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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 16 through 30 of 49 found.


Ecosmos: A Procreative Organic Habitable UniVerse

Animate Cosmos > Organic > Biology Physics

Choi, Jeong-Mo, et al. Physical Principles Underlying the Complex Biology of Intracellular Phase Transitions. Annual Review of Biophysics. 49/107, 2020. Washington University, St. Louis biomedical scientists describe and illustrate another way that life’s intrinsic genetic, metabolic vitality can be traced to, rooted in and manifestly exhibit this substantial phenomena.

Many biomolecular condensates appear to form via spontaneous or driven processes that have the hallmarks of intracellular phase transitions. This suggests that a common underlying physical framework might govern the formation of functionally and compositionally unrelated compositions. In this review, we summarize recent work that leverages a stickers-and-spacers framework adapted from the field of associative polymers for understanding how multivalent protein and RNA molecules drive phase transitions that give rise to biomolecular condensates. (Abstract excerpt)

Animate Cosmos > Organic > Chemistry

Ueltzhoffer, Kai, et al. A Drive towards Thermodynamic Efficiency for Dissipative Structures in Chemical Reaction Networks. Entropy. 23/9, 2021. In a paper for a Foundations of Biological Computation issue edited by David Wolpert and Jessica Flack, University College London theorists including Karl Friston describe the apparent activity of natural forces which might impel and foster an oriented emergence of substantial complexities. See also Memory and Markov Blankets by the collegial group et al in this journal. However see Non-equilibrium Thermodynamics and the Free Energy Principle by M. Colombo and P. Palacios in Biology and Philosophy (August 2021) for some issues.

thermodynamically favoured whenever they dissipate free energy that could not be accessed otherwise. These accounts apply as well to relatively simple systems such as convection cells, hurricanes, candle flames, or lightning strikes as they do to complex biological systems. Computational properties such as predictive representations of environmental dynamics can then be linked to the thermodynamics of underlying physical processes. However, the selection of dissipative structures with efficient subprocesses is not well understood. Here we explain how bifurcation-based, work-harvesting processes which sustain complex dissipative structures might be driven towards thermodynamic efficiency. We cite a simple mechanism that leads to self-selection in a chemical reaction network and discuss how this can emerge naturally in a hierarchy of self-similar dissipative forms. (Abstract excerpt)

Animate Cosmos > Organic > Chemistry

Ueltzhoffer, Kai, et al. A Drive towards Thermodynamic Efficiency for Dissipative Structures in Chemical Reaction Networks. Entropy. 23/9, 2021. In a paper for a Foundations of Biological Computation issue edited by David Wolpert and Jessica Flack, University College London theorists including Karl Friston describe the apparent activity of natural forces and potentials so as to impel and foster an oriented emergence of substantial complexities. By our 2021 worldwise lights, a philosophic view could well allow and reveal an independent, phenomenal ecosmic genesis. See also Memory and Markov Blankets by the collegial group et al in this journal. However see Non-equilibrium Thermodynamics and the Free Energy Principle by M. Colombo and P. Palacios in Biology and Philosophy (August 2021) for some issues.

counts of complex structure formation show that their self-organisation is thermodynamically favoured whenever they dissipate free energy that could not be accessed otherwise. These accounts apply as well to relatively simple systems such as convection cells, hurricanes, candle flames, or lightning strikes as they do to complex biological systems. Computational properties such as predictive representations of environmental dynamics can then be linked to the thermodynamics of underlying physical processes. However, the selection of dissipative structures with efficient subprocesses is not well understood. Here we explain how bifurcation-based, work-harvesting processes which sustain complex dissipative structures might be driven towards thermodynamic efficiency. We cite a simple mechanism that leads to self-selection in a chemical reaction network and discuss how this can emerge naturally in a hierarchy of self-similar dissipative forms. (Abstract excerpt)

Animate Cosmos > Organic > Universal

Zurek, Wojciech. Emergence of the Classical from Within the Quantum Universe. arXiv:2107.03378. The veteran LANL theoretical physicist (search) continues his collegial endeavor to finesse the essence of this deepest, fundamental realm. In some way a John Wheeler-like observer function is a necessary activity, which then involves an informational receive/record aspect. By a wider view, our Earthuman phenomenon seems to serve as a microcosmic agent of universal self-articulation, which yet remains an arduous process of to express what may be actually going on.

Decoherence shows how the openness of quantum systems -- interaction with their environment -- suppresses flagrant manifestations of quantumness. Einselection accounts for the emergence of preferred quasi-classical pointer states. Quantum Darwinism goes beyond decoherence. It posits that the information acquired by the monitoring environment responsible for decoherence is disseminated, in many copies, in the environment, and thus becomes accessible to observers. (Abstract excerpt)

Animate Cosmos > Thermodynamics > quant therm

Binder, Felix, et al, eds. Thermodynamics in the Quantum Regime. International: Springer, 2021. This new collection is a good example that nature’s deep domain has become recognized as a substantial field in this energetic regard. It opens with Introduction to Quantum Thermodynamics by Robert Alicki and Ronnie Kosloff, which can be PDF downloaded from the Springer site.

Quantum Thermodynamics is a novel research field which explores its basis in quantum theory and addresses such phenomena which appear in finite-size, non-equilibrium and finite-time contexts. Blending elements from open quantum systems, statistical mechanics, many-body physics, and information theory, it pinpoints thermodynamic advantages and barriers emerging from quantum coherence and correlations. In six sections the book covers topics such as quantum heat engines and refrigerators, fluctuation theorems, the emergence of thermodynamic equilibrium, strongly coupled systems, as well as various information theoretic approaches including Landauer's principle and thermal operations.

Animate Cosmos > Fractal

Feinstein, Adina, et al. Testing Self-Organized Criticality Across the Main Sequence using Stellar Flares from TESS. arXiv:2109.07011.. University of Chicago, MIT and University of Michigan (Fred Adams) add a latest confirmation of nature’s celestial innate preference to reside at this state of optimum efficiency in every disparate instance.

Stars produce explosive flares, which are believed to be powered by the release of energy stored in coronal magnetic field configurations. It has been shown that solar flares exhibit energy distributions typical of self-organized critical systems. This study applies a novel flare detection technique to data obtained by NASA's TESS mission and identifies ∼106 flaring events on ∼105 stars across spectral types. Our results suggest that magnetic reconnection events that maintain the topology of the magnetic field in a self-organized critical state are ubiquitous among stellar coronae. (Abstract)

While the sand pile analogy is simplistic by construction, self-organized criticality naturally manifests in a variety of physical systems. Applications have been found in hydrodynamical turbulence, forest fires and other percolation systems, landslides, neuroscience, climate fluctuations, rainfall, accretion disks, traffic jams, evolution, extinction, financial markets and even Conway's game of Life, to name a non-comprehensive list. (1)

Animate Cosmos > Astrobiology

Mason, Nigel, et al. Systems Astrochemistry: A New Doctrine for Experimental Studies. arXiv:2107.02924. Akin to other unified fields, University of Kent, UK astroscientists propose a comprehensive regimen so as to better quantify an innate ecosmic fertility which seems made and meant to complexify into organic life and our curious speciesphere sapience.

Laboratory experiments are vital to deciphering the chemistry of the interstellar medium (ISM) and the role that complex organic molecules (COMs) play in the origins of life. To date, most studies in experimental astrochemistry have used reductionist approaches. Here we propose a new systems astrochemistry method which draws on current work in the field of prebiotic chemistry, This integral synthesis would focus on the emergent properties of the chemical system by performing the simultaneous variation of multiple parameters. (Abstract excerpt)

Animate Cosmos > exoearths

Shorttle, Oliver, et al. Why Geosciences and Exoplanetary Sciences Need Each Other. arXiv:2108.08382. In an article to appear in a special Geoscience Beyond the Solar System issue (17/4) of Elements: An International Magazine of Mineralology, Geochemistry and Petrology, Cambridge University and Southwest Research Institute astrogeologists including Cayman Unterborn contribute to this grand project going forward as our fittest global genius begins to explore and quantify near and farther orbital environs. A glossary from Abiogenesis Zone and Albedo to Tidal Lock and White Dwarf suits the wild frontier. See also Compositional Diversity of Rocky Exoplanets at 2108.08383, and The Diversity of Exoplanets: From Interior Dynamics to Surface Expressions st 2198L09385, for this issue.

The study of planets outside our solar system may lead to major advances in our understanding of the Earth, and provide insight into the universal set of rules by which planets form and evolve. To achieve these goals requires applying geoscience's wealth of Earth observations to fill in the blanks left by the necessarily minimalist exoplanetary observations. In turn, Earth's many one-offs, e.g., plate tectonics, surface liquid water, a large moon, and life - which have long presented chicken and egg type conundrums for geoscientists - may find resolution in the study of exoplanets possessing only a subset of these phenomena. (Abstract)

Ecosmomics: A Survey of Genomic Complex Network System Sources

Cosmic Code

Renken, Elena. Turing Patterns Turn Up in a Tiny Crystal. Quanta. August 10,, 2021. A science editor gathers an array of 21st century findings along with new evidence that serves to affirm Alan Turing’s 1952 chemical reaction-diffusion theory. The title is about a Nature Physics paper, Nanometric Turing Patterns: Morphogenesis in a Bismuth Monolayer by Yuki Fuseya, et al (July 2021), as a first report of their appearance even on an atomic scale. Other instances are bacterial colonies, animal stripes, Zebra fish embryos, sea shells and more. Of especial note across a widest span is Galactic Disks as Reaction-Diffusion Systems by Lee Smolin (arXiv:astro-ph/9612033) and Turing Instability in an Economic-Demographic Dynamical System can Lead to Pattern Formation on a Geographical Scale by Anna Zincenko, et al (2006.01664). Again from mid 2021, newly due to our EarthWise collaborators, the actual independent presence of nature’s ecosmic generative mathematical code-script is found to be in effect everywhere.

Cosmic Code > nonlinear > networks

Yang, Ruochen, et al. Hidden Network Generating Rules from Partially Observed Complex Networks. Communications Physics. 4/199, 2021. USC (RY and Paul Bogdan) and University of Wisconsin (Frederic Sala) systems theorists (search PB) continue to discern and quantify the presence of common self-organized structural dynamics (as the abstract notes) at each and every natural and human phase. Herein an advanced method is described by which to better elucidate their node/link multiplex occurrence. See also in this journal Unified Treatment of Synchronization Patterns in Generalized Networks with Higher-order, Multilayer, and Temporal Interactions by Yuanzhao Zhang, et al (4/195, 2021).

Complex biological, neuroscience, geoscience and social networks exhibit heterogeneous self-similar higher order structures that are usually characterized as multifractal in nature. However, describing their topologies by a mathematical description and deciphering their governing rules has been elusive and prevents a comprehensive understanding of their networks. Here, we propose a weighted graph model which can reveal the underlying generating rules of complex systems and characterize their node heterogeneity and pairwise interactions. The proposed network generator framework is able to reproduce network properties, differentiate varying structures in brain networks and chromosomal interactions, and detect topologically associating domain regions in conformation maps of the human genome. (Abstract excerpt)

Cosmic Code > nonlinear > 2015 universal

Katsnelson, Mikhail, et al. Self-Organized Criticality in Neural Networks. arXiv:2107.03402. As MK and Tom Westerhout, Radboud University and Vitality Vanchurin, NIH, Bethesda (search VV and MK) continue to propose that such cognitive connectivities have a common natural prevalence, they advance that this SOC optimum condition ought to be appreciated for its definitive advantage. If taken to a farthest implication, the whole ecosmic uniVerse might take on the cerebral semblance of a neural net learning process. See also Emergent Quantumness in Neural Networks at 2012.05082 for another entry by the authors.

We demonstrate, both analytically and numerically, that learning dynamics of neural networks is generically attracted towards a self-organized critical state. The effect can be modeled with quartic interactions between non-trainable variables (e.g. states of neurons) and trainable variables (e.g. weight matrix). Non-trainable variables are rapidly driven towards stochastic equilibrium and trainable variables are slowly driven towards learning equilibrium described by a scale-invariant distribution on a wide range of scales. Our results suggest that the scale invariance observed in many physical and biological systems might be due to some kind of learning dynamics and support the claim that the universe might be a neural network. (Abstract)

Cosmic Code > nonlinear > 2015 universal

Morales, Guillermo and Miguel Munoz. Optimal Input Representation in Neural Systems at the Edge of Chaos. arXiv:2107.05709. University of Granada, Spain complexity theorists (search Munoz) contribute to the latest articulations of nature’s insistent preference for an active balance and poise composed of more or less conserve and create, fixed or flexible, closed or open, modes. Here this optimum occasion is shown to offer much benefit to active informational learning tasks. As such entries typically say nowadays, it is noted that many other physical, biological, cerebral and societal phases are similarly distinguished by this “sweet spot” fittest condition.

Shedding light onto how biological systems represent, process and store information in noisy environments is a key and challenging goal. An innovative hypothesis in the making poses that operating in dynamical regimes near the edge of a phase transition, i.e. at criticality, can provide information-processing living systems with operational advantages as poised between robustness and flexibility. Our contribution in this regard will be to construct an artificial neural network and train it to classify images. Indeed, we find that the best performance is obtained when the network operates near the critical point, at which the eigenspectrum of its covariance matrix follows the same statistics as actual neurons do. Thus, we conclude that operating near criticality can also have the benefit of allowing for flexible, robust and efficient input representations. (Abstract excerpt)

A popular concept from artificial neural networks is that information-processing complex systems, which are composed of many individual interacting units, are best suited to encode, respond, process, and store information if they operate in the dynamical critical point regime of a phase transition, i.e. at the edge between "order" and "disorder.” In regard, there needs to be some trade-off between order and disorder that can be stated in a number of ways, e.g., between "stability and responsiveness" or "robustness and flexibility". The criticality hypothesis poses that such a contrast is resolved near criticality. (1-2)

Cosmic Code > nonlinear > 2015 universal

Munoz, Miguel. Colloquium: Criticality and Dynamical Scaling in Living Systems. Reviews of Modern Physics. 90/031001, 2018. This entry by the veteran University of Granada complexity theorist is reviewed more in Chap. IV Ecosmomics. It has since become considered as a premier exposition of the 21st century vivifying revolution.

Cosmic Code > Genetic Info > Genome CS

Daban, Joan-Ramon. Soft-Matter Properties of Multilayer Chromosomes. Physical Biology. 18/5, 2021. An Autonomous University of Barcelona biochemist offers a latest orientation to the apparently autonomous properties of nature’s fertile materiality, by which to apply them to active genomic phenomena. In each case, self-organizing processes serve to generate vital forms: Chromatin structure is locally dynamic like a liquid crystal fluid. Altogether another example of mid 2021 revolutionary discoveries.

This perspective will identify relationships between the structural and dynamic properties of chromosomes as states of soft-matter systems. Our previous studies, using transmission electron microscopy, atomic force microscopy, and cryo-electron tomography, suggested that metaphase chromosomes have a multilayered structure. The self-assembly of multilayer chromatin plates suggests that metaphase chromosomes are self-organized hydrogels with an internal liquid-crystal order produced by the stacking of chromatin layers along the chromosome axis. The spontaneous assembly of large structures has been studied in different soft-matter systems and the self-organization of chromosomes could be justified by the interplay between weak interactions of repetitive nucleosome building blocks and thermal fluctuations. Furthermore, at the end of mitosis, condensed chromosomes undergo a phase transition into a more fluid structure. (Abstract excerpt)

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Noble, Denis. The Illusions of the Modern Synthesis. Biosemiotics. 14/1, 2021. The octogenarian Oxford University philosophical physiologist (search) continues his career quest to right the wrongs of this misguided theory which persists as the textbook version.. Indeed, a prime purpose of this Natural Genesis resource is to provide annotated documentation for an integral 21st century Genesis Evolutionary Synthesis. Noble’s view is that the MS was cobbled from mid-20th century opinions which took on its own gene-centric cast removed from actual realities. His main suggestion is that an emphasis on individual agencies whose proactive relational behaviors would replace prior passivities. His novel take struck a chord with commentators such as Signs of Consciousness? by Eva Jablonka, Agency and Choice in Evolution by Jonathon Delafield-Butt, The Plurality of Evolutionary Worldviews by Nathalie Gontier and Towards a Biosemiotic Theory of Evolution by Alexei Sharov, along with Tyler Volk, Louise Westling, Kalevi Kull. Aaron Gare and Guenther Witzany. Into these 2020s, whence a global sapiensphere may learn on her/his own (Charlotte and Charles EarthWin), such endeavors to get clear and correct on life’s oriented emergence make a vital contribution.

The Modern Synthesis (MS) has dominated biology for 80 years. It was first formulated in 1942, a decade before the major achievements of molecular biology, including the Double Helix and the Central Dogma (CD). These discoveries and concepts seemed to justify the genetic MS assumptions of accurate nucleotide replication, while the (DNA to RNA to Protein) CD was viewed as excluding the inheritance of acquired characteristics. This article examines the language of the MS to show how it is based on several misinterpretations of what molecular biology has found. In this regard, I cite these four Illusions: 1. Natural Selection; 2. The Weismann Barrier; 3. The Rejection of Darwin’s Gemmules; 4. The Central Dogma itself. An expansive multi-level view of life’s evolution avoids these miscues through the principle of biological relativity. (Abstract excerpt)

In this commentary I expand on the first of Noble’s illusions, the selection metaphor. Building on my work with Simona Ginsburg on the evolution of minimal consciousness, I argue that the existence of some complex sensory and motor patterns in the living world can be accounted for only through the evolution of conscious choice. (Jablonka)

Denis Noble has produced a succinct analysis of the ‘Illusions of the Modern Synthesis’. At the heart of the matter is the place of agency in organisms. This paper examines the nature of conscious agent action in organisms, and the role of affects in shaping agent choice. It examines the dual role these have in shaping evolution, and in the social worlds of scientists that shape evolutionary theory. Its central claim follows Noble, that agency is central to the structure of organisms, and raises careful consideration for the role animal agency and affective evaluations in biology, and in biologists. (Delafield-Butt)

The target article by Denis Noble is an excellent overview of the illusions of the Modern Synthesis that remain in textbooks. Overcoming these illusions shows the active role of organisms in the evolutionary process such as embryo development, epigenetic heredity, multilevel selection and niche construction. But what is still missing is the presence of individual agency, autonomy, semiosis, and goal-directedness. (Sharov)

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