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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 61 through 75 of 118 found.


Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution > Intel Ev

Pinero, Jordi and Ricard Sole. Statistical Physics of Liquid Brains. Philosophical Transactions of the Royal Society B. 374/20180376, 2018. In a special Liquid Brains, Solid Brains issue (search Forrest), Institut de Biologia Evolutiva, Universitat Pompeu Fabra, Barcelona theorists consider a universal recurrence in kind of the same generic complex network system across natural and social domains. While akin to genomes and ecosystems, an apt model is cerebral cognition, broadly conceived, by way of agental neurons and synaptic links in multiplex arrays. A prime attribute is a cross-conveyance of intelligence and information, aka biological computation, which is how animal groupings from invertebrates to mammals to people achieve a collective decision-making.

Liquid neural networks (or ‘liquid brains’) are a widespread class of cognitive living networks characterized by a common feature: the agents move in space. Thus, no fixed, long-term agent-agent connections are maintained, in contrast with standard neural systems. How is this class of systems capable of displaying cognitive abilities, from learning to decision-making? In this paper, the collective dynamics, memory and learning properties of liquid brains is explored under the perspective of statistical physics. We review the generic properties of three large classes of systems, namely: standard neural networks (solid brains), ant colonies and the immune system. It is shown that, despite their intrinsic differences, these systems share key properties with neural systems in terms of formal descriptions, but depart in other ways. (Abstract excerpt)

Quickening Evolution > Intel Ev

Sole, Ricard, et al. Liquid Brains, Solid Brains: How Distributed Cognitive Architectures Process Information. Philosophical Transactions of the Royal Society B. 374/20190040, 2019. With Melanie Moses and Stephanie Moses, an introduction to papers from a December 2017 Santa Fe Institute seminar with this title, which represents how many domains across life’s evolution universe to human can actually be perceived as some manner of neural-like intelligent process. We note, for example, Metabolic Basis of Brain-like Electrical Signalling in Bacterial Communities, Plant Behavior in Response to the Environment (Duran-Nebreda & Bassel herein), Statistical Physics of Liquid Brains (Pinero & Sole), The Compositional Stance in Biology, and A Brief History of Liquid Computers. A tacit theme for this work is a further major evolutionary transition in individuality.

Cognitive networks have evolved a broad range of solutions to the problem of gathering, storing and responding to information. Some of these networks are describable as static sets of neurons linked in an adaptive web of connections. These are ‘solid’ networks, with a well-defined and physically persistent architecture. Other systems are formed by sets of agents that exchange, store and process information but without persistent connections or move relative to each other in physical space. We refer to these networks that lack stable connections and static elements as ‘liquid’ brains, a category that includes ant and termite colonies, immune systems and some microbiomes and slime moulds. What are the key differences between solid and liquid brains, particularly in their cognitive potential, ability to solve particular problems and environments, and information-processing strategies? To answer this question requires a new, integrative framework. (Abstract)

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

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 > Nest > Life Origin

Pascal, Robert. A Possible Non-Biological Reaction Framework for Metabolic Processes on Early Earth. Nature. 569/47, 2019. The University of Montpellier biochemist comments on a paper, Synthesis and Breakdown of Universal Metabolic Precursors Promoted by Iron, in the same issue (569/104) by Kamila Muchowaka, et al (University of Strasbourg) which reports how a network of reactions for converting carbon dioxide into organic compounds could have fostered the advent and advance of original life.

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

Bosch, Thomas, et al. Evolutionary “Experiments” in Symbiosis. BioEssays. Online May, 2019. TB, University of Kiel, Karen Guillemin, University of Oregon, and Margaret McFall-Ngai, University of Hawaii propose novel ways to properly and fully perceive the breadth and depth of communal reciprocities that so distinguish the many phases of natural life.

Nature has given us an overwhelming diversity of animals to study, and recent technological advances have greatly accelerated the ability to generate genetic and genomic tools to develop model organisms for research on host–microbe interactions. With the help of such models the authors therefore hope to construct a more complete picture of the mechanisms that underlie crucial interactions in a given metaorganism (entity consisting of a eukaryotic host with all its associated microbial partners). As reviewed here, new knowledge of the diversity of host–microbe interactions found across the animal kingdom will provide new insights into how animals develop, evolve, and succumb to the disease. (Abstract)

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)

Earth Life > Nest > Symbiotic

Serra, Denise, et al. Self-Organization and Symmetry Breaking in Intestinal Organoid Development. Nature. 569/66, 2019. A 13 person team at Friedrich Miescher Institute for Biomedical Research, Basel, Switzerland perform detailed studies which exemplify how cellular life can indeed be known to have a capacity to organize itself during its evolutionary development.

Intestinal organoids are complex three-dimensional structures that mimic the cell-type composition and tissue organization of the intestine by recapitulating the self-organizing ability of cell populations derived from a single intestinal stem cell. Our findings reveal how single cells exposed to a uniform growth-promoting environment have the intrinsic ability to generate emergent, self-organized behaviour that results in the formation of complex multicellular asymmetric structures. (Abstract excerpt)

Earth Life > Nest > Symbiotic

Shahbazi, Marta, et al. Self-Organization of Stem Cells into Embryos: A Window on Early Mammalian Development. Science. 364/948, 2019. It is vital to make note in this late year of how much a natural self-organizing process has become wholly accepted in cell biology, which was rarely considered just a decade ago. In a special section about Organoids, Cambridge University and Rockefeller University led by Magdalena Zernicka-Goetz present a visual articulation of how organisms come to form and flourish by virtue of this intrinsic formative method. Within this website, whenever could it be possible to imagine life’s whole evolutionary development as a self-organizing embryonic gestation? See also in this issue Organoids by Design by Takebe and Wells, second Abstract.

Embryonic development is orchestrated by robust and complex regulatory mechanisms acting at different scales of organization. In vivo studies are challenging for mammals after implantation, owing to the small size and inaccessibility of the embryo. The generation of stem cell models of the embryo represents a powerful system with which to dissect this complexity. Control of geometry, modulation of the physical environment, and priming with chemical signals reveal the intrinsic capacity of embryonic stem cells to make patterns. Here, we review the principles of self-organization and how they set cells in motion to create an embryo. (Shahbazi Abstract)

Organoids are multicellular structures that can be derived from adult organs or pluripotent stem cells. Early versions of organoids range from simple epithelial structures to complex, disorganized tissues with large cellular diversity. The current challenge is to engineer cellular complexity into organoids in a controlled manner that results in organized assembly and acquisition of tissue function. We discuss how the next generation of organoids can be designed by means of an engineering-based narrative design to control patterning, assembly, morphogenesis, growth, and function. (Takebe Abstract)

Earth Life > Nest > Multicellular

Duclos, Kevin, et al. Investigating the Evolution and Development of Biological Complexity under the Framework of Epigenetics. Evolution & Development. Online July, 2019. University of Calgary cell biologists contribute to this nonlinear revolution, while it goes on largely unawares, to reinterpret life’s gestation by way of innate, iterative, scalar topologies and source forces. Here the recent expansion of genomic activity to include influences beyond nucleotides, aka epigenetics broadly conceived, is applied as one more generative factor at work in evolutionary developments.

Biological complexity is a key component of evolvability, yet its study has been hampered by a focus on evolutionary trends of complexification and inconsistent definitions. Here, we demonstrate the utility of bringing complexity into the framework of epigenetics to better investigate its utility as a concept in evolutionary biology. We first analyze the existing metrics of complexity and explore its link with adaptation and developmental mechanisms. We then consider how epigenetics shapes developmental and evolutionary trajectories. We argue that epigenetics itself could have emerged from complexity because of a need to self‐regulate. Our goal is not to explain trends in biological complexity but to help develop and elucidate novel questions in the investigation of biological complexity and its evolution. (Abstract excerpt)

Earth Life > Nest > Multicellular

Grossnickle, David, et al. Untangling the Multiple Ecological Radiations of Early Mammals. Trends in Ecology and Evolution. Online June, 2019. DG and Gregory Wilson, University of Washington along with Stephanie Smith, Field Museum of Natural History, Chicago, provide an extensive illustrated survey of our latest collective reconstruction of how life’s myriad creaturely species evolved and emerged. We muse and wonder whatever phenomenal contribution are we homo to Anthropo sapiens here by achieving for a self-revealing and auto-creating ecosmos.

The ecological diversification of early mammals is a globally transformative event in Earth’s history, largely due to the Cretaceous Terrestrial Revolution mass extinction. A confounding issue is that it comprised nested radiations of mammalian subclades within the broader scope of their evolution. In the past 200 million years, various independent groups experienced large-scale radiations involving ecological diversification from ancestral lineages of small insectivores such as include Jurassic mammalia forms, Late Cretaceous metatherians, and Cenozoic placentals. Here, we review these speciations which reveal the nuanced complexity of early mammal evolution, the value of ecomorphological fossil data, and phylogenetic context in macroevolutionary studies. (Abstract)

Earth Life > Nest > Societies

Cavagna, Andrea, et al. Dynamical Renormalization Group Approach to the Collective Behavior of Swarms. arXiv:1905.01227. This is the first of two postings by a six member team of Italian and Argentine systems theorists including Irene Giardina. The second is Renormalization Group Crossover in the Critical Dynamics of Field Theories with Mode Coupling Terms at arXiv:1905.01228 (see quote). As a general review, by since there can only be one extant nature, whether it is variously described by RG, network, complexity, fractal, computational or other methods. By 2019 each version in its way cites a dual node and link-like interactives reciprocity. This innate cosmic vitality is now seen to consistently seek and reside at an optimum critical poise such as brains, animal groupings, or protein webs. By this analysis, once again a deep rooting in condensed matter physics is achieved. As we log in along with Dante Chialvo 2019, since the 1980s when this complexity revolution began, and intimated much earlier, we may finally glimpse the epic achievement *magnum opus) of this universe to human source code.

The success of the theory of critical phenomena is based upon a simple observation: systems with very different microscopic details behave in strikingly similar ways when correlations are sufficiently strong. This experimental fact eventually crossed over into theory with the formulation of the phenomenological scaling laws, whose key idea is that the only relevant scale ruling the spatio-temporal behaviour of a system near its critical point is the correlation length. Eventually, the great conceptual edifice of the Renormalization Group (RG) tied everything together, explaining why microscopically different systems shared so much at the macroscopic level, giving a demonstration of universality through the concept of attractive fixed points, and providing a method to calculate experimentally accessible quantities, most conspicuously the critical exponents. (1905.01228, 1)

Earth Life > Nest > Societies

Su, Qi, et al. Evolutionary Dynamics with Stochastic Game Transitions. arXiv:1905.10269. Harvard University mathematicians including Martin Nowak explain why creaturely groupings seem to have an inherent drive and incentive toward beneficial cooperative behaviors versus negative selfishness. See also Su, Qi, et al Spatial Reciprocity in the Evolution of Cooperation by Qi Su, et al in the Proceedings of the Royal Society B. (Vol.286/Iss.1900, 2019) for another analysis that reaches a similar conclusion.

The environment has a strong influence on a population's evolutionary dynamics. Driven by both intrinsic and external factors, the environment is subject to continuous change in nature. To model an ever-changing environment, we develop a framework of evolutionary dynamics with stochastic game transitions, where individuals' behaviors together with the games they play in one time step decide the games to be played next time step. We then study the evolution of cooperation in structured populations and find a simple rule: natural selection can favor cooperation over defection. We show that even if each individual game opposes cooperation, allowing for a transition between them can result in a favorable outcome for cooperation. Our work suggests that interdependence between the environment and the individuals' behaviors may explain the large-scale cooperation in realistic systems even when it is expensive relative to its benefit. (Abstract excerpt)

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