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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 31 through 45 of 66 found.


Ecosmos: A 21st Century Fertile, Habitable, Solar-Bioplanet Lifescape

Animate Cosmos > Fractal

Sowmya, G., et al. Supergranular Fractal Dimension and Solar Radiation. arXiv:2207.10490. In these 2020s, CSSS Institute of Engineering and Technology for Women, Karnataka, Poornaprajna Institute of Scientific Research, Devanahalli, and Bangalore University astrophysicists proceed to find and quantify evidence of deep self-similarities even in the sun’s rays.

In regard, see The Sun’s Supergranulation by Francois Rincon and Michel Rieutord in Living Reviews in Solar Physics (15/6, 2018) whence Supergranulation is a fluid-dynamical phenomenon in the solar photosphere in the form of a vigorous cellular flow pattern.

We present findings from an analysis of the fractal dimension of solar supergranulation as a function of latitude, cell size and solar rotation, by way of spectroheliographic data. We find that the fractal dimension tends to decrease from about 1.37 at the equator to about 1 at 20 degree latitude in either hemisphere, suggesting that solar rotation rate has the effect of augmenting the irregularity of supergranular boundaries. (Excerpt)

Animate Cosmos > exoearths

Gerrit, Horstmann, et al. Tidally Forced Planetary Waves in the Tachocline of Solar-like Stars. arXiv:2208.00644. We cite this entry by German (Dresden), Georgian (Tbilisi) and Austrian (Graz) astrophysicists as a current worldwide finding about solar system phenomena to an extent that the composite sun and its orbital orrery appear to act as an integral whole unit.

The tachocline is the transition region of stars of more than 0.3 solar masses, between the radiative interior and the differentially rotating outer convective zone.

Animate Cosmos > exoearths

Sibony, Yves, et al. The Rotation of Planet-Hosting Stars. arXiv:2204.01421. University of Geneva and University of Zurich researchers perform initial analyses that indicate the presence of whole solar system interactivities between physical stellar forces and nascent orbital worlds.

Ecosmomics: An Independent Source Script of Generative, Self-Similar, Complex Network Systems

Cosmic Code

De Marzo, Giordano, et al. Quantifying the Unexpected: A Scientific Approach to Black Swans. Physical Review Research. 4/033079, 2022. The prolific collaboration of these Centro Ricerche Enrico Fermi, Rome system physicists including Luciano Pietronero here continues to apply their innovative analyses from sidereal realms to, in this instance, the pesky problem of whether sudden complex bursty behaviors (wild weather, market crashes, tipping points) can be found to have a quantifiable basis. While many prior efforts were not satisfactory, by virtue of a better perception of endemic fractal affinities this endeavor allows that some manner of an actual mathematic basis seems to be discernible. See also Using Machine Learning to Anticipate Tipping Points and Extrapolate to Post-Tipping Dynamics of Non-Stationary Dynamical Systems by Dhruvit Patel and Edward Ott at arXiv:2207.00521 for another contribution.

Many natural and socio-economic systems are characterized by power-law distributions that make the occurrence of extreme events not negligible. Such events are sometimes referred to as Black Swans, but a quantitative definition is still lacking. By leveraging on the properties of Zipf-Mandelbrot law, we investigate the relations between such events and the dynamics of the upper cutoff of the inherent distribution. This analysis provides a method to classify White, Grey, or Black Swans. The systematic and quantitative methodology we developed allows a scientific and immediate categorization of rare events, along with new insights into their generative mechanism. (Abstract excerpt)

Cosmic Code > nonlinear > networks

Carletti, Timoteo, et al. Global Topological Synchronization on Simplical and Cell Complexes. arXiv:2208.14783. TC, Lorenzo Giambagli, University of Namur, Belgium and Ginestra Bianconi, Queen Mary University, London theorists press their studies of network phenomena, which as an ecosmic anatomy and physiology seems ever graced by such innate facilities. See also Solitary States in Complex Networks: Impact of Topology by Anna Zakharova, et al (2208.14911).

Cosmic Code > nonlinear > networks

Frottier, Theo, et al. Harmonic Structures of Beethoven Quarters: A Complex Network Approach. arXiv:2201.08796. Into these 2020s, system physicists TF and Bertrand Georgeot, University of Toulouse and Olivier Giraud, University of Paris provide novel insights into how even musical compositions are distinguished by a common interconnective topology. As we may perceive, a universal anatomy and physiology, a music of the universe and humanverse, is just now being revealed. See also How Network-based Approaches can Complement Studies in Dementia by Cemile Kocoglu, et al in Trends in Genetics. (38/9, 2022) for another example.

We propose a complex network approach to the harmonic structure which underlies western tonal music. From a database of Beethoven's string quartets, we construct a directed network whose nodes are musical chords and edges connect chords. We show that the network is scale-free and has specific properties when ranking algorithms are applied. We explore its community structure and musical interpretation, and propose statistical measures from network theory to distinguish stylistically between periods of composition. (Excerpt)

The present work shows that the complex network approach can be fruitfully applied to the harmonic structure of musical works. Based on the example of Beethoven string quartets, we specified the properties of this new type of networks, and in particular we discussed the relationship between the spectrum of the Google matrix, the community structures, and musical specificities of the scores. (6)

Cosmic Code > Genetic Info

Stenseth, Nils, et al.. Gregor Johann Mendel and the Development of Modern Evolutionary Biology. PNAS. 119/30, 2022. A Gregor Johann Mendel and Modern Evolutionary Biology Special Feature herein to mark the 200th anniversary of his birth is introduced by NS, University of Oslo, Leif Andersson, Uppsala University and Hopi Hoekstra, Harvard University. Some other contents are Mendel and Darwin by Andrew Berry and Janet Browne, the “New Synthesis” by Nicholas Barton and Three Problems in the Genetics of Speciation by Selection by Dolph Schluter and Loren Rieseberg.

This year we celebrate the 200th anniversary of the birth of Gregor Johann Mendel, who discovered the missing component of Darwin’s evolutionary theory, the genetic mechanism of trait inheritance. The eight articles in this Special Feature collection cover various aspects of Mendel’s life, his work, and his contribution to science, with a special focus on his impact in evolutionary biology. In this introductory paper, we provide the context for the eight papers, as well as summarize how Mendel’s work has contributed to the development of modern evolutionary biology.

Cosmic Code > Genetic Info > Genome CS

Roman-Vicharra, Cristhian and James Cai. Quantum Gene Regulatory Networks. arXiv:2206.15362. We note this entry by Texas A & M University bioresearchers (see J. Cai website) for its innovative consideration of a deeper physical basis for GRNs, and as an exemplary instance whereby inquisitive human beings, lately members of a global knowsphere, will be moved take up, contribute to and carry forward this historic scientific learning endeavor. The content itself opens to and outlines a fertile quantum ground for to genetic structures to form and process.

In this work, we present a quantum circuit model for inferring gene regulatory networks (GRNs). The model is based on the idea of using qubit-qubit entanglement to simulate interactions between genes. We present results derived from the single-cell transcriptomic data of human cell lines from genes in involved with innate immunity regulation. We demonstrate that our quantum circuit model can predict the presence or absence of regulatory interactions between genes and estimate the strength and direction of the interactions. Based on these results, we suggest that quantum algorithmns can serve the data-driven life sciences. (Excerpt)

Life's Corporeal Evolution Encodes and Organizes Itself: An EarthWin Genesis Synthesis

Quickening Evolution

Brun-Usan,, Miguel, et al. Beyond Genotype-Phenotype Maps: Toward a Phenotype-Centered Perspective on Evolution. BioEssays. August, 2022. Lund University, Sweden, University of Southamption, UK and University of Lyon, France including Tobias Uller contribute a thorough, graphic hypothesis as a way to surmount the conflicts and misunderstandings that inhibit a viable union of life’s evolutionary aspects with the somatic development of organisms. The paper is much a result of a 2018 Integrating Development and Inheritance workshop at the Santa Fe Institute.

Evolutionary biology is paying increasing attention to the mechanisms that enable phenotypic plasticity, evolvability, and extra-genetic inheritance. Yet, there is a concern that these phenomena are not well integrated within evolutionary theory. Understanding their implications would require focusing on phenotypes and their variation, but this does not always fit well with the prevalent genetic representation that screens off developmental mechanisms. Here, we instead use development as a starting point, and represent it in a way that allows genetic, environmental and epigenetic sources of phenotypic variation to be independent. We show why this approach illumes the consequences of both genetic and non-genetic phenotype determinants, and note future areas of empirical and theoretical research

Quickening Evolution

Delisle, Richard, ed.. Natural Selection: Revisiting its Explanatory Role in Evolutionary Biology. Switzerland: Springer, 2021. The subject book is part of a new Springer series Evolutionary Biology: New Perspectives which is also edited by the University of Lethbridge, Canada philosopher. As the quotes allude, the intent is to gather and report a historic, overdue revolution far beyond Darwinism which is open to and can include the many advances of the later 20th century and in the 21st century. (See our Chapter V for a long litany and documentation.)

Evolutionary biology has been a remarkably dynamic area since its foundation. Its true complexity, however, has been concealed in the last 50 years under an assumed opposition between the "Extended Evolutionary Synthesis" and an "Alternative to the Evolutionary Synthesis". This multidisciplinary book series aims to move beyond the notion that the development of evolutionary biology is structured around a lasting tension between a Darwinian tradition and a non-Darwinian tradition, once dominated by categories like Darwinian Revolution, Eclipse of Darwinism, Evolutionary Synthesis, and Post-Synthetic Developments. (Series summary)

This book contests the general view that natural selection constitutes the explanatory core of evolutionary biology. It invites the reader to consider an alternative view which favors a more complete and multidimensional interpretation. The 1950s Modern Synthesis to date ihas two main bases: (1) Gradual evolution due to small genetic variations oriented by natural selection, a process leading to adaptation and (2) Evolutionary trends and speciation events as macroevolutionary events from processes and mechanisms occurring at a microevolutionary level. But if one reads the new papers herein by biologists, historians and philosophers, this decades old school is being set aside in preparation for a dynamic developmental paradigm. (Natural Selection)

Quickening Evolution

hsieh, Shannon, et al. Hsieh, Shannon, et al. The Phanerozoic Aftermath of the Cambrian Information Revolution. Paleobiology. 48/3, 2022. Akin to Cellular Self-Organization: An Overdrive in Cambrian Diversity by Filip Vujovic, et al in BioEssays (July 2022), University of Illinois, Chicago and University of Connecticut paleoecologists including Roy Plotnick achieve a similar perception of rapid, wide-spread cerebral and cognitive advances as organic forms suddenly leapt forward from simpler stages. Many studies from the Burgess Shale to Devonian phases of “nervous system complexities” provided an empirical basis. As a result, a graphic radiation can be sketched from no CNS to ganglia onto a relative brain. In their rare purview, soma and sensory together are seen to constitute life’s radical emergent, quicker transition (on its way to our late planetary reconstruction).

The Cambrian information revolution describes how biotic increases in signals, sensory abilities, behavioral interactions, and landscape spatial complexity led to a rapid increase in animal cognition concurrent with the Cambrian radiation. Here, we compare neural and cognitive complexity in pre- and post-Cambrian marine ecosystems. We do not find a trend in this regard, nor in macroscopic sense organs These results suggest that sophisticated information processing was already common in early Phanerozoic ecosystems, comparable with behavioral evidence from the trace fossil record. The overall rise in cognitive sophistication in the Cambrian was likely a unique event in the history of life. (Abstract)

Comparisons of faunal lists from Cambrian and post-Cambrian ecosystems reveal similarly high shares of animal genera with brains as well as macroscopic sensory organs. Our results show that the Cambrian radiation generated ecosystems that were “modern” in sensory- and information-processing complexity, comparable to ecosystems in the later Phanerozoic. A major difference, however, is that most sensorially and cognitively complex animals in the Cambrian were panarthropods, since chordates and mollusks had not yet diversified. In both Cambrian and recent times, nervous systems permitted a variety of life modes, but the most active are associated with brains, which first appear in the Cambrian. (414-415)

Quickening Evolution

Vujovic, Filip, et al. Cellular Self-Organization: An Overdrive in Cambrian Diversity? BioEssays. July, 2022. University of Sydney system biophysicians contribute another frontier perception of life’s evolutionary motive occasion as more primarily due to these mathematic procreative agencies, rather than post-selection alone. Their certain subject area is this profuse emergence some 540 mys ago. Some sections are Self-Organization: A Decentralized Algorithm to Transform Chaos into Predictability, Self-Organization and Emergence of Morphological Patterns and Emergence of Form and Function in Cellular Self-Organization. Along with 135 references, graphic displays show how this deep drive (natural genesis) provides a formative, organismic effect prior to selection.

See also The Phanerozoic Aftermath of the Cambrian Information Revolution by Shannon Hsieh, et al in Paleobiology, (48/3, 2022) about a concurrent cerebral and cognitive florescence within this expansive era and Self-Organization as a New Paradigm in Evolutionary Biology, Anne Malasse, ed., for a 2022 book-length report of life’s innate creative source.

occupy multiple ecological niches on earth. A variety of explanations have been proposed for this major evolutionary event termed the “Cambrian explosion.” While most address environmental, developmental, and ecological factors, the biological basis for this accelerated species diversity remains largely open. Here we posit that morphogenesis by self-organization enables an uncoupling of the genomic mutational landscape from phenotypic diversification. We thus suggest that accelerated morphological diversification in the Cambrian transition occurred by an activation dormant (reserved) morphological novelties whose molecular underpinnings were seeded in the Precambrian period. (Excerpt)

The basic tenet of the proposed hypothesis is that evolution of metazoan animals with self-organization capacity provided a dormant opportunity for rapid divergence. The same machinery that stabilizes multicellular structure after development, instructs morphogenesis by self-organization during development. Self-organization not only amplifies phenotypic novelties associated with genomic changes but also enables generation of dormant novelties by uncoupling genotype and phenotype. We propose that mutagenesis in the Precambrian era combined with inherent hypermutability of the self-organization lexicon could have contributed to accelerated occupancy of morphospace in transition to the Cambrian period by emergence of dormant novelties as opposed to de novo generation of these novelties. (11)

Quickening Evolution > major

Heylighen, Francis, et al. The Role of Self-Maintaining Resilient Reaction Networks in the Origin and Evolution of Life. Biosystems. Vol. 219, September, 2022. Free University of Brussels bioscholars FH, Shima Beigi and Evo Busseniers provide a paper for a special edition about how life’s emergent development from earliest nucleotide origins all the way to our linguistic version is now widely accepted as a nested, recurrent, encoded, quickening sequence. Here, better explanations are detailed maybe just how living systems actually proceed on their way to us. By some EarthKinder-like vista, we peoples seem to move closer to its global gestation phase.

We characterize living systems as resilient “chemical organizations”, i.e. self-maintaining networks of reactions that are able to resist a wide range of perturbations. We try to understand how life could have originated from such self-organized structures, and evolved on by acquiring various mechanisms to increase resilience. An example is a use of catalysts, such as enzymes, to enable reactions to deal with perturbations. This activity can be regulated by “memory” molecules, such as DNA. We suggest that major evolutionary transitions then take place when living cells of different types or species form a higher-order organization by way of special functions so reduce interference between them. (Abstract)

The present paper is part of a special issue on evolutionary transformations in biological systems. The focus is on the processes that give rise to the emergence of complex organizations with qualitatively new characteristics. This includes what are known as “major transitions” such as eukaryotes and multicellular organisms, and of life itself. What characterizes such transitions is that initially independent units, such as molecules, cells or individuals, become integrated into a larger, self-maintaining organization. This encompassing system behaves like a distinct individual with its own goals. This emergent system both constrains and enables certain interactions between its components. (1)

However, the emergence of synergetic arrangements becomes clearer when you look at these cellular units as processes that depend on each other to produce their inputs or consume outputs. Therefore, we will start from an ontology based on processes, which we have recently called “relational agency.” Thus the components that make up a living system should not be seen as independent objects but as interconnected processes and agencies. The present paper intends to show how the perspective of relational agency with formal reaction networks can help elucidate the origin of life and evolution of life. (2)

Quickening Evolution > Teleology

Clawson, Wesley and Michael Levin. Endless Forms Most Beautiful 2.0: Teleonomy and the Bioengineering of Chimaeric and Synthetic Organisms. Biological Journal of the Linnean Society. August, 2022. We cite this paper by Allen Discovery Center, Tufts University researchers because it looks forward to future beingness in themselves and to gain insights about life’s corporeal, cognitive and collective ascent to date.

A rich variety of biological forms and behaviours arises from evolutionary history on Earth, often via frozen accidents and environmental selection. But this standard view of model species does not factor the swarm intelligence of active cellular collectives. A view of novel living forms can reveal design principles of life as it yet can be. To foster experimental progress in multicellular synthetic morphology, we propose a teleonomic (goal-seeking, problem-solving) behaviour across such diverse possible beings. We suggest that a multi-scale competency architecture primes the evolution of robust problem-solving entities to come. Such imaginations can aid the emergence of diverse intelligences, along with implications for regenerative medicine, robotics and ethics. (Excerpt)

Quickening Evolution > Teleology

Crespi, Bernard and Nancy Yang. Three Laws of Teleonometrics. Biological Journal of the Linnean Society. 137/1, 2022. Simon Fraser University, BC, Canada biopsychologists contribute to an overdue 2020s admission which this premier publication (1798 -) has seen fit to report (see issues), that living, evolving organisms do actually possess their own intrinsic self-purposes within groups and environs. The essay goes into intricate genetic, physiological and medical malady aspects so as to factor in these evident appreciations, which can then add another veracity to the major transitions scale. We append five quotes to convey its import.

We define teleonometrics as the theoretical and empirical study of teleonomy (see below) for which we propose three laws. The first describes the hierarchical organization of teleonomic, goal-directed behaviors across biological levels from genes to individuals. The second law describes the operation of teleonomic functions under trade-offs, coadaptations and pleiotropies, which are common in biological systems. The third law contends that the major transitions in evolution are due to novel, emergent purposes and new divisions of labour. We illustrate the application of these laws using data from empirical vignettes, which help to show the usefulness of teleonometric views for understanding the interfaces between function, trade-offs and disease dysfunctions. (Abstract excerpt)

Teleonomy is central to biology because it epitomizes the organized and functional results of evolutionary change. As such, it leads us to ask questions about what a phenotype, or a gene, is for, in the proximate sense of serving some functional goal and in the ultimate sense of maximizing fitness. Literally, teleonomy (from τελεονομία in the original Greek) means τέλος referring to ‘goal, purpose or end’, plus νόμος nomos, referring to ‘law’. Although population genetics and quantitative genetics have ‘laws’ in the forms of mathematical abstractions that describe and predict evolutionary processes, teleonomy, the conceptual evolutionary core of adaptation, does not. (112)

The Third Law: The minor transitions in evolution are driven mainly by quantitative shifts in adaptive teleonomic functional goals. These shifts are largely deterministic and predictable in the short time scales of microevolution. Many major transitions in evolution are driven by qualitative shifts involving the origins of novel and emergent adaptive functions. These shifts typically involve: (1) increased resources, sizes and numbers of constituent units, or time; (2) novel divisions of labour; (3) the breaking, reduction and reorganization of trade-offs; and (4) new forms of ‘cooperation’ within and across levels of biological organization. (115)

The third law of teleonometrics builds on Maynard Smith and Szathmary’s work by emphasizing the roles of trade-offs and how they are overcome, then reshaped in major evolutionary transitions, thus extending the second law to a macroevolutionary scale. The general model of major transitions described here, based on roles for enhanced resources and divisions of labour in overcoming trade-offs, and new forms of cooperation that preclude or reduce conflicts within and between levels of organization, is amenable to study in research systems or clades that abut or straddle the transition points, as in some social insects. (122)

Teleonomy is the apparent purposefulness and goal-direction of living organisms. The concept is contrasted with teleology, which is understood as a purposeful goal-directedness brought about through human or innate intention. Teleonomy derives from an evolutionary adaptation for reproductive success, and/or the operation of a some manner of a (computational) program. (Wikipedia)

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