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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
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Genesis Vision
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Organic Universe
Earth Life Emerge
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Recent Additions

Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 46 through 60 of 82 found.

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution > Systems Biology

Shubin, Neil. Gene Regulatory Networks and Network Models in Development and Evolution. Proceedings of the National Academy of Sciences. 114/Vol. 23, 2017. An introduction to this September 2015 Sackler Colloquium organized by Shubin in honor and memory of Eric Davidson (1937-2015), the CalTech biologist (search both) who since the early 2000s studied and advocated the genomic and evolutionary importance of active nucleotide connectivities. Among the papers are Causes and Evolutionary Consequences of Primordial Germ-cell Specification in Metazoans, Gene Regulation During Drosophila Eggshell Patterning, Applying Gene Regulatory Network Logic to the Evolution of Social Behavior (search Baran) and Assessing Regulatory Information in Developmental Gene Regulatory Networks by Eric Davidson and Isabelle Peter (abstract next). This “conceptual revolution” is now in full force as many more entries in the new section attest.

Gene regulatory networks (GRNs) provide a transformation function between the static genomic sequence and the spatial specifications operating development. We address regulatory information at different levels of network organization from single node to subcircuit to large-scale GRNs and how design features such as architecture, hierarchical organization, and cis-regulatory logic contribute to developmental functions. Using subcircuits from the sea urchin endomesoderm GRN, we evaluate by Boolean modeling and in silico perturbations the import of circuit features. Thus, we begin to see how regulatory information encoded at individual nodes is integrated at all levels of network organization to control developmental process. (IP & ED Abstract excerpt)

Quickening Evolution > Systems Biology

Stephanou, Angelique, et al. Systems Biology, Systems Medicine, Systems Pharmacology. Acta Biotheretica. 66/4, 2018. University of Grenoble, North Wales Cancer Centre, University of Paris and University of Warwick system physicians advise how a turn to an integral “omics” perspective can much inform and guide these palliative services.

Systems biology is today such a widespread discipline that it becomes difficult to propose a clear definition of what it really is. For some, it remains restricted to the genomic field. For many, it designates the integrated approach or the corpus of computational methods employed to handle the vast amount of biological or medical data and investigate the complexity of the living. Systems biology, with its subfields of medicine, pharmacology and others, aims at making sense of complex observations/experimental and clinical datasets to improve our understanding of diseases and their treatments without putting aside the context in which they appear and develop.. (Abstract)

Quickening Evolution > Systems Biology

Uller, Tobias, et al. Developmental Bias and Evolution: A Regulatory Network Perspective. Genetics. 209/4, 2017. Five senior biologists, TU Lund University, Armin Moczek Indiana University, Richard Watson University of Southampton, Paul Brakefield Cambridge University and Kevin Laland University of St. Andrews propose a way to evoke life’s “directionality” by a factoring in novel appreciations of gene regulatory networks. Organism phenotypes as characteristics of an organism due to interactions of its genotype with its environment can thus be influenced and guided by this integrative quality. A prime feature is the presence of “analogous structures” which repeat, rise and further trace a homologous continuity.

Phenotypic variation is generated by the processes of development, with some variants arising more readily than others - a phenomenon known as “developmental bias.” Developmental bias and natural selection have often been portrayed as alternative explanations but developmental bias can evolve through natural selection, and bias and selection jointly influence phenotypic evolution. Here we describe recent theory on regulatory networks that explains why the influence of genetic and environmental perturbation on phenotypes is typically not uniform, and may even be biased toward adaptive phenotypic variation. We show how bias produced by developmental processes constitutes an evolving property able to impose direction on adaptive evolution and influence patterns of taxonomic and phenotypic diversity. We argue that it is not sufficient to accommodate developmental bias into evolutionary theory merely as a constraint on adaptation. A regulatory network perspective on phenotypic evolution thus helps to integrate the generation of phenotypic variation with natural selection, leaving evolutionary biology better placed to explain how organisms adapt and diversify. (Abstract excerpt)

Quickening Evolution > Intel Ev

Khajehabdollahi, Sina and Olaf Witkowski. Critical Learning vs. Evolution. Ikegami, Takashi, et al, eds.. ALIFE 2018 Conference Proceedings. Cambridge: MIT Press, 2018. A select paper from this online volume (Ikegami) by University of Western Ontario and Earth-Life Science Institute, Tokyo biophysicists who seek better insights into life’s quickening sentience by way of inherent complexity principles. By current turns, these dynamic phenomena appear to be increasingly cerebral in kind and function. In an extension of this view, just as brains are found to prefer and reside in a critically poised optimum state, so it seems that so does evolutionary developmental emergence.

Criticality is thought to be crucial for complex systems to adapt, at the boundary between regimes with different dynamics, where the system may transition from one phase to another. Numerous systems, from sandpiles to gene regulatory networks, to swarms and human brains, seem to work towards preserving a precarious balance right at their critical point. Understanding criticality therefore seems strongly related to a broad, fundamental theory for the physics of life as it could be, which still lacks a clear description of how it can arise and maintain itself in complex systems. (Abstract excerpt)

Understanding the utility of criticality in artificial life systems is important for understanding how complexity can self-organize into predictable but adaptive systems. This project applied the methods of critical learning to a community of Ising-embodied organisms subject to evolutionary selection pressures in order to understand how criticality affects the behavior and genotypes of the organisms and how these changes in turn affect the fitness and adaptability of the community. (53)

Olaf Witkowski’s research tackles distributed intelligence in living systems and societies, employing the tools of artificial life, connectionist learning, and information theory, to reach a better understanding of the following triptych of complex phenomena: the emergence of information flows that led to the origins of life, the evolution of intelligence in the major evolutionary transitions, the expansion of communication and cooperation in the future of the bio- and technosphere. (OW website)

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

Earth Life > Common Code

Schack, Carolann, et al. Modularity is the Mother of Invention: A Review of Polymorphism in Bryozoans. Biological Reviews. Online November, 2018. Victoria University of Wellington, New Zealand biologists post a 35 page study of how pervasive nature’s evolutionary and biological employ of semi-autonomous modular units within larger assemblies such as bodies and brains actually is. Some two decades after their initial view by Gunter Wagner and others, this efficient structural composition, famously noted by Herbert Simon (search) in the 1960s, can now be well affirmed across the Metazoan lineages.

Modularity is a fundamental concept in biology. Most taxa within the colonial invertebrate phylum Bryozoa have achieved division of labour through the development of specialized modules (polymorphs), and this group is well exemplifies this phenomenon. We provide a comprehensive description of the diversity, morphology and function of these polymorphs and the significance of modularity to the evolutionary success of the phylum, which has >21000 described fossil and living species. Modular diversity likely arose from heterogeneous microenvironmental conditions, and repeated module clusters are an emergent property of zooid plasticity. (Abstract excerpt)

Earth Life > Nest > Geological

Biswas, Soumyajyoti, et al. Statistical Physics of Fracture and Earthquakes. Philosophical Transactions of the Royal Society A. Vol.377/Iss.2136, 2018. An introduction to an issue with this title which is a good example, for this section and throughout, how the presence and study of complex network systems has now expanded to and gained theoretical roots in this substantial domain. See also, for example, New Trends in Statistical Physics of Complex Systems by Antonio Scarfone in Entropy (20/12, 2018).

Manifestations of emergent properties in stressed disordered materials are often the result of an interplay between strong perturbations in the stress field around defects. The collective response of a long-ranged correlated multi-component system is an ideal playing field for statistical physics. Hence, many aspects of such collective responses in widely spread length and energy scales can be addressed by the tools of statistical physics. In this theme issue, some of these aspects are treated from various angles of experiments, simulations and analytical methods, and connected together by their common base of complex-system dynamics. (Abstract)

Earth Life > Nest > Geological

Bui, Dieu Tien, et al. Novel Hybrid Evolutionary Algorithms for Spatial Prediction of Floods. Nature Scientific Reports. 8/15364, 2018. An eleven member team from Vietnam, Iran, the USA, China and Malaysia achieve a sophisticated analysis of interrelated geo-hydro landscape and river dynamics. After proving its veracity, the mathematical method is offered as a way to predict and mitigate future catastrophic events. We also cite as a 2010s global collaboration, via a common scientific language across locales beset by historic strife. On this website, we again ask Whom is this nascent personsphere still unknown to us? However might we altogether be able to appreciate and learn?

Adaptive neuro-fuzzy inference system (ANFIS) includes two novel GIS-based ensemble artificial intelligence approaches called imperialistic competitive algorithm (ICA) and firefly algorithm (FA). This combination could result in ANFIS-ICA and ANFIS-FA models, which were applied to flood spatial modelling and its mapping in the Haraz watershed in Northern Province of Mazandaran, Iran. Ten influential factors including slope angle, elevation, stream power index (SPI), curvature, topographic wetness index (TWI), lithology, rainfall, land use, stream density, and the distance to river were selected for flood modelling. The validity of the models was assessed using statistical error-indices, statistical tests, and the area under the curve of success. The results confirmed the goodness of fit and appropriate prediction accuracy of the two ensemble models. (Abstract)

Earth Life > Nest > Life Origin

Bray, Marcus, et al. Multiple Prebiotic Metals Mediate Translation. Proceedings of the National Academy of Sciences. Online November 9, 2018. By way of a “bioinorganic chemistry” which studies the role of metals in biology, Georgia Tech biochemists including Nicholas Hud and Jennifer Glass explain the importance of ferrous elements during life’s animating origin and early evolution.

Ribosomes are found in every living organism, where they are responsible for the translation of messenger RNA into protein. The ribosome’s centrality to cell function is underscored by its evolutionary conservation; the core structure has changed little since its inception ∼4 billion years ago when ecosystems were anoxic and metal-rich. The ribosome is a model system for the study of bioinorganic chemistry, owing to the many highly coordinated divalent metal cations that are essential to its function. We studied the structure, function, and cation content of the ribosome under early Earth conditions. Our results expand the roles of Fe2+ and Mn2+ in ancient and extant biochemistry as cofactors for ribosomal structure and function. (Abstract)

Earth Life > Nest > Life Origin

Menor-Salvan, Cesar. ed. Prebiotic Chemistry and Chemical Evolution of Nucleic Acids. International: Springer, 2018. A Universidad de Alcala, Spain astrobiologist assembles ten authoritative chapters which provide strong evidence for an innate natural occasion and forward progress of living, evolving complex entities. We note Mineral-Organic Interactions in Prebiotic Synthesis by Stephen Benner, et al, Nucleobases on the Primitive Earth by James Cleaves, and Self-Assembly Hypothesis for the Origin of Proto-RNA by Brian Cafferty, et al. Of especial import is Network Theory in Prebiotic Evolution by Sara Imari Walker and Cole Mathis which is reviewed below for its inclusion of this essential feature.

Chemical evolution encompasses the processes and interactions conducive to self-assembly and supramolecular organization, leading to an increase of complexity and the emergence of life. The book starts with the pioneering work of Stanley Miller and Jeffrey Bada on the Chemistry of Origins of Life and how the development of organic chemistry beginning in the 19th century led to the emergence of the field of prebiotic chemistry, situated between organic, geo- and biochemistry. It continues with current central topics regarding the organization of nucleic acids: the origin of nucleobases and nucleosides, their phosphorylation and polymerization and ultimately, their self-assembly and supramolecular organization at the inception of life. (Publisher)

Earth Life > Nest > Life Origin

Nowak, Martin and Hisashi Ohtsuki. Prevolutionary Dynamics and the Origin of Evolution. Proceedings of the National Academy of Sciences. 105/14924, 2008. We enter a paper by Harvard biologists referenced in Walker and Mathis 2018 as an example of how a much decade of global collaboration can advance scientific studies from patchy rudiments to a robust integral finding.

Life is that which replicates and evolves. A fundamental question is when do chemical kinetics become evolutionary dynamics? Here we formulate a general mathematical theory for the origin of evolution. All known life on earth is based on biological polymers, which act as information carriers and catalysts. We describe prelife as an alphabet of active monomers that form random polymers. Prelife is a generative system that can produce information. Prevolutionary dynamics have selection and mutation, but no replication. Life marches in with the ability of replication as polymers act as templates for their own reproduction. Prelife is a scaffold that builds life. (Abstract)

Earth Life > Nest > Life Origin

Walker, Sara Imari and Cole Mathis. Network Theory in Prebiotic Evolution. Menor-Salvan, Cesar, ed. Prebiotic Chemistry and Chemical Evolution of Nucleic Acids. International: Springer, 2018. In a final chapter, Arizona State University astrobiology theorists expand the theoretical basis of this aboriginal advent with an intrinsic interconnective quality that joins discrete biochemicals and nucleotides into a whole dynamic living system. These node/link lineaments are also seen to foster and carry generative information. As many other fields, the “universal properties” of multiplex nets provides a formative physiology as a natural fertile materiality came to life and evolution. A further section extends the composite system onto Planetary Biospheres by way of a “network theory of biogeochemistry.”

A most challenging aspect of origins of life research is that we do not know precisely what life is. In recent years, the use of network theory has revolutionized our understanding of living systems by permitting a mathematical framework for understanding life as an emergent, collective property of many interacting entities. So far, complex systems science has seen little direct application to the origins of life, particularly in laboratory science. Yet, networks are important mathematical descriptors where the structure of interactions matters more than individual component parts – which is what we envision happens as matter transitions to life. We review notable examples of the use of network theory in prebiotic evolution, and discuss the promise of systems approaches to life’s origin. Our end goal is to develop a statistical mechanics that deals with interactions of system components (rather than parts alone) and is thus equipped to model life as an emergent phenomena. (Abstract)

Earth Life > Nest > Microbial

Allen, Rosalind and Bartlomiej Waclaw. Bacterial Growth: A Statistical Physicist’s Guide. Reports on Progress in Physics. 82/1, 2018. University of Edinburgh researchers post a joint tutorial for microbiologists and physicists so as to illustrate new findings of persistent cross-affinities such as modularity and self-propelled activity.

Bacterial growth presents many beautiful phenomena that pose new theoretical challenges to statistical physicists, and are also amenable to laboratory experimentation. This review provides some of the essential biological background, discusses recent applications of statistical physics in this field, and highlights the potential for future research. (Abstract) In this review we argue that the dynamics of growing bacterial populations provides another class of systems to which the methods of statistical physics can naturally be applied. To briefly illustrate this, we notice that the above example of the growth of an antibiotic resistant infection involves stochastic phenomena on scale ranging from macroscopic to molecular. (1)

Earth Life > Nest > Microbial

Marlow, Jeffrey and Rogier Braakman. Team Players. Scientific American. November, 2018. Harvard and MIT biologists present a popular, graphic article about how prevalent and important reciprocal cooperation is beyond a prior emphasis on competition among isolate microbes.

Earth Life > Nest > Multicellular

Cooper, Rory, et al. An Ancient Turing-like Patterning Mechanism Regulates Skin Denticle Development in Sharks. Science Advances. 4/11, 2018. We cite this paper by University of Sheffield, Oxford and Florida biologists as another current finding that natural evolution seems to avail an independent mathematical source code which then appears in exemplary, recurrent effect across the anatomy and physiology of Metazoan creaturely kingdoms.

Vertebrates have a vast array of epithelial appendages, including scales, feathers, and hair. The developmental patterning of these diverse structures can be theoretically explained by Alan Turing’s reaction-diffusion system. However, the role of this system in epithelial appendage patterning of early diverging lineages such as the cartilaginous fishes is poorly understood.. We demonstrate through simulation models that a Turing-like mechanism can explain shark denticle patterning. This mechanism bears remarkable similarity to avian feather patterning, suggesting deep homology of the system. We propose that a diverse range of vertebrate appendages, from shark denticles to avian feathers and mammalian hair, use this ancient and conserved system. (Abstract)

Earth Life > Nest > Multicellular

Fernandez-Valverde, Selene, et al. Inference of Developmental Gene Regulatory Networks Beyond Classical Systems: New Approaches in the Post-genomic Era. Integrative and Comparative Biology. 58/4, 2018. The entry by research biologists from Mexico and Chile within a Genomic, Ecological and Paleontological Insights into the Early Evolution of Animals section is a good example, after decades of isolate gene studies, of realizations that equally active interlinkages are a major complementary factor. (Once again the particulate elements need be found first before connected altogether.) For concurrent views see The Vertebrate Limb: An Evolving Complex of Self-Organizing Systems by Stuart Newman, et al below and Monostability, Bistability, Periodicity and Chaos in Gene Regulatory Networks (search Qiang Lai in GCS). We also note The Molecular Quest for the Origin of the Animal Kingdom by Jordi Paps and Oxygen and the Energetic Requirements of the First Multicellular Animals by Sally Leys and Amanda Kahn.

The advent of high-throughput sequencing technologies has revolutionized the way we understand the transformation of genetic information into morphological traits. Elucidating the network of interactions between genes that govern cell differentiation through development is one of the core challenges in genome research. These networks are known as developmental gene regulatory networks (dGRNs) and consist largely of the functional linkage between developmental control genes, cis-regulatory modules, and differentiation genes. Much progress has been made in determining these gene interactions mainly in classical model systems, including human, mouse, sea urchin, fruit fly, and worm. Here, we give a historical overview on the architecture and elucidation of the dGRNs and summarize approaches to unravel them, highlighting the range of possibilities of integrating multiple technical advances. Such new knowledge will not only lead to greater insights into the evolution of molecular mechanisms underlying cell identity and animal body plans, but also into the evolution of morphological key innovations in animals. (Abstract excerpts)

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