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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 31 through 45 of 110 found.

An Organic, Conducive, Habitable MultiUniVerse

Animate Cosmos > Quantum Cosmology > quantum CS

Jia, Ding. Correlational Quantum Theory. arXiv:2001.03142. We cite this entry by a University of Waterloo doctoral student also associated with the Perimeter Institute for novel views of how this field might continue to advance, as the quotes say. His implication of a correlative organic cosmos would serve to bridge once and future millennia. A further notice is an employ of the “qudit” term to represent higher level combinations (search) above two “qubits.”

A correlational dialect is introduced within the quantum theory language to give a unified treatment of finite-dimensional informational/operational quantum theories, infinite-dimensional quantum field theories, and quantum gravity. Theories are written in terms of correlation diagrams which specify correlation types and strengths. Feynman diagrams emerge as topological classes of correlation diagrams without any perturbative considerations. The correlational formalism is applied in a study of correlation constraints, revealing new classes of quantum processes that evade previous characterizations of general quantum processes including quantum causal structure. (Abstract)

Quantum theory has gone through several phases of evolution. It started as the quantum mechanics of particles, and as a theory of fields. More recently the quantum theory of information has been on the rise. Will the future reveal yet new phases of quantum phenomena? Our vision is that besides particles, fields, and bits (dits), correlations should also be used as a fundamental concept in constructing quantum theories. Generally, we understand quantum correlation as anything that is mediated and has a quantifiable strength in a quantum theory. As such correlations transcend the distinction between particles and fields, which both involve mediated quantifiable correlations, and go beyond qubits, which are limited to finite dimensions). (1)

Qudit: The unit of quantum information described by a superposition of d states, where d is an integer greater than two; the generalization to base d of a qubit. (Wiktionary)

Animate Cosmos > Quantum Cosmology > physics

Ansari, Mohammad and Lee Smolin. Self-Organized Criticality in Quantum Gravity. Classical and Quantum Gravity. 25/095016, 2008. Perimeter Institute theorists advance an early glimpse of nature’s actual innate tendency to seek and maintain itself in an active balance between two coincidental, often complementary opposite states.

We study a simple model of spin network evolution motivated by the hypothesis that the emergence of classical spacetime from a discrete microscopic dynamics may be a self-organized critical process. Self-organized critical systems are statistical systems that naturally evolve without fine tuning to critical states in which correlation functions are scale invariant. We study several rules for evolution of frozen spin networks in which the spins labeling the edges evolve on a fixed graph. We find evidence for a set of rules which behaves analogously to sand pile models in which a critical state emerges without fine tuning, in which some correlation functions become scale invariant. (Abstract)

Animate Cosmos > Organic

Garcia-Ruiz, Juan Manuel, et al. Mineral Self-Organization on a Lifeless Planet. Physics of Life Reviews. January, 2020. JM G-R, University of Granada, Laboratory for the Study of Crystallogenesis, Mark van Zuilen, University of Paris, Institute of Earth Physics, and Wolfgang Bach, University of Bremen, each a veteran geoscientist, post a decisive report to date that Earth’s primordial land and sea materiality has an intrinsic propensity to catalyze, vivify, and develop into a prebiotic chemical milieu. As the 2010 decade of intensely accelerating worldwide research comes to a fruitful close like this, it is becoming possible to quantify and affirm that an organic universal genesis, an oriented evolutionary gestation to our curious, learned humankinder, does indeed exist on its independent own. See also for example, Inorganic Reactions Self-organize Life-like Microstructures Far from Equilibrium Knoll, Pamela and Oliver Steinbock by Pamela Knoll and Oliver Steinbock in the Israel Journal of Chemistry (58/6, 2018).

It has been experimentally found that, under alkaline conditions, silica is able to induce the formation of self-assembled inorganic-inorganic composite materials similar in morphology, texture and nanostructure to hybrid biomineral structures that, millions of years later, life was able to self-organize. These mineral self-organized structures (MISOS) have been shown to be effective catalyzers for prebiotic chemical reactions and to create compartmentalization within the solutions where they form. We reason that, during the very earliest history of this planet, there was a geochemical scenario that inevitably led to the existence of a large array of simple and complex organic compounds, many of which were relevant to prebiotic chemistry.

The primal phase involves a silica-rich high-pH ocean and is powered by two main factors: a) a quasi-infinite source of carbon molecules synthesized abiotically from serpentinization reaction, and b) the formation of self-organized silica-metal mineral composites that catalyze the condensation of molecules in a methane-rich reduced atmosphere. We discuss the plausibility of this geochemical scenario, review the details of the formation of MISOS and its catalytic properties and the transition towards a slightly alkaline to neutral ocean. (Abstract)

Animate Cosmos > Organic > Biology Physics

Gadiyaram, Vasundhara, et al. From Quantum Chemistry to Networks in Biology: A Graph Spectral Approach to Protein Structure Analyses. arXiv:1912.11609. Indian Institute of Science, Karnataka and University of Illinois, Urbana researchers provide a good example of the present integrative frontiers as 2020 science fulfills its stage of common unification from universe to humankinder.

This perspective presents a multidisciplinary characterization of protein structure networks. Our approach will be to synthesize concepts from quantum chemistry, polymer conformations, matrix mathematics, and percolation theory. We then construct protein networks in terms of non-covalently interacting amino acid side chains and to distill information from their graph spectra such as structural integrity. In conclusion, we suggest a further unifying approach to protein structure analyses for larger, more complex networks, such as metabolic and disease networks. (Abstract excerpt)

Animate Cosmos > Organic > Biology Physics

Klosta, Daphne. As Above, So Below, and also in Between: Mesoscale Active Matter in Fluids. Soft Matter. 15/8946, 2019. After a decade of diverse particle (molecules, colloids, microbes, swimmers) studies, a University of North Carolina biomaterials physicist extends the approach onto macro systems such as bird flocks, insect swarms and whale pods. By so doing, it is found that the same phenomena can be observed at each and every wide scale and instance. Into the 21st century this traditional adage can gain its worldwise quantification. See also The Most Active Matter of All by Nicholas Ouellette in the new Cell Press journal Matter (1/2, 2019, third quote).

Living matter, such as biological tissue, can be viewed as a nonequilibrium hierarchical assembly, where self-driven components come together by consuming energy to form increasingly complex structures. The remarkable properties of such living or “active-matter” systems have prompted these questions: (1) do we understand the biology and biophysics that give rise to these properties? (2) can we achieve similar functionality with synthetic active materials? Here we study active matter in liquids and gases for aquatic and avian movements with finite inertia and expect collective behavior to emerge by way of nonlinearities and many-body interactions. The organisms/particles can become quite complex leading to flocking states and nonequilibrium phase transitions. (Abstract edits)

Nature has perfected obtaining robust collective behavior and global order from simple local interactions. The challenge for us is to engineer similar systems at various scales that are composed of many agents, ranging from self-propelled nanoparticles in solution to cars in traffic, and to be able to control their emergent collective properties, their emergent “intelligence.” Our group does computational research on active matter and related topics in order to bridge the gap between emergent phenomena, smart materials and robot swarming. (DK lab website)

The term “matter” encompasses everything from molecules to mountains. It also includes living, sentient beings. If matter composes all physical things, and materials science considers the behavior of such things, can materials science describe the most active matter of all? (Ouellette)

Animate Cosmos > Thermodynamics

Conte, Tom, et al. Thermodynamic Computing. arXiv:1911.01968. This is a report from an NSF supported CCC (Computing Community Consortium) workshop held January 3-5, 2019 at the Prince Wakiki Hotel, Honolulu. Some 40 expert invitees such as Jim Crutchfield, Lidia del Rio, Massimiliano Esposito, Ilya Nemenman, Gavin Crooks, Seth Lloyd, and David Wolpert came together to scope out the necessary transit from earlier macro stages (see Abstract) into deeper energetic, complex, intrinsically self-organizing domains. Its opening phase revisited contacts between physics, information, and thermodynamics over 200 years in a table which runs from Carnot and Babbage through Gibbs, Boltzmann, Turing, Shannon, Prigogine, onto to Hopfield, Landauer, and Hinton. Current interfaces are then noted between past and future via a passage from classical to thermal to quantum methods. In sum, the endeavor continues to trace a path to better mimic natural cosmic, biological, and neural processes.

The hardware and software basics laid in the 20th Century have transformed the world, but the current paradigm faces limits from several perspectives. In terms of hardware, devices have become so small that the effects of thermodynamic fluctuations take over, which are unavoidable at the nanometer scale. In terms of software, our ability to imagine and program implementations are challenged in several domains. These difficulties - device scaling, software complexity, adaptability, energy consumption, and fabrication economics – have run their course. We propose that progress in computing can continue under a united, physically grounded, computational paradigm centered on thermodynamics. We propose a research agenda that accordingly involves complex, non-equilibrium, self-organizing systems in a holistic way that will harness nature's innate computational capacity. (Abstract excerpts)

Animate Cosmos > Thermodynamics

Jeffery, Kate, et al. On the Statistical Mechanics of Life: Schrodinger Revisited. Entropy. 21/12, 2019. At the verge of 2020, senior scientists Kate Jeffery, a University College London psychologist, Robert Pollack, a Columbia University biologist, and Carlo Rovelli, a University of Toulon polymath physicist proceed to revision cosmic, Earthly and human evolution as a single progression that arises from intrinsic energies and structures. Some 75 years after Erwin S. mused that the emergence of living beings must be rooted in and allowed by physical nature, his prescience can now be quantified and verified. To wit, novel insights about thermodynamic forces, (as herein reported), can indeed be seen to engender animate, evolving, recurrent, biospheric systems. One might even imagine we add, a “statistical organics” going forward also for quantum phenomena.

As an extended Abstract alludes, rather than entropic losses being a detriment, in this unique conception these currents are seen to foster orderly, oriented spatial and temporal growth. This vital process is well evinced by gregarious DNA nucleotides as they contain and convey prescriptive information. In this view, the major evolutionary transitions scale, here expanded to twelve steps from replicators to symbolic linguistics, can attributed to entropic and informative flows, as the second quote cites. A further significant consequence is a return of human beings to a consummate position, as per Section 12 and the third quote. Yet, within this grand scenario the word ”random” continues to appear. To reflect, if life’s informed ascent could be taken a big step further to its worldwise personsphere fulfillment, as V. Vernadsky and P. Teilhard did long ago and this site seeks to document, with a 2020 bicameral vision, a phenomenal discovery and destiny might accrue.

We study the statistical underpinnings of life and its increase in order and complexity over evolutionary time. We question some common assumptions about the thermodynamics of life. We recall that contrary to widespread belief, even in a closed system entropy growth can accompany an increase in macroscopic order. We view metabolism in living things as microscopic variables driven by the second law of thermodynamics, while viewing the macroscopic variables of structure, complexity and homeostasis as entropically favored because they open channels for entropy to grow via metabolism. This perspective reverses the conventional relation between structure and metabolism by emphasizing the role of structure for metabolism rather than the converse.

Structure extends in time, preserving information across generations, mainly in the genetic code, but also in human culture. We argue that increasing complexity is an inevitable tendency for systems with these dynamics and explain by way of metastable states, which are enclosed regions of the phase-space that we call “bubbles.” We consider that more complex systems inhabit larger bubbles, and also that larger bubbles are more easily entered than small bubbles. The result is that the system entropically wanders into ever-larger bubbles in the foamy phase space. This formulation makes intuitive why the increase in order/complexity over time is often stepwise and sometimes collapses as in biological extinction (Abstract)

The reason for this step structure can be explained by the statistical interpretation of life developed here: if life is the opening of stable channels for entropy to grow, then evolution, which is a slow random exploration of its phase space, reflects this effect by discovering new major channels into higher-entropy regions of the phase space. Each transition comes with an increase in biological diversity, understood as the acquisition of new stable pathways for entropy to grow, stabilised by the preservation of information in DNA. The earliest transitions were occasional – photosynthesis did not appear for around 2 billion years after life began, for example, while neurons arose only around 600 million years ago. Language appeared a mere 100,000 years ago, and has had a strong effect on the biosphere, via human culture and technological advance. (13)

To close, we turn to the human species; the product of a transitional step in evolution that has further increased the complexity of life’s activities. Humans have evolved a cognitive representational capability that allows us to create new correlations across time and space – that is, new forms of macroscopic order to funnel entropy into metabolism. This is manifest in many ways. For example, the experiential time of our species is much dilated, giving us a wide sense of time flow. We are aware of distant past and can plan far more ahead than any other species. Language allows humans to cooperate in learning and planning; the experience of one individual can be propagated to many others. Writing, and more recently electronic media, has amplified cultural transmissions, allowing us to develop technology that has extended our lifespans and our reach across the planet, and beyond. (14)

Animate Cosmos > Thermodynamics

Nigmatullin, Ramil and Mikhail Prokopenko. Thermodynamic Efficiency of Interactions in Self-Organizing Systems. arXiv:1912.08948. As the century enters its third decade, we cite this posting by University of Sydney complexity scientists as an example of how it has become assumed and affirmed that a natural cosmic genesis does proceed to internally organize itself into quickening complexities from cosmic phenomena to our own intelligent phase.

The emergence of global order in complex systems with locally interacting components is most striking at criticality, where small changes in control parameters result in a global re-organization. We introduce a measure of thermodynamic interaction efficiency in self-organizing systems to quantify the change in order per unit work carried out or extracted. Our analysis formalizes an intuitive understanding of thermodynamic efficiency across diverse self-organizing dynamics in physical, biological and social domains. (Excerpt)

Animate Cosmos > Thermodynamics > quant therm

International Workshop Open Quantum Dynamics and Thermodynamics. https://pcs.ibs.re.kr/PCS_Workshops/PCS_OpeQ. A meeting to be held at PCS IBS (Center for Theoretical Physics of Complex Systems, Institute for Basic Science) Daejeon, South Korea from March 30 to April 2, 2020. We cite as an0ther example of the “second quantum revolution” now well underway, as the summary notes. A recent paper from this group is Nonlinear Topological Photonics at arXiv:1912.01784.

The field of open quantum systems is undergoing rapid development due to new devices based on quantum superposition and coherence. In this context, it is crucial to understand: (i) the thermodynamic behavior of small quantum systems, in particular when in contact with an environment; (ii) the related fluctuation relations that connect thermodynamic quantities such as work and free energy of the device; (iii) effects of intermediate and strong coupling to the environment; (iv) many-body effects and their persistence in the presence of dissipation. The aim of the workshop is to bring together leading researchers to present new results and appropriate methodologies to identify and solve the relevant problems of the field. (Summary)

Animate Cosmos > Thermodynamics > autocat

Peng, Peng, Zhen, et al. An Ecological Framework for the Analysis of Prebiotic Chemical Reaction Networks. arXiv:2001.02533. Wisconsin Institute for Discovery investigators including David Baum describe detailed experimental results that evince the vital role played by primordial autocatalytic chemicals and reactions so that biocomplex systems could together and grow on their way to life’s evolutionary development.

It is becoming widely accepted that very early in the origin of life, even before the emergence of genetic encoding, reaction networks of diverse chemicals might have manifested key properties of life, namely self-propagation and adaptive evolution. Our experiments reveal that seeding an autocatalytic cycle (AC) with tiny amounts of one or more of its energy/food chemicals results in logistic growth of cyclical biochemicals. This finding justifies drawing an instructive analogy between an AC and the population of a biological species. This finding shows that pairs of ACs can have competitive, predator-prey, or mutualistic associations just like biological species. In a stochastic environment, chemical ecosystems with complex dynamics can resemble evolution. (Abstract excerpt, edits)

Animate Cosmos > Thermodynamics > autocat

Wang, Qingpu and Oliver Steinbock. Materials Synthesis and Catalysis in Microfluidic Devices: Prebiotic Chemistry in Mineral Membranes. ChemCatChem. 12/1, 2020. In this ChemPubSoc Europe journal, Florida State University chemists (search OS) add further confirmation of auto-creative processes by which living systems bootstrapped themselves into biocomplex emergence. In this edition, “self-organized compositional gradients,” among other forces are seen in progressive evolutionary effect. See also in this journal Thermodynamically and Kinetically Controlled Reactions in Biocatalysis by Stefan Marsden, et al (12/2) and Nature is the Cure: Engineering Redox Cofactors for Biomimetic and Bioinspired Catalysts by Marine Desage El Murr (12/1).

The processes that led to the origins of life possibly occurred in the inorganic precipitate membranes of alkaline hydrothermal vents. These geochemical systems provide spatial confinement, cross‐membrane gradients, and catalytic surfaces. Their study is challenging due to the vast parameter space and the need to maintain nonequilibrium conditions for long times. Microfluidic approaches offer an efficient solution by allowing the formation of mineral membranes at the interface of flowing reactant solutions and the control of steep gradients. In this minireview, we summarize recent progress with this approach and discuss their catalytic properties in the context of prebiotic chemistry. (Abstract excerpt)

Animate Cosmos > Fractal

Maeder, Andre and Vesselio Gueorguiev. Scale-Invariant Dynamics of Galaxies, MOND, Dark Matter and Dwarf Spheriodals. arXiv:2001.04978. Geneva Observatory and Institute for Advanced Physical Studies, Sofia astrophysicists report further evidence for nature’s pervasive celestial self-similarity. In regard, when we first posted this section in the early 2000s, a detection of any fractal forms in space was spurious and patchy. At this new 2020 decade dawns, their presence in every feature across the spatial raiment and its temporal course are now well proven. By a natural philoSophia, might we contemplate where do these ordained, non-random mathematical regularities come from. Might we wonder and as whatever reality put them there in the first place.

The Scale-Invariant Vacuum (SIV) theory is based on (Herman) Weyl's Integrable Geometry, endowed with a gauge scalar field. The main difference between MOND (Modified Newtonian Dynamics) and the SIV theory is that the first considers a global invariance of space and time, where the scale factor λ is constant, while the second considers λ as a function of time. The SIV theory shows an excellent agreement with observations and with MOND for baryonic gravities. These results support the view that there is no need for dark matter and that the RAR (Radial Acceleration Relation) and dynamical galaxies can be interpreted by a modification of gravitation. (Abstract excerpt)

A Dwarf Spheroidal Galaxy is a term in astronomy applied to small, low-luminosity galaxies with very little dust and an older stellar population. They are found in the Local Group as companions to the Milky Way and to the Andromeda Galaxy. (Wikipedia)

Animate Cosmos > Astrobiology

Yamagishi, Akihiko, et al. Astrobiology: From the Origins of Life to the Search for Extraterrestrial Intelligence. Singapore: Springer, 2019. The Japanese astroscientist editors, posted at the University of Toyko, Tohoku University and the Tokyo Institute of Technology, achieve a comprehensive volume for this field with 31 chapters from Prebiotic Complex Organic Molecules in Space to An RNA World, Eukaryotes and Photosynthesis, Formation of Planetary Systems, and onto the Evolution of Intelligence on Earth and Cosmolinguistics: The Emergence of Language-Like Communication on a Habitable Planet (Abstract below).

The emergence of human language is one of the biggest wonders in the universe. In this chapter, I define "a language-like communication system" and examine the components for the emergence of such a system, not only on Earth but in any habitable planet. Language is a way to transmit an infinite variety of meanings by combining a finite number of tokens based on a set of rules. Thus, it enables compositional semantics. At least three components are necessary: segmentation of context and behavior, the association between them, and the honesty of the emitted signals. I also discuss the possibility of "language as it could be" on other planets. (Cosmolinguistics, Kazuo Okanoya)

Cosmomics: A Genomic Source Code in Procreative Effect

Cosmic Code

Plamen Ch. Ivanov website. physics.bu.edu/people/show/plamen. We cite this home page of the Bulgarian-American, Boston University research professor as an example of the creative, worldwide frontiers of nonlinear, self-organizing complex network theories. From this site, the Keck Laboratory for Network Physiology which Ivanov directs, can be accessed with its rich array of projects, people, and publications. A recent contribution is the discovery of non-equilibrium critical dynamics in bursts of cortical dynamics in sleep/wake cycles (search for 2019 paper). His collegial research across a wide range from condensed matter to cardiac, neural, somatic onto societies well attests to nature’s universally recurrent manifestation of the same mathematical dynamics everywhere.

My research group has introduced several innovative approaches to analyze physiologic data by adapting concepts from modern statistical physics, nonlinear dynamics, and applied mathematics. These methods have been successfully applied to cardiac, respiratory, locomotion, and brain systems, along with sleep-stage transitions and circadian rhythms. Those data-driven approaches enabled us to discover basic laws of physiologic regulation of individual systems whose results were published in leading journals such as Nature, PNAS and Physical Review Letters. Our overall research objective is to develop a new interdisciplinary field, Network Physiology, integrating efforts across statistical and computational physics, biomedical engineering, human physiology, and medicine.

Cosmic Code

Altan-Bonnet, Gregoire, et al. Quantitative Immunology for Physicists. Physics Reports. Online January, 2020. Veteran complexity theorists G A-B, National Cancer Institute, USA, with Thierry Mora Aleksandra Walczak, CNRS Sorbonne University, Paris post a 70 page tutorial which reviews the latest perceptions of this important biological process. It then shows how much the immune system has become understood as another vital manifestation of nature’s universal complexities. Some sections are Ligand-Receptor Interaction, Antigen Diiscrimination, Cel to Cell Communication, and Populations Dynamics of Pathogens and Hosts.

The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of different cells, molecules and sub-systems is often also petrifying. Despite this complexity, as experiments on different scales of the adaptive immune system become more quantitative, many physicists have made both theoretical and experimental contributions that help predict the behaviour of ensembles of cells and molecules that participate in an immune response. Here we review some recent contributions with an emphasis on quantitative questions and methodologies. We also provide a more general methods section that presents some of the wide array of theoretical tools used in the field. (Abstract)

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