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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 114 found.


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

Earth Life > Nest > Symbiotic

Shahbazi, Marta, et al. Self-Organization of Stem Cells into Embryos: A Window on Early Mammalian Development. Science. 364/948, 2019. It is vital to make note in this late year of how much a natural self-organizing process has become wholly accepted in cell biology, which was rarely considered just a decade ago. In a special section about Organoids, Cambridge University and Rockefeller University led by Magdalena Zernicka-Goetz present a visual articulation of how organisms come to form and flourish by virtue of this intrinsic formative method. Within this website, whenever could it be possible to imagine life’s whole evolutionary development as a self-organizing embryonic gestation? See also in this issue Organoids by Design by Takebe and Wells, second Abstract.

Embryonic development is orchestrated by robust and complex regulatory mechanisms acting at different scales of organization. In vivo studies are challenging for mammals after implantation, owing to the small size and inaccessibility of the embryo. The generation of stem cell models of the embryo represents a powerful system with which to dissect this complexity. Control of geometry, modulation of the physical environment, and priming with chemical signals reveal the intrinsic capacity of embryonic stem cells to make patterns. Here, we review the principles of self-organization and how they set cells in motion to create an embryo. (Shahbazi Abstract)

Organoids are multicellular structures that can be derived from adult organs or pluripotent stem cells. Early versions of organoids range from simple epithelial structures to complex, disorganized tissues with large cellular diversity. The current challenge is to engineer cellular complexity into organoids in a controlled manner that results in organized assembly and acquisition of tissue function. We discuss how the next generation of organoids can be designed by means of an engineering-based narrative design to control patterning, assembly, morphogenesis, growth, and function. (Takebe Abstract)

Earth Life > Nest > Multicellular

Duclos, Kevin, et al. Investigating the Evolution and Development of Biological Complexity under the Framework of Epigenetics. Evolution & Development. Online July, 2019. University of Calgary cell biologists contribute to this nonlinear revolution, while it goes on largely unawares, to reinterpret life’s gestation by way of innate, iterative, scalar topologies and source forces. Here the recent expansion of genomic activity to include influences beyond nucleotides, aka epigenetics broadly conceived, is applied as one more generative factor at work in evolutionary developments.

Biological complexity is a key component of evolvability, yet its study has been hampered by a focus on evolutionary trends of complexification and inconsistent definitions. Here, we demonstrate the utility of bringing complexity into the framework of epigenetics to better investigate its utility as a concept in evolutionary biology. We first analyze the existing metrics of complexity and explore its link with adaptation and developmental mechanisms. We then consider how epigenetics shapes developmental and evolutionary trajectories. We argue that epigenetics itself could have emerged from complexity because of a need to self‐regulate. Our goal is not to explain trends in biological complexity but to help develop and elucidate novel questions in the investigation of biological complexity and its evolution. (Abstract excerpt)

Earth Life > Nest > Multicellular

Grossnickle, David, et al. Untangling the Multiple Ecological Radiations of Early Mammals. Trends in Ecology and Evolution. Online June, 2019. DG and Gregory Wilson, University of Washington along with Stephanie Smith, Field Museum of Natural History, Chicago, provide an extensive illustrated survey of our latest collective reconstruction of how life’s myriad creaturely species evolved and emerged. We muse and wonder whatever phenomenal contribution are we homo to Anthropo sapiens here by achieving for a self-revealing and auto-creating ecosmos.

The ecological diversification of early mammals is a globally transformative event in Earth’s history, largely due to the Cretaceous Terrestrial Revolution mass extinction. A confounding issue is that it comprised nested radiations of mammalian subclades within the broader scope of their evolution. In the past 200 million years, various independent groups experienced large-scale radiations involving ecological diversification from ancestral lineages of small insectivores such as include Jurassic mammalia forms, Late Cretaceous metatherians, and Cenozoic placentals. Here, we review these speciations which reveal the nuanced complexity of early mammal evolution, the value of ecomorphological fossil data, and phylogenetic context in macroevolutionary studies. (Abstract)

Earth Life > Nest > Multicellular

Sogabe, Shunsuke, et al. Pluripotency and the Origin of Animal Multicellularity. Nature. 570/519, 2019. Nine University of Queensland biologists including Sandie and Bernard Degnan contribute to a revisionary understanding of how organisms got going on their evolutionary way. Instead of a single step via clumped unicells, ancestral ur-cells are seen to differentiate at various stages in a life cycle before actual multicellularity. This effect is conveyed by the term pluripotency for cellular material capable to developing into several forms such as stem cells. See a commentary on this work as Scientists Debate the Origin of Cell Types in the First Animals by Jordana Cepelewicz in Quanta Magazine (Online July 17, 2019).

A widely held but rarely tested hypothesis for the origin of animals is that they evolved from a unicellular ancestor that structurally resembled modern sponge choanocytes and choanoflagellates. Here we test this by comparing the transcriptomes, fates and behaviours of the three primary sponge cell types. Together, these analyses argue against homology of sponge choanocytes and choanoflagellates, and the view that the first multicellular animals were simple balls of cells with limited capacity to differentiate. Instead, our results are consistent with the first animal cell being able to transition between multiple states in a manner similar to modern transdifferentiating and stem cells. (Abstract excerpt)

Earth Life > Nest > Ecosystems

Chuang, John, et al. Homeorhesis and Ecological Succession Quantified in Synthetic Microbial Ecosystems. Proceedings of the National Academy of Sciences. 116/14852, 2019. Rockefeller University, NYC systems biologists provide a unique way to identify the presence of reliable mathematic patterns which underlie and shape seemingly contingent environmental changes. Bacteria colonies in a laboratory are found to be representative model of actual field phenomena, which also implies that the nonlinear forces are at invariant effect for any creaturely activities.

Many ecological processes are largely stochastic in nature. Nevertheless, the dynamics occurring in ecosystems following a major change, such as regrowth of a forest after a fire, often follow regular temporal patterns, a condition called ecological succession. We observed similar succession in simple microbial communities consisting of algae and ciliates colonizing a new environment and studied it by measuring many replicates over several days. Abundances, which were initially highly variable across replicates, rapidly converged to similar trajectories, a phenomenon called homeorhesis. (Significance)

Earth Life > Nest > Ecosystems

Pigolotti, Simone, et al. Stochastic Spatial Models in Ecology. Journal of Statistical Physics. 172/1, 2018. SP, Okinawa Institute of Science, Massimo Cencini and Consiglio Nazionale delle Ricerch, Rome, Daniel Molina, Basque Center for Applied Mathematics, and Miguel Munoz, University of Granada, Spain provide a good example of later 2010s (re)unifications across this widest span from lively physical substrates to active flora and fauna environments.

Ecosystems display a complex spatial organization. Ecologists have long tried to characterize them by looking at how different measures of biodiversity change across spatial scales. Ecological neutral theory has provided simple predictions accounting for general empirical patterns in communities of competing species. In this review, we emphasize the connection between spatial ecological models and the physics of non-equilibrium phase transitions and how concepts developed in statistical physics translate in population dynamics, and vice versa. We conclude by discussing models incorporating non-neutral effects in the form of spatial and temporal disorder, and analyze how their predictions deviate from those of purely neutral theories. (Abstract excerpt)

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 > Sentience > Animal Intelligence

Rowlands, Mark. Can Animals Be Persons? New York: Oxford University Press, 2019. The University of Miami philosopher provides a long argument that after decades of study, and common knowledge, our creaturely co-inhabitants of all kinds are indeed as integrally personal, aware, sensitive, communicative and social as our human selves.

Earth Life > Sentience > Animal Intelligence

Whiten, Andrew. Cultural Evolution in Animals. Annual Review of Ecology, Evolution, and Systematics. Volume, 2019. The University of St. Andrews social psychologist contends that recent field and laboratory studies quite indicate that contrary to past beliefs, all manner of Metazoan creaturely groupings do indeed possess what could be seen as relative culture-like qualities.

Earth Life > Sentience > Evolution Language

Chemla, Emmanuel, et al. Constraints on the Lexicons of Human Languages have Cognitive Roots Present in Baboons. Proceedings of the National Academy of Sciences. 116/14926, 2019. Four French linguists proceed to identify a relative “connectedness” between words or signs as the methodic quality by which a meaningful message can be perceived. By virtue of these broadly conceived associations, non-human simians can similarly be seen to form a relative lexical array. See also Assessing the Uniqueness of Language: Animal Grammatical Abilities by Carel ten Cate in the Psychonomic Bulletin & Review (24/91, 2017). In all, by our late vantage life’s long emergent evolution seems intent on gaining a linguistic, expressive capacity.

Universals in language are hard to come by, yet one candidate is that words across the lexicons of the world’s languages are, by and large, connected: When a word applies to two objects, it also applies to any objects “between” those two. A natural hypothesis is that the source of this regularity is a learning bias for connected patterns, a hypothesis supported by recent experimental studies. Is this learning bias typically human? Is it language related? We ask whether other animals show the same bias. We present an experiment that reveals that learning biases for connectedness are present in baboons, suggesting that the shape of the world’s languages (both content and logical words) has roots in general, nonlinguistic, cognitive biases. (Significance)

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 > 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.

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