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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 115 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 > Bicameral Brain

Gunturkun, Onur and Sebastian Ocklenburg. The Lateralized Brain: The Neuroscience and Evolution of Hemispheric Asymmetries. Cambridge, MA: Academic Press, 2017. Ruhr-University Bochum, Germany neuroscientists provide a latest survey of 21st century findings about a complementary neural faculty which graces every creature from ourselves all the way to rudimentary invertebrates. Chapters range from Brain Asymmetries: Two Millennia of Speculation, Research and Discoveries to The Role of the Corpus Callosum, Spatial Attention, Self Perception and the Right Hemisphere, and Sex Differences. See also Ontogenesis of Lateraliztion by the authors in Neuron. 94/2, 2017.

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

Boel, Gregory, et al. Omnipresent Maxwell’s Demons Orchestrate Information Management in Living Cells. Microbial Biotechnology. 12/2, 2019. French and Italian biologists including Antoine Danchin seek better explanations for life’s vital interactive conversations as organisms survive and evolve, which are in opposition to entropic losses. By this approach, a biological complementarity between cellular discrimination and recognition modes is glimpsed, along with allusions of a natural self-organization.

Synthetic biology advances require understandings of the critical functions that allow the construction and operation of a living cell. Besides coding for ubiquitous structures, minimal genomes encode a wealth of functions that dissipate energy. Analysis of these functions shows that they manage information under noisy conditions when discrimination of substrates is preferred over a recognition process. We show that such functions, including transporters and the ribosome constructors, behave as an informational agent theorized by (James Clerk) Maxwell, circa 1870, and well known as Maxwell's demon. Altogether these features form the minimal genome required to allow the construction of an autonomous cell and allow them to perform computations in an energy‐efficient way. (Abstract)

Earth Life > Genetic Info

Eastman, Peter and Vijay Pande. Predicting Gene Expression between Species with Neural Networks. arXiv:1907.03041. This study is a proof of concept that a neural network can predict gene expression levels in one species based on experimental data from a different species. We cite this entry by Stanford University bioengineers to report how geno-informatic phenomena can be treated with these the same cerebral dynamics found to well apply everywhere else. The second author is a leading, creative source in this endeavor, which is evident by his Pande Lab website at pande.stanford.edu. See also, e.g., Physical Machine Learning Outperforms “Human Learning” in Quantum Chemistry by Pande and Anton Sinitskiy at arXiv:1908.00971.

We train a neural network to predict human gene expression levels based on experimental data for rat cells. The network is trained with paired human/rat samples from the Open TG-GATES database, where paired samples were treated with the same compound at the same dose. When evaluated on a test set of held out compounds, the network successfully predicts human expression levels. On the majority of the test compounds, the list of differentially expressed genes determined from predicted expression levels agrees well with the list of differentially expressed genes determined from actual human experimental data. (Abstract)

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