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Displaying entries 16 through 30 of 82 found.
Animate Cosmos > Organic > Biology Physics
Weber, Christoph, et al.
Physics of Active Emulsions.
As nature comes to life, MPI Physics of Complex Systems and Imperial College London biophysicists provide new appreciations of this broad class of colloidal, multi-droplet chemicals so to reveal their innate mobility. See also a later entry Novel Physics Arising from Phase Transitions in Biology at 1809.11117.
In summary, we have discussed a new class of physical systems which we refer to as active emulsions. These emulsions are relevant to cell biology. They may allow to develop novel applications in the field of chemical engineering or aqueous computing and could help explain how life could have emerged from an inanimate mixture composed of set of simple chemically active molecules. However, the class of active emulsions also challenge our theoretical understanding of spatially heterogeneous systems driven far away from thermal equilibrium and can be used to refine existing theoretical concepts. In particular, active emulsions are characterised by non-equilibrium fluxes that maintain these system away from thermal equilibrium. (37)
Animate Cosmos > Information > Quant Info
Making Better Sense of Quantum Mechanics.
Reports on Progress in Physics.
The veteran Cornell University physicist rightly observes that quantum studies have been impeded and burdened by an absence of philosophical thought or vision. (The late Stephen Hawking often claimed this.) So it remains an historical collection of disparate opinions. The first half of the paper is a shorter and longer essay on Quantum Bayesism (QBism) perspectives. It then broadly compares this model with writings from John Bell and Niels Bohr alphabetically to Erwin Schrodinger and Stephen Weinberg, 15 men in all. This leads to a section entitled There is no Classical World and a consequent new physics of Now. Mermin closes with his 2017 talk in the Czech Republic, as noted in the second quote.
We still lack any real consensus about what quantum mechanics means. The absence of conceptual clarity for almost a century suggests that the problem might lie in some implicit misconceptions about how scientific explanations are reached. I describe here some unvoiced but widely shared assumptions. This new view of physics requires physicists to think about science in an unfamiliar way. My primary purpose is to explain the new perspective and urge that it be taken seriously. My secondary aims are to explain why this perspective differs significantly from what Bohr, Heisenberg, and Pauli had been saying, and why it is not solipsism. To emphasize that this is a general view of science, and not just of quantum mechanics, I apply it to a long-standing puzzle in classical physics: the apparent inability of physics to give any meaning to 'Now' - the present moment. (Abstract)
Animate Cosmos > Intelligence
Science starts with mind, the private library of experience for each of us. From the contents of our own experience each of us strives to assemble what that experience means about the world that gives rise to it. An all too common misreading of QBism in the popular scientific press is “It’s all mind”. This is as wrong as the opinion most physicists have about physics, that it’s all world. There is mind and there is a world. Quantum mechanics has taught us that we cannot understand what we are talking about without paying attention to both. What links the contents of my mind to the world that induces them is the meaning I construct for my experience. If I had to design a coat of arms for QBism, it would display three words: mysl, smysl, sv ̆et in poetic Czech which is Mind, Meaning, World. (15-16)
Universe, Life, Consciousness.
This is a talk by the Russian-American, Stanford University philosophical cosmologist given at a 2015 Science and Nonduality Conference in California. Long ago I was fortunate to attend his first public lecture in the USA in September 1983 at Harvard where he spoke about a novel inflationary origin and a fractal multiverse of bubbling cosmoses. In the years since this theory has become an accepted version (with objections) as global science advanced from overhead slides to streaming videos. But Linde has a visionary side and here evokes an “eternally existing self-reproducing inflationary universe” due to quantum wave fluctuations which leads to the unusually important role played by the concept of an observer in cosmology. A mid 2010s result is another inference of a self-observing, participant universe. By these lights, the presence of informed, personal awareness would seem to be a phenomenal imperative by which to bring a genesis cosmos into being.
Is it not possible that consciousness, like space-time, has its own intrinsic degrees of freedom, and that neglecting these will lead to a description of the universe that is fundamentally incomplete? What if our perceptions are more real than material objects? Is it possible to introduce a “space of elements of consciousness,” and investigate that consciousness may exist by itself, even in the absence of matter, just like gravitational waves, exist in the absence of protons and electrons? Will it not turn out, with the further development of science, that the study of the universe and the study of consciousness will be inseparably linked? After the development of a unified geometrical description of the weak, strong, electromagnetic, and gravitational interactions, will the next important step be the development of a unified approach include the world of consciousness? (12)
Animate Cosmos > Thermodynamics > autocat
Jee, Ah-Young, et al.
Catalytic Enzymes are Active Matter.
Proceedings of the National Academy of Sciences.
Center for Soft and Living Matter, Institute for Basic Science, South Korea researchers including Tsvi Tlusty cite theoretical and experimental reasons why this biological substance can well exhibit spontaneous activity.
Using a microscopic theory to analyze experiments, we demonstrate that enzymes are active matter. Superresolution fluorescence measurements—performed across four orders of magnitude of substrate concentration—show that catalysis boosts the motion of enzymes to be superdiffusive for a few microseconds, enhancing their effective diffusivity over longer timescales. Occurring at the catalytic turnover rate, these fast ballistic leaps maintain direction over a duration limited by rotational diffusion, driving enzymes to execute wormlike trajectories by piconewton forces. These findings violate the classical paradigm that chemical reaction and motility are distinct processes, and suggest reaction–motion coupling as a general principle of catalysis. (Abstract excerpt)
Animate Cosmos > Fractal
Anitas, Eugen Mircea and Azat Slyamov.
Emergence of Surface Fractals in Cellular Automata.
Annalen der Physik.
In this German journal since 1799, Joint Institute for Nuclear Research, Dubna, Russia physicists, with other postings in Almaty, Kazakhstan and Bucharest, Romania describe a clever method for visualizing this topological presence. Our interest extends beyond the global research facility only now possible to a mindfulness that we phenomenal learners are witnessing an intrinsic geometry and mathematics, as Galileo and others foresaw, that does exist on its prior own. Such nascent realizations then one to wonder “whomever “put it all there in the first place.
Self‐similar (fractal) structures are present at every scale ranging from galaxies down to aggregates of atoms to elementary particles. For surface fractals, the self‐similarity is inherited from the superposition of non‐overlapping mass fractals. Despite long‐standing theoretical investigations, no generic framework exists yet to describe the nature and generation of surface fractal systems. Here, cellular automata (CA) are identified as a generic mathematical system and, by exploring the associated small‐angle scattering (neutrons, X‐rays, light) intensity curves, the emergence of surface fractals is reported. The finding on the emergence of surface fractals in CA will enrich the understanding of their structural properties while the approximation of independent objects can provide a route toward testing randomness generated by CA. (Abstract excerpt)
Animate Cosmos > Fractal
Cosmai, Leonardo, et al.
Fractal Universe and Cosmic Acceleration in a Lemaitre-Tolmon-Bondi Scenario.
When we began this section in the early 2000s, the presence of self-similar structures was suspected but their verification, still open to question, across many scales was just beginning. Here Italian astrophysicists including Luciano Pietronero and Francesco Labini (search each) can now affirm, some 90 years after Lemaitre and 4 centuries after Galileo, that an intrinsic mathematical geometry does indeed suffuse the celestial raiment.
In this paper we attempt to answer the question: can cosmic acceleration of the Universe have a fractal solution? We give an exact solution of a Lemaitre-Tolman-Bondi (LTB) Universe based on the assumption that such a smooth metric is able to describe, on average, a fractal distribution of matter. While the LTB model has a center, we speculate that, when the fractal dimension is not very different from the space dimension, this metric applies to any point of the fractal structure when chosen as center so that there is not any special point or direction. We examine the observed magnitude-redshift relation of type Ia supernovae, showing that the apparent acceleration of the cosmic expansion can be explained as a consequence of the fractal distribution of matter. (Abstract)
Animate Cosmos > Astrobiology
Maiolino, Roberto and Filippo Mannucci.
De Re Metallica: The Cosmic Chemical Evolution of Galaxies.
In an invited review for Astronomy & Astrophysics, Cambridge University and Arcetri Observatory, Italy astrophysicists post a latest 119 page review of our collaborative, instrumental ability to quantify and describe to any extent the elemental and compound makeup of ancient stellar and galactic formations.
The evolution of the content of heavy elements in galaxies, the relative chemical abundances, their spatial distribution, and how these scale with various galactic properties, provide unique information on the galactic evolutionary processes across the cosmic epochs. In recent years major progress has been made in constraining the chemical evolution of galaxies and inferring key information relevant to our understanding of the main mechanisms involved in galaxy evolution. After an overview, we discuss the observed scaling relations between metallicity and galaxy properties, the observed relative chemical abundances, how the chemical elements are distributed within galaxies, and how these properties evolve across the cosmic epochs. (Abstract excerpt)
Animate Cosmos > Astrobiology
Sadjadi, SeyedAbdolreza and Quentin Parker.
The Astrochemistry Implications of Quantum Chemical Modes Vibrational Analysis.
We note this entry by University of Hong Kong, Laboratory for Space Research astroscientists for its evidence of how cosmic materiality seems innately made to form biomolecular complexities, and as another instance of how collective human intellect can so readily explore and quantify any width and depth of this universal spacescape. Surely there must be some grand reason and purpose if me + We might just be able to ask.
Animate Cosmos > Astrobiology
Introduction to Astrochemistry: Chemical Evolution from Interstellar Clouds to Star and Planet Formation..
A University of Tokyo biophysicist provides a later 2010s comprehensive technical survey from Molecular Abundances and Diffuse Clouds to Star and Planet Forming Regions.
This important book describes the basic principles of astrochemistry — an interdisciplinary field combining astronomy, physics, and chemistry — with particular emphasis on its physical and chemical background. Chemical processes in diffuse clouds, dense quiescent molecular clouds, star-forming regions, and protoplanetary disks are discussed, along with molecular spectroscopy and observational techniques. These contents provide astronomers with a comprehensive understanding of how interstellar matter is evolved and brought into stars and planets, which is ultimately related to the origin of the solar system.
Turnbull, Laura, et al.
Connectivity and Complex Systems: Learning from a Multi-Disciplinary Perspective.
Applied Network Science.
As an example of our present integrative phase after years of special studies, eleven generalists from the UK, Germany, the Netherlands, Cyprus, and Sweden proceed to identify and describe a common feature, as the Abstract cites, which plays a formative role from geology to ecology. The paper first describes this fundamental associative property being found to join the prior pieces, as underway in genomic relations and neural networks. In this necessary turn isolate parts are brought into an actual unitary whole. Six subject areas as below are then reviewed to show how the same lineaments are in similar effect everywhere. With this in place, basic “toolbox” methods are specified to define connective features from the biosphere to cultures going forward. Several reference pages over the past decades document the research divergence and convergence.
In recent years, parallel developments in disparate disciplines have focused on what has come to be termed connectivity; a concept used in understanding and describing complex systems. Conceptualizations have evolved largely within their disciplinary boundaries, yet similarities in this concept and its application among disciplines are evident. This situation leads us to ask if there an approach to connectivity that might be applied to all disciplines. In this review we explore four ontological and epistemological challenges. These are: (i) defining the fundamental unit for the study of connectivity; (ii) separating structural connectivity from functional connectivity; (iii) understanding emergent behaviour; and (iv) measuring connectivity. We draw upon insights from Computational Neuroscience, Ecology, Geomorphology, Neuroscience, Social Network Science and Systems Biology to explore the use of connectivity among these disciplines. (Abstract excerpt)
Cosmic Code > Algorithms
Chu, Dominique, et al.
Computation by Natural Systems.
University of Kent, Sydney, and Kansas researchers including Mikhail Prokopenko introduce an issue with this title about the many ways that evolutionary, organic and cerebral life seems to be primarilly engaged in mathematical processes. Some papers are Computational Modelling Unravels the Clockwork of Cyanobacteria, Haematopoietic Stem Cells, and Semantic Information Autonomous Agency and Non-Equilibrium Statistical Physics (Artemy Kolchinsky and David Wolpert.
Computation is a useful concept far beyond the disciplinary boundaries of computer science. Perhaps the most important class of natural computers can be found in biological systems that perform computation on multiple levels. From molecular and cellular information processing networks to ecologies, economies and brains, life computes. Despite ubiquitous agreement on this fact going back as far as von Neumann automata and McCulloch–Pitts neural nets, we so far lack principles to understand rigorously how computation is done in living, or active, matter. What is the ultimate nature of natural computation that has evolved, and how can we use these principles to engineer intelligent technologies and biological tissues? (Abstract)
Cosmic Code > Algorithms
Ikegami, Takashi, et al, eds.
ALIFE 2018 Conference Proceedings.
Cambridge: MIT Press,
The edition is from a combined meeting of the European Artificial Life and Synthesis and Simulation of Living Systems groups held in Tokyo in July. It is available online as abstracts and full papers at www.mitpressjournals.org/toc/isal/30, Typical sessions are Hybrid Life: Approaches to Integrate Biological, Artificial and Cognitive Systems, Evolutionary Dynamics and Information Theory and Flow. Amongst the titles are The Self-Assembling Brain by Robin Hiesinger, Integrated Information and Autonomy in the Thermodynamic Limit by Miguel Aguilera and Ezequiel Di Paolo, Interfacing Synthetic Cells with Biological Cells by Giordano Rampioni, Socio-Technical Evolution by Martin Rosenlyst, et al, Holonomic Cellular Automata by Ada Diaconescu, et al, and An Iterated Learning Approach to the Origins of the Standard Genetic Code by Tom Froese, at al. In addition, we review (search) Major Transitions in Planetary Evolution by Hikaru Furukawa and Sara Walker, and Critical Learning vs. Evolution by Sina Khajehabdollahi and Olaf Witkowski.
Cosmic Code > 2015 universal
Aguilera, Miguel and Manuel Bedia.
Adaptation to Criticality through Organizational Invariance in Embodied Agents.
When we posted this site in the early 2000s, a theoretical and evidential basis for a universally recurrent iconic image was iffy and patchy at best. Back to the 1980s at the Santa Fe Institute, to general systems theory in the 1960s, and before, it was a Grail-like hope and goal. But in these later 2010s, University of Zaragoza, Spain biophysicists, for example, now immersed in a global sapiensphere can describe, the natural presence of a complementary, dynamic reciprocal balance between archetypal fixed and fluid, conservative and procreative, states and options. See also, e.g., physicist Gai Dvali for a cosmic and neural correspondence. In regard, perennial east and west wisdom has long intimated a common, bigender code which graces and moves this fraught existence. By this deep quality, it is made and meant to be humanly known, palliated, and created anew. If me + We = US may at last decipher, read and practice, a genesis code can inform and guide personal and planetary abidance.
Many biological and cognitive systems do not operate deep within one or other regime of activity. Instead, they are poised at critical points located at phase transitions in their parameter space. The pervasiveness of criticality suggests that there may be general principles inducing this behaviour, yet there is no well-founded theory for understanding how criticality is generated at a wide span of levels and contexts. In order to explore how criticality might emerge from general adaptive mechanisms, we propose a simple learning rule that maintains an internal organizational structure from a specific family of systems at criticality. (Abstract excerpt)
Cosmic Code > 2015 universal
In physics, the concept of universality allows to group a great variety of different critical phenomena into a small number of universality classes in such a way that all systems belonging to a given universality class are essentially identical near the critical point. Thus, systems belonging to the same universality class, even if defined by very different material parameters or physical properties, have the same critical exponents. (2) This surprising property provides a perspective on criticality in terms of universal relations, suggesting that we could model criticality using simple and non-specific mechanisms independently of the individual parameters of the system. (2)
Life at the Edge: Complexity and Criticality in Biological Function.
The Center for Complex Systems & Brain Sciences, National University of San Martin, Buenos Aires polyphysicist posts his tutorial lecture from June at Jagellonian University, Poland, in cooperation with UNSAM, Argentina. As the Abstract cites, Chialvo (search) has been a leading researcher for two decades of self-organized critical phenomena across nature, especially in cerebral form and function. (I heard Per Bak speak in 2000.) But in this 2018 entry, a deep and wide veracity and synthesis can now be reported. In addition to neural activity, an innate tendency for natural systems such as proteins, microbes and groupings to seek and reach an optimum poise of more or less orderly states is strongly evident. A dynamic duality of conserve/create, control/liberate, segmented/integrated, me entity and We empathy, and ever more, from which complexity, phase transitions and consciousness arise, is found to be a common preference. Yet as I edit this on the day after the US elections, however can it dawn, as it must, that so many 50 – 50 splits are an epitome of this cosmic complementarity?
By virtue of these findings, DC proposes that integrated information theory (Tononi) also resides in a critical balance by which foster consciousness. Now in the worldwise context of this website, a once and future confirmation of universal yang/ying (bigender) principles in a whole Taome is being achieved. See also, for example, Homeostatic Plasticity and Emergence of Functional Networks in a Whole-Brain Model at Criticality Nature Scientific Reports (8/15682) and Growing Critical: Self-Organized Criticality in a Developing Neural Brain at (1811.02861). But in the later 2010s, bereft of any integral reality, political dichotomies remain locked in destructive battle.
Why life is complex and importantly what is the origin of the over abundance of complexity in nature? This is a fundamental scientific question which, paraphrasing the late Per Bak (1946-2002), "is screaming to be answered but seldom is even being asked". In these lectures we review recent attempts across several scales to understand the origins of complex biological problems from the perspective of critical phenomena. To illustrate the approach three cases are discussed, namely the large scale brain dynamics, the characterisation of spontaneous fluctuations of proteins and the physiological complexity of the cell mitochondria network. (Abstract)
Cosmic Code > 2015 universal
The next sections will progressively introduce the problem of complexity and how its origin can be related to critical phenomena. The examples were chosen with the intention to persuade the reader that the same simple laws apply exactly to very different complex phenomena, a notion known in physics as universality. (1) Phase transitions occur in all the matter that surrounds us, and its study has been systematised recently in a great variety of collective phenomena that occur whenever a large number of non-linear elements interact. It is known, for example, that the correlations between the parts that make up a system obey statistically identical rules, regardless of whether the constituent elements are neurons, ants, grains of sand or water molecules. In all cases, the same theory explains how the system is ordered or disordered, what types of collective behavior
can be expected, how stable or unstable they will be, how it can be disturbed etc. The fact that all these disparate phenomena obey the same laws is what is known in physics as universality. (3)
The universality discussed here suggests that the way in which complexity emerges in the example of the magnetization can be seen generically in phase transitions at systems very different from one another. Indeed many examples can be found in the recent literature such as bird flocks, large groups of neurons, stockbrokers, etc. We will discuss three examples including important aspect of cerebral dynamics, as well as proteins and mitochondrial dynamics, all governed by common universal principles. (4) Complexity is Always Critical: The preceding paragraphs summarize one of the lessons of statistical physics: complexity and criticality are almost synonymous: what makes a system complex are exactly the same properties exhibited by a system when it approaches the critical point of an order-disorder phase transition. (4)
It is remarkable how universality allows us to use the exact same framework to study complex phenomena of very different nature and scales, from a culture of few thousand neurons to the entire brain, from a small protein molecule to a network spanning the entire cell. (11)
Frank, Steven A..
The Price Equation Program: Simple Invariances Unify Population Dynamics, Thermodynamics, Probability, Information and Inference.
The UC Irvine biologist continues his project (search SAF website) to finesse and expand evolutionary and selective theories by way of affinities with and rootings in physical, mathematical, energetic, and communicative domains. Into the 2010s by contributions as this, it is increasingly apparent that a universal recurrence in kind of a common iconic source code is in independent, procreative effect. See also Universal Expressions of Population Change by the Price Equation by SAF in Ecology and Evolution (7/3381, 2017).
The fundamental equations of various disciplines often seem to share the same basic structure. Natural selection increases information in the same way that Bayesian updating does. Thermodynamics and probability distributions express maximum increase in entropy, which appears mathematically as loss of information. Physical mechanics follows paths of change that maximize Fisher information. This web of vague analogies hints at a deeper common mathematical structure. I suggest that the abstract Price equation expresses that underlying universal structure as it describes dynamics as the change between two sets. One component of dynamics expresses the change in the frequency of things, holding constant the values associated with things. The other component of dynamics expresses the change in the values of things, holding constant the frequency of things. From that perspective, interpretations such as selection, information, entropy, force, acceleration, and physical work arise from the same underlying geometry expressed by the Price equation. (Abstract excerpts)
My goal has been to reveal the common mathematical structure that unifies seemingly disparate results from different subjects. The common mathematical structure arises primarily through simple invariances and their expression in geometry. (15)
In the theory of evolution and natural selection, the Price equation (George R. 1922-1975) describes how a trait or gene changes in frequency over time. The equation uses a covariance between a trait and fitness to give a mathematical description of evolution and natural selection. It provides a way to understand the effects that gene transmission and natural selection have on the proportion of genes within each new generation of a population. (Wikipedia)