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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 106 found.


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

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 > Life Origin

Benner, Steven, et al. When did Life Likely Emerge on Earth in an RNA-First Process?. arXiv:1908.11327. A ten person team from the Foundation for Applied Molecular Evolution, Florida (SB), UCLA, Tokyo Institute of Technology, Ludwig-Maximilians University, Munich, University of Colorado, University of South Florida and University of Rochester prepare a plausible scenario via recreations of an original biochemical and nucleotide milieu under Hadean geological to atmospheric environs some 4.6 to 4.0 billion years ago. Graphic visualizations illustrate our incredible global capability as the universe’s way of converting itself into consciously perceived description.

The widespread presence of ribonucleic acid catalysts and cofactors in Earth's biosphere today suggests that RNA was the first biopolymer to support Darwinian evolution. However, most "path-hypotheses" to generate RNA precursors require reduced nitrogen-containing compounds not made in useful amounts in the CO2-N2-H2O atmospheres of the Hadean. We review models for Earth's impact history that invoke a ~10^23 kg meteor to account for measured amounts of platinum, gold, and other siderophilic elements on the Earth and Moon. A sterilizing impactor would have reduced the atmosphere but not its mantle, opening a "window of opportunity" for RNA synthesis, a period with surface oxidized minerals that stabilize advanced RNA precursors and RNA. Surprisingly, this combination of physics, geology, and chemistry suggests a time when RNA formation was most probable, ~120 +/- 100 million years after a meteor, or ~4.36 +/- 0.1 billion years ago. (Abstract edits)

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

Bublitz, DeAnna, et al. Peptidoglycan Production by an Insect-Bacterial Mosaic. Cell. 179/1, 2019. We cite this entry by eleven Caltech, University of Montana, and University of Sheffield, UK scientists including John McCutcheon for its recognition of how much endosymbiotic structures and processes are in primary effect. A notice Cell Bacteria Mergers Offer Clues to How Organelles Evolved by Vivane Callier in Quanta Magazine (October 3, 2019) cites an import of this work.

Earth Life > Nest > Symbiotic

Gilbert, Scott. Evolutionary Transitions Revisited: Holobiont Evo-Devo. Journal of Experimental Zoology B. Online September 29, 2019. The Swarthmore College biologist and author contributes to this John Bonner issue, which altogether supports an inherent structural view of life’s oriented emergence from physical sources all the way to curious peoples. Gilbert is a prime advocate of this integrative realization that organisms and selves are actually communal entities by way of myriad microbes. See also Suarez & Trivino herein for a recent endorsement.

The Swarthmore College biologist and author contributes to this John Bonner issue, which altogether supports an inherent structural view of life’s oriented emergence from physical sources all the way to curious peoples. Gilbert is a prime advocate of this integrative realization that organisms and selves are actually communal entities by way of myriad microbes. See also Suarez & Trivino herein for a recent endorsement.

Earth Life > Nest > Symbiotic

Lloyd, Elisabeth and Michael Wade. Criteria for Holobionts from Community Genetics. Biological Theory. 14/3, 2019. We note this entry by a veteran Indiana University philosopher and biologist as a thorough, evenhanded review of this increasingly popular symbiotic concept of organisms from critters to sapiens. After some clarifications and caveats, by a proper understanding of life’s levels of selection, the holobiont model is a viable model of internal and external mutualisms.

Earth Life > Nest > Symbiotic

Suarez, Javier and Vanessa Trivino. A Metaphysical Approach to Holobiont Individuality. Quaderns de Filosofia. 6/1, 2019. In this journal of the Societat de Filosofia del País Valencià, this entry by University of Barcelona and University of Murcia philosophers opens with Life on Earth does not walk alone. It is becoming evident nowadays that individuals do not exist in isolation apart from each other and their ecological region. Rather everyone’s internal, and external milieu and identity are actually a symbiotic, interactive unity between me and We, small and large, so as to compose a viable US. In regard a tripartite universal, iconome principle is thus being revealed.

Holobionts are symbiotic assemblages composed by a host plus its microbiome. The status of holobionts as individuals has recently been a subject of continuous controversy, which has given rise to two main positions: on the one hand, holobiont advocates argue that holobionts are biological individuals; on the other, detractors argue that they are just chimeras or ecological communities. Both parties argue over what it takes for a “conglomerate” to be an individual from a biological point of view. This paper presents a meta-physical approach which draws on a conception of natural selection that supports the thesis that holobionts are units of selection which bear emergent traits and exert downward powers over the entities that compose them. In this vein, it is reasonable to conceive holobionts as emergent biological individuals. (Abstract excerpt)

Earth Life > Nest > Multicellular

Brunet, Thibaut and Nicole King. The Origin of Animal Multicellularity and Cell Differentiation. Developmental Cell. 43/2, 2017. By way of several graphic displays UC Berkeley biologists advance hyper-quantifications of life’s evolutionary to join simpler, diverse, reciprocal entities into viable, complex, holobiont organisms.

Over 600 million years ago, animals evolved from a unicellular or colonial organism whose cell(s) captured bacteria with a collar complex, a flagellum surrounded by a microvillar collar. Using principles from evolutionary cell biology, we reason that the transition to multicellularity required modification of pre-existing mechanisms for extracellular matrix synthesis and cytokinesis. We discuss two hypotheses for the origin of animal cell types: division of labor from ancient plurifunctional cells and conversion of temporally alternating phenotypes into spatially juxtaposed cell types. (Abstract)

Earth Life > Nest > Societies

Chen, Xiaowen, et al. Searching for Collective Behavior in a Small Brain. Physical Review. 99, 052418, 2019. Princeton University systems physicists including William Bialek travel to the minimum edge of life’s sensory cognizance and still find an inherent tendency form networks of beneficial coordinated action.

In large neuronal networks, it is believed that functions emerge through the collective behavior of many interconnected neurons. Recently, the development of techniques that allow recordings of calcium concentration from a large fraction of all neurons in Caenorhabditis elegans - a nematode with 302 neurons – leads us to ask if such emergence is universal, reaching down to even the smallest brains. Our various models exhibit signatures of collective behavior: the state of single cells can be predicted from the state of the rest of the network; the network, despite being sparse in a way similar to the structural connectome, distributes its response globally when locally perturbed; and the parameters that describe the real network are close to a critical surface in this family of models. (Abstract excerpt)

Earth Life > Nest > Societies

Gordon, Deborah. Measuring Collective Behavior: An Ecological Approach. Theory in Biosciences. Online September, 2019. For a special Quantifying Collectivity issue, the Stanford University bioecologist and expert ant colony student in the Arizona desert adds one more affirmation of life’s organic persistence to join into social groupings for their many benefits.

Collective behavior is ubiquitous throughout nature. Many systems from brains to ant colonies are regulated by interactions among the individual participants without central control. Interactions create feedback that produce the outcome, the behavior that we observe: Brains via neurons think and remember, ant colonies collect food or move nests, flocks of birds turn, human societies develop new forms of social organization. But the processes by which interactions produce outcomes are as diverse as the behavior itself. Just as convergent evolution has led to organs, such as the eye, that are similar in function but based on different physiological processes, so it has led to forms of collective behavior that appear similar but arise from different social processes. (Abstract)

Earth Life > Nest > Societies

Ling, Hangjian, et al. Costs and Benefits of Social Relationships in the Collective Motion of Bird Flocks. Nature Ecology & Evolution. 3/948, 2019. A six person team from Stanford University, University of Exeter and Simon Fraser University including Nicholas Ouellette contend that prior models underplay local, individual interactions between semi-autonomous group members, which in reality can be a major component of successful swarm patterns.

Earth Life > Nest > Homo Sapiens

Cepelewicz, Jordana. Fossil DNA Reveals New Twists in Modern Human Origins. Quanta Magazine. August 30, 2019. A science writer reports the latest retrospective findings and revisions as ancient genome sequencing expands its reach and depth. As the Bard would say, Oh, what a tangled species web we have woven. The work of Joshua Akey at Princeton, Adam Siepel at Cold Spring Harbor Laboratory, John Hawks at the University of Wisconsin, and others, with reference links, are drawn upon.

Earth Life > Nest > Homo Sapiens

Mounier, Aurelien and Marta Mirazon Lahr. Deciphering African Late Middle Pleistocene Hominin Diversity and the Origin of Our Species. Nature Communications. 10/3406, 2019. Leverhulme Centre for Human Evolutionary Studies, University of Cambridge anthropologists avail graphic computational morphings to better serve our Anthropocene reconstructions of the sapient beings whom altogether got us to this point. The work merited a New York Times review by Carl Zimmer. Scientists Find the Skull of Humanity’s Ancestor, on a Computer (Sept. 10, 2019).

The origin of Homo sapiens remains a matter of debate. Here we use a phylogenetic modelling method to predict possible morphologies of a last common ancestor of all modern humans, which we compare to LMP African fossils. Our results support a complex process for the evolution of H. sapiens, with the recognition of different, geographically localised, populations and lineages in Africa. Based on the available fossils, H. sapiens appears to have originated from the coalescence of South and, possibly, East-African source populations, while North-African fossils may represent a population which introgressed into Neandertals during the LMP. (Abstract excerpt)

Earth Life > Nest > Homo Sapiens

Overmann, Karenleigh and Frederick Coolidge, eds. Squeezing Minds from Stones: Cognitive Archaeology and the Evolution of the Human Mind. Oxford: Oxford University Press, 2019. This volume is a 40 year review of the title academic field which broadly studies, in addition to fossils, a recovery of hominin cerebral and communal experience. It was conceived by Thomas Wynn, now at the University of Colorado and a coauthor, from his idea that stone tools, carvings, along with markings, could serve this task, as it surely has. Among chapters, we note Homo Artifex by Dietrich Stout, Sticks, Stones, and the Origins of Sapience by Philip Bernard and The Origin of Cumulative Culture by Miriam Haidle. Working themes which run through are Robin Dunbar’s social brain, and niche construction via an extended evolutionary model. See especially In Three Minds by Cory Stade and Clive Gamble, reviewed herein.

Cognitive archaeology is a relatively new interdisciplinary science that uses cognitive and psychological models to explain archeological artifacts like stone tools, figurines, and art. Squeezing Minds From Stones is a collection of essays from early pioneers in the field, like archaeologists Thomas Wynn and Iain Davidson, and evolutionary primatologist William McGrew, to 'up and coming' newcomers like Shelby Putt, Ceri Shipton, Mark Moore, James Cole, Natalie Uomini, and Lana Ruck. Their essays address a wide variety of cognitive archaeology topics, including the value of experimental archaeology, primate archaeology, the intent of ancient tool makers, and how they may have lived and thought.

Earth Life > Nest > Homo Sapiens

Stade, Cory and Clive Gamble. In Three Minds: Extending Cognitive Archaeology with the Social Brain. Overmann, Karenleigh and Frederick Coolidge, eds. Squeezing Minds from Stones. Oxford: Oxford University Press, 2019. In this major volume reviewed herein, University of Southampton scholars (search CG) propose a triune cerebral emphasis of Rational, Experiential, and Relational functions. Altogether, they serve a materially based communal cognition (which might seen as left, right, and whole brain/mind phases). By another view, a member/group reciprocity, in some early ubuntu way, quite aids sustenance and survival.

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