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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 115 found.


Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Heyduk, Karolina, et al. The Genetics of Convergent Evolution. Nature Reviews Genetics. 20/485, 2019. Convergent evolution has been pervasive throughout the history of life. Even very complicated adaptations, such as camera eyes in animals, sex determination systems in eukaryotes and eusociality in insects, have evolved multiple times. (485) Yale University biologists open with these statements, which are a good example of 2019 conclusions that an inherent propensity repeats as similar forms and features in kind. In this paper insightful evidence from flora photosynthesis is seen to build the case that life’ development knows what it is doing and where it is going. (Look for Convergent Evolution on Earth by George McGhee due in October from MIT Press.)

The tree of life is resplendent with examples of convergent evolution, whereby distinct species evolve the same trait independently. Many highly convergent adaptations are also complex, which makes their repeated emergence surprising. In plants, the evolutionary history of two carbon concentrating mechanisms (CCMs) — C4 and crassulacean acid metabolism (CAM) photosynthesis — presents such a paradox. Here, we propose that many of the complexities often associated with C4 and CAM photosynthesis may have evolved during a post-emergence optimization phase. (Abstract excerpt)

Quickening Evolution

Huneman, Philippe. Revisiting Darwinian Teleology: A Case for Inclusive Fittness as Design Explanation. Studies in History and Philosophy of Biological and Biomedical Sciences. Online July, 2019. The University of Paris Sorbonne evolutionary theorist offers a latest attempt sort and clarify ways to view life’s relative appearance as having some innate directional course. That is to say, how to thread a narrow path between its olden mainstream rejection and the fact that something must be going on which resulted in our human presence.

Quickening Evolution

Newman, Stuart. Inherency of Form and Function in Animal Development and Evolution. Frontiers in Physiology. Online June 19, 2019. As the Abstract describes, the New York Medical College cell biologist continues to advance his deep insights by which to appreciate life’s iterative anatomical and physiological emergence as arising from innate physical propensities. See also Inherency and Homomorphy in the Evolution of Development by SAN in Current Opinion in Genetics & Development (Vol. 37, August 2019).

I discuss recent work on the origins of morphology and cell-type diversification in Metazoa – collectively the animals – and propose a scenario for how these two features became integrated by way of a third set of cellular pattern formation processes. These inherent propensities to generate familiar forms and cell types are exhibited by present-day organisms. The structural motifs of animal bodies and organs, e.g., multilayered, hollow, elongated and segmented tissues, internal and external appendages, branched tubes, and modular endoskeletons, result from the recruitment of “generic” physical forces and mechanisms such as adhesion, contraction, polarity, chemical oscillation, and diffusion. Cellular pattern, mediated by released morphogens interacting with biochemically responsive and excitable tissues, drew on inherent self-organizing processes in proto-metazoans to transform clusters of holozoan cells into animal embryos. (Abstract excerpt)

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

Earth Life > Common Code

Asllani, Malbor, et al. A Universal Route to Pattern Formation. arXiv:1906.05946. When this resource website was first posted around 2004, the scientific perception of pervasive self-assembled topologies was quite fragmentary. A decade and a half later, University of Limerick, University of Namur, Belgium, University of Firenze, and Oxford University (Philip Maini) theorists (as many others) can assume and attest to an intrinsic computational propensity of material and organic patternings everywhere in kind.

Self-organization, the ability of a system of microscopically interacting entities to shape macroscopically ordered structures, is ubiquitous in Nature. Spatio-temporal patterns are observed in a large plethora such the coat or skin of animals, the spatial distribution of vegetation in arid areas, colonies of insects in host-parasitoid systems and the architecture of complex ecosystems. Spatial self-organization can be described following the visionary intuition of Alan Turing, who showed how non-linear interactions between slow diffusing activators and fast diffusing inhibitors could induce patterns. We here propose a novel framework for the generation of short wavelength patterns which overcomes the limitation inherent in the Turing formulation. Macroscopic patterns that follow the onset of the instability are robust and show oscillatory or steady-state behavior. (Abstract excerpt)

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)

Earth Life > Common Code

Frank, Steven and Jordi Bascompte. Invariance in Ecological Pattern. arXiv:1906.06979. UC Irvine and University of Zurich system theorists join their common studies across life’s evolutionary and environmental species to presently be able to advance and affirm nature’s infinite propensity to repeat self-similar forms and processes in kind at each and every creaturely and communal scale and instance.

The abundance of different species in a community often follows the log series distribution. Why does the complexity and variability of ecological systems reduce to such simplicity? This article proposes a more general answer based on the concept of invariance, the property by which a pattern remains the same after transformation. Invariance has a long tradition in physics. By bringing this unifying invariance approach into ecology, one can see that the log series pattern of species abundances dominates when the consequences of density dependent processes are invariant to addition or multiplication. Recognizing how these invariances connect pattern to process leads to a synthesis of previous approaches. (Abstract excerpt)

Earth Life > Common Code

Friston, Karl. A Free Energy Principle for a Particular Physics. arXiv:1906.10184. The Wellcome Centre for Human Neuroimaging, London collegial neurotheorist posts a 148 page draft manuscript which seeks to join his self-composing and cognizing Bayesian brain theories with a conducive, natural, cosmic affinity. Search KF as this view gains a growing number of supporters. Akin to Integrated Information theory (Tononi) and other entries, these fluid perceptions take on their own iterative course in quest of better explanations, albeit in arcane terms which ought to gain a common clarity.

This monograph attempts a theory of every 'thing' that can be distinguished from other things in a statistical sense. The ensuing independencies, mediated by Markov blankets (see below), speak to a recursive composition of ensembles (things) at increasingly higher spatiotemporal scales. This decomposition provides a broad description of small things via quantum mechanics and the Schrodinger equation, then statistical mechanics and related fluctuation theorems, and through to big things in classical mechanics. Our main contribution is to examine the implications of Markov blankets for self-organisation to nonequilibrium steady-state. In so doing, we recover an information geometry and accompanying free energy principle that allows one to interpret the internal states as they represent and infer external states. (Abstract edits)

In statistics and machine learning, the Markov blanket for a node in a graphical model contains all the variables that shield the node from the rest of the network. This means that the Markov blanket of a node is the only knowledge needed to predict the behavior of that node and its children. In a Bayesian network, the values of the parents and children of a node evidently give information about that node. In a Bayesian network, the Markov blanket of node A includes its parents, children and the other parents of all of its children. (WikiPedia)

Earth Life > Common Code

Zhang, Mengsen, et al. Connecting Empirical Phenomena and Theoretical Models of Biological Coordination across Scales. Journal of the Royal Society Interface. Online August, 2019. By way of sophisticated procedures, Center for Complex Systems and Brain Sciences, Florida Atlantic University researchers MZ, Chris Beetle, Scott Kelso and Emmanuelle Tognoli (search SK & ET) uncover intrinsic mathematic reciprocities which seem to imbue and guide small group social interactions. These patterns are then seen to suffuse organic and cerebral behaviors so at to reveal a broader scale-invariance. See also Critical Diversity: Divided or United States of Social Coordination by this group in PLoS One (April 4, 2018) which alludes to a chimeric dynamics.

Coordination in living systems—from cells to people—must be understood at multiple levels of description. Analyses and modelling of patterns of biological coordination often focus either on large-scale systems with many components, or on detailed dynamics in small-scale systems with few components. To bridge this gap, we have conducted a mid-scale human social experiment designed to reveal coordination at multiple levels (ensemble, subgroups and dyads) simultaneously. The present paper shows that a single system of equations captures key observations at all relevant levels. It also connects empirically validated models of both large- and small-scale biological coordination. Only by incorporating both of these features simultaneously can we reproduce the essential coordination behaviour observed in our experiment. (Abstract excerpt)

This cross-scale consistency of experimental observations may be explained by the scale-invariant nature of the critical coupling ratio, the transition point between monostability and multistability. The scale invariance suggests that experimental methods and conclusions for small-scale coordination dynamics have implications for multistability, phase transitions and metastability at larger scales, and enables a unified approach to biological coordination that meshes statistical mechanics and nonlinear dynamics. (7)

Earth Life > Nest > Geological

Meng, Fanzhen, et al. Power Law Relations in Earthquakes from Microscopic to Macroscopic Scales. Nature Scientific Reports. 9/10705, 2019. University of Hong Kong, and Chinese Academy of Sciences, Wuhan systems geologists provide a latest technical analysis of Earth shaking catastrophic events by way of self-similar complexity theories. As they become more common in China, Iran and the USA, these insights can aid better warning systems.

Understanding the physics of earthquakes is a crucial step towards improving their prediction accuracy. Scale invariance or fractal features are often reported in earthquakes, such as the size distribution, the spatial distribution of hypocenters, and the frequency of aftershocks. Here we assess whether other key parameters and quantities involved in earthquakes also conform to the power law. By analyzing a large amount of data collected from the laboratory experiments and field monitoring of earthquakes, we find that the crack density on the two sides of small scale fracture or large scale fault decreases with increasing distance following the power law, and the crack number-crack length distribution is also scale invariant like natural faults. (Abstract excerpt)

Earth Life > Nest > Geological

sarker, Shiblu, et al. Critical Nodes in River Networks. Nature Scientific Reports. 9/11178, 2019. By way of a novel application of network theory even to this geological realm, University of Central Florida civil engineers are able to perceive their inherent presence. Once again nature’s universal mathematical program can be seen in formative effect.

River drainage networks are important landscape features that have been studied from a range of geomorphological and hydrological perspectives. However, identifying the most vital (critical) nodes on river networks and their relationships with geomorphic and climatic properties has not yet been addressed. In this study, we use an algorithm that determines the set of critical nodes whose removal results in network fragmentation and apply it to simulated and natural river networks. Our results indicate a power-law relationship between the number of connected node pairs in the remaining network and the number of removed critical nodes. (Abstract excerpt)

Earth Life > Nest > Life Origin

Cafferty, Brian, et al. Robustness, Entrainment, and Hybridization in Dissipative Molecular Networks, and the Origin of Life. Journal of the American Chemical Society. 141/20, 2019. A seven person Harvard University team led by George Whitesides describe a prebiotic propensity to generate robust complex behaviors, instead of damping them out. More evidence thus accrues for a cosmic, vital inherency to bear, form and develop in an organic fashion. A commentary on this breakthrough is Rhythm before Life by Nathaniel Wagner and Gonen Ashkenasy in Nature Chemistry (11/680, 2019).

How simple chemical reactions self-assembled into complex, robust networks at the origin of life is unknown. This general problem—self-assembly of dissipative molecular networks—is also important in understanding the growth of complexity from simplicity in molecular and biomolecular systems. Here, we describe how heterogeneity in the composition of a small network of oscillatory organic reactions can sustain (rather than stop) these oscillations, when homogeneity in their composition does not. Remarkably, a mixture of two reactants of different structure—neither of which produces oscillations individually—oscillates when combined. These results demonstrate that molecular heterogeneity present in mixtures of reactants can promote rather than suppress complex behaviors. (Abstract)

Earth Life > Nest > Life Origin

De la Escosura, Andres. The Informational Substrate of Chemical Evolution. Life. Online August 8, 2019. A Universidad Autonoma of Madrid chemist group leader (search) contributes to “abiogenesis” studies, aka how could living organisms have arisen from seemingly inanimate or inorganic substrates, via novel perceptions that precursor biochemistries can similarly be understood to possess a semantic communicative quality. In regard, this earlier material phase or stage can thus accrue an inherent, lively genetic-like content. See also Permeability-driven Selection in a Semi-empirical Protocell Model: The Roots of Prebiotic Systems Evolution by Gabriel Piedrafita, et al in Nature Scientific Reports (7/3141, 2017) for a companion Spanish study.

A key aspect of biological evolution is the capacity of living systems to process information coded in DNA. The overall picture indicates that information processing in cells occurs through a hierarchy of genes regulating other genes through metabolic networks. There is an implicit semiotic character based on functional molecules that act as signs to self-regulate the whole network. In contrast to cells, chemical systems not seen as able to process information, yet they have preceded biological organisms, and evolved into them. Hence, there must have been prebiotic molecular assemblies that could regulate their constituent reactions and supramolecular organization processes. This essay will consider distinctive features of information in living and non-living matter, and how the capacity of biological information processing might be rooted in an autonomous chemical system which could self-sustain and reproduce through organizational closure. (Abstract)

Earth Life > Nest > Microbial

Cepelewicz, Jordana. Bacterial Complexity Revises Ideas About ‘Which Came First?’. Quanta. Online June 12, 2019. A science writer conducts a wide survey of microbiologists such as Arash Komeili, Damien Devos, Michael Rout, Mark Field, Kate Adamala (see her lab page), Joel Dacks, and Anthony Poole about revolutionary rethinkings in this field about the appearance, composition and import of prokaryotic and eukaryotic microbial cells. With a main reference to Ectosymbiotic Bacteria at the Origin of Magnetoreception in a Marine Protist by Caroline Monteil, et al in Nature Microbiology (4/1088, 2019), once more a formative symbiosis is in effect everywhere.

Earth Life > Nest > Symbiotic

Geva-Zatorsky, Naama, et al. When Cultures Meet: The Landscape of “Social” Interactions between the Host and Its Indigenous Microbes. BioEssays. Online August, 2019. As this composite organism model gains use acceptance, with some resistance, N G-Z, Technicon-Israel Institute of Technology, with Eran Elinav and Sven Pettersson, Canadian Institute for Advanced Research, Toronto, provide a comparative sociological and cultural dimension. To paraphrase, we contain multitudes which in turn make up our integral persona, which is here cleverly enhanced and expanded to health, psychological, and urbane realms.

Animals exist as biodiverse composite organisms that include microbes, eukaryotic cells, and organs. Through an interdependent relationship and an inherent ability to transmit and reciprocate stimuli in a bidirectional way, a human body, aka holobiont, secures growth, health, and reproduction. In this review an overview is provided on the communications between microbes and their host in mutually nurturing biochemical, biological, and social interconnected relationships.. Nutrition, immunology, and sexual dimorphism have been traversed extensively to reflect on health and mind states, social interactions, and urbanization defects/effects. Finally, examples of molecular mechanisms potentially orchestrating these complex trans-kingdom interactions are provided. (Abstract excerpt)

Earth Life > Nest > Symbiotic

Mason, Alexander, et al. Mimicking Cellular Compartmentalization in a Hierarchical Protocell through Spontaneous Spatial Organization. ACS Central Science. Online July 3, 2019. We include this entry about synthetic cells in this section because it shows how these title findings of life’s scalar self-organization are well evident across cellular forms. Eight Eindhoven University of Technology chemists apply this natural archetype of bounded whole units composed of symbiotic members to intentionally scope out how new beneficial and benign procreations could be conceived to well serve person and planet.

A systemic feature of eukaryotic cells is the spatial organization of functional components through compartmentalization. Developing protocells with compartmentalized synthetic organelles is a critical step toward one of the core characteristics of cellular life. Here we demonstrate the bottom-up, multistep, noncovalent, assembly of rudimentary subcompartmentalized protocells through the spontaneous encapsulation of semipermeable, polymersome proto-organelles inside cell-sized coacervates. The coacervate microdroplets are membranized using tailor-made terpolymers, to complete the hierarchical self-assembly of protocells, a system that mimics both the condensed cytosol and the structure of a cell membrane. In this way, the spatial organization of enzymes can be finely tuned, leading to an enhancement of functionality. (Abstract)

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