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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 38 found.


> Geonativity

Tsakmakidis, Kosmos, et al. Quantum Coherence-driven Self-Organized Criticality and Nonequilibrium Light Localization. Science Advances. May, 2018. UC Berkeley research physicists discern one more actual presence of nature’s optimum dynamic phase ineven at this deepest energetic stage. As a reflection, when I began these studies long ago (e.g., 1987 at the Santa Fe Institute to hear Harold Morowitz) the SO universality of the second quote was a remote hope. Today, in these critical condition 2020s, due to John Beggs and many others, it is vital that our worldwise natural philosopher sapience once again is able at last to perceive and realize what an epochal, numinous discovery has been achieved.

Self-organized criticality emerges in dynamical complex systems driven out of equilibrium and characterizes a wide range of classical phenomena in physics, geology, and biology. We report on a quantum coherence–controlled self-organized critical transition observed in the light localization behavior of a coherence-driven nanophotonic configuration. Our system is composed of a gain-enhanced plasmonic heterostructure controlled by a coherent drive, in which photons close to the stopped-light regime interact in the presence of the active nonlinearities. In this system we observe quantum coherence–controlled self-organized criticality in the emergence of light localization arising from the synchronization of the photons. (Excerpt)

The self-organization of many nonequilibrium complex systems toward an “ordered” state is a profound concept in basic science, ranging from biochemistry to physics.. Examples include the group movement of flocks of birds (, motions of human crowds, neutrino oscillations in the early universe, and the formation of shapes (morphogenesis) in biological organisms. An intriguing trait of this nonequilibrium, driven-dissipative systems is that their self-organization can lead them to a phase transition and to critical behavior — a phenomenon known as self-organized criticality. (1)

> Geonativity

Wang, Zi-Han, et al. Power-law Distribution and Scale Invariant Structure from the First CHIME/FRB Fast Radio Burst Catalog. arXiv:2212.05229. As the abstract notes, Center for Gravitation and Cosmology, Yangzhou University and Frontier Research Center for Gravitational Waves, Shanghai Jiao Tong University physicists describe a strong. pervasive presence across levels and realms of hyper-active celestial phenomena of a tendency to arrive at a self-organized critical state. See also Scale Invariance in X-ray Flares of Gamma-ray Bursts at 2212.08813 for another SOC instance effect.

We study the statistical property of fast radio bursts (FRBs) based on a selected sample of 190 one-off FRBs in the first CHIME/FRB catalog. Three power law models are used in the analysis, and we find the cumulative distribution functions of energy can be well fitted by power law models. The q values in the Tsallis q-Gaussian distribution are constant with small fluctuations for different temporal scale intervals, indicating a scale-invariant structure of the bursts. The earthquakes and soft gamma repeaters show similar properties, which are consistent with the predictions of self-organized criticality systems. (Abstract)

> Geonativity

Wei, Jun-Jie. Scale Invariance in X-ray Flares of Gamma-ray Bursts.. arXiv:2212.08813.. In advanced studies of these wide-spread celestial phenomena, a Purple Mountain Observatory, Chinese Academy of China astronomer once again winds up with a notice and explanation of their intrinsic SOC character.

X-ray flares are produced by the reactivation of the central energy source with a dissipation mechanism as the prompt emission of gamma-ray bursts (GRBs). In this work, we study for the first time the differential size and return distributions of X-ray flares with known redshifts. We find that the duration, energy, and waiting time can be well fitted by a power-law function. The q-Gaussian distributions keep steady for temporal interval scales, imply a scale-invariant structure of GRB X-ray flares. These statistical features can be well explained within the physical framework of a self-organizing criticality system. (Excerpt)

> Geonativity

Zimatore, Giovanna, et al. Self-organization of Whole-Gene Expression through Coordinated Chromatin Structural Transition. Biophysics Reviews. September, 2021. Five geneticists posted in Italy, Japan, and Poland including Masa Tsuchiya provide still another, significant genomic example of nature’s persistence to reach and reside at an optimum reciprocal poise.

The human DNA molecule is a long polymer collapsed into the micrometer space of the cell nucleus. This simple consideration leads to gene-by-gene regulation which better contrasts with the physical reality in the presence of cell state transitions that involvef thousands of genes. This state of affairs invites a statistical mechanics approach where specificity arises from a selective unfolding of chromatin driving the rewiring of gene expression patterns. The arising of “expression waves” marking state transitions can be related to chromatin reorganization through self-organized critical control of whole-genome. (Excerpt)

Our Planatural Edition: A 21st Century PhiloSophia, Earthropo Ecosmic PediaVersion

The Genesis Vision > News

From Computation to Life: The Challenge of a Science of Organization. www.walterfontana.zone/writings. This entry is the Inaugural Lecture for the Chair in Informatics and Computational Sciences 2019-2020 at the Collège de France, Paris by the veteran Harvard Medical School systems biologist (see website). He was notably the coauthor with Leo Buss of The Arrival of the Fittest (1994, search) about an innate evolutionary course. Some 25 years later, this richly composed edition proceeds to describe a deep integration of chemical phenomena with complexity theories and physical substrates which altogether can be expressed b informative computer programs. As the quotes convey, along with a catalytic force, the whole package can well presage a natural genesis synthesis with a global 2020s research agenda. For a current example, see Representing Catalytic Mechanisms with Rule Composition by Jakob Andersen, WF, et al at arXiv:2201.04515,

(3) In addition to statistical models, researchers also construct mechanistic models to gain insight into the dynamical processes that generate the system state reflected in the data. Analyzing the behavior of a molecular interaction network is helpful for understanding how and why a biological system might function. Such networks are modeled at various levels of abstraction. One recent approach represents each interaction as an instruction in a purpose-made programming language. A model then effectively represents a biological system as a program. This is more subtle than just using a computer; it is about representing a complex system using ideas from computation. (E-1)

(4) At a more fundamental level, many systems in nature are composed of components that mutually construct each other in a way that glues them together into a unit: metabolisms, cells, organisms, ecologies, cognitive systems, economies, cultures. All these systems are functional organizations. What kind of dynamics produces organizations of this sort? How much of their architecture is contingent and how much of it is inevitable? The idea of computation is the modern formalization of the idea of mechanism. However, unlike its predecessors, the clockwork and the steam engine, computation emphasizes a constructive aspect of interaction. (E-1)

Auto-catalysis is relevant in origin-of-life scenarios, because it concentrates the mass of a system in the autocatalytic loop, while suppressing many side reactions that could be a kinetic threat. It would be of great interest to understand whether, given hypotheses about the chemical substances and the chemical rules available 3.5–4 billion years ago, this cycle was the only solution in the accessible chemical space, or whether there are other paths. In other words: is the universality in the functional organization of metabolism that we observe today one of many options, or is it necessary? (E-11)

In closing, I would like to take in the whole picture. I tried to span an arc between three chemistries and representations of their interactions founded on ideas from computer science. When endowed with dynamics, all three give rise to aspects I associate with functional organization. At the beginning I asked about such aspects as self-maintaining organizations of logic whose change is constrained, the auto-catalytic chemical networks present in living systems, and the causal structures that organize the signaling processes in cells. These dynamics are a constructive force based on interactions that directly build new objects with new interactive properties. The challenge of a science of (chemical) organization consists in formalizing and understanding this constructive dynamics. (E-16, 17)

The Genesis Vision > News

Jafari, Sajad, et al. Collective Behavior of Nonlinear Dynamical Oscillators. European Physical Journal Special Topics. December, 2022. Teheran Polytechnic and Changzhou University physicists introduce, survey, and summarize a collection of 35 entries herein and elsewhere about the recently quantified presence of a universal propensity to seek and reside at an optimum dynamic, reciprocal condition. Some technical papers are Complete Synchronization Analysis of a Neocortical Network Model, Impact of Repulsive Coupling in Exhibiting Distinct Collective Dynamical States, and Dynamics and Chimera State in a Neural Network with Memristor Coupling as researchers try to define and express this favored feature. And we also wish to record that while Iran, China along with the USA, Russia and everywhere else is in total chaos, such current findings yet remain unknown, not supposed to exist, cut off and unable to contribute this phenomenal resolve.

The Genesis Vision > News

Van der Kolk,, Jasper, et al. Emergence of Geometric Turing Patterns in Complex Networks. arXiv:2211.11311. In November 2022, five Spanish systems theorists including Angeles Serrano and Marian Boguna post an extensive study about how various spatial topologies and shape-shiftings can lead to a wide array of morphogenetic effects across physical, biological and neural phenomena. A further deep affirmation of nature’s invariant, connective vitalities is evidently achieved, once more to prove the independent, ubiquitous presence in kind of these genotype-like mathematics. See also Network Geometry at (2001.03241) and Network Cosmology (1310.6272) by this collegial group.

The Turing instability due competing species of diffusive particles is an important framework for describing non-equilibrium self-organization across chemical and biological systems. These patterns have recently been observed in large complex networks with scale-free degree distributions and the small world property. In this work we study geometric random graph models, where the network topology arises from the fact that nodes live in an underlying similarity space. These results indicate that there is a profound connection between network functions and its hidden reaction-diffusion processes. (Excerpt)

Pedia Sapiens: A Planetary Progeny Comes to Her/His Own Actual Factual Knowledge

A Learning Planet > The Spiral of Science > deep

Russell, Stuart. Human Compatible: Artificial Intelligence and the Problem of Control. New York: Penguin, 2020. A timely volume by the senior UC Berkeley computer scientist authority which is a basic guide for this disparate, frontier field. See his latest article If We Succeed in Daedulus for April 2022, along with a 2019 book and current articles by Melanie Mitchell.

Superhuman artificial intelligence is an tidal wave that threatens not just jobs and human relationships, but civilization itself. AI researcher Stuart Russell argues that this scenario can be avoided, but only if we rethink AI from the ground up. Russell begins by exploring the idea of intelligence in humans and in machines. He describes the near-term benefits we can expect, from intelligent personal assistants to accelerated scientific research. He also spells out the ways humans are already finding to misuse AI, from lethal autonomous weapons to viral sabotage. Russell suggests that we can rebuild AI on a new foundation, according to which machines are designed to be inherently uncertain about the human preferences they are required to satisfy. (Publisher)

Since its inception, AI has operated within a standard model whereby systems are designed to optimize a fixed, known objective. This model has been increasingly successful. I briefly summarize the state of the art and its likely evolution over the next decade. At the same time, the standard model will become progressively untenable in real-world applications because of the difficulty of specifying objectives completely and correctly. I propose a new model for AI development in which the machine’s uncertainty about the true objective leads to qualitatively new modes of behavior that are more robust, controllable, and deferential. (Article)

Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet Lifescape

Animate Cosmos > Organic > Gaia

Arthur, Rudy and Arwen Nicholson. A Gaian Habitable Zone. arXiv:2301.02150. This present paper can serve to note a flow of perceptive work by the University of Exeter computer scientist and astronomer team. See also Does God Play Dice: Simple Models of Non-Darwinian Selection at 2301.06223 and There’s No Planet B in Aeon Magazine for January 2023. Their contribution seems to be a recognition that any favorable candidate, like our home Earth, should be seen a self-regulating biosphere over its evolutionary span. But an implication becomes that space travel to another world will not work because any other world will take to long to become a vital, sustainable place. Still another aspect is that any search for atmospheric biosignatures need be aware of this.

Animate Cosmos > Information

Bawden, David and Lyn Robinson. Still Minding the Gap? Reflecting on Transitions between Concepts of Information. Information. 11/2, 2020. City University of London, Centre for Information Science scholars continue to consider ways to achieve an integrative definition and synthesis of the prior, disparate expressions of this prime feature of living systems. In regard they specifically cite many entries in this subject section. But again, without any sense of a common, independent existence which proceeds with an evolutionary development, this vital unity will ever allude.

This contribution to the tenth anniversary Special Issue of Information gives a cross-disciplinary review of conceptual theories of information. A selective literature survey is used to update our 2013 article on different views across the physical and biological sciences, and onto the humanities (philosophy) and social sciences. The dissonances between these versions remain, although there has been an increasing interest in a common convergence. The solution is likely to be either a general theory of sufficient flexibility to cope with multiple meanings of information, or multiple and distinct theories for different domains, but with a complementary nature. (Abstract excerpt)

Animate Cosmos > Thermodynamics > autocat

Fontana, Walter and Phillpp Honegger. Translation of a 1971 Paper by Otto Rossler and a Commentary. arXiv:2209.04731.. Otto Rossler’s paper is a landmark in the chemical landscape that was all but missed despite providing a consequential refinement of the idea of generalized autocatalysis, which refers to a system that facilitates its own growth. Harvard Medical School system biologists (search WF) post a once and future survey over 50 years about how many domains across a long evolutionary development can be factually appreciated as a catalytic process by which living systems proceed to make themselves The author’s commentary continues from Rossler onto classic versions by Manfred Eigen, Stuart Kauffman, Tibor Ganti and others.

Animate Cosmos > Thermodynamics > autocat

Kutner, Corinna, et al. The Photophysics of Nucleic Acids: Consequences for the Emergence of Life. ChemSystemsChem. 4/6, 2022. Harvard Smithsonian Center for Astrophysics quantify even more explanatory reasons about an innate vitality which serves to engender an increasing, oriented series of complex biomolecules and procreative processes.

Absorption of ultraviolet (UV) radiation can trigger a variety of photophysical and photochemical reactions in nucleic acids. In the prebiotic era, on the surface of the early Earth, UV light could have played a major role in the selection of biomolecules via a balance between synthetic and destructive pathways. As nucleic acid monomers assembled into polymers, their non-enzymatic replication hinged on a photo-stability and self-repair of lesions by UV charge transfer. This review summarizes the photophysical processes in nucleic acids and their implications for chemical and genetic selection at the emergence of life and the origin of translation. (Abstract)

Animate Cosmos > Astrobiology

Rennie, John and Allison Parshall.. Inside Ancient Asteroids, Gamma Rays Made Building Blocks of Life. Quanta. January 4, 2023. Science writers consider a latest research paper about how such astro-energies might have actually fostered life’s advancing biomolecular complexities. The subject entry is Gamma-Ray-Induced Amino Acid Formation in Aqueous Small Bodies in the Early Solar System by Yoko, Kebukawa, et al (Yokohama National University, Japan) in ACS Central Science, December 7, 2022, which is reachable from the text.

A new radiation-based mechanism adds to the ways that amino acids could have been made in space and brought to the young Earth. But where did these amino acids come from? The amino acids flowing through our ecosystems are products of cellular metabolism, mostly in plants. What nonbiological mechanism could have put them in meteorites and asteroids? Scientists have thought of several ways, and recent work by researchers in Japan points to a significant new one: a mechanism that uses gamma rays to forge amino acids. Their discovery makes it seem even more likely that meteorites could have contributed to the origin of life on Earth.

Carbonaceous chondrites contain life’s essential building blocks, including amino acids, and their delivery of organic compounds would have played a key role in life’s emergence on Earth. Aqueous alteration of carbonaceous chondrites is a widespread process induced by the heat produced by radioactive decay of nuclides like 26Al. Simple ubiquitous molecules like formaldehyde and ammonia could produce various organic compounds, including amino acids and complex organic macromolecules. However, the effects of radiation on such organic chemistry are unknown. In this paper, we propose a new prebiotic amino acid formation pathway that contributes to life’s origin. (Kebukawa Excerpt)

Animate Cosmos > exoearths

Inutsuka, Shu-ichiro, editor in chief. Protostars & Planets VII. Tempe: University of Arizona Press, 2023. This entry will be about this latest series (search) volume, and the international conference in Japan in April 2023 from which its chapters are drawn. We note, for example, Offner, Stella, et al. The Origin and Evolution of Multiple Star Systems by Stella Offner, et al, Organic Chemistry in the First Phases of Solar-type Protostars by Ceccarelli, Cecilia, Ceccarelli,et al, Architectures of Compact Multi-Planet Systems by Lauren Weiss, et al and Chemical Habitability: Supply and Retention of Life's Essential Elements During Planet Formation by Krijt, Sebastiaan, Krijt, et al. Our EarthMost global and galactic quest picks up again going forward.

Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus and Sulfur (CHNOPS) play key roles in the origin and rise of life on Earth. We begin by citing the CHNOPS budget on Earth, their role in shaping our biosphere, and origins in the Solar Nebula. We then view how these elements are distributed in diverse astrophysical settings, tracing their journeys from synthesis in dying stars to molecular clouds, and onto temperate rocky planets around main sequence stars. (Krijt, S. excerpt)

Animate Cosmos > exouniverse

Wood, Charlie. Why This Universe? A New Calculation Suggest Our Cosmos is Typicall. Quanta. November 17,, 2022. A science writer surveys the latest conjectures about what kind of spatial and temporal environs we Earthlings may actually find ourselves. As a gloss, our scientific scenario this far may be legitimate due to a new array of physical and energetic features. Latham Boyle, Perimeter Institute and Neil Turok, its once director and now at the University of Edinburgh post novel theoretical reasons, which cast back to the 1970s, as to why this is the phenomenal case. See, for example, their Thermodynamic Solution of the Homogeneity, Isotropy and Flatness Puzzles. (arXiv:2210.01142) and The Big Bang as a Mirror: A Solution of the Strong CP Problem (2208.10396) papers.

Two physicists have calculated that the universe has a higher entropy — and is therefore more likely — than alternative possible universes. The calculation is “an answer to a question that is yet to be fully understood.” The properties of our universe — smooth, flat, just a pinch of dark energy — are what we should expect to see, according to a new calculation.

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