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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 120 found.


Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution > Intel Ev

Hasson, Uri, et al. Direct Fit to Nature: An Evolutionary Perspective on Biological and Artificial Neural Networks. Neuron. 105/3, 2020. In another example of cerebral cognition methods being readily applied everywhere, Princeton University neuroscientists point out how brain-based topologies and operations can have analytic utility in many other areas. Section headings include Interpolation and Extrapolation, Generalization Based on Partial and Big Data, and The Power of Adaptive Fit in Evolution. As the quotes allude, parallels can then be drawn between human cerebration and life’s neoDarwinian course whence organisms via sensory apparatus and activities must find a good enough way to survive and evolve. See also A Critique of Pure Learning and What Artificial Neural Networks can Learn from Animal Brains by Anthony Zador in Nature Communications (10/3770, 2019).

Evolution is a blind fitting process by which organisms become adapted to their environment. Does the brain use similar brute-force fitting processes to learn how to perceive and act upon the world? Recent advances in artificial neural networks have exposed the power of optimizing millions of synaptic weights over millions of observations to operate robustly in real-world contexts. These models do not learn simple, human-interpretable rules or representations of the world; rather, they use local computations to interpolate over task-relevant manifolds in a high-dimensional parameter space. Similar to evolutionary processes, over-parameterized models can be simple and parsimonious, as they provide a versatile, robust solution for learning a diverse set of functions. This new family of direct-fit models are a radical challenge to many of the theoretical assumptions in psychology and neuroscience. (Abstract)

Evolution Is an Iterative Optimization Process over Many Generations: Evolution by natural selection is a mindless optimization process by which organisms are adapted over many generations according to environmental constraints. This artistic rendition of the phylogenetic tree highlights how all living organisms on Earth can be traced back to the same ancestral organisms. Humans and other mammals descend from shrew-like mammals that lived 150 million years ago; mammals, birds, reptiles, amphibians, and fish share a common ancestor; and all plants and animals derive from bacteria-like microorganisms that originated more than 3 billion years ago. (Figure 3, evogeneao.com)

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

Earth Life > Common Code

Amgalan, Anar, et al. Unique Scales Preserve Self-Similar Integrate-and-Fire Functionality of Neuronal Clusters. arXiv:2002.10568. SUNY Stony Brook and UM Amherst computational neuroscientists including Hava Siegelmann post a strongest statement to date of the actual presence of a “functional scale-invariance or fractality” which spans its dynamic multiplex architecture. In regard, here is another current affirmation of a microcosmic instantiation of nature’s universal genetic complexities in our very own cerebral faculty.

Identifying the brain's neuronal cluster size as nodes in a network computation is critical to both neuroscience and artificial intelligence. Experiments support many forms and sizes of neural clustering, while neural mass models (NMM) assume scale-invariant functionality. Here, we use simulations within a fMRI network to show that a brains stay structurally self-similar continuously across scales. As such, we propose a coarse-graining of network of neurons to ensemble-nodes, with multiple spikes making up its ensemble-spike, and time re-scaling factor defining its ensemble-time step. The fractal-like spatiotemporal structure and function that emerges allows strategic choices across experimental scales for computational modeling, along with regulatory constraints on developmental and/or evolutionary "growth spurts" in brain size. (Abstract excerpt)

Earth Life > Common Code

Keil, Petr, et al. Macroecological and Macroevolutionary Patterns Emerge in the Universe of GNU/Linux Operating Systems. Ecography. 41/11, 2018. When we first posted this section in the early 2000s, any notice of environmental regularities was sparsely evident. In these later 2010s, eight European theoretical ecologists based at the German Centre for Intergrative Biodiversity Research, Leipzig not only aver their wide, constant presence, indeed an untangled bank, but go on to find a cross-affinity with computer software. A true universality across nature’s diversities is becoming patently apparent. See also Evolution in the Debian GNU/Linux Software Network: Analogies and Differences with Gene Regulatory Networks by Pablo Villegas, et al in the Journal of the Royal Society Interface (February 2020) which cites this paper.

What leads to classically recognized patterns of biodiversity remains an open question. Here, we employ analogies between GNU/Linux operating systems, and biodiversity. We demonstrate that patterns of the Linux universe generally match macroecological patterns. Moreover, the composition of functional traits (software packages) exhibits significant phylogenetic signal. The emergence of macroecological patterns across Linux suggests that the patterns are produced independently of the system identity, which points to the possibility of non‐biological drivers of fundamental biodiversity patterns. (Abstract excerpt)

To explain these patterns, we can invoke uniquely ecological and evolutionary processes: the patterns could be an outcome of assembly rules, natural selection, behavior, species interactions, or interplay between specific functional traits and environments. However, it has been demonstrated that some of the patterns are not unique to ecological and evolutionary systems, and often emerge in other complex systems. Examples are: species‐abundance distributions of music festival setlists, frequency distributions of components of software, latitudinal gradients of language diversity, species–area relationships in corporations, industrial codes, and minerals. However, structural constraints are not the only way that biological and non‐biological systems can resemble one another – similarity may also arise from analogous underlying processes. (2)

Earth Life > Common Code

Schwab, Julian, et al. Concepts in Boolean Network Modeling. Computational and Structural Biotechnology Journal. March, 2020. Ulm University system biochemists contribute some latest verifications of Stuart Kauffman’s first 1969 notice that living nature can be described by these mathematical topologies. The paper reviews their technical features and a few biological applications. In closing it notes that in contrast to a reductive focus, if in addition the presence of these real interconnective dynamics is allowed, then an integral model of life’s evolutionary animation can be achieved. The 140 references from this composite 21st century endeavor (search Villani, et al) well augurs for a 2020 discovery.

Boolean network models are one of the simplest models to study complex dynamic behavior in biological systems. They can be applied to unravel the mechanisms regulating the properties of the system or to identify promising intervention targets. Since its introduction by Stuart Kauffman in 1969 for describing gene regulatory networks, various biologically based networks and tools for their analysis were developed. Here, we summarize and explain the concepts for Boolean network modeling. We also present application examples and guidelines to work with and analyze Boolean network models. (Abstract)

Boolean networks are well-studied discrete models of biological networks such as gene regulatory networks where DNA segments in a cell interact with each other indirectly through their RNA and protein expression products or with other substances in the cell, thereby governing the rates at which genes in the network are transcribed into mRNA. (Google BN)

Earth Life > Common Code

Villegas, Pablo, et al. Evolution in the Debian GNU/Linux Software Network: Analogies and Differences with Gene Regulatory Networks. Journal of the Royal Society Interface. February, 2020. In this visionary, consummate year, University of Granada, Spain including Miguel Munoz (search) proceed to recognize many structural and operational parallels between these widely separate domains as they both engage in information processing and conveyance. Convergent comparisons such as this quite imply the reality of an independent mathematical program with a generic neural and genomic essence across all natural and social realms. See also Keil, Petr, et al. Macroecological and Macroevolutionary Patterns Emerge in the Universe of GNU/Linux Operating Systems by Petr Keil et al in Ecography (41/11, 2018).

Gene regulatory networks GRN as they process information in the cell display non-trivial architectural features such as scale-free degree distributions, high modularity and low average distance between connected genes. Such networks result from complex evolutionary and adaptive processes difficult to track empirically. On the other hand, the developmental (or evolutionary) stages of open-software networks that result from self-organized growth across versions are well known. Here, we study the evolution of the Debian GNU/Linux software network, focusing on changes of key structural and statistical features over time. Our results show that this has led to a structure in which the out-degree distribution is scale-free and the in-degree distribution is a stretched exponential. These features resemble closely those shown by GRNs, which suggests the existence of common adaptive pathways for the architectural design of information-processing networks. (Abstract)

Understanding the collective properties stemming from the interactions of a large number of units such as genes, proteins or metabolites is of paramount importance in biology. Theoretical work focusing on the changes over time of self-organizing networks can provide key information about these natural systems. Particularly, network theory provides us with a highly insightful systems-level perspective to extremely complicated biological problems, which has helped advance knowledge in fields such as neuroscience, ecology and epidemiology. The study of information processing in living systems has greatly benefited from this network perspective, complementing parallel endeavours for the analysis of single pathways, and providing a much richer understanding of collective phenomena emerging from a large number of basic inter-related units. (1)

Earth Life > Nest > Geological

Bonetti, Sara, et al. Channelization Cascade in Landscape Evolution. Proceedings of the National Academy of Sciences. 117/1375, 2020. ETH Zurich, Princeton and Polytechnic Institute of Torino systems geologists including Amilcare Porporato achieve another current proof that it is possible to verify the manifest, exemplary presence of a self-organizing, self-similar mathematics even across mountainous arête terrains.

We show that increasingly complex ridge and valley networks are produced by nonlinear partial differential equations as a minimalist landscape evolution model to describe the interplay between soil creep, runoff erosion, and tectonic uplift. We identify critical conditions for the transition from a smooth to a channelized topography and highlight striking similarities with fluid dynamic turbulence. The results shed light on the physical mechanisms responsible for the observed landscape self-organization. The formation of regular prefractal networks reveals a tendency to evolve toward optimal configurations typical of nonequilibrium complex systems. (Significance)

Sara Bonetti I am an ecohydrologist at ETH Zurich with a strong interest in the quantitative description of ecosystem functioning. My past and current research focuses on the analysis and modeling of i) vadose zone processes, ii) plant hydraulics, iii) landscape topography and evolution under natural and disturbed conditions, iv) vegetation pattern formation, and v) soil-plant atmosphere interactions.

Dr. (Amilcare) Porporato's research at Princeton University focuses on the quantitative description of the complex dynamics of the terrestrial water cycle. He uses both theoretical and experimental approaches to describe dynamical components of these physical and biological interactions. Because of an inherent interdisciplinarity, his research methods draw from fluid mechanics, soil physics, plant physiology, statistical physics, nonlinear dynamics, non-equilibrium thermodynamics, and complex system science.

Earth Life > Nest > Geological

Ma, Hongbo, et al. Universal Relation with Regime Transition for Sediment Transport in Fine-Grained Rivers. Proceedings of the National Academy of Sciences. 117/171, 2020. A thirteen member team of geoscientists from across China and the USA, with a global cast of names, uncover and quantify a common mathematical basis which underlie and guide such sediment flows and depositions across the world’s waterways. We also cite as more current proof that a natural genesis is graced by an independent generative source code across land, sea, air and space.

Fine-grained sediment transport systems (grain size under 2,000 μm) are ubiquitous over time and space on Earth and extraplanetary surfaces, and include rivers, deltaic coastal settings, and submarine, subglacial systems. Forecasting the evolution of Earth’s surface requires a predictive algorithm for sediment transport. Herein we provide a universal relation for sediment transport in fine-grained rivers. Surprisingly, it is shown that sediment flux differs by up to 2 orders of magnitude as grain size changes only slightly near the boundary between very fine sand and fine sand. The universal applicability of the sediment transport formulation enables quantitative understanding of the sedimentology and morphology of fine-grained rivers. (Significance)

Earth Life > Nest > Geological

Rak, Rafal, et al. Universal Features of Mountain Ridge Networks on Earth. Journal of Complex Networks. May, 2019. We cite this entry by Polish systems geophysicists including Jaroslaw Kwapien and Stanislaw Drozdz (search) as another instance of how every phenomenal aspect is being found to exhibit the generative presence of fractal, self-similar, multiplex topologies. These late 2010s abilities strongly imply and represent an independent mathematical source program which manifests at every scale and instance from quantum inflation to our deep bicameral brains.

In this paper, we analyse different mountain ranges by means of a network approach so to reveal grasp essential features of their branching structure. We employ a fractal method as especially good at describing properties of rough objects and surfaces. We study ridge network structure by way of empirical elevation data from the Shuttle Radar Topography Mission across mountain ranges from different geological periods and geographical locations. We observe that the topographic networks do display fractal scales of the mountain ranges and by another view show the power-law degree distributions. Since the various aretes differ in many properties, these values seem to be universal for Earthly mountainous terrains. (Abstract excerpt, edits)

Earth Life > Nest > Life Origin

Camprubi, Eloi, et al. The Emergence of Life. Space Science Reviews. 215/56, 2019. Eight researchers posted in the Netherlands, France, and the USA including Frances Westall and Michael Russell provide a comprehensive illustrated survey to date of both Earthly and astronomic environs such as watery moons, along with candidate RNA, geologic surface, first prokaryote and other aspects as they may have served to foster our late sentience and present reconstructive vista.

The aim of this article is to provide an overview of possible scenarios for the emergence of life, to critically assess them and to analyze whether similar processes could have been conducive to independent origins of life on the several icy moons of the Solar System. Instead of proposing an unequivocal cradle of life on Earth, we describe the different requirements that seem to be needed for the transition between non-life to life from geological, biological, and chemical perspectives in an integrative manner. Based on the conclusions extracted, we address whether the conditions for abiogenesis are/were met in any of the oceanic moons. (Abstract excerpt)

Earth Life > Nest > Life Origin

Preiner, Martina, et al. The Future of Origin of Life Research: Bridging Decades Old-Divisions. Life. 10/3, 2020. This is a conference summary by twenty five “early career” scientists as a unique retrospect of this field over its past decades, so that an integrative resolve going forward can be scoped out. The overview allows prior aspects such as prebiotic catalysis, thermal sea vents, mineral surfaces, first replicators, encapsulations, some 21 in all, to be gathered into a graphic display. A further issue has been a broad split between an RNA replicator or bounded metabolism preference, see Iris Fry 2011 herein. New synoptic pathways will involve better theories, common trends, and clever experiment. In this regard, this intentional project is a good example of an intentional shift to a coordinated, worldwide scientific pursuit.

Research on the origin of life is highly heterogeneous. After a peculiar historical development, it still includes strongly opposed views which potentially hinder progress. In the 1st Interdisciplinary Origin of Life Meeting, early-career researchers gathered to explore the commonalities between theories and approaches, critical divergence points, and expectations for the future. We find that even though classical approaches and theories—e.g. bottom-up and top-down, RNA world vs. metabolism-first—have been prevalent in origin of life research, they are ceasing to be mutually exclusive and they can and should feed integrating approaches. Here we focus on pressing questions and recent developments that bridge the classical disciplines and approaches, and highlight expectations for future endeavours in origin of life research. (Abstract)

Earth Life > Nest > Microbial

Schleper, Christa and Filipa Sousa. Meet the Relatives of Our Cellular Ancestor. Nature. 577/519, 2020. University of Vienna, Archaea Biology and Ecogenomics Group bioscientists cite a paper, Isolation of an Archaeon at the Prokaryote-Eukaryote Interface by Hiroyuki Imachi, et al in the same issue, as a significant quantification of how rudimentary microbal cells seem to have internal propensity (drive) to become nucleated cells on their long course to multicellularity.

Microorganisms related to lineages of the Asgard archaea group are thought to have evolved into complex eukaryotic cells. Now the first Asgard archaeal species to be grown in the laboratory reveals its metabolism and cell biology.

Earth Life > Nest > Symbiotic

Lim, Shen Jean and Seth Bordenstein. An Introduction to Phylosymbiosis. Proceedings of the Royal Society B. Vol. 287/Iss. 1922, 2020. Vanderbilt University biologists (search SB) describe and illustrate this new found way that life well avails the benefits of myriad microbe-host communities. The survey covers, for example, plant roots, insect guts, aquatic creatures, land animals such as rodents and primates, and more. See also A Bird’s Eye View of Phylosymbiosis by Brian Trevelline, et al in this journal, Issue 1923, which reports upon avian instances.

Phylosymbiosis was formulated to support a hypothesis-driven framework for the characterization of a cross-system trend in host-associated microbiomes. Defining phylosymbiosis as ‘microbial community relationships that recapitulate the phylogeny of their host’, we review its literature and data. Quantitative proof is provided by statistical methods evaluating higher microbiome variation between host species than within host species, and a positive association between host genetic relationships and microbiome beta diversity. Significant degrees of phylosymbiosis are prevalent in microbiomes of plants and animals from terrestrial and aquatic habitats. Its pervasiveness carries several important implications for advancing knowledge of eco-evolutionary processes that impact host–microbiome interactions and future applications of precision microbiology. (Abstract excerpt)

Earth Life > Nest > Symbiotic

Nalaban, Valeriu, et al. Quantifying Emergence and Self-Organization of Enterobacter cloacae Microbial Communities. Nature Scientific Reports. 8/12416, 2020. We cite this entry by University of Southern California bioengineers as an example of the late 2010s full scale admission of these innate title forces and forms as they serve to distinguish and pervade life’s oriented gestation.

From microbial communities to cancer cells, many complex collectives embody emergent and self-organising behaviour. As a result, cells develop composite features such as formation of aggregates or expression of specific genes due to cell-cell interactions. Currently, we lack a universal mathematics to analyze the collective behaviour of biological swarms. We propose a multifractal inspired framework to measure the degree of emergent self-organisation from scarce spatial data and apply it to evolution of the arrangement of Enterobacter cloacae aggregates. Our method could identify these patterns and dynamics changes within the bacterial population. (Abstract)

Earth Life > Nest > Symbiotic

Singharoy, Abhishek, et al. Atoms to Phenotypes: Molecular Design Principles of Cellular Energy Metabolism. Cell. 179/1098, 2019. At the culmination of the global 2010s, nineteen Arizona State University, Center for Applied Structural Discovery, molecular biologists present an illustrated report which proceeds to root life’s vesicular development phases deeply into a fertile physical substrate. In this expansive view, the scientific studies of cellular organisms which began decades, and centuries ago can now by way of detailed experiment, graphic display, and computational verity connect with a vital conducive ecosmos. From our late vantage, universe and human are rejoined as one and the same. As the quotes say, a further aspect is an advent and passage of a self-creative natural genesis to our collaborative, respectful, informed mitigation and continuance. A commentary herein is Dynamic Modeling of a 100 Million Atom Organelle at the Source of Life by Jean-David Rochaix (179/1012).

At the culmination of the global 2010s, nineteen Arizona State University, Center for Applied Structural Discovery, molecular biologists present an illustrated report which proceeds to root life’s vesicular development phases deeply into a fertile physical substrate. In this expansive view, the scientific studies of cellular organisms which began decades, and centuries ago can now by way of detailed experiment, graphic display, and computational verity connect with a vital conducive ecosmos. From our late vantage, universe and human are rejoined as one and the same. As the quotes say, a further aspect is an advent and passage of a self-creative natural genesis to our collaborative, respectful, informed mitigation and continuance. A commentary herein is Dynamic Modeling of a 100 Million Atom Organelle at the Source of Life by Jean-David Rochaix (179/1012).

Earth Life > Nest > Symbiotic

Sorensen, Megan, et al. Comparison of Independent Evolutionary Origins Reveals both Convergence and Divergence in the Metabolic Mechanisms of Symbiosis. Current Biology. 30/2, 2020. University of Sheffield, Exeter, and York biologists describe sophisticated experiments to elucidate the primary role played by nature’s tendency for all manner of cellular entities to join together in mutual benefit. Although difficult to recover because not readily evident, their procreative influence in life’s episodic emergence grows in importance. But in the article or references the life work of Lynn Margulis (1938-2011) as an advocate this vital feature, against much opposition, is not mentioned. A decade later one might imagine a second worldwide phase which at last confirms a universal symbiotic synthesis. See also a commentary Evolution: Convergent Pathways to Symbiosis by Levi Morran in the same issue.

Through the merger of previously independent lineages, symbiosis promotes the acquisition of new traits and exploitation of ecological niches, driving evolutionary innovation and vital ecosystem functions. In order to study this convergent process, independent we compared the metabolic mechanisms of two independent origins of Paramecium bursaria-Chlorella photosymbiosis using a reciprocal metabolomic pulse-chase method. This showed convergent patterns of nutrient exchange and utilization for host-derived nitrogen in the Chlorella genotypes and symbiont-derived carbon in the P. bursaria genotypes. Altogether our data suggests that the multiple origins of P. bursaria-Chlorella symbiosis use a convergent nutrient exchange. (Abstract excerpt)

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