

Information avalanches in social media are typically studied in a similar fashion as avalanches of neuronal activity in the brain. Whereas much literature reveals a substantial agreement about a unique process that characterizes neuronal activity across organisms, the dynamics of information in online social media is far less understood. Here, we analyze almost 1 billion time-stamped events collected from a multitude of platforms (Telegram, Twitter and Weibo) over some 10 years to show that the propagation of information in social media is a universal and critical process. Universality arises from the observation of identical macroscopic patterns, irrespective of the specific system. Critical behavior is deduced from the power-law distributions, and their hyperscaling relations, which control the size and duration of avalanches of information. (Abstract excerpt)

For example, there is large agreement on the fact that neuronal activity in the brain is universal and critical. Universality is the notion that nearly identical avalanche statistics are observed for a multitude of organisms. Criticality instead refers to the fact that avalanche statistics are characterized by algebraic distributions. (4)

We speculate that our results extend beyond the six platforms considered here. If so, there must be a mechanism that explains the universality shown by the data, involving a critical dynamics that is independent of the peculiarities implemented in the individual platforms. Understanding where this mechanism is rooted in and how to exploit it for the prediction of the propagation of information in online social media remain open challenges for future research. (10)

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution > major

Cooney, Daniel, et al. A PDE Model for Protocell Evolution and the Origin of Chromosomes via Multilevel Selection. arXiv:2109.09357. University of Pennsylvania, Princeton, and UCLA biotheorists including Simon Levin contribute 75 pages to the increasing flow of universality proofs by way of mathematically situating emergent genetic phenomena within the popular major emergent transitions scale. As the Abstract notes, an array of “fast and slow replicators” mix and match to help get life going on its oriented way to our retro-quantification.

The evolution of complex life involved major transitions such as the aggregation of individual genes into a replicating genome and the encapsulation of self-replicating genetic entities into cellular units. Here we model the evolution of proto-chromosomes within protocells as composed of two types of genes: "fast" for gene-level self-replication and "gene" which facilitates protocell-level reproduction. Our results suggest that dimerization can overcome lower-level effects and work in concert with multilevel selection to allow for complementary genes that coexist at the protocell-level but compete at the level of individual gene-level replication. (Abstract excerpt)

Quickening Evolution > major

Kun, Adam. The Major Evolutionary Transitions and Codes of Life. Biosystems. September, 2021. In this journal which is more open to holistic vistas, a Parmenides Center for the Conceptual Foundations of Science, Munich and collaborator with Eors Szathmary at Eotvos Lorand University, Budapest provides a novel synthesis between this popular view of life’s oriented developmental scales, and an expanded presence of many genetic-like code qualities. As they cross-fertilize and inform, both aspects benefit and grow in explanatory import. Can yet we move closer to truth and real discovery in time?

Major evolutionary transitions as well as the evolution of codes of life are key elements in macroevolution which are characterized by increase in complexity. These nested emergences ensue by a transition in individuality and by the evolution of a novel mode of using, transmitting or storing information. Here is where codes of life enter the picture. This flexibility allows information to be employed in a variety of ways, which can fuel evolutionary innovation. The collation of the list of major evolutionary transitions and the list of codes of life show a clear pattern: codes evolved prior to a major evolutionary transition and then played roles in the transition and/or in the transformation of the new individual. The evolution of a new code of life then can facilitate major evolutionary transitions. This effect could help us to identify new organic codes.

Marcello Barbieri lists five characteristics of codes of life that are important for the history of life. (1) Discontinuity: Codes of life represent something abruptly novel, not just gradual improvement of something that already exists. (2) Invariance: Codes of life do not change in the sense that there is a strong selection for their conservation. (3) Additivity: More than one types of code can be included in the same lineage, and one code does not erase the other. (4) Stability: Each code remains a viable form, and organism harbouring them still exist, thus the appearance of a new code does not invalidate former codes of life. And (5) Complexity: The evolution of a new code increases complexity. If we contrast this list with characteristics of the major evolutionary transitions, then we nearly find the same list. They are fundamental events in the history of life (cf. discontinuity) which always increase complexity. METs are also mostly irreversible (cf. invariance). METs happen in succession too and an organism can be the product of multiple METs. (2)

Quickening Evolution > Biosemiotics

Code Biology 2021. codebiology.org/conferences/Luznica2021. This is the website for the Seventh International Conference of the Code Biology Society which was held in September in Luznica, Croatia. The Society was founded by Marcello Barbieri and colleagues around 2010 as an offspring from a biosemiotic endeavor which is still active with a journal by this name. An extensive Abstracts book includes entries by Abir Igamberdiev (his Biosystems journal is a locus for papers in this field), Anna Aragno (NYC), Diego Gonzalez, et al (Mathematical Regularities in the Genetic Code), Elena Fimmel, Jacques Demongeot, et al and Joao Major (Jungian Archetypes). An overarching subject theme is an articulation of how much physical, natural, biological and social phases are deeply suffused by codes, signs, literary content writ large and small.

Quickening Evolution > Biosemiotics

Deacon, Terrence. How Molecules Became Signs. Biosemiotics. October, 2021. The veteran UC Berkeley bioanthropologist continues his project to explain and emphasize life’s loquacious evolution by way of an apparent codifications which manifestly appear wherever possible. For example, Fig. 7 depicts three ways that a nucleic acid template can serve to regulate a complex autogenic process. Fig. 9 shows how a recursive course between genes and proteins becomes a basis for epigenetic processes. In essence, the endeavor is seeking to parse life’s biochemical dynamics as some manner of an innate literature (liferature, iiferate).

As a target article, several critiques herein such as Does Autogenic Semiosis Underpin Minimal Cognition? by M. Garcia-Valdecasas and Data and Context by T. Dickins laud and embellish the dialogue. But a remarkable response is Symbol Grounding Precedes Interpretation by Harold Pattee (reviewed below) since Deacon casts back and dedicates this article to Pattee’s 1969 original essay, How Does a Molecule Become a Message?.

To explore this occasion I will ask: “What sort of process is necessary and sufficient to treat a molecule as a sign?” In regard I develop and specify a simple molecular model system assumes known physics and chemistry but can represent the interpretive properties of interest. Three complex variants are then sketched that parallel an “icon-index-symbol” hierarchic scaffolding logic. This analysis reverses a molecular and evolutionary biology which treats DNA and RNA as the original sources of biological information. Instead I argue that the structural characteristics of these molecules have provided semiotic affordances which the interpretive dynamics of viruses and cells have taken advantage of. (Abstract excerpt)

To summarize the argument so far: there are 5 holistic properties that even a simple autogenic system exhibits which are not reducible its physical–chemical properties of its components and emerge from the whole integrated system. They are 1. individuation (an intrinsic maintenance of a self/non-self distinction); 2. autonomy (it sustains its own boundary conditions via component processes); 3. recursive self-maintenance3 (it repairs and replicates these same critical boundary conditions); 4. normativity (it is disposed to produce these result); and 5. interpretive competence (by being able to re-present itself in new instantiations). (10)

Quickening Evolution > Biosemiotics

Pattee, Harold. Symbol Grounding Precedes Interpretation. Biosemiotics. October, 2021. The entry is a response to Terrence Deacon’s entry How Molecules Become Signs in this journal (Oct. 2021, above) which was posted to honor my 1969 paper How Does a Molecule Become a Message?. In extraordinary regard, the eminent CalTech logician, physicist, and mathematician (search) is still on his message at 96 years of age. As a result, a remarkable comparison over a half century span can well illume and emphasize life’s textual articulation. Fortunately Pattee’s original paper has been reprinted in a 2012 collection, Laws, Language and Life, with many other diverse, erudite writings (search Joanna Leonardi, Polish philosopher editor).

Deacon speculates on the origin of interpretation of signs using autocatalytic origin of life models and Peircean terminology. I explain why interpretation evolved only later as a triadic intervention between symbols and actions. In all organisms the passive one-dimensional genetic informational symbol sequences are converted to active functional proteins or nucleic acids by three-dimensional folding. This symbol grounding is a direct symbol-to-action conversion. It is universal throughout all evolution. Folding is entirely a lawful physical process, leaving neither freedom nor necessity for interpretation. Similarly, the initial converse action-to-symbol conversion of sensory inputs also leaves no freedom for interpretation until after the action-to-symbol conversion. (Abstract)

Quickening Evolution > Intel Ev

Vanchurin, Vitaly, et al. Towards a Theory of Evolution as Multilevel Learning. arXiv:2110.14602. VV, Yuri Wolf, and Eugene Koonin, US National Library of Medicine, along with Mikhail Katsnelson, Radboud University (search each) continue their expansive, multi-faceted project, which broadly reflects their Russian heritage and holistic worldview. Amongst other contributions, this entry takes the growing sense that life’s sensory development is distinguished by an ascendant cerebral intelligence and cognitive knowledge to its fullest implications. In regard, the major transitions scale can be further tracked by information processing abilities by way of deep neural network methods. An overall vista proceeds from a physical basis by sequential stages to our human phase as some manner of a natural self-discovery. See also a companion paper Thermodynamics of Evolution and the Origin of Life by this team herein and at (2110.15066).

We apply the theory of learning to physically renormalizable systems as a way to develop a theory of biological evolution, and the origin of life, as an oriented process of multilevel learning. We formulate seven vital evolutionary principles so to show how they entail replication, natural selection and more and follow naturally from the theory of learning. A further approach uses the mathematical framework of neural networks so to indicate their presence in life’s cognitive advance. evolutionary phenomena. More complex phenomena, such as major transitions in evolution are studied at their thermodynamic limit, which is described in the accompanying paper (V. Vitaly, 2110.15066, herein). (Abstract excerpt)

Modern evolutionary theory gives a detailed quantitative description of processes that occur within evolving populations of organisms, but its transitional scale and the emergence of multiple complex levels remain less understood. Here we establish a correspondence between the key features of evolution, renormalized physical theories and learning dynamics. In this way life’s development can be gain a unified mathematical framework which emphasizes intelligence and knowledge content. Under this theory the same learning phenomena occurs on multiple levels or on different scales, similar to the case of renormalizable physical theories. (Significance excerpt)

Earth Life Emergence: Development of Body, Brain, Selves and Societies

Earth Life > Common Code

Mondal, Shrabani, et al. Universal Dynamic Scaling in Chemical Reactions At and Away from Equilibrium. arXiv:2101.01613. UM Boston, Center for Quantum and Nonequilibrium Systems contribute to on-going endeavors which are finding the expansive presence of an invariant, active self-similarity beyond the usual realms of living phenomena. See also On the Conditions for Mimicking Natural Selection in Chemical Systems by Gregoire Danger, et al in Nature Reviews Chemistry (4/102, 2020) for another example. As these efforts grow an spread in the 2020s, they achieve still deeper evidence for an organic fertility with an independent generative source.

Physical kinetic processes are known to exhibit universal scaling of observables that fluctuate in space and time. Are there analogous dynamic scaling laws that are unique to the chemical reaction mechanisms available to and natural and synthetic conditions? Here, we formulate two complementary approaches to the dynamic scaling of stochastic fluctuations in thermodynamic phenomena at and away from an equilibrium state. A survey of common chemical mechanisms reveals classes that organize according to the molecularity of the reactions, (non) equilibrium phases, and the extent of autocatalysis in the reaction network. Altogether, these results establish dynamic universality for the thermodynamic fluctuations well-mixed chemical reactions. (Abstract excerpt)

Universal scaling behavior has been found in biochemical networks [8], the stochastic exponential growth and division of bacterial cells [9, 10], the growth of human cancers [11], and dissipative self-assembly [12]. Formal analogies have expanded the scope of kinetic roughening theory [13, 14] even further by treating the fluctuations of mathematical functions as surrogates for the physical interface [1]. Examples include biological systems such as DNA [15], complex networks [16], crudeoil prices [17], heartbeat signals [18], strongly interacting gases [19], and material fracture [20). (1)


Universal behaviors have been extensively explored for physical phenomena, and here we have shown that universal dynamical scaling extends to the thermodynamic observables of chemical phenomena at and away from equilibrium. These observables satisfy three interconnected dynamic scaling classes we have tested of chemistry from simple, elementary reactions to complex, coupled autocatalytic reactions. Dynamical universality classes are typically determined by the dimensionality, conservation laws, symmetry of the order parameter, range of the interactions, and the coupling of the order parameter to conserved quantities. (16)

Earth Life > Common Code

Yang, Haiqian, et al. Configural Fingerprints of Multicellular Living Systems. Proceedings of the National Academy of Sciences. 118/44, 2021. Seven bioengineers from MIT, University of Ottawa, and Northeastern University quantify deeper rootings of life’s evolutionary sequential course into invariant physical phenomena such as dynamic state transitions. As substantial matter is found to possess an active spontaneity, it becomes a fertile soil for regnant flora and fauna.

Cells cooperate as groups to achieve structure and function at the tissue level, during which specific material characteristics emerge. Analogous to phase transitions in classical physics, transformations in multicellular assemblies are essential for a variety of vital processes including morphogenesis, wound healing, and cancer. In this work, we develop configurational fingerprints of particulate and multicellular assemblies and extract volumetric and shear order parameters to quantify the system disorder. These two parameters form a complete and unique pair of signatures for the structural disorder of a multicellular system. (Abstract excerpt)

Tissues are composed of many cells that coordinate in space, through which structural formations emerge. While recent progress has shown that many biological processes are analogous to material phase transitions, a systematic framework to describe the spatial order of complex living systems has not yet occurred. We develop a unified method to quantify the evolution of spatial order across different types of disordered systems, including jammed thermal systems, 2D cell monolayers, 3D epithelial spheroids, and Drosophila embryos. Using scaling analysis, we show successful differentiation of gas-like, liquid-like, and solid-like phases in various living systems. (Significance)

Earth Life > Nest > Life Origin

Danger, Gregiore, et al. On the Conditions for Mimicking Natural Selection in Chemical Systems. Nature Reviews Chenistry. 4/102, 2020. Aix-Marseille Universite, CNRS physical chemists including Robert Pascal provide a latest contribution to an integral synthesis of substantial, self-organizing agencies with nature’s winnowing optimization processes from many variant candidates. An array of ensuing biomolecular constraints then need be factored into origin of life scenarios.

The emergence of natural selection which requires that reproducing entities have variations that may be inherited and passed on, was an important breakthrough in the self-organization of life. In this Perspective, the assumptions about biological reproduction are confronted with known physico-chemical principles that control the evolution of material systems. Here we see that chemical replicators can behave in a similar fashion to living entities, provided that the reproduction cycle proceeds in a unidirectional way. For this to be the case, the system must be held far from equilibrium and fed with a non-degraded (low-entropy) form of energy. (Abstract excerpt)

Earth Life > Nest > Life Origin

Higgs, Paul. When is a Reaction Network a Metabolism? Criteria for Simple Metabolisms that Support Growth and Division of Protocells. Life. 11/9, 2021. In a paper for a special Prebiotic Systems Chemistry issue, the McMaster University, Ontario biochemist (search) continues his project to reconstruct and explain how living systems came to form, develop and evolve eons ago. Something was going on by itself, which is becoming intelligible to an individual and global collaboration. One wonders by what sufficient veracity might it dawn that a greater phenomenal genesis from which we arise exists on its independent own.

As a way to better understand the nature of metabolism in the first cells, and life’s metabolic origin, we propose three criteria that a chemical reaction must satisfy to sustain the growth and division of a protocell. (1) Biomolecules produced by the reaction system must be at high concentration inside the cell while they remain at low or zero on the outside. (2) The solute concentration inside the cell must be higher than outside. (3) These criteria can be met if the reaction system is bistable, because different concentrations can exist inside and out while all the reactions are the same. (Abstract excerpt)

Earth Life > Nest > Life Origin

Vanchurin, Vitaly, et al. Thermodynamics of Evolution and the Origin of Life. arXiv:2110.15066. This is a companion paper by Vanchurin, Wolf, Koonin and Katsnelson to their Evolution as Multilevel Learning entry (2110.14602) so to provide a physical and chemical basis for life’s evident proclivity to progressively achieve an referential accumulated knowledge repository. Along the way a maximum entropy principle is seen to be involved. A Table compares thermodynamic qualities with machine learning methods and evolutionary biology, which are then fitted into a major transitions frame. Into the 2020s, these postings suggest that a composite explanatory synthesis which links many heretofore separate aspects into a single sweep from universe to us is newly possible.

We outline a phenomenological theory of evolution and the origin of life by combining classical thermodynamics with a statistical description of learning. The maximum entropy principle is employed to derive a canonical ensemble of organisms (population), their macroscopic fitness and free energy of additive fitness). We model evolution as a function of the biological temperature and potential development, This thermodynamics framework then allows major transitions in evolution such as from biomolecular stages to an ensemble organisms to be identified. As a further result, the origin of life, can be appreciated as a special case of physical phase transitions. (Abstract)

We employ the conceptual apparatus of thermodynamics to develop a phenomenological theory of evolution and of the origin of life that incorporates both equilibrium and non-equilibrium evolutionary processes within a mathematical framework of the theory of learning. The threefold correspondence is traced between the fundamental quantities of thermodynamics, the theory of learning and the theory of evolution. Under this theory, major transitions in evolution, including the origin of life, represent specific types of physical phase transitions. (Significance)

The key idea of our theoretical construction is the interplay between the entropy increase in the environment dictated by the second law of thermodynamics and the entropy decrease in evolving systems (such as organisms or populations) dictated by the second law of learning (19)

Earth Life > Nest > Microbial

Astacioa, Luis, et al. Closed Microbial Communities Self-Organize to Persistently Cycle Carbon. Proceedings of the National Academy of Sciences. 118/45, 2021. University of Illinois, Center for the Physics of Living Cells and University of Chicago, Center for the Physics of Evolving Systems researchers describe a robust tendency to spontaneously form a conserved set of metabolic processes. In regard, as the late Eshel Ben Jacob foresaw years ago, bacterial colonies can well serve as archetypal ecosystem exemplars.

Life on Earth depends on ecologically driven nutrient cycles to regenerate resources. Understanding how nutrient cycles emerge from a complex web of ecological processes is a central challenge in ecology. However, we lack model ecosystems that can be replicated, manipulated, and quantified in the laboratory, making it hard to quantify how changes in composition and the environment impact cycling. Enabled by a new high-precision method, we show that microbial ecosystems (CES) with only light self-organize can robustly cycle carbon. Our study helps establish CES as model biospheres for studying how ecosystems persistently cycle nutrients. (Significance)

Earth Life > Nest > Multicellular

Simpson, Carl. Adaptation to a Viscous Snowball Earth Ocean as a Path to Complex Multicellularity. American Naturalist. 198.5, 2021. As our collaborative studies proceed to reconstruct past planetary environs from which we all arose, the University of Colorado Museum of Natural History geobiologist (search) presents a thorough scenario of colder, glacial and milder, conducive phases that have affected complex organisms. It again amazes that our sapient issue can turn and retrace such a circuitous, stressful course, which reveals how chancy and perilous it was. See also Reproductive Innovations and Pulsed Rise in Plant Complexity by A. Leslie, C. Simpson and L. Mander in Science (373/1308, 2021).

Animals, fungi, and algae with complex multicellular bodies all evolved independently from unicellular ancestors. The early history of these major eukaryotic multicellular clades co-occur with an extreme phase of global glaciations known as the Snowball Earth. Here, I propose that the long-term loss of low-viscosity environments due to several rounds global glaciation drove the multiple origins of complex multicellularity in eukaryotes and the subsequent radiation of complex multicellular groups into previously unoccupied niches. In this scenario, life adapts to Snowball Earth oceans by evolving larger bodies and faster speeds for high-viscosity seawater. Warm, low-viscosity seawater returned with the melting of the glaciers which gave rise to new vital complexities. (Abstract)

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