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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 76 through 90 of 118 found.


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

Earth Life > Nest > Ecosystems

Zhao, Li-Xia, et al. The Shaping Role of Self-Organization: Linking Vegetation Patterning, Plant Traits and Ecosystem Functioning. Proceedings of the Royal Society B. Vol.286/Iss.1900, 2019. When this section was first posted in the early 2000s, perceptions of self-organized natural complex dynamics were just beginning to dawn. A decade and a half later East China Normal University, Nanjing University, and Utrecht University ecologists contribute to recognitions of their broad scale, formative, beneficial presence. Notable factors in this achievement involve better (remote) sensing techniques, along with global research analysis and communications.

Self-organized spatial patterns are increasingly recognized for their contribution to ecosystem functioning, productivity, stability, and species diversity in terrestrial as well as marine ecosystems. Most studies of self-organization have focused on regular patterns. However, there is an abundance of patterns which are not strictly regular. Understanding of how they are formed and affect ecosystem function is crucial for the broad acceptance of self-organization in ecological theory. Field observations and experiments have revealed that self-organization involves a range of plant traits, including shoot-to-root ratio, rhizome orientation, node number and length, and enhances vegetation productivity. Moreover, patchiness in self-organized salt marshes can support a microhabitat for macrobenthos promoting a spatial heterogeneity of species richness. Our results extend existing concepts of self-organization and its effects on productivity and biodiversity to the spatial irregular patterns observed in many systems. (Abstract edits)

Earth Life > Nest > Homo Sapiens

Finlayson, Clive. The Smart Neanderthal: Cave Art, Bird Catching, and the Cognitive Revolution. Oxford: Oxford University Press, 2019. The British behavioral ecologist has been a director of archaeology excavations in Gibraltar. After many years of field studies, he seeks to correct the olden view of a brutish, dim-witted hominid. By virtue of these title abilities and much more, this Anthropo ancestral stage actually participated in and contributed to evolutionary stirrings of intellectual faculties and social cultures. OK

Earth Life > Nest > Homo Sapiens

Godsen, Chris and Lambros Malafouris. Process Archaeology. World Archaeology. 47/5, 2015. Oxford University archaeologists advocate moving beyond artifact relics to admit the equally real, important presence of creative groupwide activities as they aided survival and relative cultural advance. See also Homo faber Revisited: Material Engagement Theory by Don Ihde and Malafouris in Philosophy and Technology (32/195, 2019).

We advocate a Process Archaeology which explores modes of becoming rather than being. We advance three theoretical postulates we feel will be useful in understanding the process of becoming. And then six temporal propositions, with the latter arranged from the briefest to the longest timescale. We lay down the basic conceptual foundation of our approach using the example of pottery making and we follow the process of creativity in between the hand of the potter and the affordances of clay. This specific creative entanglement of flow and form on a fast bodily timescale provides our grounding metaphor for an archaeology of becoming over the long term. Subsequent propositions provide the basis for exploring issues of longer-term material engagement and change. (Abstract)

Earth Life > Nest > Gaia

Doolittle, W. Ford. Making Evolutionary Sense of Gaia. Trends in Ecology & Evolution. Online May, 2019. The veteran Dalhousie University biologist has long disavowed this hypothesis of a steady self-regulating biosphere. It just does not square with or be explained by standard Darwinian selection. However as this vital theory has steadily grown by way of robust study and application, the author offers a novel rationale, much to his credit, as to how this presence is indeed possible.

The Gaia hypothesis in a strong and frequently criticized form assumes that global homeostatic mechanisms have evolved by natural selection favoring the maintenance of conditions suitable for life. Traditional neoDarwinists hold this to be impossible in theory. But the hypothesis does make sense if one treats the clade that comprises the biological component of Gaia as an individual and allows differential persistence – as well as differential reproduction – to be an outcome of evolution by natural selection. Recent developments in theoretical and experimental evolutionary biology may justify both maneuvers. (Abstract)

Earth Life > Sentience > Evolution Language

Brown, Steven. A Joint Prosodic Origin of Language and Music. Frontiers in Psychology. October 30, 2017. A McMaster University, Canada psychologist and director of the NeuroArts Lab advances the view that creaturely and primate communications have a common gestural musilanguage origin. Akin to Ma, Weiyi, et al herein, this initial phase evolved into dual, complementary rhythmic and linguistic modes, broadly conceived. So once more every instance natural and social phenomena can be seen to take on dual connective flow and discrete detail archetypes. See Brown’s publication list on the NeuroArts site for other articles such as The Narration/Coordination Model (2019).

Vocal theories of the origin of language rarely make a case for the precursor functions that underlay the evolution of speech. The vocal expression of emotion is unquestionably the best candidate for such a precursor, although most evolutionary models of both language and speech ignore emotion and prosody altogether. I present here a model for a joint prosodic precursor of language and music in which ritualized group-level vocalizations served as the ancestral state. This precursor combined not only affective and intonational aspects of prosody, but also holistic and combinatorial mechanisms of phrase generation. From this common stage, there was a bifurcation to form language and music as separate, though homologous, specializations. (Abstract)

Earth Life > Sentience > Evolution Language

Frohlich, Marlen, et al. Multimodal Communication and Language Origins: Integrating Gestures and Vocalizations. Biological Reviews. Online June, 2019. As the Abstract notes, University of Zurich, Basel, and Geneva behavioral anthropologists including Carel van Schaik gather altogether many modes of signed contact between creatures from somatic to semiotic conveyance. Overall one gets a sense of life’s regnant evolution ever try to gain its expressive voice and vision.

The presence of independent research traditions in the gestural and vocal domains of primate communication has led to discrepancies in how cognitive concepts came to be. Recent evidence from behavioural and neurobiological research now implies that both human and primate communication is inherently multimodal. We review evidence that there is no clear difference between primate gestures and vocalizations for language intentionality, reference, iconicity and turn‐taking. We note that in great apes, gestures seem to fulfill an informative role in close communication, whereas the opposite holds for human interactions. This suggests an evolutionary transition in the carrying role from the gestural to the vocal stream. (Abstract edits)

Earth Life > Sentience > Evolution Language

Searcy, William. Animal Communication, Cognition, and the Evolution of Language. Animal Behavior. Online April, 2019. An editorial introduction to a special issue with this title. As scientific realizations form that all manner of creatures from primates and birds onto invertebrate insects. See for example Evolutionary Roads to Syntax (Klaus Zuberbuhler), Rules, Rhythm and Grouping: Pattern Perception by Birds, Communication in Social Insects, and Syntactic Rules in Avian Vocal Sequences and the Evolution of Compositionality (Suzuki herein).

Earth Life > Sentience > Evolution Language

Suzuki, Toshitaka, et al. Syntactic Rules in Avian Vocal Sequences as a Window into the Evolution of Compositionality. Animal Behavior. Online April, 2019. In a special issue on Cognition and Language, University of Tokyo, Zurich, and Uppsala neurolinguists consider how birds achieve meaningful content and communication from their rhythmic twitters. An overall message might be that life’s long evolutionary development has altogether been trying to compose itself unto our late sapience expression and hopefully, if we can come to our individual and collective senses, reprise and recognition.

Understanding the origins and evolution of language remains a deep challenge, because its complexity and expressive power are unparalleled in the animal world. One of the key features of language is that the meaning of an expression is determined both by the meanings of its constituent parts and the syntactic rules used to combine them; known as the principle of compositionality. Although compositionality has been considered unique to language, recent field studies suggest that compositionality may have also evolved in vocal combinations in nonhuman animals. Here, we discuss how compositionality can be explored in animal communication systems and review recent evidence that birds use an ordering
rule to generate compositional expressions composed of meaningful calls. (Abstract)

Earth Life > Genetic Info

Miranda-Dominguez, Oscar, et al. Heritability of the Human Connectome. Network Neuroscience. 2/2, 2018. In an issue on New Trends in Connectomics, Oregon Health and Science University and Emory University behavioral neuroscientists propose a familial “connectotype” akin to a bodily phenotype to likewise represent a person’s cerebral endowment. In a similar way, ancestral histories can then be traced.

Earth Life > Genetic Info

Nussimov, Ruth, et al. Protein Ensembles Link Genotype to Phenotype. PLoS Computational Biology. June, 2019. National Cancer Institute researchers contribute a latest insight into how genetic phenomena proceeds to actively inform and array into evolving organisms. Rather than a prior one gene to one trait, now mostly set aside, it is “ensembles” of biochemical generative guidance which are the pathway by which life forms and vivifies itself. See also The Energy Landscapes of Biomolecular Function by Nussimov and Peter Wolynes in Physical Chemistry Chemical Physics (16/6321, 2014) for a setup piece.

Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical studies aim to project phenotypic likelihoods from genotypic patterns. The traditional genotype-to-phenotype theory embraces the view that the encoded protein shape together with gene expression level largely determines the resulting phenotypic trait. Here, we point out that the molecular biology revolution at the turn of the century explained that the gene actually encodes ensembles of conformations. A dynamic ensemble view can better reveal the linkage between genetic change and observable physical or biochemical features. An ensemble view, rather than the genotype–phenotype paradigm, clarifies how even small genetic alterations can lead to pleiotropic traits in adaptive evolution and in disease, why cellular pathways can be modified in monogenic and polygenic traits, and how the environment may tweak protein function. (Abstract excerpts)

The terms genotype and phenotype have been in use at least since the turn of the last century. Genotype has been defined as the genetic makeup of an organism or of a specific characteristic. Phenotype has been construed as the composite of the organism’s observable characteristics or traits, such as morphology, development, biochemical, and physiological properties. Classically, the genotype of an organism has been described as the inherited genetic material coding for all processes in the organism’s life. (1)

Earth Life > Genetic Info > DNA word

Eetemadi, Ameen and Ilias Tagkopoulos. Genetic Neural Networks: An Artificial Neural Network Architecture for Capturing Gene Expression Relationships. Bioinformatics. 35/13, 2019. We cite this entry by UC Davis computer scientists to show how readily these popular analytic methods seem to find similar application everywhere, even in this case so as to parse life’s heredity. Could commonality infer that brains and genomes and all else are deeply cerebral, information bearing, relative aware in kind?

Results: We present the Genetic Neural Network (GNN), an artificial neural network for predicting genome-wide gene expression given gene knockouts and master regulator perturbations. In its core, the GNN maps existing gene regulatory information in its architecture and it uses cell nodes that have been specifically designed to capture the dependencies and non-linear dynamics that exist in gene networks. Our results argue that GNNs can become the architecture of choice when building predictors of gene expression from the growing corpus of genome-wide transcriptomics data.

Earth Life > Genetic Info > Genome CS

Rubenstein, Dustin, et al. Coevolution of Genome Architecture and Social Behavior. Trends in Ecology & Evolution. Online May, 2019. An eleven member international team including Hans Hofmann report the presence of a dynamic reciprocal relation between creaturely social activities and their malleable genetic composition.

Although social behavior can have a strong genetic component, it can also result in selection on genome structure and function, thereby influencing the evolution of the genome itself. Here we explore the bidirectional links between social behavior and genome architecture by considering variation in social and/or mating behavior among populations (social polymorphisms) and across closely related species. We propose that social behavior can influence genome architecture via demographic changes. We establish guidelines to exploit emerging whole-genome sequences using analytical ways to examine genome structure and function at different levels (regulatory vs. structural variation) from an ecological perspective of both molecular biology and population genetics. (Abstract)

Earth Life > Integral Persons > Somatic

Altan-Bonnet, Gregoire, et al. Quantitative Immunology for Physicists. arXiv:1907:03891. G A-B, National Cancer Institute, USA, with Thierry Mora and Aleksandra Walczak, Sorbonne University, Paris post a 78 page, 328 reference advanced synthesis of life’s immune systems by way of generic complex network dynamics. Thus in one more candidate realm, nature’s universal nonlinear self-viabilities are found to be similarly in effect. Search Albert Tauber for prior glimpses of this manifest exemplar.

The adaptive immune system is a dynamical, self-organized multiscale system that protects vertebrates from both pathogens and internal irregularities, such as tumours. For these reason it fascinates physicists, yet the multitude of different cells, molecules and sub-systems is often also petrifying. Despite this complexity, as experiments on different scales of the adaptive immune system become more quantitative, many physicists have made both theoretical and experimental contributions that help predict the behaviour of ensembles of cells and molecules that participate in an immune response. Here we review some recent contributions with an emphasis on quantitative questions and methodologies. We also provide a more general methods section that presents some of the wide array of theoretical tools used in the field. (Abstract)

Earth Life > Integral Persons > Somatic

Bonzanni, Mattia, et al. On the Generalization of Habituation. BioEssays. 41/7, 2019. With a Novel Model of Habituation that is Independent of any Biological System subtitle, Tufts University, Allen Discovery Center, biomedical engineers including Michael Levin offer notices and explanations of how an entity becomes accustomed to their daily environs is a common occurrence across nature and society. A commentary, Describing Atypical Instances of Intelligence by Fred Keijzer in the same issue, appreciates its content.

Habituation, a form of non‐associative learning, is no longer studied exclusively within psychology and neuroscience. Indeed, the same stimulus–response pattern has now been observed at the molecular, cellular, and organismal scales. Hence, a more inclusive theory is required to accommodate aneural forms. Here an abstraction of the habituation process that does not rely upon particular biological pathways or substrates is presented. Its formulation can be applied to interrogate systems as they respond to several stimulation paradigms, providing new insights and supporting existing behavioral data. The results suggest that habituation serves as a general biological strategy that any system can implement to adaptively respond to harmless, repetitive stimuli. (Abstract)

Earth Life > Integral Persons > Somatic

Dahmen, David, et al. Second Type of Criticality in the Brain Uncovers Rich Multiple-Neuron Dynamics. Proceedings of the National Academy of Sciences. 116/13051, 2019. Julich Research Center, Germany neuroresearchers at once confirm a cerebral tendency to settle at this optimum state, while teasing out another neural way that brains avail this productive balance.

Parallel recordings of motor cortex show weak pairwise correlations on average but a wide dispersion across cells. This observation runs counter to the prevailing notion that optimal information processing requires networks to operate at a critical point, entailing strong correlations. We here reconcile this apparent contradiction by showing that the observed structure of correlations is consistent with network models that operate close to a critical point of a different nature than previously considered: dynamics that is dominated by inhibition yet nearly unstable due to heterogeneous connectivity. Our findings provide a different perspective on criticality in neural systems: network topology and heterogeneity endow the brain with two complementary substrates for critical dynamics of largely different complexities. (Significance)

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