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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 31 through 45 of 112 found.


An Organic, Conducive, Habitable MultiUniVerse

Animate Cosmos > Thermodynamics

Avanzini, Fransesco, et al. Thermodynamics of Chemical Waves. arXiv:1904.08874. University of Luxembourg systems theorists FA, Gianmaria Falasco and Massimiliano Esposito (search) proceed to quantify vital energetic aspects of these organic transmissions.

Chemical waves constitute a known class of dissipative structures emerging in reaction-diffusion systems. They play a crucial role in biology, spreading information rapidly to synchronize and coordinate biological events. We develop a rigorous thermodynamic theory of reaction-diffusion systems to characterize chemical waves. Our main result is the definition of the proper thermodynamic potential of the local dynamics as a nonequilibrium free energy density and establishing its balance equation. This enables us to identify the dynamics of the free energy, of the dissipation, and of the work spent to sustain the wave propagation. Given the fundamental role of chemical waves as message carriers in biosystems, our thermodynamic theory constitutes an important step toward an understanding of information transfers and processing in biology. (Abstract excerpt)

Animate Cosmos > Thermodynamics > autocat

Kamimura, Atsushi and Kunihiko Kaneko. Molecular Diversity and Network Complexity in Growing Protocells. arXiv:1904.08094. University of Tokyo, Universal Biology Institute researchers continue their project (search KK) to explain how life gained its cellular vitalities by here adding an important presence of catalytic activities.

A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address an essential role of the huge diversity of cellular components, we study a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. We then study how the molecule species diversify and complex catalytic reaction networks develop through the evolutionary course. It is shown that molecule species first appear, at some generations, as parasitic ones that do not contribute to replication of other molecules. With this successive increase of host species, a complex joint network evolves. The present study sheds new light on the origin of molecular diversity and complex reaction network at the primitive stage of a cell. (Abstract excerpt)

Animate Cosmos > Thermodynamics > autocat

Piotto, Stefano, et al. Plausible Emergence of Autocatalytic Cycles under Prebiotic Conditions. Life. Online April 4, 2019. For a special collection about The Origin and Early Evolution of Life, University of Salerno biochemists deftly discern the evident presence of such self-initiating bootstrap processes which served to get vitality and development on its long ascent to our present retro-quantification.

The emergence of life in a prebiotic world is an enormous scientific question of paramount philosophical importance. Even when life (in any sense we can define it) can be observed and replicated in the laboratory, it is only an indication of one possible pathway for life emergence, and is by no means be a demonstration of how life really emerged. The best we can hope for is to indicate plausible chemical–physical conditions and mechanisms that might lead to self-organizing and autopoietic systems. Here we present a stochastic simulation, based on chemical reactions already observed in prebiotic environments, that might help in the design of new experiments. We will show how the definition of simple rules for the synthesis of random peptides may lead to the appearance of networks of autocatalytic cycles and the emergence of memory. (Abstract)

Animate Cosmos > exoearths

Hinkel, Natalie, et al. Stellar Characterization Necessary to Define Holistic Planetary Habitability. arXiv:1904.01089. Natalie H., Southwest Research Institute, Irina Kitiashvili, NASA along with Patrick Young and Ben Rackham, ASU propose an Astro2020 Science White Paper to study this vital interrelation. The significant insight is that prior views of planets and stars in separate isolation misses their integral, symbiotic interaction. In regard, a benign sun with an orbital Earth and planets as some manner of incubator-like solar system would be appreciated as the most characteristic cosmic feature.

It is a truism within the exoplanet field that "to know the planet, you must know the star." This pertains to the physical properties of the star (i.e. mass, radius, luminosity, age, multiplicity), the activity and magnetic fields, as well as the stellar elemental abundances which can be used as a proxy for planetary composition. In this white paper, we discuss important stellar characteristics that require attention in upcoming ground- and space-based missions, such that their processes can be understood and either detangled from that of the planet, correlated with the presence of a planet, or utilized in lieu of direct planetary observations. (Abstract)

Animate Cosmos > exoearths

Kaltenegger, Lisa, et al. TESS Habitable Zone Star Catalog. Astrophysical Journal Letters. 874/1, 2019. (TESS = Transiting Exoplanet Survey Satellite). We cite this report by Cornell, Lehigh, and Vanderbilt University researchers as an example of an initial EarthKinder cosmic census going forward.

Animate Cosmos > exoearths

Shahar, Anat, et al, Anat, et al. What Makes a Planet Habitable. Science. 364/434, 2019. Carnegie Institute of Washington geochemists add another requirement for life’s long-term viability. Suitable internal core conditions are a vital factor within the overall conduciveness for living systems to appear and evolve.

The Milky Way Galaxy teems with planetary systems, most of which are unlike our own. It is tempting to assume that life can only originate on a planet that is similar to Earth, but different planets able to sustain Earth-like features could be important for habitability studies. To aud the search for extraterrestrial life, scientists must assess which features of Earth are essential to the development and sustenance of life for billions of years and whether the formation of such planets is common. External effects such as stellar variability and orbital stability affect habitability, but internal processes that sustain a clement surface are also vital. A combination of observations, experiments, and modeling of planetary interiors can guide the search for extraterrestrial life. (Summary)

Animate Cosmos > exoearths

Zeng, Li, et al. Growth Model Interpretation of Planet Size Distribution. Proceedings of the National Academy of Sciences. 116/9723, 2019. A 16 member team based at Harvard including Dimitar Sasselov provide a good example of how later 2010s exoplanet studies, now an intense global activity (search Astro2020), have begun to identify topological features across an array from rocky asteroids to gas giants. As the Abstract alludes, it is noted again how chancy and rare the presence of just the right size and location might be so to hold a benign atmosphere without becoming all dry or wet. A concurrent entry As Planetary Discoveries Pile Up, a Gap Appears in the Pattern by Rebecca Boyle in Quanta Magazine (May 16, 2019) which links to a similar Astrophysical Journal paper.

The radii and orbital periods of 4,000+ confirmed/candidate exoplanets have been precisely measured by the Kepler mission. The radii show a bimodal distribution, with two peaks corresponding to smaller planets (likely rocky) and larger intermediate-size planets, respectively. While only the masses of the planets orbiting the brightest stars can be determined by ground-based spectroscopic observations, these observations allow calculation of their average densities placing constraints on the bulk compositions and internal structures. However, an important question about the composition of planets ranging from 2 to 4 Earth radii (R⊕) still remains. They may either have a rocky core enveloped in a H2–He gaseous envelope (gas dwarfs) or contain a significant amount of multicomponent, H2O-dominated ices/fluids (water worlds). Planets in the mass range of 10–15 M⊕, if half-ice and half-rock by mass, have radii of 2.5 R⊕, which exactly match the second peak of the exoplanet radius bimodal distribution. (Abstract excerpt)

Cosmomics: A Genomic Source Code in Procreative Effect

Cosmic Code

Virgo, Nathaniel. The Necessity of Extended Autopoiesis. Adaptive Behavior. Online April 16, 2019. Amongst an ongoing discussion of how living organisms continue to vitalize and compose themselves, an Earth-Life Science Institute, Tokyo research professor defends a wider view, which the Abstract notes, which expands beyond just a bodily locus. The target article for this commentary is Are Living Beings Extended Autopoietic Systems? by Mario Villalobos and Pablo Razeto-Barry (online January).

The theory of autopoiesis holds that an organism can be defined as a network of processes. However, an organism also has a physical body. The relationship between these two things—network and body—has been raised in this issue of Adaptive Behaviour, with reference to an extended interpretation of autopoiesis. This perspective holds that the network and the body are distinct things, and that the network should be thought of as extending beyond the boundaries of the body. The relationship between body and network is subtle, and I revisit it here from the extended perspective. I conclude that from an organism = network perspective, the body is a biological solution to the problem of maintaining both the distinctness of an organism, separate from but engaged with its environment and other organisms, and its distinctiveness as a particular individual. (Abstract)

Cosmic Code > Algorithms

Berges, Jurgen. Scaling Up Quantum Simulations. Nature. 569/339, 2019. . A Heidelberg University physicist lauds a paper Self-Verifying Variational Quantum Simulation of Lattice Models by eleven University of Innsbruck researchers in the same issue (Kokail, 569/355) about a composite digital-analog computational method which can span and join quantum and classical phases. Once again this complementarity is found to work best.

It is difficult to carry out and verify digital quantum simulations that use many quantum bits. A hybrid device based on a digital classical computer and an analog quantum processor suggests a way forward.

Cosmic Code > Algorithms

Cardinot, Marcos, et al. Evoplex: A Platform for Agent-Based Modeling on Networks. SoftwareX. 9/199, 2019. We cite this entry from the National University of Ireland, Galway and University of Maribor, Slovenia (Matjaz Perc) as an example of how computer code programs can likewise be found to take on these ubiquitous complexity formats.

Agent-based modeling and network science have been used extensively to advance our understanding of emergent collective behavior in systems that are composed of a large number of simple interacting individuals or agents. Evoplex meets this need by providing a fast, robust and extensible platform for developing agent-based models and multi-agent systems on networks. Each agent is represented as a node and interacts with its neighbors, as defined by the network structure. Evoplex is ideal for modeling complex systems, for example in evolutionary game theory and computational social science. (Abstract excerpt)

Cosmic Code > Algorithms

Erwig, Martin. Once Upon an Algorithm: How Stories Explain Computing. Cambridge: MIT Press, 2017. An Oregon State University professor of computer science draws an extended analogy between familiar stories and songs as an effective way to convey an array of algorithmic principles. For example, Hansel and Gretel and Sherlock Holmes can illustrate problem solving, representation and data structures, while Over the Rainbow and Harry Potter express language and meaning, control loops, recursion and abstraction. A copious glossary for each chapter adds pertinent definitions. But for this website, another inference surely comes to mind. If a cross-comparison between literary narratives and computational practice can indeed be parsed, it could well imply that nature’s animate processes are truly textual in kind, a cosmic script and score made and meant for we peoples to decipher, read and write a new story and score.

In Once Upon an Algorithm, Martin Erwig explains computation as something that takes place beyond electronic computers, and computer science as the study of systematic problem solving. He points out that many daily activities involve problem solving. In computer science, such a routine is called an algorithm. Here Erwig deftly illustrates concepts in computing with examples from familiar stories. Hansel and Gretel, for example, execute an algorithm to get home from the forest. Sherlock Holmes handles data structures when solving a crime; and the magic in Harry Potter's world is understood through types and abstraction. He also discusses representations and ways to organize data; “intractable” problems; language, syntax, and ambiguity; control structures, loops, and the halting problem; different forms of recursion; and more.

Since recursion is a general control structure and a mechanism for organizing data, it is part of many software systems. In addition, there are several direct applications of recursion. The feedback loop is a recursive description of the repetitious effect. Fractals are self-similar geometric patterns that can be described through recursive equations. Fractals can be found in nature, for example, in snowflakes and crystals, and are also used in analyzing protein and DNA structures. (9)

Cosmic Code > Algorithms

Gosciniak, Ireneusz. Semi-Multifractal Optimization Algorithm. Soft Computing. 23/5, 2019. A University of Silesia, Poland computer scientist illustrates that self-similar geometries can be seen to appear even in these software program iterations.

Observations on living organism systems are the inspiration for the creation of modern computational techniques. The article presents an algorithm implementing the division of a solution space in the optimization process. A method for the algorithm operation controlling shows the wide range of its use possibilities. The article presents properties of fractal dimensions of subareas created in the process of optimization. The paper also presents the possibilities of using this method to determine function extremes. The approach proposed in the paper gives more opportunities for its use. (Abstract)

Cosmic Code > 2015 universal

Aschwanden, Markus. Self-Organized Criticality in Solar and Stellar Flares. arXiv:1906.05840. The Lockheed Martin, Palo Alto astrophysicist and leading researcher of cosmic SOC phenomena (search) finds that seemingly unpredictable extreme events are actually very rare or not at all, so that a prior mathematical model (Sornette, et al, search) for them does not apply to spacescape dynamics. We cite to note the total presence of SOC just being found everywhere.

We search for outliers in extreme events of statistical size distributions of astrophysical data sets, motivated by the {Dragon-King hypothesis} of (Didier) Sornette, which suggests that the most extreme events in a statistical distribution may belong to a different population, and thus may be generated by a different physical mechanism, in contrast to the strict power law behavior of self-organized criticality models. Identifying such disparate outliers is important for space weather predictions. However, we find that Dragon-King events are not common in solar and stellar flares. Consequently, small, large, and extreme flares remain scale-free with a single physical mechanism. (Abstract excerpt)

Cosmic Code > 2015 universal

Chialvo, Dante, at al. Controlling a Complex System near its Critical Point via Temporal Correlations. arXiv:1905.11758. Argentinian and NIH, USA (Dietmar Plenz) neuroscientists provide a further theoretical and evidential basis for a dynamically creative nature which seeks to ever “tune itself” to an optimum state of complementary balance. See also by DC, et al How Ants Move: Individual and Collective Scaling Properties at 1707.07135 and Critical Fluctuations in Proteins Native State at 1601.03420 for a far afield example for this constant propensity.

A wide variety of complex systems exhibit large fluctuations both in space and time that often can be attributed to the presence of some kind of critical phenomena. Under such critical scenario it is well known that the properties of the correlation functions in space and time are two sides of the same coin. Here we test whether systems exhibiting a phase transition could self-tune to its critical point taking advantage of such correlation properties. We describe results in three models: the 2D Ising ferromagnetic model, the 3D Vicsek flocking model and a small-world neuronal network model. Since the results rely on universal properties they are expected to be relevant to a variety of other settings. (Abstract)

Cosmic Code > 2015 universal

Del Papa, Bruno, et al. Criticality Meets Learning: Criticality Signatures in a Self-Organizing Recurrent Neural Network. PLoS One. May 26, 2017. Computational neuroscientists BDP and Jochen Triesch, Goethe University, Frankfurt, and Viola Priesemann, MPI Dynamics and Self-Organization press on with studies of a neural propensity to seek and reside at a preferred, simultaneous poise of more or less orderly states.

Many experiments suggest that the brain operates close to a critical state, based on signatures such as power-law distributed neuronal avalanches. In neural network models, criticality is a dynamical state that maximizes information processing capacities, e.g. sensitivity to input, dynamical range and storage capacity. Although models that self-organize towards a critical state have been proposed, the relation between criticality signatures and learning is still unclear. Here, we investigate criticality in a self-organizing recurrent neural network (SORN). We show that, after a transient, the SORN spontaneously self-organizes into a dynamical state that shows criticality signatures comparable to those found in experiments. Overall, our work shows that the biologically inspired plasticity and homeostasis mechanisms responsible for the SORN’s spatio-temporal learning abilities can give rise to criticality signatures in its activity. (Abstract excerpt)

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