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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 46 through 60 of 114 found.


An Organic, Conducive, Habitable MultiUniVerse

Animate Cosmos > exoearths

Airapetian, Vladimir, et al. Impact of Space Weather on Climate and Habitability of Terrestrial-type Exoplanets. International Journal of Astrobiology. Online August, 2019. A forty-five member collaboration from NASA, across the USA, Austria, Germany, Japan, and Ireland provide an extended review and preview of this “astro-spheric” phase of a biocosmic spacescape which fills itself with evolutionary life bearing planets in solar incubators. A 206 page edition is accessible at arXiv:1905.05093.

Animate Cosmos > exoearths

Cooke, Ilsa and Ian Sims. Experimental Studies of Gas-Phase Reactivity in Relation to Complex Organic Molecules in Star-Forming Regions. ACS Earth and Space Chemistry. Online June, 2019. We note this entry by University of Rennes, CNRS, France astrophysical chemists as an example in this new journal of how sophisticated these research endeavors have become as they quantify ever increasing evidence of an intrinsic biocosmic essence which brings forth, complexifies, develops and evolves as it reaches our human ability and purpose to retrospectively learn and take form here.

The field of astrochemistry concerns the formation and abundance of molecules in the interstellar medium, star-forming regions, exoplanets, and solar system bodies. These astrophysical objects contain the chemical material from which new planets and solar systems are formed. Around 200 molecules have thus far been observed in the interstellar medium; almost half containing six or more atoms and considered “complex” by astronomical standards. All of these complex molecules consist of at least one carbon atom and thus the term complex organic molecules (COMs) has been coined by the astrochemical community. In the following review, we present recent laboratory efforts to produce quantitative kinetic data for gas-phase reactions at low temperatures. (Abstract excerpt)

The scope of ACS Earth and Space Chemistry includes the application of analytical, experimental and theoretical chemistry to investigate research questions relevant to the Earth and Space. The journal notes the highly interdisciplinary nature of research in this area, with chemistry and chemical research tools as the unifying theme. It publishes broadly in the domains of high- and low-temperature geochemistry, atmospheric chemistry, marine chemistry, planetary chemistry, astrochemistry, and analytical geochemistry.

Animate Cosmos > exoearths

Kovacs, Tamas. Recurrence Network Analysis of Exoplanetary Observables. . We cite this entry by an Eotvos University, Budapest physicist as an example of how network complexity researchers are beginning to detect and quantify an intrinsic, independent, self-organizing mathematics which seems to apply even to the cosmic realm of dynamic solar systems.

Recent advancements of complex network representation among several disciplines motivated the investigation of exoplanetary dynamics by means of recurrence networks. We are able to recover different dynamical regimes by means of various network measures obtained from synthetic time series of a model planetary system. The framework of complex networks is also applied to real astronomical observations acquired by recent state-of-the-art surveys. The outcome of the analysis is consistent with earlier studies opening new directions to investigate planetary dynamics.

Cosmomics: A Genomic Source Code in Procreative Effect

Cosmic Code

Krakauer, David, ed. Worlds Hidden in Plain Sight: The Evolving Idea of Complexity at the Santa Fe Institute 1984 – 2019. Santa Fe, NM: Santa Fe Institute Press, 2019. The SFI evolutionary biologist and current president gathers 35 years of contributions from events, seminars, projects, talks, and more which can well track the revolutionary discovery of a natural anatomy, physiology, cerebral, and cultural essence. A 1984 - 1999 section notes Mavericks such as John Holland, Murray Gell-Mann, and Simon Levin. 2000 - 2014 turns to Unifers like Harold Morowitz, Jessica Flack and Brian Arthur. 2015 and Beyond then completes 37 chapters with entries by Luis Bettencourt, Geoffrey West, Mirta Galesic, Simon DeDeo, Samuel Bowles, and Jennifer Dunne.

The book opens with a yearly topical list from initial glimpses of a nonlinear physics across astral and material systems all the way to active societies and economies. 2019 titles are Humans in Ecological Networks and Eco-Evolutionary Synthesis. A prime SFI founder George Cowan saw the promise of an iconic, common motif which similarly recurred everywhere. Three and a half decades later, as we try to document, a self-organizing complex adaptive network system of node element and link relation within a whole, viable entity seems to well fulfill this goal. I visited SFI in 1987 to hear a talk by Morowitz, when one sensed that a new animate frontier was opening. We cite a prescient 1992 affirmation by Murray Gell-Mann, another founder, along with a 2015 verification by David Krakauer.

Ultimately, we can argue that it is the self-similarity of the structure of fundamental physical law that dictates the continuing usefulness of mathematics. At the modest level of earlier science, this sort of self-similarity is strikingly apparent. Electricity, gravitation, and magnetism all have the same force, and Newton suggested that there might be some short-range force. Now that scientists are paying attention to scaling phenomena, we see in the study of complex systems astonishing power laws extending over many orders of magnitude. The renormalization group turns out to apply not only to condensed matter but to numerous other subjects. The biological and social sciences are just as much involved in these discoveries of scaling behavior as the physical sciences. We are always dealing with nature consonant and conformable to herself. So the approximate self-similarity of the laws of nature runs the gamut from underlying laws of physics to the phenomenological laws of the most complex realms. (Murray Gell-Mann, 1992, 38-39)

For the last few decades we have been steadily surveying the landscape of complex phenomena, and it is gratify that along the way we find that complex systems nominally unrelated bear strong family resemblances. These similarities include how the structure of evolutionary adaption looks a lot like the mathematics of learning, that the distribution of energy within a body made of tissues and fluids follows rules similar to those governing the flow of energy in a society, that networks within cells adhere to the geometric principles we find on the internet, and that the rise and fall of ancient civilizations follow a sequence similar to the present growth of urban centers. (David Krakauer, 2015, 230)

Cosmic Code

Moore, Douglas, et al. Cancer as a Disorder of Patterning Information: Computational and Biophysical Perspectives. Convergent Science Physical Oncology. 3/043001, 2017. DM and Michael Levin, Tufts University and Sara Walker, Arizona State University, who represent a new generation of complexity scientists, contribute a 30 page, 478 reference posting of the 2010s turn to factor in a mathematical presence of multiplex network phenomena. By this advance, previously identified cellular elements gain the missing dimension of their fluid interactive linkage. Their compass includes integrated information theory from neural studies as another way that agents form spatiotemporal patterns. See also in this journal The Physics of Life: Clinical, Biological and Physical Science Approaches for Cancer Research by Katharine Arney (4/040201, 2018), second quote. In the broader scheme of an ecosmos genesis, we might witness life’s long evolution as a self-healing, curing and now preventative process by virtue of such an emergent knowledge corpus which, in its genomic essence, can be fed back to heal, cure the beings it arose from.

The current paradigm views cancer as a clonally degradation of genetic information in single cells. A novel perspective is that cancer is due to a system disorder of algorithms that normally guide individual cell activities toward anatomical features and away from tumorigenesis. A view of cancer as a disease of geometry can focus on pathways that allow cells to cooperate, form and maintain large-scale patterning. Cancer may result when cells lose coherent structures and their computational selves reverts to a single-cell, self-serving stage. Here, we highlight two recent areas of theoretical advance. First, we review the roles that endogenous bioelectrical networks across many tissues in vivo foster information processing in tumor suppression, progression, and reprogramming. Second, we provide a primer to the development of computational methods for quantifying causal control structures in cancer and other complex biological systems. Finally, specific ways in which a synthesis of novel integrative biophysics and mathematical analysis may better understand and address cancer are stated. (Abstract edits)

Bringing together the physical and biological sciences will ultimately lead to new frameworks for understanding cancer as a complex adaptive system with measurable and predictable physical characteristics. And from this standpoint we can hope to develop better diagnostic and monitoring techniques to spot cancer early, track it as it grows, changes and spreads, and apply this knowledge to treat it more effectively. (Arney, 4)

Cosmic Code

Parker, Michael and Chris Jeynes. Maximum Entropy (Most Likely) Double Helical and Double Logarithmic Spiral Trajectories in Space-Time. Nature Scientific Reports. 9/10779, 2019. University of Essex and University of Surrey computational physicists post a unique mathematical procedure to explain how natural phenomena so often adopt into this dynamic patterning. By this view, a common affinity between genomes and galaxies can provide another glimpse of nature’s geometric universality.

The ubiquity of double helical and logarithmic spirals in nature is well observed, but no real explanation is offered for their prevalence. DNA and the Milky Way galaxy are examples, which we study using an information-theoretic complex-vector analysis to calculate the Gibbs free energy difference between B-DNA and P-DNA, and the galactic virial mass. We define conjugate hyperbolic space and entropic momentum co-ordinates to describe these spiral structures in Minkowski space-time, enabling a consistent, holographic Hamiltonian-Lagrangian system that is isomorphic and complementary to that of conventional kinematics. (Abstract excerpt)

Cosmic Code

Sole, Ricard and Sergei Valverde. Evolving Complexity: How Tinkering Shapes Cells, Software and Ecological Networks. arXiv:1907.05528. Barcelona systems theorists (search) provide a 21st century retrospective survey of their studies and this revolutionary witness by a worldwide faculty of a cosmos to creature to cognition proto-evolution which is suffused by a common multiplex anatomy and physiology. In 2019 this phenomenal animate reality is set within a scenario that implies a dynamic interplay of endemic self-organizing principles and constraints, along with many candidates subject to chancy selective forces. The main gist draws upon Francois Jacob’s 1977 Evolution and Tinkering paper (French Nobel geneticist, see Science 196/1161) to emphasize how nature seems to constantly repurpose organelle components as life strives to develop and emerge. Some four decades later, by way of novel network connectivities a balanced synthesis of non-random rules and working adaptations can be broached.

A prime trait of complex systems is that they can be represented as a network of interacting parts. These organizational propensities are the main source of higher-level properties, which are not reducible to the individual parts. Can the topological features of these webs provide insight into their evolutionary origins? Both biological and artificial networks are heterogeneous and sparse, and exhibit small-world modular or hierarchical patterns. Against the standard selection-optimization argument, some networks reveal the inevitable generation of complex patterns resulting from reuse which can be modelled using duplication-rewiring rules. These give rise to scale-free and modular architectures observed in the real case studies.

Tinkering is a universal mechanism that drives not only biological evolution but also the large-scale dynamics of some technological designs. Here we examine the evidence for tinkering in cellular, technological and ecological webs and its impact in shaping their architecture and deeply affecting their functional properties. Our analysis suggests to seriously reconsider the role played by selection forces or design principles as main drivers of network evolution. (Abstract)

The fabric of complexity is made of networks. The presence of collective-level, system properties necessarily requires a description grounded in a map of connections between individual parts. Such view has been around much longer than is usually acknowledged within the field of Network Science. Long before small worlds and scale-free structures were identified, the importance of interactions and their embodiment within graphs was already in place in ecology and neuroscience. Classic studies on trophic webs and their stability had an enormous impact on our understanding of communities. Similarly, since (Santiago) Ramon y Cajal the realization that cognition was associated to complex webs
has been percolating through the entire field. (1)

It has been suggested (Sole et al., 2003) that inspecting the organisation of complex networks can reveal the evolutionary design or evolutionary principles that shaped them. In a nutshell, identifying the generative rules responsible for their topology could be used to find their origins and the contributions of randomness, architectural constraints or self-organisation. In other words, the paths followed by each system can be deeply limited by fundamental principles of mathematical nature. In this paper, we will review the evidence for this idea and its deep implications for our understanding of network complexity. This includes the presence of mechanisms of network growth that are dominated by extensive reuse of extant components. Such a ”tinkering” process was early suggested by the French biologist Francois Jacob and has enormous importance in evolution. (3)

The findings described above strongly support the idea that the proteome map contains a considerable amount of statistical correlations that are a byproduct of the duplication-rewiring set of rules. The presence of modularity or non-random distributions of motifs cannot be taken (alone) as a signature of selection. This finding, as shown below, is far from accidental. (5)

Cosmic Code > Algorithms

Aerts, Diederik, et al. Quantum Entanglement in Physical and Cognitive Systems. arXiv:1903.09103. A seven person team based at Brussels Free University with other postings in Switzerland, the UK and Chile enter their latest work-in-progress toward a theoretical and conceptual, quantum and classical, physical and biological, cosmic integrative whole. Into mid 2019, per the second quote, as new understandings join quantum and human phenomena, we can begin to glimpse a universal Copernican revolution. Physics and people are at last reunited, which in turn implies a lively, literate ecosmos. On this eprint site, over a hundred papers by D. Aerts, this group, and many colleagues can be accessed going back to 2008. An example is The Emergence and Evolution of Integrated Worldviews by DA with Liane Gabora at 1001.1399. Another current posting is Quantum-Theoretic Modeling in Computer Science at 1901.04299 and Quantum Entanglement in Corpuses of Documents 1810.12114.

We provide a general description of the phenomenon of entanglement in bipartite systems, as it manifests in micro and macro physical systems, as well as in human cognitive processes. We do so by observing that when genuine coincidence measurements are considered, the violation of the 'marginal laws', in addition to the Bell-CHSH inequality, is also to be expected. The situation can be described in the quantum formalism by considering the presence of entanglement not only at the level of the states, but also at the level of the measurements. (Abstract excerpt)

But nowadays the predictions of quantum theory are no longer put into question, not only as regards entanglement, which has been shown to be preservable over distances of a thousand kilometers, but also with respect to many other effects such the delocalization of large organic molecules. On the other hand, the debate about the profound meaning of the theory never stopped, and in fact has constantly renewed and expanded over the years, so much so that one can envisage this will produce in the end a Copernican-like revolution in the way we understand the nature of our physical reality. Such a debate, however, is not confined to physicists or philosophers of science, but also reached new fields of investigation, in particular that of psychology, due to the development of that research domain called ‘quantum cognition.’ (2)

Quantum entanglement is a physical phenomenon that occurs when pairs or groups of particles are generated, interact, or share spatial proximity in ways such that the quantum state of each particle cannot be described independently of the state of the others, even when the particles are separated by a large distance.

In physics, the CHSH inequality can be used in the proof of Bell's theorem, which states that certain consequences of entanglement in quantum mechanics cannot be reproduced by local hidden variable theories. Experimental verification of violation of the inequalities is seen as experimental confirmation that nature cannot be described by local hidden variables theories. CHSH stands for John Clauser, Michael Horne, Abner Shimony, and Richard Holt, who described it in 1969.

Cosmic Code > Algorithms

Beltran, Lester and Suzette Geriente. Quantum Entanglement in Corpuses of Documents. arXiv:1810.12114. Brussels Free University, Interdisciplinary Studies Group researchers led by Diederik Aerts explore how recent clarifications and integrative expansions of quantum theory can reveal how such deep phenomena is actively present even in human literary writings. As if a library of cosmos (taking license), in addition to fractal network complexities, our textual linguistic corpora is found to possess a physical affinity and generative source. And we note, by turns, this extant cosmos becomes graced by a natural narrative (more license). See also Quantum-Theoretic Modeling in Computer Science by these authors and group at 1901.04299 for a later finesse. A parallel effort goes on in Bob Coecke’s Oxford University group, such as The Mathematics of Text Structure at 1904.03478.

Cosmic Code > Algorithms

Fernandez, Jose and Francisco Vico. AI Methods in Algorithmic Composition. Journal of Artificial Intelligence Research. Volume 48, 2013. This entry by University of Malaga, Spain computer scientists is cited in A. Wagner’s Life Finds a Way (2019) to show how evolution seems guided by source programs which can be modeled by artificial neural networks. By such perceptions, the natural presence of iterative cellular automata and self-similar patterns can be noticed. Its mathematical form and flow also appear as a musical or written composition. In regard, are we coming upon an proactive ecosmos which is composing itself by way of sapient species as our global own? Please visit F. Vico’s website to read about his “Melomics” or genetics of melody project.

Algorithmic composition is the partial or total automation of the process of music composition by using computers. Since the 1950s, different computational techniques related to Artificial Intelligence have been used for algorithmic composition, including grammatical representations, probabilistic methods, neural networks, symbolic rule-based systems, constraint programming and evolutionary algorithms. This survey aims to be a comprehensive account of research on algorithmic composition, presenting a thorough view of the field for researchers in Artificial Intelligence. (Abstract)

The purpose of this survey is to review and bring together existing research on a specific style of Computational Creativity: algorithmic composition. Interpreted literally, algorithmic composition is a self-explanatory term: the use of algorithms to compose music. (1)

Cosmic Code > Algorithms

Sloss, Andrew and Steven Gustafson. 2019 Evolutionary Algorithm Review. arXiv:1906.08870. Bellevue, WA software scientists post a thorough survey as the field of artificial intelligence, broadly conceived, becomes ever more biological in its basis. By turns, life’s genetically programmed development is broached as an “Idealized Darwinism.” Section 5.1 is an Auto-Constructive Evolution, while 5.2 is Deep Neuroevolution and 5.3 Self-Replicating Neural Networks.

In this review, we explore a new taxonomy of evolutionary algorithms and classifications that look at five main areas: the ability to manage the control of the environment with limiters, how to explain and repeat the search process, understandings of input and output causality within a solution, the ability to manage algorithm bias due to data or user design, and lastly, and how to add corrective measures. As many reviews of evolutionary algorithms exist, after motivating this new taxonomy, we briefly classify a broad range of algorithms and identify areas of future research. (Abstract excerpt)

Cosmic Code > 2015 universal

Nagata, Shintaro and Macoto Kikuchi. Emergence of Cooperative Bistability and Robustness of Gene Regulatory Networks. . An Osaka University biochemist and a biophysicist report that the common bistability state (Wikipedia) of dynamical systems can likewise be recognized in this genomic mode, whence GRNs reside in two coordinated, genes on and off, positions at once. See also a slide presentation Simultaneous emergence of Cooperative Response and Mutational Robustness in Gene Regulatory Networks by the authors at www.cp.cmc.osaka-u.ac.jp/~kikuchi/presentation/CCS2018.

Gene regulatory networks (GRNs) are complex systems in which many genes mutually regulate their expressions for changing the cell state adaptively to environmental conditions. The GRNs utilized by living systems possess several kinds of robustness which here means that they do not lose their functions when exposed to mutation or noises. In this study, we explore the fitness landscape of GRNs and investigate how the robust feature emerges in the "well-fitted" GRNs. Thus the more sensitively a GRN responds to the input, the fitter it is. To do this, they exhibit bistability, which necessarily emerges as the fitness becomes high. These properties are universal irrespective of the evolutionary pathway, because we did not perform evolutionary simulations. (Abstract excerpt)

The emergence of the new fixed points can be considered as an innovation or a big evolutionary jump. Then, what can we infer about the evolution based on them? The cooperative bistability and the robustness against noises are the consequence of the high fitness. Thus, we can say that this evolutional jump occurs inevitably as the fitness increases irrespective of the evolutionary pathway. We may identify this as the universality of evolution. (9)

Cosmic Code > 2015 universal

Norman, Andreas and Lukasz Rudnicki. Quantum Correlations and Complementarity of Vectorial Light Fields. arXiv:1904.07533. We review this entry by MPI Science of Light researchers much more in Quantum Organics, especially for its introduction of a “triality” concept to join and unite complements.

Cosmic Code > 2015 universal

Peruzzo, Fabio, et al. Spatial Patterns Emerging from a Stochastic Process near Criticality. arXiv:1907.08852. Into the year 2019, University of Leeds mathematicians including Sandro Azaele (search), draw upon a wealth of 21st century science so as to assert that living systems across every natural and social phase can be seen to seek and reach a preferred state of critical balance. As many other entries prove, this finding bodes well for a discovery of the universal complex recurrence of a dynamic complementarity. This constant phenomena arises from “nonlinearities of interacting agents,” that is nodal, particulate entities and relational, wave-like links, which are rooted in the physical cosmos, as it come to life again.

There is mounting empirical evidence that many communities of living organisms display key features which closely resemble those of physical systems at criticality. We here introduce a model framework for the dynamics of a community of individuals which undergoes local birth-death, immigration and local jumps on a regular lattice. We study these properties when the system is close to its critical point. Within a physically relevant regime dominated by fluctuations, it is possible to calculate analytically the probability density function of the number of individuals living in a given volume, which captures the close-to-critical behavior of the community across spatial scales. We discuss how this model in the critical-like regime is in agreement with several biodiversity patterns observed in tropical rain forests. (Abstract)

Cosmic Code > 2015 universal

Wolchover, Natalie. The Universal Law that Aims Time’s Arrow. Quanta. August 1, 2019. A new look at a ubiquitous phenomenon has uncovered unexpected fractal behavior that could give us clues about the early universe and the arrow of time. The science journalist reports on a confluence of findings which seem to quantify and affirm an intrinsic cosmic self-similarity. By way of a natural philosophia view, if of a mind to perceive, a worldwide human quest may at last be closing on a phenomenal discovery. As long intimated, an infinite recurrence of the same pattern and process in kind really does exist and emerge on its own. As a nascent sapiensphere can prove and realize this, organic nature’s genome-like source code can reach, as planned, our intentional, procreative furtherance.

Notable papers are Prescaling and Far from Equilibrium Hydrodynamics in the Quark-Gluon Plasma by Alekson Mazeliauskas and Jurgen Berges in Physical Review Letters (122/122301, 2019), Universal Dynamics Far from Equilibrium by C. M. Schmied, et al at arXiv:1810.08143, Observation of Universal Dynamics in a Spinor Gas by Max Prufer, et al in Nature (563/217, 2018) and Prescaling in a Far from Equilibrium Bose Gas by C. M. Schmied, et al in Physical Review Letters (122/170404, 2019). See also Bubble Experiment finds Universal Laws by Charlie Wood in Quanta for July 31, 2019.

In the new work, researchers see far-from-equilibrium systems undergoing fractal-like universal scaling across both time and space. Take the birth of the universe. After cosmic inflation, the hypothetical oscillating, space-filling condensate would have quickly transformed into a dense field of quantum particles all moving with the same characteristic speed. (Jurgen) Berges and his colleagues conjecture that these non-equilibrium particles then exhibited fractal scaling governed by universal scaling exponents as they began the thermal evolution of the universe.

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