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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 1 through 15 of 22 found.


Earth Learn: A Planetary Prodigy Comes to Her/His Own Knowledge

A Learning Planet > Original Wisdom > World Philosophy

Abede, Rediet, et al. Narratives and Counternarratives on Data Sharing in Africa. arXiv:2103.01168. A seven person team posted at UC Berkeley (RD), University of the Witwatersrand, UC Dublin, Carnegie Mellon University, IBM Research Africa, and Deloitte Africa contend that the Global South is graced by a different, relational culture than particulate bytes. Their essence is more about integral storytelling, drama rather than data, which by a prosodic integrity can convey an ethical message, which “data” alone cannot. For more about the lead author, an Ethiopian-American AI scientist, and this project see A Computer Scientist Who Tackles Inequality Through Algorithms in Quanta Magazine (April 2021)

As machine learning and data science applications grow ever more prevalent, there is an increased focus on data sharing and open data initiatives in the context of the African continent. Many argue that data sharing can support research and policy design to alleviate poverty, inequality, and derivative effects in Africa. But conversations around accessing and sharing African data are too often driven by nonAfrican stakeholders. These perspectives employ deficit narratives, focusing on lack of education, training, and technological resources as the causes of problems in the data ecosystem. We argue that these narratives obscure the full complexity of African data efforts. We use storytelling via fictional personas built from interviews with African data experts to provide alternative versions. Along with studies on data practices within the continent, we identify recurring impediments and inequities in sharing data benefits. We discuss issues arising from power imbalances resulting from the legacies of colonialism, ethno-centrism, and slavery, disinvestment in building trust, and Western-centric policies that are ill-suited to the African context. (Abstract excerpt)

A Learning Planet > Original Wisdom > World Philosophy

Abede, Rediet, et al. Narratives and Counternarratives on Data Sharing in Africa. arXiv:2103.01168. A seven person team posted at UC Berkeley (RD), University of the Witwatersrand, UC Dublin, Carnegie Mellon University, IBM Research Africa, and Deloitte Africa contend that the Global South is actually graced by a different, relational culture than North/West particulate bytes. Their essence is more about integral storytelling, drama rather than data, which by a prosodic integrity can convey a meaningful, ethical message. For more about the lead author, an Ethiopian-American AI scientist, and this project see A Computer Scientist Who Tackles Inequality Through Algorithms in Quanta Magazine (April 2021)

As machine learning and data science applications grow ever more prevalent, there is an increased focus on data sharing and open data initiatives in the context of the African continent. Many argue that data sharing can support research and policy design to alleviate poverty, inequality, and derivative effects in Africa. But conversations around accessing and sharing African data are too often driven by nonAfrican stakeholders. These perspectives employ deficit narratives, focusing on lack of education, training, and technological resources as the causes of problems in the data ecosystem. We argue that these narratives obscure the full complexity of African data efforts. We use storytelling via fictional personas built from interviews with African data experts to provide alternative versions. Along with studies on data practices within the continent, we identify recurring impediments and inequities in sharing data benefits. We discuss issues arising from power imbalances resulting from the legacies of colonialism, ethno-centrism, and slavery, disinvestment in building trust, and Western-centric policies that are ill-suited to the African context. (Abstract excerpt)

A Learning Planet > The Spiral of Science

Connor, Thomas, et al. Enhanced X-ray Emission for the Most Radio-Powerful Quasar in the Universe’s First Billion Years. arXiv:2103.03879. We cite this entry by eleven astronomers based in the USA, Germany, the UK, Italy, and Chile as one example among many of active worldwise studies about every aspect from quantum to, in this case, quasar phenomena. How could it be so that we tiny human beings who can yet now communicate in a super-organic way are able to gain such infinite knowledge. On the face of it, our global sapience seems as the phenomenal way that a self-creative universe can necessarily achieve a written, quantified description of itself.

We present deep Chandra X-ray observations of a quasar that, with a radio-to-optical flux ratio of R>1000, is one of the radio-loudest quasars in the early universe. Modeling the X-ray spectrum of the quasar with a power law, we identify a diffuse structure 50 kpc to the NW of the quasar along the jet axis that corresponds to a 3σ enhancement in the angular density of emission. (Abstract excerpt)

A quasar is an extremely luminous active galactic nucleus, in which a supermassive black hole with mass ranging from millions to billions of times the mass of the Sun is surrounded by a gaseous accretion disk.

Ecosmos: A Revolutionary Organic Habitable UniVerse

Animate Cosmos > Quantum Cosmology > cosmos

Scharf, Caleb. Is Physical Law an Alien Intelligence? Nautilus. Issue 42, 2016. The Columbia University astrobiologist (search) muses about how trending evidence with regard to universal, and also multiversal appearances, lead to inklings that maybe lively systems equations and systems are an intrinsic essence which suffuses our reality. Our interest, as the text alludes, is that such a conceptual revolution can imply that akin to Gaian self-regulation on Earth, animate forces might similarly begin to influence the entire ecosmos

The universe began to expand at an accelerated rate about 5 billion years ago. This acceleration is conventionally chalked up to dark energy. In fact, one explanation is that the timing has to do with life—an anthropic argument. The dark energy didn’t become significant until enough time had gone by for life to take hold on Earth. For many cosmologists, that means our universe must be part of a vast multiverse where the strength of dark energy varies from place to place. We live in one of the places suitable for life like us. Elsewhere, dark energy is stronger and blows the universe apart too quickly for cosmic structures to form and life to take root. But perhaps there is another reason for the timing coincidence: that dark energy is related to the activities of living things. After all, any very early life in the universe would have already experienced 8 billion years of evolutionary time by the time expansion began to accelerate. It’s a stretch, but maybe there’s something about life itself that affects the cosmos.

Animate Cosmos > exoearths

Kaltenegger, Lisa and Zifan Lin. Finding Signs of Life in Transits: High-resolution Transmission Spectra of Earth-Like Planets around FGKM Host Star. Astrophysical Journal Letters. 909/1, 2021. (arXiv:2102.12011) Cornell University astronomers contribute to this frontier field of how to detect and distinguish biosignatures as our exoplanet neighborhood census proceeds apace. Subject topics are high resolution and transmission spectroscopy, atmosphere compositions, observational views, and more as our Earthomo sapience takes up the exploratory task of quantifying and learning all about whom or what might, or may not, be out there. The grand project then feeds back to situate and identify we valiant Earthlings.

Thousands of transiting exoplanets have already been detected orbiting a wide range of host stars, including the first planets that could potentially be similar to Earth. The upcoming Extremely Large Telescopes and the James Webb Space Telescope will enable the first searches for signatures of life in transiting exoplanet atmospheres. Here, we quantify the strength of spectral features that could indicate a similar biosphere on exoplanets orbiting a wide grid of host stars (F0 to M8). In the search for life in the cosmos, transiting planets provide the first opportunity to discover whether or not we are alone, with this database as one of the keys to optimize the search strategies. (Abstract)

Ecosmomics: A Survey of Genomic Complex Network System Sources

Cosmic Code > nonlinear > Algorithms

Gregor, Karol and Frederic Besse.. Self-Organizing Intelligent Matter: A Blueprint for an AI Generating Algorithm. arXiv:2010.07627. DeepMind, UK computer theorists pick up on a 2019 paper by Jeff Clune (University of Wyoming) entitled Ai-generating Algorithms as an Alternate Paradigm for General Artificial Intelligence (1905.10985) about a better natural basis for evolutionary computation. The authors continue and enhance this method by way of further perceptions of life’s origin and complex, quickening course as a prime exemplar. In respect, this approach can provide another window upon of some manner of computational program and process at work in animate generation.

We propose an artificial life framework aimed at facilitating the emergence of intelligent organisms. In this framework there is no explicit notion of an agent: instead there is an environment made of atomic elements. These elements contain neural operations and interact through exchanges of information and through physics-like rules contained in the environment. We discuss how an evolutionary process can lead to the emergence of different organisms made of many such atomic elements which can coexist and thrive in the environment. (Abstract)

An AI generating algorithm is a computational system that runs by itself without outside interventions and after a certain amount of time generates intelligence. Evolution on earth is the only known successful system thus far that we know of. (1) In this paper we proposed a framework for achieving intelligence by evolutionary process in an environment that is built out of interacting elements implementing computationally efficient and general learning. (9)

Cosmic Code > nonlinear > 2015 universal

Manicka, Santosh, et al. Effective Connectivity Determines the Critical Dynamics of Biochemical Networks. arXiv:2101.08111. Into 2021, Indiana University, Center for Social and Biomedical Complexity theorists including Luis Rocha (see his website at IU) advance understandings of the phenomena of self-organized criticality which is seen to naturally mediate life’s need to conserve and preserve, along with an openness to creative change. And if this golden middle way might ever at be confirmed and comprehended, it could revise our awful politics which now pits one mode vs. the other.

Living systems operate in a critical dynamical regime between order and chaos where they are both resilient to perturbation, and flexible enough to evolve. To characterize such critical dynamics, the present method uses automata network connectivity and node bias (to be on or off) as tuning parameters, which can lead to uncertain predictions. We derive a more accurate approach by way of canalization, a redundancy that buffers response to inputs and traits keeping them close to optimal states despite genetic and environmental perturbations. The new 'canalization theory' of criticality is based on a measure of effective connectivity, which resolves how to find precise ways to design or control network models of biochemical regulation. (Abstract excerpt)

Cosmic Code > nonlinear > 2015 universal

Plenz, Dietmar, et al. Self-Organized Criticality in the Brain. arXiv:2102.09124. Into the 2020s, National Institute of Mental Health, Critical Brain Dynamics Section (D. Plenz director, search) neuroscientists report on a decade and more of convergent research findings which now have reached a proven validity that human cerebral activity does indeed seek and reside at an optimum dynamic poise. In respect, one more robust exemplar, on the way to an invariant universality, is achieved by virtue of our own microcosmic cognizance.

Self-organized criticality (SOC) refers to the ability of complex systems to evolve towards a phase transition at which interactions between system components lead to scale-invariant events beneficial for overall performance. For the last two decades, considerable experimental evidence has accumulated that the mammalian cortex with its diversity in cell types, interconnectivity, and plasticity might exhibit SOC. Here we review experimental findings of isolated, layered cortex preparations to self-organize towards the four dynamical motifs of up-states, oscillations, neuronal avalanches, and coherence potentials. The precise interaction between up-states, nested oscillations and avalanches in layered cortex provides compelling evidence for SOC in the brain. (Abstract excerpt)

Cosmic Code > nonlinear > 2015 universal

Zhang, Yuanzhao and Adilson Motter. Mechanism for Strong Chimeras. arXiv:2101.12230. Northwestern University systems physicists (search AM) provide a deeply technical explanation of why so many natural phenomena are found to exhibit this optimum state of both order and disorder at once.

Chimera states have attracted significant attention as symmetry-broken states exhibiting the unexpected coexistence of coherence and incoherence. Despite the valuable insights gained from analyzing specific systems, an understanding of the general physical mechanism underlying the emergence of chimeras is still lacking. Here, we show that many stable chimeras arise because coherence in part of the system is sustained by incoherence in the rest of the system. Recognizing this mechanism offers a new meaning to the interpretation that chimeras are a natural link between coherence and incoherence. (Abstract)

Cosmic Code > Genetic Info > DNA word

Kaye, Alice and Wyeth Wasserman. The Genome Atlas: Navigating a New Era of Reference Genomes. Trends in Genetics. January, 2021. Children's Hospital Research Institute, University of British Columbia scholars conceive, specify and finesse some better ways to display and access all manner of burgeoning genetic data bases. Our further interest is their strong employ of a ready cross-affinity between genomic scriptomes and literate, library-like textual analogies.

The reference genome serves two distinct purposes within the field of genomics. First, it provides a persistent structure against which findings can be reported, which then allows for universal knowledge exchange between users. Second, it reduces the computational costs and time required to process genomic data by creating a software scaffold that can be relied upon. Here, we posit that current efforts to extend the linear reference to a graph-based structure will face a trade-off between comprehensiveness and computational efficiency. In this article, we explore how the reference genome is used and suggest an alternative structure, The Genome Atlas (TGA), to fulfill the bipartite role of the reference genome. (Abstract)

Box 1. The Library Analogy Consider a library of books that represents our collective knowledge regarding the human genome. In place of the words of a story, a book contains a DNA sequence that is an allele or a stretch of immutable nucleotide. The complete diploid genome of an individual can be constructed through two series of books read in a specific order. Each book has two sets of information associated with it: (i) meta-information (e.g., author, publisher, or genre); and (ii) the text within. This divide extends to searching for books, or looking within a specific book. The utilization of meta-information for feature identification and the functional implications of the differences between genomes or populations of genomes form ‘knowledge exchange’ with regards to a reference genome.

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

Earth Life > Nest > Symbiotic

Igamberdiev, Abir, et al, eds. Symbiogenesis and Progressive Evolution. Biosystems. April, 2021. is a special collection edited by AI, Richard Gordon, and George Mikhailovsky which into the 2020s seeks to report frontier insights and evidence that nature’s constant preference for a mutual convergent synthesis of diverse members is in primary procreative effect everywhere. We note in this issue From Empedocles to Symbiogenetics: Lynn Margulis's Revolutionary Influence on Evolutionary Biology by Dorion Sagan and Symbiogenesis as a Driving Force of Evolution: The Legacy of Boris Kozo-Polyansky by Vladimir Agafonov, et al, Serial Endosymbiosis Theory: From Biology to Astronomy and Back to the Origin of Life by Predrag Slijepcevic (search) and Archaeal Origins of Eckaryotic Cells by Frantisek Baluska and Sherrie Lyons.

Symbiogenesis played a crucial role in the origin of eukaryotic cells and onto life’s emergence. It led to a complexification of coding systems as a result of merging individual genomes of prokaryotic cells. This issue will explore the role of horizontal gene transfer and symbiogenesis onto complex multicellular organisms. The papers herein will seek to understand the role of symbiogenesis in the evolutionary process and suggest computational models to describe the emergence of complex biological systems. The issue is dedicated to the founders of the concept of symbiogenesis Boris Kozo-Polyansky (1890-1957) and Lynn Margulis (1938-2011), the former chief editor of BioSystems, who proved this concept and introduced it into the mainstream of evolutionary theory. (Issue Introduction excerpt)

Earth Life > Nest > Symbiotic

Prosdocimi, Francisco, et al. The Theory of Chemical Symbiosis: A Margulian View for the Emergence of Biological Systems. Acta Biotheoretica. 69/1, 2021. We note this entry by Universidade Federal do Rio de Janeiro, Universidad Nacional Autónoma de México and Universidade Federal do Rio de Janeiro, Universidade Federal da Paraíba, Brazil biochemists as an example of how symbiotic phenomena are being found in increasingly widespread areas as in this case of life’s origins. As the title cites, some ten years after Lynn Margulis’ passing, there is strong effort is going forth to give prime credit to her four decades of study, explanation and defense.

The theory of chemical symbiosis (TCS) suggests that biological systems started with the collaboration of two polymeric molecules existing in early Earth: nucleic acids and peptides. Chemical symbiosis emerged when RNA-like nucleic acid polymers happened to fold into 3D structures capable to bind amino acids together, forming a proto peptidyl-transferase center. TCS suggests that there is no chicken-and-egg problem into the emergence of biological systems as RNAs and peptides were of equal importance to the origin of life. Life has initially emerged when these two macromolecules started to interact in molecular symbiosis. Mutualism is the strongest force in biology, capable to create novelties by emergent principles; on which the whole is bigger than the sum of the parts. (Abstract excerpt)

Earth Life > Nest > Symbiotic

Slijepcevic, Predrag. Serial Endosymbiosis Theory: From Biology to Astronomy and Back to the Origin of Life. Biosystems. April, 2021. Into this late year for a Symbiogenesis and Progressive Evolution issue, a Brunel University ecosmic philosopher (search) can post a widest-ranging survey and endorsement of nature’s propensity to combine into nested, mutually reciprocal units. The paper opens with an account of early Russian work, so as to proceed onto the lifetime contribution of Lynn Margulis (1938-2011) to quantify that such diverse unifications were a prime mover of life’s organismic development. The essay goes on to add Freeman Dyson’s later 1990s perception of symbiotic phenomena across interstellar and galactic reaches, along with Dyson’s 1999 Origins of Life book which finds such convergent, additive effects likewise in effect at this early stage.

Serial Endosymbiosis Theory, or SET, was conceived and developed by Lynn Margulis to best explain the origin of eukaryotic cells. In this paper, I focus on two aspects of SET. First, using the concept of “universal symbiogenesis”, proposed by Freeman Dyson to search for commonalities in astronomy and biology, I contend that SET can apply beyond eukaryogenesis. Second, I contrast a recent “viral eukaryogenesis” hypothesis, according to which the nucleus evolved from a complex DNA virus, with a view closer to SET, whence the nucleus evolved through the interplay of the archaeal host, the eubacterial symbiont, and a non-LTR transposon, or telomerase. (Abstract excerpt)

Earth Life > Nest > Societies

Guo, H., et al. Evolutionary Games on Simplical Complexes. arXiv:2103.03498. Eleven system theorists based in China, Spain, Chile, Russia, and Italy including Stefano Boccaletti consider a novel explanation of life’s cooperative propensities by way of complex network principles. It is concluded that this mathematical structuration is realistically present and an appropriate method to study.

Elucidating the mechanisms that lead to cooperation is still one of the main scientific challenges of current times, as many common cooperative scenarios remain at odds with Darwin's natural selection theory. Here, we study evolutionary games beyond pairwise interactions by way of situations in which indirect interactions via a neighbor or a group of neighbors. We report a number of results that: (i) support that higher-order games allow for non-dominant strategists to emerge and coexist with dominant ones; (ii) characterize a novel transition from defection to cooperation as a function of the simplicial structure of the population; and (iii) demonstrate that 2-simplex interactions are a source of strategy diversity. Our study constitutes a step toward understanding the roots of cooperation and the mechanisms that sustain it. (Abstract excerpt)

Earth Life > Recapitulation

Kohsokabe, Takahiro and Kunihiko Kaneko. Dynamical Systems Approach to Evolution–Development Congruence: Revisiting Haeckel's Recapitulation Theory. Journal of Experimental Biology. B. February, 2021. Some 140 years later, RIKEN Center for Biosystem Dynamics and Universal Biology Institute, University of Tokyo veteran researchers (search KK) provide a novel 21st century qualification for general parallels between ontogeny and phylogeny. The main novel resource is the active presence of gene regulatory networks, along with complex system influences. See also Recapitulation-like Developmental Transitions of Chromatin Accessibility in Vertebrates by Masahiro Uesaka, et al in Zoological Letters (5:33, 2019).

It is acknowledged that embryonic development has a tendency to proceed from common toward specific. Ernst Haeckel (1834-1919) raised the question of why that tendency prevailed through evolution, and the question remains unsolved. Here, we revisit his recapitulation theory of a parallel between evolution and development through numerical evolution and dynamical systems theory. By using intracellular gene expression dynamics with cell‐to‐cell interaction over spatially aligned cells to represent the developmental process, gene regulation networks (GRN) that govern these dynamics evolve under the selection pressure to achieve a prescribed spatial gene expression pattern. For most numerical evolutionary experiments, the evolutionary pattern changes over generations, as well as the developmental pattern changes governed by the evolved GRN exhibit remarkable similarity. (Abstract excerpt)

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