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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 46 through 60 of 78 found.


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

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 Evolutionary Development Organizes Itself: A 2020s 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

Dambricourt Malasse, Anne, ed. Self-Organization as a New Paradigm in Evolutionary Biology. International: Springer Frontiers, 2022. The editor is a senior paleo-anthropologist at the French National Center for Scientific Research. The volume appears in a new Springer series Evolutionary Biology: New Perspectives (search Richard Delisle) and can represent a latest, strongly evident affirmation of this missing innate, common source force for life’s oriented, emergent development. In regard the work well serves to establish an absent, animating, informative, genome-like basis which can at last inform, explain, qualify and brace a valid 2020s genesis synthesis within a revolutionary ecosmos uniVerse.

We note these chapters to convey the book’s inclusive reach and deep veracity: Self-Organization Meets Evolution: Ernst Haeckel and Abiogenesis (Georgy Levit and Uwe Hossfeld, see review), Self-Organization in Embryonic Development (Stuart Newman, search), Biological Evolution of Microorganisms (Werner Arber) From Dissipative Structures to Biological Evolution: A Thermodynamic Perspective (Dilip Kondepudi, et al, see review), and Quantum Fractal Thermodynamics to Describe the Log-Periodicity Law in Species Evolution and Human Organizations (Diogo Queiros-Conde, et al). Anne Malasse then posts a final wrap as Sapiens and Cognition: The Last Threshold of Self-Organized and Self-Memorizing Increasing Complexity.

A new evolutionary synthesis is proceeding to integrate the scientific models of self-organization in occurrence since the later 20th century as based on the laws of physics, thermodynamics, and mathematics. This book shows how self-organization is by now integrated across a 21st century span from life’s origins to our human phase. The first part attends to the modern observations in paleontology and biology, with prior presciences such as Immanuel Kant, d’Arcy Thompson, Henri Bergson, and Ilya Prigogine. The second part views emergent evolutionary models drawn from the complexity sciences, the non-linear dynamical systems, fractals, attractors, epigenesis, and other system approaches such as embryogenesis-morphogenesis phenomena. (Publisher)

Global warming, anthropocene extinctions along with astrobiology efforts to look for primitive life forms are prompting thinkers to view life’s evolution as the prime reality for species biodiversity and indeed our own civilization. This discernment leads to better understandings of the origin of the organization of dynamic forms and processes from the smallest cellular unit to the most complex interactions within the organism and then between organisms. Such novel insights and vista just coming into view can illume over geological and cosmic time scales how principles of self-organization of complex systems and generic laws of adaptation and complexification are at procreative work. (Anne Malasse, The Origin and Evolution of Living Organisms: A Convergence between Old and New Paradigms.)

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

Forestiero, Saveiro. The Historical Nature of Biological Complexity and the Ineffectiveness of the Mathematical Approach. Theory in Biosciences. 141/213, 2022. A University of Rome biotheorist clarifies and contributes to overdue, course correction, revisions of life’s inherent vitalities and oriented emergence as they naturally arise from biomolecules to ourselves. Four main aspects are identified as Organization, Individuality,
Diverse Variation and Relationality. By an overall surmise, it becomes evident, once again, some orthogenetic self-organization seems to be organizing her/his self.

Contemporary scientific knowledge is mainly based on a reductionism epistemology and method. But its limitations prevent mathematical treatment of physical properties such as complex patterns and processes. The article will review the biological complexity debate and differences between living and inert matter. With these preparations, biological complexity can be viewed as a global, relational, and historical phenomenon at the individual and species level. (Abstract edits)

Along with that between order and disorder (life as per “Entre le cristal et la fumée” by Henri Atlan 1979), there is the opposition between stability and instability, variation an its opposite, differentiation and integration, openness and closure (with respect to the internal organization), there are the (internal metabolic oscillators, the seasonal rhythms, periodicity or aperiodicity of signals external phase-shifted from the internal rhythms), and many more. (1-2)

Quickening Evolution

Gontier, Nathalie and Michael Bradie. Evolutionary Epistemology: Two Research Avenues, Three Schools and a Single, Shared Agenda. Journal for General Philosophy of Science.. 52/2, 2021. University of Lisbon and Bowling Green State University, Ohio scholars edit this latest survey of philosophical endeavors about how to get a read and bead on life’s long developmental course that brought us to such ruminations. Among entries are Cognitive Niche Construction and Extragenetic Information: A Sense of Purposefulness in Evolution by Lorenzo Magnani, Jierarchies, Networks and Causality by N. Gontier, United in Diversity: An Organic Overview of Non-Adaptationist Evolutionary Epistemology by Marta Facoetti, and Principles of Information Processing and natural Learning in Biological Systems by Predrag Slijepcevidic.

This special issue is devoted to the impact and ramifications of current research in evolutionary epistemology, an inter- and multi- disciplinary areas that can be sorted into two inclusive research avenues. One approach is an expansive study of the appropriate comprehension of life’s evolution (see below). The other program, by turns, considers the evolution of epistemology. Since its 1990s origins, EE has adopted three schools of thought: adaptationist, non-adaptationist, and applied EE. Although diverse in outlook, these several versions share and advance similar agendas about how knowledge evolves and relates to the world. (Excerpt)

Biosphere as the Communicative Network The final task is to put all categories of biological systems in the context of the biosphere. Heinz von Foerster argued that information is a purely relational concept that can be actualized only when related to cognitive systems. If we accept his dictum and assume that the biosphere is the supersystem that accommodates all seven categories of biological systems, it becomes the network of communicative interactions between them. The totality of all communicative interactions in the biosphere may be termed the “interactome” as the distributed network of biological information that holds organism–environment altogether. (Predrag S., 240-241)

The term “Epistemology comes from the Greek “episteme” and “logos”. Episteme means knowledge and understanding while logos translates as account or reason. In all historic these historic cases (Plato to B. Russell), epistemology seeks to comprehend one or another kind of cognitive success. (Stanford Encyclopedia)

Quickening Evolution > Biosemiotics

Pagni, Elena and Richard Simanke, eds. Biosemiotics and Evolution: The Natural Foundations of Meaning and Symbolism. Switzerland: Springer, 2022. Federal University of Juiz De Fora, Brazil philosophers collect a wide range of authors and papers which serve to advance this present informative synthesis between living, personal systems and our pervasive communications. See for example Life Sciences and the Natural History of Signs by Franco Giorgi, Physical Intentionality: The Phenomenological Roost of Biosemiotics by Roberta Lanfredidi, and How Information Gets its Meaning by Vinciius Romanini.

This book reviews the evolution of Biosemiotics and an outlook on the future of this interdisciplinary new discipline. In this volume, the foundations of symbolism are transformed into a phenomenological, technological, philosophical and psychological discussion. The book is divided into three parts: Life, Meaning, and Information, Semiosis and Evolution, Physics, medicine, and bioenergetics. The authors shed new light on the processes underlying the origins and evolution of knowledge, the boundary between teleonomic and teleological paradigms of evolution and their possible integration, the relationship between linguistics and biological sciences, biological information and its transmission, physical and biosemiotic intentionality and models for culture, digitalization and proto-design. (Publisher)

Quickening Evolution > Intel Ev

Ng, Eden Tian Hwa and Akira Kinjo. Computational Modelling of Plasticity-Led Evolution. arXiv:2208.00649. In our late day of a global knowsphere whose composite EarthKinder contents are commonly accessible, University of Brunei, Darussalam, Island of Borneo biomathematicians advance and finesse alternative views upon how life might have arisen along with an especial educative capacity. By this vista, into the 2020s a natural, necessary affinity between genomic and cerebral networks and functions is becoming newly apparent.

In a plasticity-led evolution, a change in the environment induces novel traits via phenotypic variability, after which such traits are genetically accommodated. While this hypothesis is served by experimental findings, here we propose computational methods to gain insight into underlying mechanisms. These models include the developmental process and gene-environment interactions, along with genetics and selection. Our results apply to such GRNs which represent consolidate the criteria of plasticity-led evolution. Since gene regulatory networks are mathematically equivalent to artificial recurrent neural networks, we discuss their analogies and discrepancies to help understand the mechanisms underlying plasticity-led evolution.

We remark that the Wagner model (Does Evolutionary Plasticity Evolve? Evolution. 50/3, 1996) is mathematically equivalent to a recurrent neural network (RNN). Numerous authors have also pointed out analogies between evolution and learning. RNNs process input data to give predictions as outputs. In development, GRNs process environmental cues to express phenotypes as outputs. However, the learning process itself differs between RNNs and GRNs. On the one hand, RNNs are often trained by changing their network parameters in order to minimize the prediction error, which bears similarity to Lamarckian evolution. (9)

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

Heylighen, Francis. The Meaning and Origin of Goal-Directedness: A Dynamical Systems Perspective. Biological Journal of the Linnean Society. July, 2022. This entry was a contribution by the Brussels bioscholar to the Evolution on “Purpose” conference sponsored by this original British naturalist periodical, as noted in this section. As the Abstract says, by virtue of this open venue it is possible again since orthogenesis decades to express the obvious presence of life’s oriented progression. Into the 21st century a robust documentation, as the site notes, now braces this universal genesis revolution.

This paper attempts to clarify the notion of goal-directedness, which is often seen as being inconsistent with standard causal mechanisms. We first note that goal-directedness does not presuppose any mysterious forces, such as intelligent design, vitalism, conscious intention or backward causation. We then review ways to define goal-directedness by more operational characteristics: equifinality, plasticity, persistence, concerted action and negative feedback. We show that such goal-like features can be interpreted as a far-from-equilibrium attractor of a dynamical system. We argue that attractors and basins with degrees of resilience tend to self-organize in complex reaction networks so as to engender self-maintaining “organizations”. (Abstract excerpt)

Quickening Evolution > Teleology

Noble, Raymond and Denis Noble. Physiology Restores Purpose to Evolutionary Biology. Biological Journal of the Linnean Society. July, 2022. This entry was a prime contribution by veteran London health and sanity provides to the Evolution on “Purpose” conference, as noted in this section. Once again it is can be exclaimed that Life is Purposefully Creative. For these reasons, the major transitions scale is given added aspects of Increasing Openness and Active Agency on the way to Self-Consciousness. See also (July 2022) Engines of Innovation: Biological Origins of Genome Evolution by James Shapiro for another conference statement.

Life is purposefully creative in a continuous process of maintaining integrity as an ongoing, iterative process.. Physiology is the study of purposeful living function. This was accepted all the way from the 17th century, through many 19th and early 20th century examples. But into the late 20th century any “teleological” views became excluded. This wrong turn must now be reversed. Even on the practical criterion of relevance to health care, gene-centrism has been a disaster, since prediction to the whole system only rarely succeeds. (Excerpt)

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

Earth Life > Nest > Life Origin

Smokers, Iris, et al. Complex Coacervation and Compartmentalizes Conversion of Prebiotically Relevant Metabolites. ChemSystemsChem. June, 2022. In this new Chemistry Europe journal, Radboud biochemists along with lab director Evan Spruijt contribute another 2020s instance whereby synthetic ideas can be fed back to help illume what went on long ago as life first came into being and on its cellular way to our curious selves.

Metabolism and compartmentalization are two of life’s most central elements. Constructing
synthetic assemblies based on prebiotically relevant molecules that combine these elements can provide insight into the formation of life-like protocells from abiotic building blocks. In this work, we show that a wide variety of anionic metabolites interact with oligoarginine to form coacervate protocells through liquid-liquid phase separation. We show that these metabolites remain reactive in compartmentalized systems. These results reveal the intricate interplay between (proto)metabolic reactions and coacervate compartments. (Abstract excerpt)

Earth Life > Nest > Microbial

Shishkov, Olga and Orit Peleg. Social Insects and Beyond: The Physics of Soft, Dense Invertebrate Aggregations. arXiv:2206.11129. Since circa 2010 when this “active matter” milieu came into being (see its Ecosmos section) University of Colorado biobehavioral researchers here achieve a thorough review to date. A novel advance is an ability to perceive these many dynamic animate, and inorganic occasions as exemplary manifestation of deep physical phenomena such as phase transitions. See also Bacterial Active Matter by Igor Aranson in Reports on Progress in Physics (85/7, 2022) for similar work. A number of current surmises become notably apparent. Once again, an independent mathematic domain seems to be in generative effect at each and every instance from mold blobs to urban areas. In regard, an emergent 21st century worldwise sapience in these 2020s can thus finally accomplish a whole scale vista of a universal genesis as it may reach it’s vital self-recognition.

Aggregation is a common behavior by which organisms arrange into cohesive groups. Whether airborne (honey bee clusters), ground dwellers (army ant bridges), or in water (sludge worm blobs), these collectives serve vital functions, Here we survey a variety of insects, arthropods, and worms as active soft matte . A group can be much larger than its members yet exist as a coherent entity. We discuss how novel aggregation physics can add to insights from ecological and physiological considerations as entities exchange information, energy, and matter as if a super-organism. With this work, we seek to scope out the inherent collective physics of dense living aggregations. (OS excerpt)

Analogies between the formation of aggregations of invertebrates to phase separation of non-living particles reveal unique properties of living aggregations. Wild-type C. elegans worms align through collisions with one another to aggregate into a nematic (oriented) phase. The process by which sludge worms water assemble into a blob is similar to polymer phase separation. These examples highlight the similarities and differences between living aggregations and non-living materials. (11)

Bacteria colonize diverse habitats and play a significant role in the oxygen, carbon, and nitrogen cycles. Suspensions of motile bacteria provide a good model of active matter as a broad class of non-equilibrium systems converting energy from the environment into motion. Concentrated suspensions, often termed active fluids, exhibit complex collective behavior such as turbulent-like swarming. The paper discusses microbial motilities from a deep physics viewpoint by way of experiments, main theories, and how visco-elasticity, liquid crystallinity, and confinement effect collective behaviors. (Aronson excerpt)

Earth Life > Nest > Microbial

Zamponi, Nahuel, et al. Scale Free Density and Fluctuations in the Dynamics of Large Microbial Ecosystems. arXiv:2206.12384. Four senior researchers with postings in the USA, Argentina, Poland, and Italy including Dante Chialvo discuss how these critically poised features, just as everywhere else from the ISM to the Internet it seems, serve suffuse and enhance bacterial assemblies. Once again a vital, dynamic poise between stability and flexibility, aka “nature’s sweet spot” as coined by Chialvo, seems best.

Microorganisms self-organize in extensive communities exhibiting complex fluctuations. But the ways that these systems can achieve variability along with a basic robustness is not well explained. Here we analyze three aspects of microbiota and plankton: density changes, the correlation structure and an avalanching fluidity. Our results find scale-free densities, anomalous variance' stages, abundance relations and stationary scale-free waves in effect. These behaviors, which typically occur in critically poised systems, suggest this active state is a way to explain both the robust and irregular phases and processes of copious microbial colonies.

Earth Life > Nest > Symbiotic

Bonfort, Adriano and Ricard Sole. Unicellular-Multicellular Evolutionary Branching Driven by Resource Limitations. Journal of the Royal Society Interface. June, . Barcelona systems bioscholars tease out reasons why and how cellular life was prompted to join into beneficial associations than go it alone.

Multicellular life (MC) forms have evolved many times, suggesting this is a common, beneficial innovation. Here we address how the first precondition for MC, namely ‘stay together’, might have taken place under spatially limited resources exploited by a population of unicellular agents. Using a minimal model of cell–cell adhesion among cells that exploit a local resource, a transition at a critical resource size does favor multicellular aggregates over a unicellularity (UC) phase. (Abstract excerpt)

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