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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 50 found.


Ecosmos: A Revolutionary Organic Habitable UniVerse

Animate Cosmos > Thermodynamics > autocat

Dufour, Gwenaelle and Steven Charnley. Astrochemical Bistability: Autocatalysis in Oxygen Chemistry. . . NASA Goddard researchers quantify the natural presence and formative contribution of self-activating chemical reactions to an ecosmic materiality as it proceeds to evolve and develop in animate complexity.

The origin of bistable solutions in the kinetic equations describing the chemistry of dense interstellar clouds is explained as being due to the autocatalysis and feedback of oxygen nuclei from the oxygen dimer. We show that these processes can produce the bistable solutions found in previous studies, as well as the dependence on various model parameters such as the helium ionization rate and the sulfur depletion. (Abstract)

We have demonstrated that interstellar chemistry is bistable due to the interaction of several autocatalytic processes involving molecular oxygen. By deconstructing a known bistable solution into ever simpler reduced models through omission of chemical elements, and then artificially removing selected reactions, we have identified four distinct modes of autocatalysis that can occur in dense molecular clouds. (6)

Animate Cosmos > Fractal

Teles, Sharon, et al. Fractal Analysis of the UltraVISTA Galaxy Survey. arXiv:2013.07164. In 2000, one could find inklings that self-similar geometries might be present across the celestial reaches. Two decades later, Valongo Observatory, Universidade Federal do Rio de Janeiro Observatório Nacional astronomers add another strong confirmation that all manner of spacescape phenomena is indeed arrayed in and sustained by fractal scales.

This paper seeks to test if the large-scale galaxy distribution can be characterized as fractal system. Tools appropriate for describing galaxy fractal structures with a single fractal dimension in relativistic settings are developed and applied to the UltraVISTA galaxy survey. A graph of volume-limited samples corresponding to the redshift limits in each redshift bins for absolute magnitude is presented. The results show two consecutive and distinct redshift ranges in both the reduced and complete samples where the data behave as a single fractal galaxy structure. (Abstract excerpt)

The fractal galaxy distribution hypothesis is an approach for the description of the large-scale structure of the Universe which assumes that this distribution is formed by a fractal system. This approach characterizes the system by means of its key feature, thefractal dimension, which is basically a way of quantifying the irregularity of the distribution. In the context of the large-scale structure of the Universe, essentially measures galactic clustering sparsity or, complementary, the dominance of voids. (1)

Differently from the single fractal approach, the multifractal one characterizes the fractal system by several fractal dimensions in the same scaling range, that is, a whole spectrum of dimensions whose maximum value corresponds to the single fractal dimension the structure would have if it were treated as a single fractal. The multifractal approach is applied when quantities like galactic luminosity or mass have a distribution, that is, they range between very different values. (1)

Animate Cosmos > exoearths

Gaudi, B. Scott, et al. The Demographics of Exoplanets. arXiv:2011.04703. SG, Ohio State University, Jessie Christiansen, Caltech, and Michael Meyer, University of Michigan post a chapter to appear in ExoFrontiers: Big Questions in Exoplanetary Science (Bristol: IOP Publishing Ltd) AAS-IOP ebooks, 2021). It is a sign of a new maturity if this fast-moving, expansive field of exoplanetary science can begin to lay out a program for a near and farther census. Amongst many aspects are the shape of the explanet, host star interactions, multiple formation paths for gas giants, and so on. But as the second quote notes, these studies come up with more evidence of how special our own Sun – Earth system really is.

In the broadest sense, the primary goal of exoplanet demographic surveys is to determine the frequency and distribution of planets as a function of as many of the physical parameters that may influence planet formation and evolution as possible, over as broad of a range of these parameters as possible. By comparing these planet distributions to the predictions of planet formation theories, we can begin to both test and refine these theories. In this chapter, we review the major results on exoplanet demographics to date. (Abstract)

How common are solar system analogs? One of the most surprising results from Kepler is that the majority of stars appear to host relatively close-in, compact systems of super-Earths and/or sub-Neptunes. As our solar system does not host any analogues of such planets; this suggests that planetary architectures like our own (with small rocky planets in the temperate zone and gas giants beyond the ice line) may not be common. (5)

Animate Cosmos > exoearths

Wiedner, Martina, et al. Origins Space Telescope: From First Light to Life: ESA Voyage 2050 White Paper. arXiv:2012.02731. A 27 member team from the European Space Agency posts their grant proposal which was one of four selected for this international project. It is based on three questions: How does the Universe work?, How did we get here?, Are we alone? And to take a philoSophia view, a nascent worldwise knowledgeable sapience becomes able to recreate and envision the whole vast scenario it arose from. Who are me/We beings that can altogether learn the the galactic baryon cycle? Might our Earthmost home be a fittest, optimum candidate? Here is another instance of a major personsphere transition proceeding to come to her/his own discoveries.

The Origins Space Telescope is one of four science and technology definition studies selected by NASA for the 2020 Astronomy and Astrophysics Decadal survey in the USA. Origins will trace our history from the time dust and heavy elements permanently altered the cosmic landscape to present-day life. It is designed to answer three major science questions: How do galaxies form stars, make metals, and grow their central supermassive black holes from reionization? How do the conditions for habitability develop during the process of planet formation? Do planets orbiting M-dwarf stars support life? (Abstract excerpt)

Animate Cosmos > exoearths

Winter, Andrew, et al. Stellar Clustering Shapes the Architecture of Planetary Systems. Nature. 586/528, 2020. University of Heidelberg and University of Leichester astrophysicists review observational and experimental studies about the ways that solar systems may form and arrange themselves. A propensity for sunny stars to bunch together in groups then becomes a factor with regard to the relative habitability of orbital worlds.

Conclusions:Our results show that stellar clustering is a key factor setting the architectures of planetary systems. This environment represents a fundamental axis along which exoplanetary and atmospheric properties may vary, and which has implications for planetary habitability and the likelihood of life in the Universe. Star formation was likely more clustered in the past, so that an influence on older planetary systems may have been even greater. (532)

Ecosmomics: A Survey of Genomic Complex Network System Sources

Cosmic Code > nonlinear > Algorithms

Chan, Bert. Lenia and Expanded Universe. arXiv:2005.03742. The Hong Kong computational scholar posts his latest, elaborate illustration of how lively and complex the algorithms of John Conway’s Game of Life (see Siobhan Roberts herein) can become. Also Google the author’s name to reach his YouTube videos of Mathematical Life Forms.

We report experimental extensions of Lenia, a continuous cellular automata family capable of producing lifelike self-organizing autonomous patterns. The rule of Lenia was generalized into higher dimensions, multiple kernels, and multiple channels with a final architecture akin to a recurrent convolutional neural network. Genetic algorithm automations led to phenomena like polyhedral symmetries, individuality, self-replication, emission, growth by ingestion, and "virtual eukaryotes" with an internal division of labor and type differentiation. (Abstract)

Cosmic Code > nonlinear > Algorithms

Gilpin, William. Cellular Automata as Convolutional Neural Networks. arXiv:1809.02942. The Stanford University physicist runs these computational programs in accord with dynamical systems theory to an extent that the results begin to look like cognitive architectures. See also his concurrent paper Cryptographic Hashing using Chaotic Hydrodynamics in the PNAS. (115/4869, 2018).

Cosmic Code > nonlinear > Algorithms

Roberts, Siobhan. The Lasting Lessons of John Conway’s Game of Life. New York Times. December 28, 2020. A science journalist and author of a 2015 Genius at Playbiography of the Princeton University mathematician reviews his prime computational innovation along with its on-going implications. Sadly, John Conway passed away at age 82 in April 2020 from the COVID virus. When at Cambridge University in 1972 he sent several puzzles to Martin Gardner who was then an editor for Scientific American. His Game of Life entry was reviewed in the October issue, and has grown in popularity ever since.

The first quote cites the simple automata algorithm sequence. By running these rules, one can generate all manner of complex life forms as they self-organize into individualities, divisions of labor, groupings, and more. For a wider survey, Roberts asked computer scholars such as Susan Stepney, Stephen Wolfram, Daniel Dennett and Rudy Rucker for their thoughts, we include other comments below. But an overall mindset or interpretation seems to pervade that such natural programs are ultimately unpredictable. In our current mindset a reliable, thematic guidance is not seen to be written in, nor does it exist.

The game of life was simple: Place any configuration of cells on a grid, then watch what transpires according to three rules that dictate how the system plays out. Birth rule: An empty, or “dead,” cell with precisely three “live” neighbors (full cells) becomes live. Death rule: A live cell with zero or one neighbors dies of isolation; a live cell with four or more neighbors dies of overcrowding. Survival rule: A live cell with two or three neighbors remains alive. With each iteration, some cells live, some die and “Life-forms” evolve, one generation to the next. (S. Roberts)

Complexity arises from simplicity! We are used to the idea that anything complex must arise out of something more complex. But the Game of Life shows us that complex virtual “organisms” arise out of the interaction of a few simple rules. (Brian Eno)

In this moment in time, it’s important to emphasize that inherent unpredictability is a feature of life in the real world as well as in the Game of Life. We have to figure out ways to flourish in spite of the vicarious uncertainty we constantly live with. (Melanie Mitchell)

The name Conway chose — the Game of Life — frames his invention as a metaphor. But I’m not sure that he anticipated how relevant Life would become, and that in 50 years we’d all be playing an emergent game of life and death. (William Poundstone)

In normal times, we can keep building stuff one component upon another, but in harder times like this pandemic, we need something that is more resilient and can prepare for the unpreparable. That would need changes in our “rules of life,” which we take for granted. (Bert Chan – see his Lenia and Expanded Universe paper above for extensive displays of this cellular method.)

Cosmic Code > nonlinear > Algorithms

Thompson, Sarah, et al. The Fractal Geometry of Fitness Landscapes at the Local Optima Level. Natural Computing. December, 2020. University of Stirling, UK and Universite du Littoral Côte d’Opale, Calais systems mathematicians show how an evolutionary dynamics meant to attain and select a fittest result can take on a self-similar topology.

A local optima network (LON) encodes local optima connectivity in the fitness landscape of a combinatorial optimisation problem. Recently, LONs have been studied for their fractal dimension which is a complexity index where a non-integer can be assigned to a pattern. We use visual analysis, correlation analysis, and machine learning to show that relationships exist and that fractal features of LONs can contribute to explaining and predicting algorithm performance. (Abstract excerpt)

A heuristic is any approach to problem solving or self-discovery that employs a practical method that is not guaranteed to be optimal, perfect, or rational, but is nevertheless sufficient for reaching an immediate, short-term goal or approximation.

Cosmic Code > nonlinear > Rosetta Cosmos

Li, Yi, et al. Incorporating Textual Network Improves Chinese Stock Market Analysis. Nature Scientific Reviews. 0/20944, 2020. At the close of this year, Shanxi University of Finance and Economics analysts offer another cross-correlation between diverse subject areas. The title network model which is broadly used for literary document analyses is here applied to similarly parse financial stock transactions. But our further interest is to note that nature’s network dynamic geometry can thus be considered to have a literary essence. We log in with Yang-Hui He’s paper Universe as Big Data with generally the same idea.

This study adopts the textual network which describes the coordination where nodes represent words which are connected if they have co-occurrence patterns across documents. To study stock movements, we then propose the sparse laplacian shrinkage logistic model which can take into account the network connectivity structure. By this approach, we studied the relationship between Shenwan index and analysts' research reports. Our study unveils some interesting findings that the efficient use of textual network is important to improve the predictive power as well as the semantic interpretability in stock market analysis. (Abstract)

Cosmic Code > nonlinear > 2015 universal

Paraslesh, Fatemeh, et al. Chimeras. Physics Reports. October, 2020. Amirkabir University of Technology, University of Western Australia, Northwestern Polytechnical University, Xi’an, China. CNR Institute of Complex Systems, Fiorentino, Italy (Stefano Boccaletti), and University of Maribor, Slovenia (Matjaz Perc) system theorists post a major 80 page, 324 reference review about this recently recognized condition. While its name is taken from organisms with a double genome, here it stands for a complex dynamism which actively resides in more or less orderly or coherent modes at the same time. The paper covers various occasions such as chemical or neural, their network topologies, and more. The import in later 2020 is to add a major explication that natural phenomena everywhere seeks and prefers a “middle way golden balance” optimum poise.

Chimeras are this year coming of age since they were first observed by Kuramoto and Battogtokh in 2002. What started as an observation of a coexistence of synchronized and desynchronized states turned out to be an important new paradigm of nonlinear dynamics at the interface of physical and life sciences. Here we present a major review of chimeras, dedicated to all aspects of their theoretical and practical existence. We cover different dynamical systems in which they have been observed along with network structure for the emergence of chimeras. (Abstract)

Cosmic Code > Genetic Info

Snyder, Michale, et al. Perspectives on ENCODE. Nature. 583/693, 2020. 21 coauthors from the ENCODE Project Consortium including Mark Gerstein post a latest status report as this Encylopedia of DNA Elements proceeds apace to sequence whole genomes for an expanding array of species.

The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated with gene regulation (for example, transcription factor binding sites, open chromatin, and histone marks) and transcript isoforms. The marks serve as sites for candidate cis-regulatory elements (cCREs) that may serve functional roles in regulating gene expression1. The project has been extended to model organisms, particularly the mouse. In the third phase of ENCODE, nearly a million and more than 300,000 cCRE annotations have been generated for human and mouse, respectively, and these have provided a valuable resource for the scientific community.

Cosmic Code > Genetic Info > DNA word

Wang, Li-Min, et al. Mechanism of Evolution Shared by Genes and Language. arXiv:2012.14309. Nine National Tsing Hua University, Taiwan biologists and linguists describe a strongest parallel between these premier modes of vital, prescriptive content. After consideration from 1970 to 2000 to today, life’s evolutionary emergence can indeed be seen as endowed with deeply similar, Rosetta-like versions of genetic and linguistic informative codesl. We log this in with Siobhan Roberts review of cellular automata models such as John Conway’s Game of Life and Bert Chan’s Lenia Universe. Within a 21st century worldwise revolution, a natural genesis now well appears to have its own uniVerse to humanVerse ecosmomic code. In further regard, our Earthomo sapience may seem meant to achieve its sentient translation, and intentional continuance.

We propose a general mechanism for evolution to explain the diversity of genes and language. To quantify their common features and reveal hidden structures, several statistical properties and patterns are examined by way of a new method called the rank-rank analysis. We find that the older relation, "domain plays the role of word in gene language", is not rigorous, and propose to replace it by protein. Based on the correspondence between (protein, domain) and (word, syllgram), we discover that both genes and language share a common scaling structure and scale-free network. Like the Rosetta stone, this work may help decipher the secret behind non-coding DNA and unknown languages. (Abstract)

Among the topics of evolution, we are particularly interested in genes and natural languages. The fact that 20 kinds of codon, composed by three nucleotides in the set A, T, C, G encode genome sequence is similar to the human written text constituted by letters that form the alphabet. Therefore, it is intuitive to make an analogy between gene and language. When choosing the “space-time” of organism as nature and that of human as society, their inheritance of survival can be recorded in gene and language, respectively. (1)

The correspondence between gene and language may be the Rosetta Stone to decipher the language of genes. Scientists have applied linguistic formalisms to this goal, such as using Zipf’s and Shannon’s approach to quantify the linguistic features of non-coding DNA sequences, and exploring information hidden in genome with the aid of natural language processing (NLP). On the other hand, linguists have investigated the relationship between language and the natural selection, and discussed the language faculty in the broad and narrow sense from the viewpoint of biolinguistics. (1)

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Sukhoverhov, Anton and Nathalie Gontier. Non-Genetic Inheritance: Evolution above the Organismal Level. Biosystems. December, 2020. Kuban State Agrarian University, Russia and University of Lisbon (search NG papers) biophilosophers propose to expand upon extended evolutionary theories by moving on up life’s episodic emergent scale. In this broader view a constant impetus to form more nested cellular communities can become evident. The evident major transitions scale can thus be shifted toward this cooperative emphasis, and also accrue a reticulated, networked anatomy.

The article proposes to develop the Extended Evolutionary Synthesis (EES) by including phenomena that occur above the organismal level. We show that the current EES view is focused more on individual traits and less on community traits of biological, ecological, social, and cultural systems. In regard, we consider communities made up of interacting populations that occupy the same place in time and space, and for which the individual members can belong as the same or different species. Examples include biofilms, ant colonies, symbiotic associations in holobiont formation, and human societies. Our proposed communities model revises major transitions in evolution theory by adding the interplay between social traits and individual traits. (Abstract excerpt)

Quickening Evolution > Intel Ev

Szilagyi, Andras, et al. Phenotypes to Remember: Evolutionary Developmental Memory Capacity and Robustness. PLoS Computational Biology. November 30, 2020. The analogy between neural and genetic regulatory networks is not superficial in that it allows knowledge transfer between fields that used to be developed separately from each other. Centre for Ecological Research, Tihany, Hungary researchers including Eors Szathmary post a latest implication that life’s course has an main orientation toward intelligence and cognition. In regard, genotype-phenotype mappings are a “highly non-linear process” which are seen to advance by reference to prior represented experiences. See also The World as a Neural Network by the cosmologist Vitaly Vanchurin (2020).

The development of individual organisms from embryo to adult state is under the control of many genes. During development the initially active genes activate other genes, which in turn change the composition of regulatory elements. The behavior of genetic regulatory systems shows similarities to neural networks, such as developmental memory, the ability to quickly adapt to environments that have occurred in the past. We investigated the properties of this system; the developmental pathways that can be “memorized”, and its robustness against disturbances affecting either the embryo state or the gene interaction networks. (Summary excerpt)

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