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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 31 through 45 of 106 found.

An Organic, Conducive, Habitable MultiUniVerse

Animate Cosmos > exoearths

Stojkovic, Neda, et al. Galactic Habitability Re-Examined: Indications of Bimodality. arXiv:1909.01742. Astronomical Observatory, Belgrade astrophysicists including Milan Cirkovic post an extensive contribution which seeks ways to better to quantify preferential places for living systems to form and evolve. As the quotes allude, this requires factoring in a range of stellar and galactic types, sizes and active shapes. See also Habitability of Galaxies and Application of Merger Trees in Astrobiology at arXiv:1908.05935 and What can Milky Way Analogues Tell us About the Star Formation Rate of Our Own Galaxy? at 1909.01654 for concurrent papers. Again how fantastic is it that homo to anthropo sapiens, phoenix-like out of war zones, can come together and move on to learn about our celestial neighborhood. The paper merits some extended quotes.

The problem of the extent of habitable zones in different kinds of galaxies is one of the outstanding challenges for contemporary astrobiology. In the present study, we investigate habitability in a large sample of simulated galaxies from the Illustris Project in order to at least roughly quantify the hospitality to life of different galactic types. In particular, we find a tentative evidence for a second mode of galactic habitability comprising metal-rich dwarfs similar to IC 225, LMC or M32. The role of the galactic environment and the observation selection effects is briefly discussed and prospects for further research on the topic outlined. (Abstract)

Hence, we have essentially two major views on the habitability of galaxies so far: (i) the conventional view based to a large degree on the “rare Earth” thinking of Gonzalez, Ward, and Brownlee limiting life to large spiral discs analogous to the Milky Way Population I, and (ii) the radical view, emerging since about 2015, that it is mostly quiescent early-type galaxies and dwarfs more similar to the local Population II that are the best abodes for life. Details may vary from study to study, but this dilemma is quickly becoming one of the central issues of astrobiology.(3)

Studies of galactic habitability are obviously in their infancy. There is a large number of galactic properties which may influence the habitability score in ways currently ill-understood, and even those whose influence is somewhat understood (like the mean metallicity or the global star-formation rate in the present study) are still only roughly represented in the models. Thus, we hereby propose an emerging picture of galactic habitability which is bimodal: high-metallicity dwarfs on one hand, and quiescent spiral discs on the other hand, represent the peaks of galactic habitability in the local universe at present. (15)

If the emerging picture is correct, one mode of habitability is based upon the following factors: large galaxies with active star formation, similar to the Milky Way, with habitable planets forming around the Pop I analog stars with high metallicities. This mode is characterized by many different kinds of planetary systems, a high level of chemical evolution and, presumably, easier routes for advancement of prebiotic chemistry in both interstellar/circumstellar medium and on planetary surfaces. Once life appears, however, it is subject to strong abiotic selection pressure of its astrophysical environment in form of frequent irradiations by supernovae and GRBs, perturbations due to the spiral-arm and galactic-plane crossings, higher cosmic-ray fluences, and other astrobiological regulation mechanisms. Part of these perturbing influences may overflow into the “Gaian windows”, which are likely to be shorter for biospheres in the giant spiral systems. (17)

Cosmomics: A Genomic Source Code in Procreative Effect

Cosmic Code > Algorithms

Palazzi, Maria, et al. Online Division of Labour: Emergent Structures in Open Source Software. Nature Scientific Reports. 9/13890, 2019. Five Internet Interdisciplinary Institute (IN3), Universitat Oberta de Catalunya computer scientists cleverly apply complex system phenomena to the multi-player process of software code development. By so doing they find this artificial field to exhibit the same features of self-organization, diverse task allotment, a scalar, nested structure and more as every other natural and social realm. Once again, another life-like domain with this common vitality is revealed, which altogether strongly implies the presence of a natural, seed-like, generative program.

The development Open Source Software depends on the participation and commitment of volunteer developers to progress on a particular task. Several strategies are in effect, but little is known on how these diverse groupings self-organise to work together: any number of contributors can join in a decentralised, distributed, and asynchronous manner. It is helpful to then see some efficient hierarchy and division of labour must be in place within human biological and cognitive limits. We analyze popular GitHub open source projects with regard to three key properties: nestedness, modularity and in-block nestedness. These typify the emergence of heterogeneities among contributors, subgroups working on specific files, and the whole activity. From a complex network perspective, our conclusions create a link between bio-cognitive constraints, group formation and online working environments. (Abstract)

Cosmic Code > Algorithms

Wolfram, Stephen. Logic, Explainability and the Future of Understanding. Complex Systems. 28/1, 2019. The polymath prodigy (bio below) now can provide a 40 page technical survey of the history, present and preview of philosophical knowledge by way of its computational basis. In this journal edited by Hector Zenil, see also On Patterns and Dynamics of Rule 22 Cellular Automaton by Genaro Martinez, et al (28/2).

Stephen Wolfram is the creator of Mathematica, Wolfram|Alpha and the Wolfram Language; the author of A New Kind of Science; and the founder CEO of Wolfram Research. Born in London in 1959, he was educated at Eton, Oxford and received his PhD in theoretical physics from Caltech at age 20. Wolfram's early scientific work was mainly in high-energy physics, quantum field theory and cosmology. Over the course of four decades, he has been responsible for many discoveries, inventions and innovations in computer science and beyond. (www.stephenwolfram.com)

Cosmic Code > Algorithms

Wolpert, David, et al, eds. The Energetics of Computing in Life and Machines. Santa Fe: Santa Fe Institute Press, 2018. These highly technical proceedings from SFI seminars consider more efficient computational methods by way a better, deeper integration with vital principles and procedures. For example see Overview of Information Theory and Stochastic Thermodynamics of Computation by Wolpert (search), Information Processing in Chemical Systems by Peter Stadler, et al, and Automatically Reducing Energy consumption of software by Stephanie Forrest, et al.

Why do computers use so much energy? What are the fundamental physical laws governing the relationship between the precise computation run by a system, whether artificial or natural, and how much energy that computation requires? Can we learn how to improve efficiency in computing by examining how biological computers manage to be so efficient? The time is ripe for a new synthesis of systems physics, computer science, and biochemistry. This volume integrates pure and applied concepts from these diverse fields, with the goal of cultivating a modern, nonequilibrium thermodynamics of computation.

Cosmic Code > networks

Lee, Sang Hoon. Network Nested as Generalized Core-Periphery Structures. arXiv:1602.00093. We cite this entry by a Korea Institute for Advanced Study physicist as an example of how such a generic recurrent scale, which seeks and reaches complementary fast dense and slower expanse phases, are gaining notice as natural archetypes from universe to human. See also later entries on this eprint site by the author and colleagues for practical applications such as 3D chromosome and power-grid geometries.

The concept of nestedness, in particular for ecological and economical networks, has been introduced as a structural characteristic of real interacting systems. We suggest that the nestedness is in fact another way to express a mesoscale network property called the core-periphery structure. With real ecological mutualistic networks and synthetic model networks, we define the network-level measures for nestedness and core-periphery-ness in the case of weighted and bipartite networks. Therefore, there must exist structurally interwoven properties in more fundamental levels of network formation, behind this seemingly obvious relation between nestedness and core-periphery structures. (Abstract)

Cosmic Code > networks

Radicchi, Filippo, et al. Classical Information Theory of Networks. arXiv:1908.03811. FR, Indiana University, with Dmitri Krioukov and Harrison Hartle, Northeastern University, and Ginestra Bianconi, Queen Mary University of London finesse a better synthesis of implicit network communicative content with nature’s ubiquitous multiplex geometries. The broad motive is a better way to recognize evident commonalities as they vitalize and inform both genomic and neuromic phases.

Heterogeneity is an important feature which characterizes real-world networks. The diverse concept provides a convenient way to analyze and enhance systemic features such as robustness, synchronization and navigability. However, a unifying information theory to explain the natural emergence of heterogeneity in complex networks does not yet exist. Here, we develop a theoretical framework by showing that among degree distributions that can generate random networks, the one emerging from the principle of maximum entropy exhibits a power law. The pertinent features of real-world air transportation networks are well described by the proposed framework. (Abstract excerpt)

The principle of maximum entropy states that the unique probability distribution, encoding all the information available about a system but not any other information, is the one with largest information entropy. Available information about the system corresponds to constraints under which entropy is maximized. The principle of maximum entropy has found applications in many different disciplines, including physics, computer science, geography, finance, molecular biology, neuroscience, learning, deep learning, etc. (1)

Cosmic Code > networks

Suvakov, Milovan, et al. Hidden Geometries in Networks Arising from Cooperative Self-Assembly. Nature Scientific Reports. 8/1987, 2018. In these later 2010s of daily global scientific discourse, Jozef Stefan Institute, Slovenia physicists including Bosiljka Tadic (search) delve deeper into nature’s phenomenal, generative topologies so as to find further dimensions. We seek to report this frontier work, along with companion studies, as growing evidence of an independent, mathematical source code in creative, exemplary effect everywhere. As a result, relatively inorganic and living systems are found to organize or assemble themselves into similarly quickening scales and activities. By these perceptions, a universal reciprocity via a particulate nodal component and a relational connectivity mode or phase, which altogether carry vital information and form a triune whole, can be identified. See also Functional Geometry of Human Connectomes in this journal (9/12060, 2019), and Simplicial Complexes and Complex Systems by Vsevolod Salnikov, et al in the European Journal of Physics (40/014001, 2018).

Multilevel self-assembly involving small structured groups of nano-particles provides new routes to novel functional materials with a sophisticated architecture. In addition to inter-particle forces, the geometrical shapes are decisive factors. A comprehensive understanding of these processes is thus vital for the design of assemblies of desired properties. Here, we introduce a computational model for cooperative self-assembly with the attachment of structured groups of particles described by simplexes (connected pairs, triangles, tetrahedrons and higher order cliques) within a growing network. Our results show that higher Q-connectedness of the appearing simplicial complexes can arise due to geometric factors alone and that it can be efficiently modulated by changing the chemical potential and the polydispersity of the binding simplexes. (Abstract excerpt)

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Bonner, John T.. The Evolution of Evolution. Journal of Experimental Zoology B. Online June, 2019. The Princeton University biologist (1920-2019) was an experimental and theoretical pioneer and author for over 60 years with regard to the course of animal morphogenesis. His especial subject was the developmental course of slime molds, but in the vein of D’Arcy Thompson (search) his thought spread across life’s soma and senses on to human beings. Among his many works are Why Size Matters (2011) and Randomness in Evolution (2013). This posthumous essay is intended as one last clarification, against the mainstream as he notes, while selection remains a force there are other innate structural factors in much effect. Its significance merited commentaries such as by Stuart Newman, Scott Gilbert, and by Russell Powell and Maureen O”Malley.

In the past, most biologists, myself included, did not think of evolution as changing over time. The wonders of natural selection were always at hand and in operation once there was life. However, with reflection it became obvious that evolution has changed. Life’s course can be separated into four phases, or eras. The first starts with the rise of life on earth, which led to single cells that multiply asexually. The second era takes advantage of sexual reproduction as evolution could now gallop forward because of more diverse offspring for natural selection. The third era begins with the introduction of multicellularity. In the fourth there is a radical innovation: the nervous system which forms in animals. This allowed major changes to proceed such as language that led to what we call civilization and no longer depends on the slow changes of gene‐controlled evolutionary steps. (Abstract)

Evolution has been from small to big, from simple to complex. Besides this obvious point, there has been another neglected but equally important trend in the control – or suppression - of the effect of randomness. In microorganisms, random events are common, but with the increase in size and complexity there has been a corresponding decrease in the role of chance. So there are three phenomena: the increase in size, the increase in complexity, and the decrease in the part played by randomness, all three go together during the course of evolution. (Randomness in Evolution, 7)

Quickening Evolution

Fusco, Giuseppe, ed. Perspectives on Evolutionary and Developmental Biology. Padova: University of Padova Press, 2019. . This 420 page volume of essays for the Italian biologist and author Alessandro Minelli’s (search) 70th birthday is online in full, just Google title + Padova. With such entries a Towards a Developmental Biology of Holobionts by Scott Gilbert, An Evolutionary Biology for the 21st Century by Armin Moczek, Evo-Devo’s Challenge to the Modern Synthesis by Gerd Muller, The Evolutionary Relationships of Neural Structures in Arthropods by Angelika Stollewerk, Humans of the Middle Pleistocene by Giorgio Manzi, and Dynamic Structures in Evo-Devo by Johannes Jaeger, the work offers a latest evocation of this overdue (re)union of phylogeny and ontogeny. This 21st century synthesis is reinforced by a pervasive notice of symbiotic mutualities from eukaryotes to organisms and groups. In addition, a “self-constructing” essence is seen in process from physical origins to social peoples.

Evolutionary developmental biology (evo-devo) has revolutionized our understanding of why and how evolution unfolds the way it does. At the same time, much of evo-devo remains steeped in traditional perspectives and established dichotomies; these need to be overcome if evo-devo is to remain relevant in the coming century. In particular our conception of developmental evolution has to embrace the nature and consequences of developmental bias, the self-constructing nature of living systems, and the reciprocal interdependencies of development and environment in evolution. (Moczek abstract)

Evolution does not act on particular stages in the life of an organism. Instead, it alters developmental processes and life cycles in response to environmental conditions to bring about phenotypic change. The structure of these processes determines evolvability, the capacity of organisms to adapt. They lead us to fundamentally reconsider the active role of organisms in evolutionary change, which raises the possibility of a new agent-based theory of evolution in which organisms and their perceived environments co-construct each other in a radically innovative dialectic dynamic. (Jaeger abstract)

Quickening Evolution

Newman, Sturat. Inherent Forms and the Evolution of Evolution. Journal of Experimental Zoology B. Online August, 2019. The New York Medical College, Valhalla, theoretical experimentalist (search) has long studied and advocated the view that life’s creaturely forms arise from and manifest an intrinsic physical and mathematical basis. Here he comments on Bonner’s paper in this journal (June) which is a capsule of his 60 prolific years guided by this persuasion. In regard, Newman cites a growing trend to view the presence of the same structure, wing to limb, in descendent organisms. See also Inherency and Homomorphy in the Evolution of Development by SN in Current Opinion in Genetics (57/1, 2019), see third quote.

John Bonner presented a provocative conjecture that the means by which organisms evolve has itself evolved. The elements of his proposed model, namely the emergence of sex and enhanced selection pressures on larger multicellular forms, centers on a close mapping of genotypic to phenotypic change. He has also studied the intrinsic organizational properties of cell aggregates in social amoebae. By comparing the mechanistic bases of morphogenesis in the embryos of metazoans (animals), closely related holozoans, onto dictyostelids and volvocine algae, I conclude that understanding the evolution of multicellular evolution does indeed require knowledge of the inherent forms of diversifying lineages. (Abstract excerpt)

This approach stands outside of, but complements, the more gene-centric, adaptationist concepts of the major transitions in evolution scale, which are echoed in Bonner’s paper. As discussed her, and previously, the evolutionary transition from aggregates of unicellular organisms to the morphogenetically prolific Matazoa was a consequence of the acquisition of novel self-organizational capabilities, a factor that eludes selectionist explanatory frameworks. (6)

Inherency: The idea that aspects of the phenotype in development and evolution are latent in the organism’s material identity and that these features will spontaneously emerge if the conditions are appropriate.

Quickening Evolution

Powell, Russell and Maureen O’Malley. Metabolic and Microbial Perspectives on the “Evolution of Evolution". Journal of Experimental Zoology B. Online September, 2019. Boston University and University of Bordeaux philosophers of biology comment on John Bonner’s article with the above title (herein June) for a special issue. But this present paper, alongside structural biologist Bonner himself, Stuart Newman and Scott Gilbert, can illustrate a deep conceptual dichotomy. The major transitions model (see Abstract), along with the nested dimensions view of Eva Jablonka and Marion Lamb, and Newman who goes on to root life in a physical inherency, quite imply a directional procession. However P & O’M’s opening section is Broad Problem 1: Progressivism, which worries that these scalar views are at odds with past, vested denials of any teleological course and aim. As this quandary persists and resists, it begs a 21st century natural philosophy to sort out, clear up, and allow an actual evolutionary gestation to be realized. (See Powell’s new book Contingency and Convergence (MIT Press, Jan. 2020) for more.)

Identifying and theorizing major turning points in the history of life generates insights not only into epochal events but also the processes that bring them about. In his treatment of these issues, John Bonner identifies the evolution of sex, multicellularity, and nervous systems as enabling the “evolution of evolution,” which involves transformations in how life develops. By comparing his framework with two decades of major transitions scale theory, we identify some issues between Bonner's view and the prevailing literature. These problems include implicit progressivism, conceptual disunity, and a limited ability to explain major transformations. In contrast with the “vertical” focus on replication, hierarchy, and morphology that preoccupies most literature on major transitions, we propose a “horizontal” dimension in which metabolism and microbial innovations play an explanatory role in the broad‐scale organization of life. (Abstract)

Quickening Evolution

Sela, Itamar, et al. Selection and Genome Plasticity as the Key Factors in the Evolution of Bacteria. Physical Review X. 9/031018, 2018. In this physics journal, aided by current affirmations of a common repetition in kind everywhere, National Center for Biotechnology Information theorists I. Sela, Yuri Wolf and Eugene Koonin report that genomic phenomena takes on the form of a nested scale across many domains or classes. As their Summary below notes, the present re-unification and re-rooting of life in an increasingly fertile cosmos is well served by such evidential findings. See also a reference Family Specific Scaling Laws in Bacterial Genomes by Eleonora De Lazzari, et al in Nucleic Acids Research (45/13, 2017, second quote).

Sela, Itamar, et al. Selection and Genome Plasticity as the Key Factors in the Evolution of Bacteria. Physical Review X. 9/031018, 2019. In this physics journal, aided by current affirmations of a common repetition in kind everywhere, National Center for Biotechnology Information theorists I. Sela, Yuri Wolf and Eugene Koonin report that genomic phenomena takes on the form of a nested scale across many domains or classes. As their Summary below notes, the present re-unification and re-rooting of life in an increasingly fertile cosmos is well served by such evidential findings. See also a reference Family Specific Scaling Laws in Bacterial Genomes by Eleonora De Lazzari, et al in Nucleic Acids Research (45/13, 2017, second quote). OK

In microbes, different functional classes of genes, such as those involved in information processing, metabolism, and regulation, show scaling exponents with the genome size. However, there is no general theory to explain these “universal laws” of microbial genome evolution. Here, we describe a mathematical model that recovers the differential scaling of functional gene classes in bacterial genomes, includes only two parameters to characterize genomes, selection coefficient and plasticity. After testing the model against genomic data, we conclude that genome plasticity is a key evolutionary factor. Our findings suggest that at least some key aspects of genome evolution can be captured by general theoretical models akin to those widely used in physics. (Sela Summary)

Among several quantitative invariants found in evolutionary genomics, one of the most striking is the scaling of the overall abundance of proteins, or protein domains, which share a specific functional annotation across genomes of given size. The size of these functional categories change, on average, as power-laws in the total number of protein-coding genes. Here, we show that such regularities are not restricted to the behavior of high-level functional categories, but exist at the level of single evolutionary families of protein domains. Under the common assumption that selection is driven solely or mainly by biological function, these findings point to fine-tuned and interdependent roles of specific protein domains. (De Lazzari Abstract)

Quickening Evolution

Svorcova, Jana and Anton Markos. Epigenetic Processes and the Evolution of Life. Boca Raton: CRC Press, 2019. Charles University, Prague theoretical biologists (search AM) achieve a consummate review to date of life’s oriented, stirring “planetogenesis.” The inclusive survey set within a biospheric milieu proceeds from rudimentary metabolic and/or replicator origins onto unicells and organisms, with an emphasis upon evolving phases of genetic heredity. An informational, semiotic quality is emphasized along with a pervasive symbiosis which leads to an I, Holobiont model. With all this in place, an extended evolutionary synthesis in the air is well scoped out.

The book covers the possible story of emergence of life and its subsequent evolution, emphasizing the necessary evolutionary step negotiation of a common "language set" which kept all inhabitants in the biosphere together, ensuring a basic level of understanding among them. The book focuses on "protocols of communication" (both genetic and epigenetic) representing norms shared and understood across the whole biosphere, enabling a plethora of holobiotic relationships. Cooperative nature of organismal evolution and epigenetic processes as a major force in evolution are also covered.

Quickening Evolution > Biosemiotics

Hendin, Yogi Hale. Meeting Report: The 18th Annual Biosemiotics Gathering. Biosemiotics. 12/2, 2019. An Erasmus University, Rotterdam philosopher reviews this UC Berkeley June convocation, organized by Terence Deacon and the author (Google title for more info and a 70 page book of abstracts). Some talks were Quantum origins of ontic emergence by Michael Epperson, Creation of the relative next by Donald Favareau, Can truth and love prevail? by Gerald Ostdick, and Do cell sing to each other? by Mark Johnson.

Over June 17–20, 2018, from dozens of countries, biosemioticians converged at the University of California, Berkeley to discuss the state of the art of Biosemiotics. The syncretic gathering, like the discipline itself, brought together scholars in natural science, social science, and the humanities, to further develop what Danish chemist and ur-biosemiotian Jesper Hoffmeyer calls “the life of signs, and the signs of life.” The conferees examined the hermeneutics of biological communication, its relevance to the Extended Evolutionary Synthesis, and went on to address primordial questions such as What is life, What Is Semiosis, and much more. (Abstract excerpt)

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

Earth Life > Common Code

Bagrow, James and Eric Bolit. An Information-Theoretic, All-Scales Approach to Comparing Networks. Applied Network Science. 4/45, 2019. University of Vermont complexity researchers conceive a common pictorial image as an effective way to represent nature’s ubiquitous propensity to join discrete elements or entities into viable communal assemblies. The novel approach is thus dubbed a Network Portrait.

As network studies proceed, it is more common to move beyond a single network to analyze multiple arrays. An important task then becomes network comparisons by way of a similarity or distance measure in between. Here we introduce a new measure as a Network Portrait Divergence which is mathematically principled, incorporates the topological characteristics at all structural scales, and is generally applicable to all types of networks. An important feature that enables many of its useful properties is that it is based on a graph invariant. We test our measure on both synthetic graphs and real world networks taken from protein interaction data, neuroscience, and computational social science applications. (Abstract edits)

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