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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 36 found.


Ecosmos: A Procreative Organic Habitable UniVerse

Animate Cosmos > Astrobiology

Navrotsky, Alexandra and Kristina Lilova. Materials of the Universe: The Final Chemical Frontier. ACS Earth and Space Chemistry. 5/8, 2021. Arizona State University astrochemists introduce a virtual collection of topical papers from refractory ceramics to organic solids.

The concept of Materials of the Universe (MotU) is to unite cosmology, astrophysics, astronomy, planetary science, mineralogy, and petrology with materials science, chemistry, physics, and biology to address their complex evolutionary chemistries. We need to understand their formation, stability, catalytic activity, and rheology over a range of temperatures, pressures, and compositions not yet imagined. This MotU Special Issue has contributions across science, technology, engineering, and mathematics (STEM) fields inspired by materials under extreme conditions at low- and high-temperature and pressure, ultrahigh-vacuum, radiation fields, and far from equilibrium conditions.

Animate Cosmos > exoearths

Shorttle, Oliver, et al. Why Geosciences and Exoplanetary Sciences Need Each Other. arXiv:2108.08382. In an article to appear in a special Geoscience Beyond the Solar System issue (17/4) of Elements: An International Magazine of Mineralology, Geochemistry and Petrology, Cambridge University and Southwest Research Institute astrogeologists including Cayman Unterborn contribute to this grand project going forward as our fittest global genius begins to explore and quantify near and farther orbital environs. A glossary from Abiogenesis Zone and Albedo to Tidal Lock and White Dwarf suits the wild frontier. See also Compositional Diversity of Rocky Exoplanets at 2108.08383, and The Diversity of Exoplanets: From Interior Dynamics to Surface Expressions st 2198L09385, for this issue.

The study of planets outside our solar system may lead to major advances in our understanding of the Earth, and provide insight into the universal set of rules by which planets form and evolve. To achieve these goals requires applying geoscience's wealth of Earth observations to fill in the blanks left by the necessarily minimalist exoplanetary observations. In turn, Earth's many one-offs, e.g., plate tectonics, surface liquid water, a large moon, and life - which have long presented chicken and egg type conundrums for geoscientists - may find resolution in the study of exoplanets possessing only a subset of these phenomena. (Abstract)

Ecosmomics: A Survey of Genomic Complex Network System Sources

Cosmic Code > nonlinear > networks

Yang, Ruochen, et al. Hidden Network Generating Rules from Partially Observed Complex Networks. Communications Physics. 4/199, 2021. USC (RY and Paul Bogdan) and University of Wisconsin (Frederic Sala) systems theorists (search PB) continue to discern and quantify the presence of common self-organized structural dynamics (as the abstract notes) at each and every natural and human phase. Herein an advanced method is described by which to better elucidate their node/link multiplex occurrence. See also in this journal Unified Treatment of Synchronization Patterns in Generalized Networks with Higher-order, Multilayer, and Temporal Interactions by Yuanzhao Zhang, et al (4/195, 2021).

Complex biological, neuroscience, geoscience and social networks exhibit heterogeneous self-similar higher order structures that are usually characterized as multifractal in nature. However, describing their topologies by a mathematical description and deciphering their governing rules has been elusive and prevents a comprehensive understanding of their networks. Here, we propose a weighted graph model which can reveal the underlying generating rules of complex systems and characterize their node heterogeneity and pairwise interactions. The proposed network generator framework is able to reproduce network properties, differentiate varying structures in brain networks and chromosomal interactions, and detect topologically associating domain regions in conformation maps of the human genome. (Abstract excerpt)

Cosmic Code > nonlinear > Rosetta Cosmos

Semple, Stuart, et al. Linguistic Laws in Biology.. Trends in Ecology and Evolution. October, 2021. SS, University of Roehampton, London, Ramon Ferrer-i-Cancho, Quantitative Linguistics, Relational Algorithmics, Learning Research Group, Polytechnic University of Catalunya, Barcelona and Morgan Gustison, Integrative Biology, UT Austin propose that recent advances so to interpret (parse) written script and oral conversation by way of self-organizing complex network theories has reached a maturity so that they can be compared with and integrated into biological phenomena. And we note how well this synthesis accords with our 2020s theme of a natural genesis narrative. A broad array of 118 references are posted in support.

Linguistic laws, the common statistical patterns of human language, have been investigated by quantitative linguists for some decades. Recently, biologists have started to note and study the prevalence of these laws beyond this field to find patterns consistent with linguistic laws across multiple levels of biological organisation from molecular (genomes, genes, and proteins) to organismal (animal behaviour) to ecological (populations and ecosystems). We propose a new conceptual framework for the study of linguistic laws in biology, comprising and integrating distinct levels from description and prediction to novel theories. Adopting this framework will provide critical new insights into the fundamental rules of organisation underpinning natural systems, unifying linguistic laws and core theory in biology. (Abstract)

Cosmic Code > nonlinear > 2015 universal

Notarmuzi, Daniele, et al. Universality, Criticality and Complexity of Information Propagation in Social Media. arXiv:2109.00116. Indiana University systems theorists including Filippo Radicchi post a strong exposition to date of how all manner of dynamic self-organizing systems can be seen to spring from and express an iconic array of similar forms and behaviors. As a result, it is noted that all this disparate phenomena quite implies an independent generative source which seems to be in eternal effect. Into these 2020s, a natural propensity to seek and reside at an active bilateral poise from galaxies to Google becomes evident.

Information avalanches in social media are typically studied in a similar fashion as avalanches of neuronal activity in the brain. Whereas much literature reveals a substantial agreement about a unique process that characterizes neuronal activity across organisms, the dynamics of information in online social media is far less understood. Here, we analyze almost 1 billion time-stamped events collected from a multitude of platforms (Telegram, Twitter and Weibo) over some 10 years to show that the propagation of information in social media is a universal and critical process. Universality arises from the observation of identical macroscopic patterns, irrespective of the specific system. Critical behavior is deduced from the power-law distributions, and their hyperscaling relations, which control the size and duration of avalanches of information. (Abstract excerpt)

For example, there is large agreement on the fact that neuronal activity in the brain is universal and critical. Universality is the notion that nearly identical avalanche statistics are observed for a multitude of organisms. Criticality instead refers to the fact that avalanche statistics are characterized by algebraic distributions. (4)

We speculate that our results extend beyond the six platforms considered here. If so, there must be a mechanism that explains the universality shown by the data, involving a critical dynamics that is independent of the peculiarities implemented in the individual platforms. Understanding where this mechanism is rooted in and how to exploit it for the prediction of the propagation of information in online social media remain open challenges for future research. (10)

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Noble, Denis. The Illusions of the Modern Synthesis. Biosemiotics. 14/1, 2021. The octogenarian Oxford University philosophical physiologist (search) continues his career quest to right the wrongs of this misguided theory which persists as the textbook version.. Indeed, a prime purpose of this Natural Genesis resource is to provide annotated documentation for an integral 21st century Genesis Evolutionary Synthesis. Noble’s view is that the MS was cobbled from mid-20th century opinions which took on its own gene-centric cast removed from actual realities. His main suggestion is that an emphasis on individual agencies whose proactive relational behaviors would replace prior passivities. His novel take struck a chord with commentators such as Signs of Consciousness? by Eva Jablonka, Agency and Choice in Evolution by Jonathon Delafield-Butt, The Plurality of Evolutionary Worldviews by Nathalie Gontier and Towards a Biosemiotic Theory of Evolution by Alexei Sharov, along with Tyler Volk, Louise Westling, Kalevi Kull. Aaron Gare and Guenther Witzany. Into these 2020s, whence a global sapiensphere may learn on her/his own (Charlotte and Charles EarthWin), such endeavors to get clear and correct on life’s oriented emergence make a vital contribution.

The Modern Synthesis (MS) has dominated biology for 80 years. It was first formulated in 1942, a decade before the major achievements of molecular biology, including the Double Helix and the Central Dogma (CD). These discoveries and concepts seemed to justify the genetic MS assumptions of accurate nucleotide replication, while the (DNA to RNA to Protein) CD was viewed as excluding the inheritance of acquired characteristics. This article examines the language of the MS to show how it is based on several misinterpretations of what molecular biology has found. In this regard, I cite these four Illusions: 1. Natural Selection; 2. The Weismann Barrier; 3. The Rejection of Darwin’s Gemmules; 4. The Central Dogma itself. An expansive multi-level view of life’s evolution avoids these miscues through the principle of biological relativity. (Abstract excerpt)

In this commentary I expand on the first of Noble’s illusions, the selection metaphor. Building on my work with Simona Ginsburg on the evolution of minimal consciousness, I argue that the existence of some complex sensory and motor patterns in the living world can be accounted for only through the evolution of conscious choice. (Jablonka)

Denis Noble has produced a succinct analysis of the ‘Illusions of the Modern Synthesis’. At the heart of the matter is the place of agency in organisms. This paper examines the nature of conscious agent action in organisms, and the role of affects in shaping agent choice. It examines the dual role these have in shaping evolution, and in the social worlds of scientists that shape evolutionary theory. Its central claim follows Noble, that agency is central to the structure of organisms, and raises careful consideration for the role animal agency and affective evaluations in biology, and in biologists. (Delafield-Butt)

The target article by Denis Noble is an excellent overview of the illusions of the Modern Synthesis that remain in textbooks. Overcoming these illusions shows the active role of organisms in the evolutionary process such as embryo development, epigenetic heredity, multilevel selection and niche construction. But what is still missing is the presence of individual agency, autonomy, semiosis, and goal-directedness. (Sharov)

Quickening Evolution

Zelditch, Miriam and Anjali Goswami. What Does Modularity Mean? Evolution and Development. August, 2021. We recall when Gunter Wagner’s 1996 paper was an initial notice of nature’s avail of diverse modules as a good way to form and bolster bodies and brains. Twenty five years later, University of Michigan and Natural History Museum, London paleontologists finesse and confirm its ubiquitous use and value. However then might it dawn that these now worldwide surveys have come upon a greater phenomenal genesis which in place on its preordained own?

Modularity is now recognized as a fundamental feature of organisms, with profound consequences for evolution. This natural propensity has become a major focus of research in organismal biology across disciplines including genetics, developmental biology, functional morphology, population and evolutionary biology. But the concept of modularity retains an ambiguity due to diverse definitions about what it means, Here we review various concepts, metrics and methods at different levels, and some other concerns. (Abstract excerpt)

Quickening Evolution > major

Kun, Adam. The Major Evolutionary Transitions and Codes of Life. Biosystems. September, 2021. In this journal which is more open to holistic vistas, a Parmenides Center for the Conceptual Foundations of Science, Munich and collaborator with Eors Szathmary at Eotvos Lorand University, Budapest provides a novel synthesis between this popular view of life’s oriented developmental scales, and an expanded presence of many genetic-like code qualities. As they cross-fertilize and inform, both aspects benefit and grow in explanatory import. Can yet we move closer to truth and real discovery in time?

Major evolutionary transitions as well as the evolution of codes of life are key elements in macroevolution which are characterized by increase in complexity. These nested emergences ensue by a transition in individuality and by the evolution of a novel mode of using, transmitting or storing information. Here is where codes of life enter the picture. This flexibility allows information to be employed in a variety of ways, which can fuel evolutionary innovation. The collation of the list of major evolutionary transitions and the list of codes of life show a clear pattern: codes evolved prior to a major evolutionary transition and then played roles in the transition and/or in the transformation of the new individual. The evolution of a new code of life then can facilitate major evolutionary transitions. This effect could help us to identify new organic codes.

Marcello Barbieri lists five characteristics of codes of life that are important for the history of life. (1) Discontinuity: Codes of life represent something abruptly novel, not just gradual improvement of something that already exists. (2) Invariance: Codes of life do not change in the sense that there is a strong selection for their conservation. (3) Additivity: More than one types of code can be included in the same lineage, and one code does not erase the other. (4) Stability: Each code remains a viable form, and organism harbouring them still exist, thus the appearance of a new code does not invalidate former codes of life. And (5) Complexity: The evolution of a new code increases complexity. If we contrast this list with characteristics of the major evolutionary transitions, then we nearly find the same list. They are fundamental events in the history of life (cf. discontinuity) which always increase complexity. METs are also mostly irreversible (cf. invariance). METs happen in succession too and an organism can be the product of multiple METs. (2)

Quickening Evolution > Biosemiotics

Lackova, Ludmila and Dan Faltynek. Can Quantitative Approaches Develop Bio/Semiotic Theory? Biosemiotics. August, 2021. The Palacky University, Olomouc, Czech Republic linguists (search) introduce a dedicated collection to consider better ways to appreciate and assimilate the vital presence of organic codes and communications across life’s animate scales. Among the entries are Application of N-Gram Based Distances to Genetic Texts Comparison by Valery Kirzhner and Zena Volkovich, and A Semiotic Modern Synthesis: Quantitative Studies in Zoosemiotics by Amelia Lewis.

This special issue addresses question about the place of quantitative methods in the field of biosemiotics. Many standpoints have been taken by contributing authors to demonstrate that the answer to this question is not straightforward. Considering quantitative methods in biosemiotics is necessarily related to inclusion of other scientific fields and interdisciplinary dialogue. (Abstract)

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

Earth Life > Common Code

Ribeiro, Tiago, et al. Scale-Free Dynamics in Animal Groups and Brain Networks. Frontiers in Systems Neuroscience. January, 2021. Into the 2020s, TR and Dietmar Plenz, NIH Critical Dynamics Group and Dante Chialvo, Universidad Nacional de San Martin, Argentina are able to perceive and delineate strong similarities between these disparate phases. An especial quality is the spontaneous presence of a self-organized criticalities in both active instances. Here then is an excellent instance of our Earthuman acumen just now attaining such a convergent synthesi of universal recurrence in kind.

The collective emergence of order in myriad interactive entities occurs over a vast range of physical and biological systems. Their key feature is an adaptive behavior beyond individual components. This article focuses on recent insights for two seemingly disparate phenomena: flocking in animal groups and neuronal ensembles in the brain. We report upon the spontaneous organization in bird flocks and whole human brain activity utilizing correlation functions and critical dynamics. Scale-free correlation functions capture the collective organization of neuronal avalanches in nonhuman primates and between neurons during visual processing in rodents. We conclude that at or near a phase-transition, neuronal information can propagate in the brain with similar efficiency to the collective adaptive response observed in some animal groups. (Abstract excerpt)

Earth Life > Nest > Microbial

Roy, Anjan, et al.. A Unifying Autocatalytic Network-based Framework for Bacterial Growth Laws. Proceedings of the National Academy of Sciences. 118/33, 2021. Ben-Gurion University of the Negev and Abdus Salam International Center for Theoretical Physics, Trieste identify how such self-assembly processes are in common metabolic effect across the prokaryotic domains. See also Growth-laws and Invariants from Ribosome Biogenesis in Lower Eukarya by Sarah Kostinski and Shlomi Reuveni at arXiv:2008.11697.

In the clash between the physics-inspired strive for simple underlying laws of bacterial physiology and the biological hard-won understanding of the intricacies of life, we end in a middle ground. On one hand, we have found valid and simple growth laws. On the other hand, we demonstrated that the validity of a given growth law does not fully reveal the physiological state of the cell. Understanding how the cellular state is determined in response to internal and external cues, and how evolutionary stresses shaped different schemes for determining it, remains a formidable challenge. (10)

Earth Life > Nest > Ecosystems

Bohdalkova, Eliska, et al. Universality in Biodiversity Patterns: Variation in Species Temperature and Species-Productivity Relationships. Ecography. 44/9, 2021. Into the 2020s, Charles University, Prague ecologists describe a sophisticated survey across near and far diverse flora and fauna environs which is now able to discern such a common recurrence of spatial and temporal patterns.

Temperature and productivity appear as universal positive large-scale correlates of species richness. However, the strength and the shape of species–temperature (STR) and species–productivity (SPR) relationships vary widely, and are insufficiently studies. We analysed species richness data for multiple taxa in various regions and different clades within global vertebrate classes to test the effects of spatial scale and taxa character on the strength and direction of STRs and SPRs. The effect of temperature on species richness is complex and context-dependent, while productivity is a more universal driver of species richness, largely independent of given region or taxon. Productivity thus appears as the main proximate driver of species richness patterns, probably due to its effect on the limits of the number of viable populations which can coexist in a given environment. (Abstract excerpt)

Earth Life > Sentience > Brain Anatomy

Tosches, Maria. From Cell Types to an Integrated Understanding of Brain Evolution: The Case of the Cerebral Cortex.. Annual Review of Cell and Developmental Biology. Vol. 37, 2021. A Columbia University neurobiologist provides a summary survey to date of her collegial project to conceptually and experimentally reconstruct how neural net faculties formed and emerged with regard to Vertebrate phylogeny, forebrain neuroanatomy, tetrapartite palliams and more across invertebrates, fishes, reptiles, birds and mammals onto curious, brilliant sapient selves.

With the discovery of the incredible diversity of neurons, Ramon y Cajal and coworkers laid the foundation of modern neuroscience. Neuron types are not only structural elements of nervous systems but evolutionary units, because their identities are encoded in genomes. With the advent of high-throughput cellular transcriptomics, neurons can be compared systematically across species. Research results now indicate that the mammalian cerebral cortex is a mosaic of deeply conserved and recently evolved neuron types. This review illustrates how various neuron types is key to observations on neural development, neuroanatomy, circuit wiring, and physiology for an integrated understanding of brain evolution. (Abstract excerpt)

Earth Life > Individuality

Molter, Daniel. On Mycorrhizal Individuality. Biology & Philosophy. 34/Art. 52, 2109. A Weber State University, Utah philosopher provides another take of life’s persistent formation of relative personal entities in communal settings at each and every chance.

This paper argues that a plant together with the symbiotic fungus attached to its roots, a mycorrhizal collective, is a true individual, and further, that this identity has important implications for evolutionary theory. Mycorrhizae in nature usually connect the roots of multiple plants, so their individuality entails overlapping entities. I suggest that the degree of evolutionary individuality in a symbiotic collective corresponds to its probability of reproducing with vertical or pseudo-vertical transmission, which could constitute a fourth parameter of graded Darwinian individuality in collective reproducers. (Abstract excerpt)

Our Earthuman Moment: A Major Evolutionary Transition in Individuality

wumanomics > Integral Persons > Complementary Brain

Singer, Wolf. Recurrent Dynamics in the Cerebral Cortex: Integration of Sensory Evidence with Stored Knowledge. Proceedings of the National Academy of Sciences. 118/33, 2021. Into the 2020s, the senior MPI Brain Research neuroscientist (search) provides a definitive (natural) exegesis of the presence of dual modes of active neural cognition. An on-going informative interplay is described between a person’s represented memory and new experiences so as to reach a viable, beneficial response. In this way, a balance and harmony can occur between one’s past familiarity and a variable external world. An accord then becomes possible of conserved values with novel occasions, rather than current politics where these conserve and create, regress or progress phases are locked in mortal combat. In August of this year, an incarnate complementarity thus achieves a strong scientific affirmation in our desperate midst. Here is the very EarthWise edification that so needs to gain a public veracity and avail in the time left.

Current concepts of sensory processing in the cerebral cortex emphasize serial extraction and recombination of features in hierarchically structured feed-forward networks in order to view the relations among the components of perceptual objects. These concepts are implemented in convolutional deep learning networks and have been validated by the astounding similarities between the functional properties of artificial systems and their natural counterparts. However, cortical architectures also display an abundance of recurrent coupling within and between the layers of the processing hierarchy. This massive recurrence gives rise to highly complex dynamics whose putative function is poorly understood. Here a concept is proposed that assigns specific functions to the dynamics of cortical networks and combines, in a unifying approach, the respective advantages of both recurrent and feed-forward processing. (Abstract excerpt)

Two Complementary Strategies for the Analysis and Encoding of Relations The virtually infinite variety of perceptual objects results from variable combinations of a relatively small set of elementary features, just like the 26 letters of the Latin alphabet suffice to compose western literature. Therefore, cognitive systems need effective strategies to identify these features and to encode the relations among them. (1)

Encoding of Relations in Feed-Forward Networks. One common strategy for the encoding of relations is based on the generation of conjunction-specific neurons in hierarchically structured feedforward networks. Neurons tuned to elementary features distribute their responses through divergent and convergent connections to neurons of the respective next layer. Dynamic Encoding of Relations in Recurrent Networks. A complementary strategy to capture relations among components relies on dynamic combinatorial codes, similar to those used by natural languages. (2)

Last but not least, there is a puzzling analogy with the processes that make quantum computing so fast and efficient. The superposition of wave functions bears similarities to the covert superposition of priors in the correlation structure of spontaneous activity, and the simultaneous and probabilistic evaluation of nested relations resembles the virtually simultaneous and holistic interaction between network nodes that represent, in a probabilistic and graded way, the presence of particular features. It would be truly fascinating if evolution had succeeded to realize, with classical mechanisms, those functions
that quantum computers are particularly good at: the parallel and therefore ultrafast evaluation of the relations between a huge number of probabilistic variables (9)

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