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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 16 through 30 of 64 found.


An Organic, Conducive, Habitable MultiUniVerse

Animate Cosmos > Quantum Cosmology > physics

Nakamura, Eita and Kunihiko Kaneko. Statistical Evolutionary Laws in Music Styles. Nature Scientific Reports.. 9/15993, 2019. In late 2019, Kyoto University and University of Tokyo, Universal Biology Institute offer a good example of our 21st century worldwise project reaching a systemic synthesis across these widest ecosmos to cultural occasions, and every other natural and social phase in between. In significant regard, a reciprocal presence even in musical compositions of dual phases of conserved tradition, and a creative originality is recorded. So once again an iconic reciprocity akin to physical energy and our bicameral brains is found to grace score and song. See also Cultural Evolution of Music by Patrick Savage in Nature Communications (5/16, 2019).

If a cultural feature is transmitted over generations and exposed to stochastic selection, its evolution may be governed by statistical laws. Music exhibits steady changes of styles over time, with new characteristics developing from traditions. Here we analyze Western classical music data and find statistical evolutionary laws. We then study an evolutionary model where creators learn from past data so to generate new data to be socially selected according to the content dissimilarity (novelty) and style conformity (typicality). The model reproduces the observed statistical laws and can make predictions for independent musical features. In addition, the same model with different parameters can predict the evolution of Japanese enka music. Our results suggest that the evolution of musical styles can partly be explained and predicted by the evolutionary model incorporating statistical learning. (Abstract excerpts)

In the evolutionary process studied here, the balance between novelty and typicality (i.e. content dissimilarity and style conformity) plays an essential role. As we saw in the classical music data and enka music data, relative values can influence the direction and speed of evolution. The novelty and typicality biases can then be important for other types of culture. Evolutionary dynamics of language, other genres of music, scientific topics, and sociological phenomena are among topics under investigation. Another relevant topic is the evolution of bird songs, where selection-based learning is important. Bird song dynamics have been studied to describe the interaction between generators (singing birds) and imitators, which is similar to the novelty-typicality dyad in this study. (7, edits)

Animate Cosmos > Organic

Branscomb, Elbert and Michael Russell. On the Beneficent Thickness of Water. Interface Focus. October, 2019. In an 80th birthday festschrift for the NASA astrobiologist Michael Russell, he and the University of Illinois biochemist (search) wax over how amazing is it that life’s fluid bath seems to inherently possess extraordinarily ideal properties so as simple and complex cells and peoples can come into being.

In the 1930s, Lars Onsager published his famous ‘reciprocal relations’ describing free energy conversion processes, which assumed that the fluxes involved in the conversion were proportional to the forces driving them. For chemical reactions, this condition holds only for systems close to equilibrium. Soon thereafter, it was observed that in some biological conversions both the reciprocal relations and linear flux–force dependency appeared to be obeyed no matter how far from equilibrium the system was being driven. No explanation for this ‘paradoxical’ behaviour has emerged and it has remained a mystery. We here argue, however, that this anomalous behaviour is simply a gift of water, of its viscosity in particular; a gift, moreover, without which life almost certainly could not have emerged. (Abstract excerpt)

Animate Cosmos > Organic

Hazen, Robert. Symphony in C: Carbon and the Evolution of (Almost) Everything. New York: Norton, 2019. The veteran geochemist director of the Deep Carbon Observatory at the Carnegie Institute, Washington and prolific, collegial author (search) writes a lyrical tribute to the most important element for the biochemical evolutionary occasion of creatures and peoples. He is also a member of a symphony orchestra as a trumpeter, so chose to arrange the work in four Earth, Air, Fire and Water movements about these prime ways carbon serves this purpose. He also led the discovery (RH 2008) of the vital role played by diverse mineral surfaces in life’s origin, whose compositions are seen evolve in tandem with biospheric and atmospheric systems (see VI. B. 1. Geosphere).

Hazen goes on here to consider a “second genesis” on myriad exoplanets, which would have a unique mineralogy but, akin to George McGhee 2019, would largely retrace and repeat the same oriented development. In so doing, he notes that Jacques Monod’s 1970 claim of chance accident over innate necessity is a false dichotomy (also McGhee 2016). While local contingency is rife, these relatively inanimate and animate materials evolve and emerge from origins, through many organisms, and unto ourselves as if along a guiding course. See also Carbon in Earth edited by R. Hazen, et al in the Reviews in Mineralogy and Geochemistry (Volume 75, 2013) for earlier views. As one peruses this luminous edition, a 21st century revolution to a truly organic ecosmos with life and persons written in becomes increasingly, profoundly evident.

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 > Organic > Chemistry

Ghosh, Abhik and Paul Kiparsky. Grammar of the Elements. American Scientist. November-December, 2019. Once in a while, a truly unique contribution comes to light. Here an Arctic University of Norway chemist and a Stanford University linguist, each veteran scholars, make a good case that Dmitri Menddeleev’s periodic table drew inspiration for its form and phrases from Sanskrit. It seems that both he and Otto von Bohtlingk, who wrote a German edition about this ancient Indian script, lived in St. Petersburg in the 1870s and knew each other. Akin to Antoine Lavoisier who used linguistic metaphors, its tabular frame and generative grammar, traced to the 4th century BCE philologist Panini, served as an initial guide for sorting and arraying the 70 or so atomic elements at the time. See also Mendeleev’s Predictions: Success and Failure by Philip Stewart in Foundations of Chemistry (21/1, 2019), Challenges for the Periodic Systems of Elements by Guillermo Restrepo in Chemistry: A European Journal (November 2019), and Mendeleev and earlier The Periodic Table by Subhash Kak at arXiv:0411080. At its 150th anniversary, this deep affinity reveals an innate connection between chemical matter and linguistic forms, so as to infer a textual uniVerse which we peoples seem meant to learn, read and write.

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 > 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 > 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 > Algorithms

Nichol, Daniel, et al. Model Genotype-Phenotype Mappings and the Algorithmic Structure of Evolution. Journal of the Royal Society Interface. 16/20190332, 2019. Oxford University and H. Lee Moffitt Cancer Center, FL computer scientists and mathematical oncologists including Peter Jeavons describe an advanced complex systems biology method which joins cellular components into a dynamic synthesis from genes to metabolism. Then a novel program-like factor is brought into play to better quantify and express the metastasis invasions. To so reflect, from our late vantage Earth life’s contingent evolution seems yet to reach a global cumulative knowledge which can be fed back to contain, heal and prevent. We are given to perceive some manner of palliative, self-medicating procreation, which seems meant to pass on to our intentional continuance. What an incredible scenario is being revealed to us.

Cancers are complex dynamic systems that undergo evolution and selection. Personalized medicine in the clinic increasingly relies on predictions of tumour response to one or more therapies, which are complicated by the phenotypic evolution of the tumour. The emergence of resistant phenotypes is not predicted from genomic data, since the relationship between genotypes and phenotypes, termed genotype–phenotype (GP) mapping, is neither injective nor functional. We review mapping models within a generalized evolutionary framework that relates genotype, phenotype, environment and fitness. The GP-mapping provides a pathway for understanding the potential routes of evolution taken by cancers, which will be necessary knowledge for improving personalized therapies. (Abstract excerpt)

Cosmic Code > 2015 universal

Kalinin, Nikita, et al. Self-organized Criticality and Pattern Emergence through the Lens of Tropical Geometry. Proceedings of the National Academy of Sciences. I115/E8135, 2018. National Research University, St. Petersburg, IBM Watson Research Center, University of Toulouse, Institute of Science and Technology, Austria, and CINVESTAV, Mexico system mathematicians provide another way to perceive and quantify nature’s constant propensity to reach an a balance beam of more or less relative order in every topological form and function. In actuality, each instantiated complement of the dual, reciprocal condition then resides in both modes at once (particle/wave). See also Introduction to Tropical Series by the authors at arXiv:1706.03062.

A simple geometric continuous model of self-organized criticality (SOC) is proposed. This model belongs to the field of tropical geometry and appears as a scaling limit of the classical sandpile model. We expect that our observation will connect the study of SOC and pattern formation to other fields (such as algebraic geometry, topology, string theory, and many practical applications) where tropical geometry has already been successfully used. (Significance)

Cosmic Code > networks

Porter, Mason. Nonlinearity + Networks: A 2020 Vision. arXiv:1911.03805. The UCLA systems mathematician (search) broadly reviews and previews to date this expansive webwork field. Sections include Centrality, Clustering and Large-Scale Structures and Time-Dependence. And whenever might it dawn that all these lively phenomena and their studies are actually quantifying a natural anatomy and physiology?

I will briefly survey several fascinating topics, methods and ideas in networks and nonlinearity, which I anticipate to be important during the next several years. These include temporal networks (in which the entities and/or their interactions change in time), stochastic and deterministic dynamical processes on networks, adaptive networks (in which a dynamical process on a network is coupled to the network structure), and "higher-order" interactions (which involve three or more entities in a network). I draw examples from a variety of scenarios such as contagion dynamics, opinion models, waves, and coupled oscillators. (Abstract)

Cosmic Code > networks

Zheng, Muhua, et al. Geometric Origins of Self-Similarity in the Evolution of Real Networks. arXiv:1912.00704. MZ, Marian Boguna and Angeles Serrano, University of Barcelona, along with Guillermo Garcia-Perez, University of Turku contribute to integrations of nature’s universe to human multiplex connectivities with deeper physical principles.

One of the aspirations of network science is to explain the growth of real networks, often through the sequential addition of new nodes that connect to older ones. However, many real systems evolve through the branching of basic units, whether those be scientific fields, countries, or species. Here, we provide empirical evidence for self-similar branching growth in real networks and present the Geometric Branching Growth model, which is designed to predict evolution and symmetries. The model produces multiscale unfolding of a network in a sequence of scaled-up replicas. (Abstract excerpt)

In the context of network science, growth is often modeled through the sequential addition of new nodes that connect to older ones by preferential attachment. Here, we take an alternative approach and explore the relation between branching growth and geometric renormalization to explain self-similar network evolution. Renormalization in networks, based on statistical physics, acts as an inverse branching process by coarse-graining nodes. Thus, branching growth can be seen as an inverse renormalization transformation: an idea that was introduced in using a purely topological approach to reproduce the structure of fractal networks, where fractality was interpreted as an evolutionary drive towards robustness. (2)

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

Earth Life > Common Code

Boldini, Alain, et al. Application of Symbolic Recurrence to Experimental Data from Firearm Prevalence to Fish Swimming. Chaos. 29/113128, 2019. NYU and Technical University of Cartagena, Spain bioengineers finesse mathematical techniques in search of better ways to parse and compare complex interactive phenomena across wide scales and instances. And coincidently we log in on the December 14 date of the 2012 Newton school shooting, which is mentioned in the paper. However then might a breadth and depth of credible, sufficient, phenomenal proof be achieved so we peoples could realize and implement an independent, universal naturome code? See also Symbolic Recurrence Plots to Analyze Dynamical Systems by Victoria Caballero-Pintado, et al in Chaos (28/063112, 2018).

Recurrence plots and recurrence quantification analysis are powerful tools to study the behavior of nonlinear dynamical systems. Previous usages, however, have led to arbitrary definitions of recurrence. Here we describe a symbolic recurrence to overcome this issue, and to better book-keep recurrent portions of the phase space and real time series. We illustrate by examining a wide range of experimental datasets from firearm prevalence and media coverage to the sexual interaction of swimming fish. These results demonstrate the potential of symbolic recurrence in real-world applications across research fields. (Abstract excerpt)

Earth Life > Common Code

Garcia-Ruiz, Ronald and Adam Vernon. Emergence of Simple Patterns in Many-Body Systems from Macroscopic Objects to the Atomic Nucleus. arXiv:1911.04819. . R. Garcia Ruiz is posted at CERN Geneva and MIT, while A. Vernon is with KU Leuven, Belgium and the University of Manchester. Among an increasing number of reports, this entry with 175 references is a good example to date of a global scientific endeavor now able to quantify a substantial nature that everywhere gives rise to common forms and flows by its own propensities. With a root basis in nuclear shell clusters, a recurrent regularity spreads in kind across micro-physical and macro-biological realms. As the second quote cites, iconic mathematical shapes can found throughout, aka “magic numbers.” See also Underlying Structure of Collective Bands and Self-Organization in Quantum Systems by Takaharu Otsuka, et al at arXiv:1907.10759, and Magic Number Colloidal Clusters as Minimum Free Energy Structures by Junwei Wang, et al in Nature Communications (9/5259, 2018.)

Strongly correlated many-body systems often display the emergence of simple patterns and regular behavior of their global properties. Phenomena such as clusterization, collective motion and shell structures are commonly observed across different size, time, and energy scales in our universe. Although at the microscopic level their individual parts are described by complex interactions, the collective behavior of these systems can exhibit strikingly regular patterns. This contribution provides an overview of the experimental signatures that are used to identify the emergence of structures and collective phenomena in distinct physical systems, along with macroscopic examples. (Abstract)

Throughout nature, driving forces give rise to the arrangement of constituents in many-body systems at almost every size. On biological scales, this manifests in collective phenomena and pattern formation such as the phyllotaxis of plants, where growth patterns appear in the leaves or flowers around a plant stem. A striking example is observed in the seeds in a sunflower head, which follows the Fibonacci sequence. Complex many-body systems often form clusters to minimise their energy by interactions between neighbours and their mean field. This can form “magic” numbers, as in the atomic nucleus, where certain integer numbers of constituents of a given system result in greater stability of its collective whole. Another instance is the abundance distribution of isotopes in the universe following nucleosynthesis. (2, edits)

In nuclear physics, a magic number is a number of nucleons (either protons or neutrons, separately) such that they are arranged into complete shells within the atomic nucleus. The seven most widely recognized magic numbers as of 2019 are 2, 8, 20, 28, 50, 82, and 126. For protons, this corresponds to the elements helium, oxygen, calcium, nickel, tin, and lead. (Wikipedia)

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