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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 42 found.

Ecosmos: A Revolutionary Fertile, Habitable, Solar-Bioplanet Lifescape

Animate Cosmos

Brandenburg, Axel and David Hochberg. Introduction to Origins of Biological Homochirality. Origins of Life and Evolution of Biospheres. 52/1-3, 2022. Stockholm University and Center for Astrobiology, Madrid editors open a special issue for the latest research on life’s deep tendency to branch into relative left or right topological phases See, for example, Symmetry Breaking by Consecutive Amplification by Laura Huber and Oliver Trapp (view his website), Biological Homochirality and the Search for Extraterrestrial Biosignatures by Marcelo Gleiser, et al, Molecular Self-Assembly as a Trigger of Life Origin and Development by Dmitry Zlenko, et al, and Frontiers in Prebiotic Chemistry and Early Earth Environments by Ulrich Muller, et al.

The chemistry of terrestrial life is based on a spatial molecular asymmetry whose three dimensional geometrical structure or conformation is not identical to that of their mirror image or spatial reflections though a mirror. The parity P, or space inversion, is a discrete symmetry transformation in physics, and is broken at the molecular level. Such molecules thus possess homochirality or handedness. Amino acids, the building blocks of proteins, and the sugar backbones present in DNA and RNA are chiral molecules. Chirality constitutes a unifying feature of the living world and is a prime driving force for genetic evolution and biologic selection. (First paragraph)

Most amino acids and sugar molecules occur in mirror, or chiral, images of each other, knowns as enantiomers. However, life on Earth is mostly homochiral: proteins contain almost exclusively L-amino acids, while only D-sugars appear in RNA and DNA. We review potential mechanisms for biological homochirality on primal Earth an their implications for astrobiology: that it is a stochastic process driven by local environmental fluctuations; second, that it is driven by circularly-polarized ultraviolet radiation in star-forming regions; and that it is driven by parity violation at the elementary particle level. (Gleiser, et al)

Homochirality is a uniformity of chirality, or handedness. Objects are chiral when they cannot be superposed on their mirror images. For example, the left and right hands of a human are approximately mirror images of each other but are not their own mirror images, so they are chiral. In biology, 19 of the 20 natural amino acids are homochiral, being L-chiral (left-handed), while sugars are D-chiral (right-handed). (Wikipedia)

Animate Cosmos > Organic > quantum CS

Economou, Sophia and Edwin Barnes. Hello Quantum World! A First-world University Course in Quantum Information Science.. arXiv:2210.02868. We note this entry by Virginia Tech physicists as a way to show how this arcane depth is now being treated as just another science subject. (but a residual weirdness persists in some areas.)

Addressing workforce shortages within the Quantum Information Science and Engineering fields requires students from diverse backgrounds early in their education. Here, we describe our undergrad course called Hello Quantum World! that introduces a broad range of quantum information and computation concepts in a rigorous way but without much mathematics beyond high-school algebra, nor quantum mechanics. Some of the topids include superposition, entanglement, quantum gates, teleportation, quantum algorithms, and more. (Abstract)

Animate Cosmos > cosmos

akrami, Yasher, et al. The Search for the Topology of the Universe has just Begun. arXiv:2210.11426. This entry by a 14 person team based at Case Western Reserve University and also in Japan, Norway, the UK and Spain ban illustrate the functional scope and open frontier quest that our valiant Earthumanity is commencing to embark upon with seemingly limitless intrinsic abilities to do so.

New large-angle cosmic microwave background anisotropies can facilitate wider searches for cosmic topology. We demonstrate that for standard geometries of flat spacetimes, off-diagonal correlations between microwave background harmonic coefficients over a wide range of scales encode significant information, even if the topology scale exceeds the diameter of the observable Universe. Observations have so far considered a small subset. (Excerpt)

Animate Cosmos > cosmos > Quantum Cosmology

Overbye, Dennis. Black Holes May Hide a Mind-Bending Secret About Our UniVerse. New York Times. October 10, 2022. Take gravity, add quantum mechanics, stir. What do you get? Just maybe, a holographic cosmos. A succinct review of attempts by quantum and astro physicists to appreciate that their fields have a deep commonality to an extent as being one and the same. A main player is Stanford’s Leonard Susskind (arxiv:1708.03040) along with many colleagues.

Animate Cosmos > cosmos > physics

Rovelli, Carlo. The Relational Interpretation of Quantum Physics. arXiv:2109.09170. The Aix Marseille University and Perimeter Institute polyphysicist provides a latest finesse of his theoretical perception since the 1990s that interactivities between objects have their own existence which may be more vital that the pieces themselves. As a general validity of this concept has come to most subject fields, this insight also gains credence for this deepest, substantial realm. See also Information is Physical: Cross Perspective Links in Relational Quantum Mechanics by CR and Emily Adlam at arXiv:2203.13342, For a popular article see The Big Idea: Why Relationships are the Key to Existence in the Manchester Guardian for September 5, 2022.

The relational interpretation (or RQM, for Relational Quantum Mechanics) solves the measurement problem by considering an ontology of sparse relative events, or "facts". Facts are realized in interactions between any two physical systems and are relative to these systems. RQM's technical core is the realisation that quantum transition amplitudes determine physical probabilities only when their arguments are facts relative to the same system. The relativity of facts can be neglected in the approximation where decoherence hides interference, thus making facts approximately stable. (Abstract)

Animate Cosmos > cosmos > Geological

Menon, Anirudha and Banasri Basu.. Uncovering the Fractal Nature of Water Vapor Distribution above the Surface of the Earth. arXiv:2211.04106. When these scientific postings began in the early 2000s, evident perceptions such as this were rarely noticed anywhere. But two decades later every realm from Earth to ecosystems is found to be inherently graced with invariant patternings. Here Indian Association for the Cultivation of Science and Indian Statistical Institute mathematicians even find a moist atmosphere to exhibit their presence.

Fractals have recently become a major aspect of geophysical and geospatial studies. We examine the emergent fractal character of water vapor distributions on Earth’s surface as a function of pixel image resolution and moisture content percentile. We calculate physically relevant quantities such as fractal dimension, number of clusters, and size of the largest cluster with varying vapor percentile using computational methods and algorithms. We show that the self-similarity distribution is exact as a function of image resolution and approximate in some regimes as a function of the vapor percentiles. (Excerpt)

Animate Cosmos > Thermodynamics

Rovelli, Carlo. How Causation is Rooted into Thermodynamics. arXiv:2211.00888. The University of Toulouse polyphysicist contributes his latest deeply considerate insights about such an aimed arrow flight of time and fate. In regard, an allusion is offer that our beingness takes on a causal factor.

The notions of cause and effect are widely employed in science. I discuss why and how they are rooted into thermodynamics. The entropy gradient (i) explains in which sense interventions affect the future rather than the past, and (ii) underpins the time orientation of the subject of knowledge as a physical system. Via these two distinct paths, it is this gradient, and only this gradient, the source of the time orientation of causation, namely the fact the cause comes before its effects.

Hence the arrow of causation is rooted into the thermodynamic arrow via two different paths. Because in the macrophysics of our actual world, intervention does in fact affect the future. And because causation is the concern of the biological systems we are, time-oriented by the biosphere’s entropy gradient. For this second reason, causation is something we read in the worlds. Our own thinking is a dissipative process by the entropy gradient. So it is hard for our intuition to accept the fact that time orientation and hence the arrow of causation, are only thermodynamic, that is statistic, approximate, perspectival, phenomena. (6)

Animate Cosmos > Thermodynamics > quant therm

Rubino, Giulia, et al. Quantum Superposition of Thermodynamic Evolution with Opposing Time’s Arrow. Communications Physics. November, 2022. . As a good example of how this deepest phase can bring novel perception not possible until just now (surely not in the later 19th century), University of Vienna and University of Bristol, UK theorists appear to define a new course as life’s evolutionary systems may wend their energetic ways.

Microscopic physical laws are time-symmetric without a preferential temporal direction. However, the second law of thermodynamics allows one to associate a “forward” direction to a positive variation of the total entropy, and a negative variation with its “time-reversal” counterpart. This definition of a temporal axis is considered to apply in both classical and quantum contexts. Yet, quantum physics admits superpositions between forward and time-reversal. In this work, we demonstrate that time’s thermodynamic time’s arrow can be restored by a quantum measurement of entropy production. (Excerpt)

Animate Cosmos > Thermodynamics > autocat

Peng, Zhen, et al. The Hierarchical Organization of Autocatalytic Reaction Networks and its Relevance to the Origin of Life. PLOS Computational Biology.. September, 2922. University of Wisconsin system biologists develop and advance the latest reasons why, long ago, some manner of innate spontaneity must have existed. Into this decade, it is more evident that deep, natural tendencies to initiate and propel living systems occur on their own, beyond any chance occasion. Our global scale as a result can turn and proclaim an autopoietic self-made activation. Are we now participant persons meant to take up a role of ecosmic catalysts going forward?

Prior work on abiogenesis, the emergence of life from non-life, suggests that it requires chemical reaction networks that contain self-amplifying motifs, namely, autocatalytic cores. However, little is known about how the presence of multiple autocatalytic cores might allow for the gradual accretion of complexity on the path to life. Here we conceive a seed-dependent autocatalytic system (SDAS) as a subnetwork that can autocatalytically maintain itself. We develop new algorithms for detecting SDASs in chemical reaction databases and parallels between multi-SDAS networks and biological ecosystems. Our work provides computational tools to study large chemical/biochemical reaction networks and suggests new approaches to studying abiogenesis in the lab. (Excerpt)

The core puzzle of abiogenesis is, given a flux of energy and water, carbon dioxide, minerals, what system could arise by itself with the capacity of self-propagation complexification. As a result, any successful theory of abiogenesis needs to specify a system, a “first evolver,” that is endowed with the capacity to evolve adaptively and accrete complexity yet is simple enough to have a reasonable probability of arising spontaneously on the prebiotic Earth. Whatever the nature of the first evolver, it must have been able to self-propagate because such a facility is required for evolution. As a result, for the first evolver to exhibit two core attributes of life, namely self-maintenance and the capacity to evolve [16], it must have been autocatalytic. (2)

Animate Cosmos > exoearths

Meadows, Victoria, et al. Community Report from the Biosignatures Standards of Evidence Workshop. arXiv:2210.14293. A major NASA, ASU plus document by over 80 astro-authorities such as Glada Arney, Laura Barge, Chris Kempes, Sanjoy Som and Sara Walker to scope out, get in front of, this vast enterprise of our Earthly search quest for other near and far animate presences. Many more contributors are cited to give this circa 2021 project a broad credibility. The comprehensive, graphic report goes on for 86 pages, with a long reference list

The search for life beyond the Earth is the premier goal of the NASA Astrobiology Program for the scientific missions that explore the environments of Solar System planets and exoplanets. However, the detection of extraterrestrial life is so challenging that many technical approaches will be needed to make a convincing claim. Current and upcoming research efforts aimed at past and extant life could avail a consensus framework to plan for, assess and discuss life detection. Given the importance of exolife searches to NASA, and its complex scientific challenges and conveyance, the astrobiology community needs to develop guidelines for biosignature findings, along with clear reporting protocols. (Executive Summary)

Ecosmomics: An Independent, Informative Source Script of Common Complex Network Systems

Cosmic Code > nonlinear > networks

Samoylenko, Ivan, et al. Why are there Six Degrees of Separation in a Social Network?. arXiv:2211.09643.. For the first time, some 14 systems theorists with postings in Russia, Taiwan, Italy, Austria, Slovenia, the USA, Israel and India including Matjaz Perc and Stefano Boccaletti achieve an explanation as to why this popular degree of personal association is built into nature’s network topologies.

A wealth of evidence shows that real world networks are endowed with a small-world format whence the maximal distance between any two nodes scales logarithmically rather than linearly with their size. In addition, most social networks are organized so that no individual is more than six links apart from any other, an empirical feature known as six degrees of separation. Why social networks have this ultra-small world organization, whereby the graph's diameter is independent of the network size over several orders of magnitude, is still unknown. Here we show that this inherent property results from the equilibrium state of any network where individuals weigh between their aspiration to improve their centrality and the costs incurred in forming connections. Thus simple evolutionary rules associated with human cooperation and altruism can also account for a most intriguing attributes of social networks. (Abstract)

Cosmic Code > nonlinear > Algorithms

Caucheteux, Charlotte and Jean-Remi King. Brains and Algorithms Partially Converge in Natural Language Processing. Communications Biology. 5/134, 2022. Facebook AI Research, Paris and University of Paris Saclay researchers find an intrinsic, parallel affinity between these disparate cognitive phases. In regard, it appears that life and mind ought to parsimoniously use the same patterns and processes in every instance.

Deep learning algorithms trained to predict words from large amount of text have recently been shown to generate activations similar to those of the human brain. However, what drives this similarity is still unknown. Here, we compare deep language models to identify computational principles that generate brain-like representations of sentences. Our analyses reveal that the similarity between the algorithms and the brain primarily depends on their ability to predict words from context. Secondly, this common mode gives rise to and maintains perceptual, lexical, and compositional representations within each cortical region. Overall, this study shows that modern language algorithms converge towards brain-like solutions, which then suggests a way to unravel the foundations of natural language processing. (Abstract)

Cosmic Code > Genetic Info > DNA word

Bepler, Tristan and Bonnie Berger. Learning the Protein Language: Evolution, Structure, and Function. Cell Systems. 12/6, 2021. We cite this by Simons Machine Learning Center, NYC and MIT computational biologists as another instance of how deep learning AI, ML (Earthificial) leading edge capabilities are beginning a new global plane of of lively analytical studies.

Language models have emerged as a machine-learning approach for distilling information from protein sequence databases. These methods can discover evolutionary, structural, and functional organization across protein spaces. Here we encode amino-acid sequences into distributed vector representations that capture their structural and functional properties, as well as evaluate the evolutionary fitness of sequence variants. Deep protein language studies thus suggest new ways to approach protein and therapeutic design. (Excerpt)

Cosmic Code > Genetic Info > DNA word

Elnaggar, A., et al. ProtTrans: Towards Cracking the Language of Life’s Code Through Self-Supervised Deep Learning and High Performance Computing. IEEE Transactions on Pattern Analysis and Machine Intelligence. 14/8, 2021. Twelve computer scientists mainly at the Technical University of Munich explore these 2020 frontiers of deep new methods and insights into the deep, natural grammars of the language of life9 from the text). A long Abstract cites many computer code methods with a facile ability facility to read, write and take up natural, ecosmomic code-scripts. See also CodeTrans: Towards Cracking the Language of Silicon's Code Through Self-Supervised Deep Learning and High Performance Computing by the same group at arXiv:2104.02443,.

Cosmic Code > Genetic Info > DNA word

Ferruz, Noelia, et al. ProtGPT2 is a Deep Unsupervised Language Model for Protein Design. Nature Communications. 13/4348, 2022. University of Bayreuth, German system biochemists describe current progress toward a deep unity of life’s two prime genetic and linguistic code domains. By virtue of AI/ML facilities, into the 2020s an infinite affinity, as long sensed, is being revealed. This worldwise phase of palliative and enhanced metabolomics then brings much promise for health and welfare.

Protein design projects aim to build novel biomolecules customized for specific purposes so to potentially solve many environmental and biomedical problems. Recent progress in Transformer-based architectures have been enabled by language models which can generate text with human-like capabilities. Here, we describe ProtGPT2, a linguistic form that can build de novo protein sequences following the principles of natural ones. AlphaFold prediction of ProtGPT2-sequences yield structures with embodiments and topologies not captured in current structure databases.

Natural language processing (NLP) has seen many advances in recent years. Analogies between protein sequences and human languages have long been described as a concatenation of letters from a chemically defined alphabet. Both amino acids, and human text arrange letters to form structural elements (“words”) which assemble into domains (“sentences”) that undertake a function (“meaning”). A vital similarity is that protein sequences, like natural languages, are information-complete: they fully store structure and function. We propose that these methods open a new approach the whole metabolicfield of proteomics. (1)

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