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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 74 found.


Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution > Systems Biology

DiFrisco, James and Johannes Jaeger. Genetic Causation in Complex Regulatory Systems: An Integrative Dynamic Perspective. BioEssays. 42/6, 2020. A biological studies advance, KU Leuven philosopher and a Complexity Science Hub, Vienna systems biologist seek to add a relational network vista which can inform the historic turn from discrete nucleotides to whole entities, be it genomes or organisms.

The logic of genetic discovery remains in place, but the focus of biology is shifting from genotype–phenotype relationships to complex metabolic, physiological, developmental, and behavioral traits. In light of this, the reductionist view of genes as privileged causes is re‐examined. The scope of genetic effects in complex regulatory systems, in which dynamics are driven by feedback and hierarchical interactions across levels, are considered. This review argues that genes can be treated as specific difference‐makers for the molecular regulation of their expression. However, they are not stable, proportional or specific as causes of the behavior of regulatory networks. Proper dynamical models can illuminate cause‐and‐effect in complex biological systems so to gain an integrative understanding of underlying complex phenotypes. (Abstract edit)

Quickening Evolution > Intel Ev

Brun-Usan, Miguel, et al.. How to Fit In: The Learning Principles of Cell Differentiation. PLoS Computational Biology.. April, 2020. University of Southampton, UK, computer scientists including Richard Watson continue their revisionary studies of biological metabolisms by viewing them through a learning lens. A cerebral perspective, as this section reports, can provide better insights into cellular processes because both evolution and learning are explorations in search of solutions. A further step is to integrate this view with gene regulatory networks so these common models can reinforce each other. Altogether this approach implies that life’s oriented emergence is trying to achieve some manner of its own self-description and comprehension.

Cell differentiation in multicellular organisms requires cells to respond to complex combinations of extracellular cues, such as morphogen concentrations. But a general theory describing how cells integrate multi-dimensional signals is still lacking. In this work, we propose a framework from learning theory to understand the relationships between environmental cues (inputs) and phenotypic responses (outputs) underlying cell plasticity.. Altogether, these results illustrate the functional parallelisms between learning in neural networks and the action of natural selection on environmentally sensitive gene regulatory networks. This offers a theoretical framework for responses that integrate information from multiple cues, a phenomenon that underpins the evolution of multicellularity and developmental robustness. (Abstract excerpt)

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

Earth Life > Nest > Microbial

Menon, Shakti, et al. Information Integration and Collective Motility in Phototactic Cyanobacteria. PLoS Computational Biology. April, 2020. Institute of Mathematical Sciences, Tamil Nadu, India researchers describe how bacterial groupings can be seen to exhibit and be modeled by active matter phenomena. In regard, quorum sensing is interpreted to proceed by way of integrating relevant information. Altogether another manifestation of universal principles and formations.

Microbial colonies in the wild often consist of large groups of heterogeneous cells that coordinate and integrate information across multiple spatio-temporal scales. We describe a computational model for the collective behavior of phototaxis in the cyanobacterium Synechocystis that move in response to light. The results suggest that tracking individual cyanobacteria may provide a way to determine their mode of information integration. Our model allows us to address the emergent nature of this class of collective bacterial motion, linking individual cell response to the large scale dynamics of the colony. (Summary)

Earth Life > Nest > Symbiotic

, Pfannschmidt. Thomas, et al. Philosophical Transactions of the Royal Society B.. May, 2020. We cite this introduction to a special collection as a good example of how much these mutualistic processes are now being found to pervade and serve the formation and activity of eukaryotic cells, a feature not considered at all a few years ago.

Earth Life > Nest > Symbiotic

Varahan, Sriram, et al. Metabolic Constraints Drive Self-Organization of Specialized Cell Groups. eLife. June 26, 2019. Five Indian systems cell biologists contribute novel understandings of the many ways that cellular activities have a vitality of their own as they innately organize themselves into preferred states and solutions.

How phenotypically distinct states in isogenic cell populations appear and stably co-exist remains unresolved. We find that within a mature, clonal yeast colony in low glucose, cells arrange into metabolically disparate cell groups. Using this system, we model and experimentally identify metabolic constraints which drive such self-assembly. Our work suggests simple physico-chemical principles that determine how isogenic cells spontaneously self-organize into structured assemblies in complimentary, specialized states. (Abstract excerpt)

Earth Life > Nest > Multicellular

Naranjo-Ortiz, Miguel and Toni Gabaldon. Fungal Evolution: Cellular, Genomic and Metabolic Complexity. Biological Reviews. April, 2020. As the life sciences proceed apace to record the anatomic presence of networks everywhere, here Barcelona Institute of Science and Technology geneticists explore in detail how these prolific microorganisms can be an exemplary way to study this interlinked and communicative phenomena. Within a sense of a transitional emergence from nucleotides and prokaryotes to mobile, varigated organisms, the fungi family do indeed provide an iconic, valuable model.

The question of how phenotypic and genomic complexity are related and shaped through evolution is a central to animal and plant biology. Recently, fungi have emerged as an alternative system of much value because they present a broad and diverse range of phenotypic traits and many different shapes. Fungal cellular organizations span from unicellular forms to complex, macroscopic multicellularity, with multiple transitions to higher or lower levels of cellular complexity occurring throughout their evolution. Similarly, fungal genomes have a diverse architecture with rapid changes in genome organization. We explore how the interplay of cellular, genomic and metabolic traits mediates the emergence of complex phenotypes. (Abstract)

Fungus compose a group of spore-producing organisms feeding on organic matter, including molds, yeast, mushrooms, and toadstools.

Earth Life > Nest > Societies

Brask, Josefine, et al. Animal Social Networks: An Introduction for Complex Systems Scientists. arXiv:2005.09598. University of Exeter animal behaviorists including Darren Croft show how equally real interactive relations between group members can reveal and achieve new insights and explanations. In regard, these topologies are not fixed or static in nature but provide a dynamic, beneficial matrix.

Many animals live in societies where individuals frequently interact socially with each other. Animal social network research, however, seems to not be well known by scientists outside of the animal behaviour field. Here we provide an introduction for complex systems researchers. In this paper, we describe what animal social networks are and how they are scientifically important; we give an overview of common methods; and highlight challenges where interaction between animal social network and general complex systems research could be valuable. We hope that this will help to facilitate future interdisciplinary collaborations and lead to better integration of these networks into the field of complex systems. (Abstract excerpt)

Earth Life > Nest > Societies

Grueter, Cyril, et al. Multilevel Organization of Animal Society. Trends in Ecology and Evolution. May, 2020. Sixteen researchers posted in Australia, China, Germany, the USA, Switzerland, and India including Larissa Swedell describe how animal groupings typically array into multiple nested networked units. And we note that a diagram display of this threading out appears as another epitome of life’s iterative evolutionary emergence whether bodies, brains or organisms.

Multilevel societies (MLSs), stable nuclear social units within a larger collective with multiple nested social levels, occur in several mammalian lineages. Their architectural complexity and size impose require their members to find adaptive solutions in disparate domains. Here, we propose a unifying terminology and operational definition of MLS. To identify new avenues for integrative research, we synthesise current literature on the selective pressures underlying the evolution of MLSs and their implications for cognition, intersexual conflict, and sexual selection. Mapping the drivers and consequences of MLS provides a reference point for the social evolution of many taxa, including our own species. (Abstract)

Earth Life > Nest > Ecosystems

vandermeer, John and Ivette Perfecto. Ecological Complexity and Agroecology. London: Routledge, 2017. University of Michigan senior professors of ecology, evolutionary biology, natural resources and environments (search) provide a unique textbook for this subject which can also represent a 2010s revolutionary, advantageous synthesis of this vital sustenance resource with nature’s innate underlay of self-organizing network patterns and processes. Chapter titles such as Multidimensionality, Coupled Oscillatory, Stochasticity and Critical Transitions discuss and apply the latest ecosmos code mathematical guidance. OK

While the science of ecology should be the basis of agroecological planning, many analysts have out-of-date ideas about contemporary ecology. Ecology has come a long way since the old days of "the balance of nature" and other notions of how ecological systems function. In this context, the new science of complexity has become vitally important in the modern science of ecology. The book’s organization consists of an introductory chapter, and a second chapter providing some of the background to basic ecological topics as they are relevant to agroecosystrems (e.g., soil biology and pest control). The core of the book consists of seven chapters on key intersecting themes of ecological complexity, including issues such as spatial patterns, network theory and tipping points, illustrated by examples from agroecology and agricultural systems from around the world.

Earth Life > Nest > Ecosystems

Vandermeer, John, et al. New Forms of Structure in Ecosystems Revealed with the Kuramoto Model. arXiv:2006.16006. University of Michigan sustainability enviromentalists including Ivette Perfecto post a latest advance of their project to better understand diverse flora and fauna biotas by way of nonlinear network complexities. It opens with a review of prior glimpses of a natural, endemic nonlinearity in formative effect. Into the 2010s, global computational and communicative efforts are now well able to quantify independent, mathematical, complex adaptive self-organizations. This paper then cites a new perception that ecosystems are composed of periodic, interactive, synchronized oscillations between transitional phases such as predator/prey, invasion/resistance and so on. Thus, even myriad ecologies are found to be defined by a “chimera” condition, similar to other reams such as brains and metabolisms.

For a series of related work, see Viewing Communities as Coupled Oscillators: Elementary Forms from Lotka and Volterra to Kuramoto by Zachary Haijan-Forooshani and John Vandermeer in bioRxiv (May 27, 2020), The Community Ecology of Herbivore Regulation in an Agroecosystem: Lessons from Complex Systems by John Vandermeer et al in BioScience (69/12, 2019, reviewed herein), Chimera Patterns Induced by Distance-Dependent Power-Law Coupling in Ecological Networks by Tanmoy Banerjee, et al in Physical Review E (94/032206, 2016) and Synchronization Unveils the Organization of Ecological Networks with Positive and Negative Interactions by Andrea, Giron, et al in Chaos (26/065302, 2016). A unique text for this ecosmic ecosystem revolution is Ecological Complexity and Agroecology by John Vandermeer and Ivette Perfecto (Routledge, 2017, search).

Ecological systems, as is often noted, are complex. Equally notable is the common generalization that complex systems tend to be oscillatory, which could provide insights into the structure of ecological systems. A popular analytical tools for such studies is the Kuramoto model of coupled oscillators. Using a well-studied system of pests and their enemies in an agroecosystem, we apply this stylized model to ask whether its actual natural history is reflected in the dynamics of the qualitatively instantiated Kuramoto model. Indeed, synchrony groups with an overlying chimeric structure, depending on the strength of the inter-oscillator coupling, are found. We conclude that the Kuramoto model presents a novel window to better understand the interactive forms of ecological systems. (Abstract)

Earth Life > Nest > Ecosystems

Vandermeer, John, et al. The Community Ecology of Herbivore Regulation in an Agroecosystem: Lessons from Complex Systems. BioScience. 69/12, 2019. With 30 authors from 4 continents, this article well represents the 21st century discovery that flora and fauna environs are indeed graced and structured by a domain of nonlinear mathematic phenomena, just as everywhere else. In regard, an application of theoretical aspects, as the Abstract notes, onto invasive pest and pathogen management for coffee growers results in advanced, beneficial results.

Whether an ecological community is controlled from above or below remains a popular framework and takes on especially important meaning in agroecosystems. We describe the regulation from above of three coffee herbivores, a leaf herbivore, a seed predator, and a plant pathogen by various natural enemies, emphasizing the remarkable complexity involved. We emphasize the intersection of classical ecology with the burgeoning field of complex systems with reference to chaos, critical transitions, hysteresis, basin or boundary collision, and spatial self-organization, all aimed at the applied question of pest control in the coffee agroecosystem. (Abstract excerpt)

Regulation of this herbivore is therefore effected through a complex system involving a Turing process, nonlinear indirect interactions, critical transitions, hysteresis, chaos, basin or boundary collisions, and a hypergraph, all elements of the burgeoning field of complex systems. (984)

Earth Life > Nest > Gaia

Payne, Jonathan, et al. The Evolution of Complex Life and the Stabilization of the Earth System. Interface Focus. June, 2020. For an issue on The Origin and Rise of Complex Life, Stanford, Tufts, Yale, and University of Hawaii biogeologists advance understandings of planetary bioregulations as they long proceeded to modify and tailor environmental conditions to organismic life’s advantage.

Earth's increasing habitability could result from: (i) a decrease in the intensity of interactions among species; (ii) a decrease in the prevalence or intensity of geological triggers; (iii) a decrease in the sensitivity of animals to environmental disturbance; or (iv) an increase in the strength of stabilizing feedbacks within the climate system and biogeochemical cycles. There is evidence from palaeontology, geochemistry and comparative physiology that animals have become more resilient to an environmental change and that the evolution of complex life has, on the whole, strengthened stabilizing feedbacks in the climate system. The differential success of certain phyla and classes appears to result from anatomical solutions to the evolution of macroscopic size that arrived during Ediacaran and Cambrian time. (Abstract excerpt)

Earth Life > Sentience > Brain Anatomy

De la Fuente, Ildefonso, et al. Evidence of Conditioned Behavior in Amoebae. Nature Communications. 10/369, 2009. Twelve Spanish systems biologists describe the clever ways by which to perceive the life’s associative learning method in effect even in these early, unicellular organisms.

Associative memory is the main type of learning by which complex organisms endowed with evolved nervous systems respond to environmental stimuli. It has been found in different multicellular species, from cephalopods to humans, but never in individual cells. Here we describe a motility pattern consistent with associative conditioned behavior in the microorganism Amoeba proteus. We confirm a similar behavior in a related species, Metamoeba leningradensis. Thus, our results indicate that unicellular organisms can modify their behavior during migration by associative conditioning. (Abstract)

Earth Life > Sentience > Brain Anatomy

Ng, Renny, et al. Neuronal Compartmentalization: A Means to Integrate Sensory Input at the Earliest Stage of Information Processing. BioEssays. July, 2020. UC San Diego neurobiologists graphically demonstrate how life’s developmental propensity to form functional modules persists from initial rudiments across the span of invertebrate and mammalian species. From the get-go, neural operations are performed by bounded cellular whole units.

In peripheral sense organs, external stimuli are detected by sensory neurons compartmentalized within structures of cuticular or epithelial tissue. Beyond developmental constraints, such compartmentalization allows grouped neurons to functionally interact. Here, we review the prevalence of these units, describe compartmentalized neurons, and consider interactions between cells. Particular attention is paid to insect olfaction with well‐characterized mechanisms of functional, cross‐neuronal interactions. (Abstract excerpt)

Earth Life > Sentience > Evolution Language

Prieur, Jacques, et al. The Origins of Gestures and Language. Biological Reviews. 95/3, 2020. Free University of Berlin and Normandie University paleolinguists advance understandings of the important role of early simian hand, eye and bodily motions as a form of rudimentary proto-language.

Investigating the deeper mechanisms of human and non‐human primate communication systems can shed light on the evolutionary roots of language. Reports on great apes suggest that gestures have been a crucial prerequisite for language. We review three processes that can explain this: phylogenetic ritualisation, ontogenetic ritualisation, and learning via social negotiation. Our scenario postulates that primates' communication is a complex trait shaped by a cost–benefit trade‐off of signal production in relation to four interlinked evolutionary and life cycle factors: species, individual and context‐related characteristics as well as behavioural characteristics. (Abstract excerpt)

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