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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 31 through 45 of 49 found.


Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Zelditch, Miriam and Anjali Goswami. What Does Modularity Mean? Evolution and Development. August, 2021. We recall when Gunter Wagner’s 1996 paper was an initial notice of nature’s avail of diverse modules as a good way to form and bolster bodies and brains. Twenty five years later, University of Michigan and Natural History Museum, London paleontologists finesse and confirm its ubiquitous use and value. However then might it dawn that these now worldwide surveys have come upon a greater phenomenal genesis which in place on its preordained own?

Modularity is now recognized as a fundamental feature of organisms, with profound consequences for evolution. This natural propensity has become a major focus of research in organismal biology across disciplines including genetics, developmental biology, functional morphology, population and evolutionary biology. But the concept of modularity retains an ambiguity due to diverse definitions about what it means, Here we review various concepts, metrics and methods at different levels, and some other concerns. (Abstract excerpt)

Quickening Evolution > Biosemiotics

Lackova, Ludmila and Dan Faltynek. Can Quantitative Approaches Develop Bio/Semiotic Theory? Biosemiotics. August, 2021. The Palacky University, Olomouc, Czech Republic linguists (search) introduce a dedicated collection to consider better ways to appreciate and assimilate the vital presence of organic codes and communications across life’s animate scales. Among the entries are Application of N-Gram Based Distances to Genetic Texts Comparison by Valery Kirzhner and Zena Volkovich, and A Semiotic Modern Synthesis: Quantitative Studies in Zoosemiotics by Amelia Lewis.

This special issue addresses question about the place of quantitative methods in the field of biosemiotics. Many standpoints have been taken by contributing authors to demonstrate that the answer to this question is not straightforward. Considering quantitative methods in biosemiotics is necessarily related to inclusion of other scientific fields and interdisciplinary dialogue. (Abstract)

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

Earth Life > Common Code

Ribeiro, Tiago, et al. Scale-Free Dynamics in Animal Groups and Brain Networks. Frontiers in Systems Neuroscience. January, 2921. Into the 2020s, TR and Dietmar Plenz, NIH Critical Dynamics Group and Dante Chialvo, Universidad Nacional de San Martin, Argentina are able to perceive and delineate strong similarities between these disparate phases. An especial quality is the spontaneous presence of a self-organized criticalities in both active instances. Here then is an excellent instance of our Earthuman acumen just now attaining such a convergent synthesi of universal recurrence in kind.

The collective emergence of order in myriad interactive entities occurs over a vast range of physical and biological systems. Their key feature is an adaptive behavior beyond individual components. This article focuses on recent insights for two seemingly disparate phenomena: flocking in animal groups and neuronal ensembles in the brain. We report upon the spontaneous organization in bird flocks and whole human brain activity utilizing correlation functions and critical dynamics. Scale-free correlation functions capture the collective organization of neuronal avalanches in nonhuman primates and between neurons during visual processing in rodents. We conclude that at or near a phase-transition, neuronal information can propagate in the brain with similar efficiency to the collective adaptive response observed in some animal groups. (Abstract excerpt)

Earth Life > Nest > Microbial

Artiga, Marc. Bacterial Communication. Biology and Philosophy. 36/4, 2021. A University of Valencia, Spain natural philosopher advances our understandings about how this microbial phase persists by way of biosemiotic molecular cross-messaging. Aka quorum sensing, this active facility informs and sustains biofilm colonies within variable environs. With a copious bibliography in support, life’s prokaryotic stage is viewed an iconic exemplar a consistent recurrence in kind of cooperative qualities along with an emergent individuality, an episodic evolution thus courses to our Earthuman sapience which can lately proceed to reconstruct all this. Into the 2020s we peoples altogether be able to glimpse a grand phenomenal discovery and vista so to carry on forward?

Recent research on bacteria and other microorganisms has provided interesting insights into the nature of life, cooperation, evolution, individuality or species. In this paper, I focus on the capacity of bacteria to produce molecules that are usually classified as ’signals’ and I defend two claims. First, I argue that certain interactions between bacteria should actually qualify as genuine forms of communication. Second, I use this case study to revise our general theories of signaling. Among other things, I argue that a plausible requirement for a state to qualify as a signal is that it is a minimal cause. (Abstract)

Earth Life > Nest > Microbial

Roy, Anjan, et al.. A Unifying Autocatalytic Network-based Framework for Bacterial Growth Laws. Proceedings of the National Academy of Sciences. 118/33, 2021. Ben-Gurion University of the Negev and Abdus Salam International Center for Theoretical Physics, Trieste identify how such self-assembly processes are in common metabolic effect across the prokaryotic domains. See also Growth-laws and Invariants from Ribosome Biogenesis in Lower Eukarya by Sarah Kostinski and Shlomi Reuveni at arXiv:2008.11697.

In the clash between the physics-inspired strive for simple underlying laws of bacterial physiology and the biological hard-won understanding of the intricacies of life, we end in a middle ground. On one hand, we have found valid and simple growth laws. On the other hand, we demonstrated that the validity of a given growth law does not fully reveal the physiological state of the cell. Understanding how the cellular state is determined in response to internal and external cues, and how evolutionary stresses shaped different schemes for determining it, remains a formidable challenge. (10)

Earth Life > Nest > Symbiotic

Mitchison, Timothy and Christine Field. Self-Organization of Cellular Units. Annual Review of Cell and Developmental Biology. Volume 37/October, 2021. In this forthcoming volume, Harvard Medical School researchers illustrate the historic paradigm shift within biological science. At present a vested, mechanistic version via natural selection alone, sans any teleological aim, exists side by side with these worldwise perceptions due to this deeper, innate agency. This paper offers an expansive array of real, quantified, instances, see also Tom Misteli for a 21st century chronicle. It is an aim of Natural Genesis to help inform, clear up, untangle and facilitate this overdue resolve. The current conflation could be one reason that vaccines are so misunderstood.

The purpose of this review is to explore self-organizing mechanisms that pattern microtubules (MTs) and spatially organize animal cell cytoplasm. We start with conceptual distinctions between self-organizing and templating mechanisms for subcellular organization. We then discuss how self-organization generates radial MT arrays and cell centers such as autocatalytic MT nucleation. We end by discussing shared mechanisms and principles for the MT-based self-organization of cellular units. (Abstract excerpt)

Earth Life > Nest > Symbiotic

Vidiella, Blai, et al. Engineering Self-Organized Criticality in Living Cells. Nature Communications. 12/4415, 2021. Seven Barcelona system scientists including Ricard Sole identify and explain how cellular processes do, in fact, avail this optimum condition for their active viability. This novel appreciation is then carried forth as a way to better conceive new, beneficial biologic formations. And once again this leading edge paper goes on to note that this fittest resolve is likewise being found everywhere else so to prove a natural, one bigender code, universality.

Complex dynamical fluctuations, from intracellular noise, brain dynamics or computer traffic typically display bursting dynamics situated at a critical state between order and disorder. Living close to the critical point has adaptive advantages to an extent that it has been conjectured that life’s evolution could select for these critical states. In regard we consider the case of living cells to see if they reside in at a self-organized criticality (SOC) state. To do so we present an engineered gene network which actually displays SOC behavior, namely the proteolytic degradation of E. coli cells by means of a negative feedback loop that reduces congestion. Our critical motif is built from a two-gene circuit, where SOC can be successfully implemented. (Abstract excerpt)

Critical states are known to be part of the cognitive equipment of multicellular organisms from simple, non-neural placozoans to neural systems and animal collectives. The SOC motif might be an efficient way of generating phenotypic diversity in a microbial population and can be relevant to expand the space of synthetic biology computational designs into collective intelligence. Finally, given the analogies between our system and critical traffic in parallel computer networks, an extension of our approach could involve a 3D spatially explicit system and the development of statistical physics models of critical intracellular activity. (8)

Earth Life > Nest > Multicellular

Bernardes, Joana, et al. The Evolution of Convex Trade-off Enables the Transition Towards Multicellularity. Nature Communications. 12/4222, 2021. A six person team from MPI Evolutionary Biology, Alfred Wegener Institute, and University of Konstanz add further experimental quantifications of how life’s cellular phases proceeded to beneficially interact on the way to animal organisms.

The evolutionary transition towards multicellular life often involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. Theory predicts that germ soma differentiation is facilitated by a convex trade-off between survival and reproduction. However, this has never been tested and these transitions remain poorly understood. Here, we study the evolution of cell groups in ten isogenic lines of unicellular green algae with exposure to a rotifer predator. We confirm that growth in cell groups is heritable and characterized by a convex curve between reproduction and survival. Overall, we show that just 500 generations of predator selection were sufficient to lead to such a trade-off and incorporate evolved changes into the prey genome. (Abstract)

Earth Life > Nest > Ecosystems

Guimaraes, Paulo. The Structure of Ecological Networks across Levels of Organization. Annual Review of Ecology, Evolution and Systematics. 51/433, 2020. As a Universidade de São Paulo researcher provides a latest exposition of how nature’s interactive networks, as a heretofore overlooked feature, suffuse and serve to join, connect, inform and sustain living systems. As we have noted, here is another way that Darwin’s famous tangled bank can yet gain a consistent comprehension.

Interactions connect the units of ecological systems, by which to form networks. Individual-based networks characterize variation in niches within populations as they merge with each other to compose species-based networks and food webs in ecological communities. At spatiotemporal scales, networks portray the structure of ecological interactions across landscapes and over macroevolutionary time, which I review across multiple levels. By such studies, regularities in network structure are seen to emerge due to the fundamental architectural patterns shared by complex networks. (Abstract excerpt)

Earth Life > Sentience > Brain Anatomy

Godfrey-Smith, Peter. Metazoa: Animal Life and the Birth of the Mind. New York: Farrar, Straus and Giroux, 2021. The Australian naturalist (search), continues his project and mission, which involves scuba-diving amongst the creatures he writes about, to emphasize that Earth’s fauna and flora developmental emergence is defined by an advancing intelligent cognizance and proactive behavior from its earliest rudiments. Our interest is to report growing appreciations (Pam Lyons, et al) that life’s uniVerse to wumanVerse ascent can be seen as an oriented learning and knowledge gaining process.

Below the ocean’s surface are forms of life that seem quite foreign to our own: sea sponges, soft corals, and serpulid worms, whose rooted bodies, intricate geometry, and flower-like appendages are reminiscent of plant life. As fellow members of the animal kingdom – Metazoa - they can teach us much about the evolutionary origins of not only our bodies, but also our minds. As he delves into what it feels like to perceive and interact with the world as other life-forms do, Godfrey-Smith shows that the appearance of the animal body over half a billion years ago was a profound innovation that set life on its way to us. Following the evolutionary paths of a glass sponge, soft coral, banded shrimp, and octopus, then moving onto land and insects, birds, and primates, Metazoa bridges the gap between mind and matter, so as to reach aware consciousness. (Publisher excerpt)

Peter Godfrey-Smith is a professor in the School of History and Philosophy of Science at the University of Sydney. He is the author of the bestselling Other Minds: The Octopus, the Sea and The Deep Origins of Consciousness, which has been published in more than twenty languages.

Earth Life > Individuality

Molter, Daniel. On Mycorrhizal Individuality. Biology & Philosophy. 34/Art. 52, 2109. A Weber State University, Utah philosopher provides another take of life’s persistent formation of relative personal entities in communal settings at each and every chance.

This paper argues that a plant together with the symbiotic fungus attached to its roots, a mycorrhizal collective, is a true individual, and further, that this identity has important implications for evolutionary theory. Mycorrhizae in nature usually connect the roots of multiple plants, so their individuality entails overlapping entities. I suggest that the degree of evolutionary individuality in a symbiotic collective corresponds to its probability of reproducing with vertical or pseudo-vertical transmission, which could constitute a fourth parameter of graded Darwinian individuality in collective reproducers. (Abstract excerpt)

Our Earthuman Moment: A Major Evolutionary Transition in Individuality

wumanomics > Integral Persons > Complementary Brain

O'Reilly, Randall, et al. The Structure of Systematicity in the Brain. arXiv.2108.03387. UC Davis computational neuroscientists continue their cerebral project (search) to discern and express the presence of distinct neural faculties which act in a complementary manner as they make up and compose our on-going human thought processes. In this entry, their “What, Where and Why” modes have become dual “structure and content” phases so to represent object and frame aspects, along with the informative message they may contain and convey. See also Complementary Structure-Learning Neural Networks for Relational Reasoning by Jacob Russin, et al at arXiv:2105.0894.

Human intelligence is distinguished by an ability to adapt to new situations by way of applying learned rules to new content (systematicity) so as to enable an open-ended array of inferences and actions (generativity). Here, we propose that the human brain accomplishes this through pathways in the parietal cortex that encode the abstract structure of space, events, and tasks, and pathways in the temporal cortex that encode information about specific people, places, and things (content). Recent neural network models show how the separation of structure and content might emerge through an interplay of architectural biases and iterative learning. As a result these networks show facilitate an improved systematic, generative behavior. (Abstract excerpt)

There is a well-established distinction between spatial and object processing in the human brain, which can be reframed as one example of how the brain separates structure and content via distinct, but interacting pathways. Visual (and auditory) networks in the brain route sensory input into distinct dorsal and ventral stream pathways with the ventral visual pathway extending from early visual cortex to inferotemporal cortex characterized as the What pathway, specialized for object or scene recognition (i.e., visual content). The dorsal pathway through the parietal lobe is specialized for spatial Where processing, based on extensive evidence that this pathway represents spatial and relational information in a relatively content-independent manner (2-3)

wumanomics > Integral Persons > Complementary Brain

Singer, Wolf. Recurrent Dynamics in the Cerebral Cortex: Integration of Sensory Evidence with Stored Knowledge. Proceedings of the National Academy of Sciences. 118/33, 2021. Into the 2020s, the senior MPI Brain Research neuroscientist (search) provides a definitive (natural) exegesis of the presence of dual modes of active neural cognition. An on-going informative interplay is described between a person’s represented memory and new experiences so as to reach a viable, beneficial response. In this way, a balance and harmony can occur between one’s past familiarity and a variable external world. An accord then becomes possible of conserved values with novel occasions, rather than current politics where these conserve and create, regress or progress phases are locked in mortal combat. In August of this year, an incarnate complementarity thus achieves a strong scientific affirmation in our desperate midst. Here is the very EarthWise edification that so needs to gain a public veracity and avail in the time left.

Current concepts of sensory processing in the cerebral cortex emphasize serial extraction and recombination of features in hierarchically structured feed-forward networks in order to view the relations among the components of perceptual objects. These concepts are implemented in convolutional deep learning networks and have been validated by the astounding similarities between the functional properties of artificial systems and their natural counterparts. However, cortical architectures also display an abundance of recurrent coupling within and between the layers of the processing hierarchy. This massive recurrence gives rise to highly complex dynamics whose putative function is poorly understood. Here a concept is proposed that assigns specific functions to the dynamics of cortical networks and combines, in a unifying approach, the respective advantages of both recurrent and feed-forward processing. (Abstract excerpt)

Two Complementary Strategies for the Analysis and Encoding of Relations The virtually infinite variety of perceptual objects results from variable combinations of a relatively small set of elementary features, just like the 26 letters of the Latin alphabet suffice to compose western literature. Therefore, cognitive systems need effective strategies to identify these features and to encode the relations among them. (1)

Encoding of Relations in Feed-Forward Networks. One common strategy for the encoding of relations is based on the generation of conjunction-specific neurons in hierarchically structured feedforward networks. Neurons tuned to elementary features distribute their responses through divergent and convergent connections to neurons of the respective next layer. Dynamic Encoding of Relations in Recurrent Networks. A complementary strategy to capture relations among components relies on dynamic combinatorial codes, similar to those used by natural languages. (2)

Last but not least, there is a puzzling analogy with the processes that make quantum computing so fast and efficient. The superposition of wave functions bears similarities to the covert superposition of priors in the correlation structure of spontaneous activity, and the simultaneous and probabilistic evaluation of nested relations resembles the virtually simultaneous and holistic interaction between network nodes that represent, in a probabilistic and graded way, the presence of particular features. It would be truly fascinating if evolution had succeeded to realize, with classical mechanisms, those functions
that quantum computers are particularly good at: the parallel and therefore ultrafast evaluation of the relations between a huge number of probabilistic variables (9)

wumanomics > Integral Persons > Gender

Fitzgerald, Angela, ed. Women’s Lived Experiences of the Gender Gap: Gender Inequalities from Multiple Global Perspectives. International: Springer, 2021. A University of Southern Queensland (an appropriate name) science teacher trainer and social activist edits a vital edition in this critical life supportcondition year because half of the procreative ecomos remains in subserivence. Some chapters are Gender Parity in Political Representation, International Responses to Regretting Motherhood and A Comparative Study of Professional Women in Puebla and Barcelona. See also, for example, Controlling Women: What We must do to Save Reproductive Freedom by Kathryn Kolbert and Julie Kay (Hachette, 2021).

wumanomics > Phenomenon > Human Societies

Laland, Kevin and Amanda Seed. Understanding Human Cognitive Uniqueness. Annual Review of Psychology. 72/689, 2020. University of St. Andrews neuropsychologists (search KL) contribute to current quantifications that our human acumen arose as an embellished ramification of intelligent, psychological, behavioral and collective which can be traced back through life’s evolution to its earliest rudiments. A graphic image depicts this long episodic course as an emergent projection of the same basic entity/network structure. In respect, once again our main premise for this collaborative bibliographic resource is that a further enveloping episode is much underway to a prodigious global progeny.

Humanity has regarded itself as intellectually superior, yet special faculties, if any, remain poorly understood. Here, we evaluate candidate traits plausibly underlying our distinctive cognition (mental imagination, tool use, problem solving, sociality, and communication) and how these features may have evolved. We conclude that there are no traits present in humans which are absent in other animals that might explain our species’ cognitive performance. Rather, there are many cognitive domains in which humans have more capabilities then those found in other, earlier species. Humans are flexible cognitive all-arounders, whose proficiency arises through interactions and reinforcement between cognitive domains at multiple scales. (Abstract)

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