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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 130 found.


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

Earth Life > Nest > Life Origin

Takeuchi, Nobuto, et al. The Origin of a Primordial Genome through Spontaneous Symmetry Breaking. Nature Communications. 8/250, 2017. Veteran theoretical and experimental biologists NT and Kunihiko Kaneko, University of Tokyo and Paulien Hogeweg, Utrecht University go on to perceive a whole genomic complementarity amongst replicative nucleotides in rudimentary bounded cells and autocatalytic processes. As the Abstract notes, an efficient self-organized critical poise between these dual functional stages is then becoming apparent.

The paper is included in an Early Earth Collection on this site which has Nucleoside and Nucleotide, Early Cells, and Early Earth Conditions segments. See, e.g., Considering Planetary Environments in Origin of Life Studies by Laura Barge, Life as a Guide to Prebiotic Nucleotide Synthesis by Stuart Harrison and Nick Lane, and Prebiotic Plausibility and Networks of Paradox-Resolving Independent Models by Stephen Benner.

The heredity of a cell is provided by a small number of non-catalytic templates. How did these genomes originate? We demonstrate the possibility that genome-like molecules arise from symmetry breaking between complementary strands of self-replicating molecules. Our model assumes a population of protocells, each containing a population of self-replicating catalytic molecules. The protocells evolve towards maximising the catalytic activities of the molecules to increase their growth rates. Conversely, the molecules evolve towards minimising their catalytic activities to increase their intracellular relative fitness.

These conflicting tendencies induce the symmetry breaking, whereby one strand of the molecules remains catalytic and increases its copy number (enzyme-like molecules), whereas the other becomes non-catalytic and decreases its copy number (genome-like molecules). This asymmetry increases the equilibrium cellular fitness by decreasing mutation pressure and increasing intracellular genetic drift. These results implicate conflicting multilevel evolution as a key cause of the origin of genetic complexity. (Abstract)

Earth Life > Nest > Symbiotic

Belcaid, Mahdi, et al. Symbiotic Organs Shaped by Distinct Modes of Genome Evolution in Cephalopods. Proceedings of the National Academy of Sciences. 116/3030, 2019. A premier twenty-two person team from the University of Hawall, Florida, Connecticut, Washington, MO, Vienna, Lyon, UC Santa Barbara and Berkeley, the Jackson Laboratory for Genomic Medicine, CT and Okinawa Institute of Science and Technology, including Margaret McFall-Ngai and Jamie Foster, provide deep evidence of how prevalent and important symbiotic assemblies are to evolutionary development and physiological anatomy. See also companion papers Squid Genomes in a Bacterial World by Thomas Bosch in PNAS (Online February 2019), Host-Microbe Coevolution by Paul O’brien, et al in mBio (10/1, 2019) and a commentary on this vital work New Squid Genome Shines Light on Symbiotic Evolution by Laura Poppick in Quanta Magazine for February 19, 2019.

Animal–microbe associations are critical drivers of evolutionary innovation, yet the origin of specialized symbiotic organs remains largely unexplored. We analyzed the genome of Euprymna scolopes, a model cephalopod, and observed large-scale genomic reorganizations compared with the ancestral bilaterian genome. We report distinct evolutionary signatures within the two symbiotic organs of E. scolopes, the light organ (LO) and the accessory nidamental gland (ANG). The LO evolved through subfunctionalization of genes expressed in the eye, indicating a deep evolutionary link between these organs. Alternatively, the ANG was enriched in novel, species-specific orphan genes suggesting these two tissues originated via different evolutionary strategies. These analyses represent the first genomic insights into the evolution of multiple symbiotic organs within a single animal host. (Significance)

Earth Life > Nest > Multicellular

Chen, Zhanqi, et al. Prolonged Milk Provisioning in a Jumping Spider. Science. 362/1052, 2018. In a paper which received popular notice, ten zoologists and botanists in China report for the first time that even insect species possess and this prime maternal attribute of vertebrate mammals. In regard, evolutionary life seems to hold to a common physiology, anatomy and behavioral repertoire which is then availed and repeated in creaturely kind.

Lactation is a mammalian attribute, and the few known nonmammal examples have distinctly different modalities. We document here milk provisioning in a jumping spider, which compares functionally and behaviorally to lactation in mammals. The spiderlings ingest nutritious milk droplets secreted from the mother’s epigastric furrow until the subadult stage. Maternal care, as for some long-lived vertebrates, continues after the offspring reach maturity. These findings demonstrate that mammal-like milk provisioning and parental care for sexually mature offspring have also evolved in invertebrates, encouraging a reevaluation of their occurrence across the animal kingdom, especially in invertebrates. (Abstract)

Earth Life > Nest > Societies

Kappeler, Peter, et al. Social Complexity: Patterns, Processes, and Evolution. Behavioral Ecology and Sociobiology. 73/1, 2019. PK, Leibniz Institute for Primatology, Gottingen, Tim Clutton-Brock, Cambridge University, Susanne Shultz, University of Manchester, and Dieter Lukas, MPI Evolutionary Anthropology introduce a Topical Collection with this title so to review and advance the field. See, e.g., A Framework of Studying social Complexity, Teaching and Curiosity as Drivers of Cumulative Cultural Evolution in the Hominin Lineage, and Kinship, Association and Social Complexity in Bats.

Animal and human societies exhibit extreme diversity in the size, composition and cohesion of their social units with regard to sex-specific reproductive skew, parental care, form and frequency of cooperation, and their competitive regime creating a wide array of complex societies. However, there is an ongoing debate about whether these are real, emergent properties of a society or only a framework for studying the diversity and evolution of societies. In this introduction, we identify three areas of current research that address the study of social complexity. First, previous studies have suffered from a lack of common concepts and shared definitions. Second, features such as intraspecific variation and interactions in social complexity have been overlooked. Third, comparative studies offer can explore biological causes and correlates but the identify the causal relationships are elusive. (Abstract edits)

Earth Life > Nest > Societies

Sasaki, Takao and Stephen Pratt. The Psychology of Superorganisms: Collective Decision Making by Insect Societies. Annual Review of Entomology. 63/259, 2018. An Oxford University zoologist and Arizona State University neurobiologist advance understandings of how such creaturely groupings can attain an overall cognitive faculty, which in turn serves their viable survival. We also cite because S. Pratt was an advisor to Paul Davies (ASU) for his 2019 book (search) about such common tendencies, aka The Logic of Life, of social communities to seek and reach a distributed intelligence, with allusions to our worldwide humanity.

Under the superorganism concept, insect societies are so tightly integrated that they possess features analogous to those of single organisms, including collective cognition. Here, we review research that uses psychological approaches to understand decision making by colonies. The application of neural models to collective choice shows basic similarities between how brains and colonies balance speed/accuracy trade-offs in decision making. Experimental analyses have explored collective rationality, cognitive capacity, and perceptual discrimination at both individual and colony levels. A major theme is the emergence of improved colony-level function from interactions among relatively less capable individuals. Collective learning is a nascent field for the further application of psychological methods to colonies. (Abstract)

Earth Life > Nest > Societies

Wright, Colin, et al. Collective Personalities: Present Knowledge and New Frontiers. Behavioral Ecology and Sociobiology. 73/3, 2019. Penn State, UC Santa Barbara, McMaster University, and Francois-Rabelais University, Tours, France behavioral biologists suffest a new realization about animal groupings of all kinds. In addition to cognitive qualities, communal personality traits can be observed as they interact with other groups.

Collective personalities refer to consistent, distinct behaviors between social groups. This phenomenon is a ubiquitous feature of social groups, as many lab and field studies to date have documented between-group differences in collective behavior, and reveal ongoing selection on these traits. Here, we summarize recent works conducted in the model systems of social spiders and eusocial insects. We used a trait-by-trait format to compare the results and trends obtained in these taxa on 10 aspects of collective personality: division of labor, foraging, exploration, boldness, defensive behavior, aggressiveness, decision-making, cognition, learning, and nest construction. We conclude that the recognition of actual communal personalities can improve understandings of all manner an animal groupings. (Abstract)

Earth Life > Nest > Ecosystems

Rocha, Juan, et al. Cascading Regime Shifts Within and Across Scales. Science. 362/1379, 2018. Stockholm Resilience Centre ecological scholars including Simon Levin provide a latest finesse of complex ecosystems as they interact and transition within local and planetary bioregions and climates. The work merited a review Seeing a Global Web of Connected Systems by Marten Scheffer and Egbert van Nes (362/1357), second quote.

The potential for regime shifts and critical transitions in ecological and Earth systems, particularly in a changing climate, has received considerable attention. However, the possibility of interactions between such shifts is poorly understood. Rocha et al. used network analysis to explore whether critical transitions in ecosystems can be coupled with each other, even when far apart (see the Perspective by Scheffer and van Nes). They report different types of potential cascading effects, including domino effects and hidden feedbacks, that can be prevalent in different systems. Such cascading effects can couple the dynamics of regime shifts in distant places, which suggests that the interactions between transitions should be borne in mind in future forecasts. (Rocha summary)

The Arab Spring, the invention of penicillin, and the recent mass bleaching of coral reefs are reminders that much of the change in nature and society happens in just a tiny portion of time. Understanding why and when such critical transitions happen remains notoriously difficult. In this issue, Rocha et al mine a database of shifts in social and ecological systems and conclude that about half of them may be causally linked on different scales. Their results highlight the importance of unraveling hidden connections in the web of ecological and social systems on which we depend. (Scheffer abstract)

Earth Life > Nest > Homo Sapiens

Buskes, Chris. The Encultured Primate: Thresholds and Transitions in Hominin Cultural Evolution. Philosophies. 4/1, 2019. With Keywords of Cultural evolution; cumulative culture; gene–culture coevolution; dual inheritance; universal Darwinism; and memetics, a Radboud University, Netherlands scholar extols the unique way that our homo sapience has achieved a collective knowledge capacity and external informed repertoire. If we might reflect on this retrospect vantage, it seems to strongly suggest the presence of a worldwise Earthcyclopedic accumulation, which a main surmise and aim of this site is to represent, document and display. See also How Humans Cooperate by R. Blanton and L. Fargher (2016, search) for another perception.

This article tries to shed light on the mystery of human culture. Human beings are the only extant species with cumulative, evolving cultures. Many animal species do have cultural traditions in the form of socially transmitted practices but they typically lack cumulative culture. Thanks to their accumulated knowledge and techniques our early ancestors were able to leave their cradle in Africa and swarm out across the planet, adjusting themselves to a whole range of new environments. In order to explain this mystery I won’t appeal to the major advances in human evolution like walking upright, crafting stone tools and controlling fire because that would be question begging. Instead I try to unearth the mechanisms that caused those evolutionary turning points to occur in the first place. It seems that unlike other animals, humans are predisposed to acquire, store and transmit cultural information in such ways that our cultures can genuinely evolve. (Abstract)

Earth Life > Nest > Homo Sapiens

Daems, Dries. On Complex Archaeologies: Conceptualizing Social Complexity and its Potential for Archaeology. Adaptive Behavior. Online February, 2019. A University of Leuven, Belgium anthropologist considers how this current mathematical approach is evident in and can help quantify early hominin groupings and their material cultures.

This article surveys a number of approaches in complex systems thinking and their relevance for applications in the field of archaeology. It focuses on the fundamental role of social interactions and information transmission as constituent elements for the development of organizational complexity on a community level. It is discussed how material surroundings – including architectural structures and objects – are used to shape and social interactions and practices. It is shown how complex structures develop through underlying mechanisms of change such as diversification, connectivity and standardization, and how these can be applied in archaeological case studies. (Abstract)

Earth Life > Sentience > Brain Anatomy

Smith-Ferguson, Jules and Madeleine Beekman. Who Needs a Brain? Slime Moulds, Behavioural Ecology and Minimal Cognition. Adaptive Behavior. Online January, 2019. University of Sydney neurobiologists contribute to current realizations that an evolutionary continuum is evident from invertebrate rudiments all the way to complex animals. For example, familiar “cognitive” behaviors are found in insects (bees can count) and even for prokaryote bacterial colonies. As our Evolutionary Intelligence section conveys, this rising, cumulative acumen seems quite traces a central track. See also Van Duijn, Marc. Phylogenetic Origins of Biological Cognition: Convergent Patterns in the Early Evolution of Learning by Marc van Duijn in Interface Focus (7/3, 2017) for a similar perception.

Although human decision making seems complex, there is evidence that many decisions are grounded in simple heuristics. Such heuristic models of decision making are widespread in nature. To understand how and why different forms of information processing evolve, it is insightful to study the minimal requirements for cognition. Here, we explore the minimally cognitive behaviour of the acellular slime mould, Physarum polycephalum, in order to discuss the ecological pressures that lead to the development of information processing mechanisms. By highlighting a few examples of common mechanisms, we conclude that all organisms contain the building blocks for more complex information processing. Returning the debate about cognition to the biological basics demystifies some of the confusion around the term ‘cognition’. (Abstract)

Earth Life > Sentience > Brain Anatomy

van Duijn, Marc. Phylogenetic Origins of Biological Cognition: Convergent Patterns in the Early Evolution of Learning. Interface Focus. 7/3, 2017. The University of Groningen paleoneurologist continues his reconstructive studies of how life gained sensory, information-based, cumulative abilities so as to survive and thrive. See also Principles of Minimal Cognition by van Duijin, et al in Adaptive Behavior (14/2, 2006) for a much cited prior entry, and Slime Moulds, Behavioural Ecology and Minimal Cognition by Jules Smith-Ferguson and Madeleine Beekman in Adaptive Behavior (January 2019). These findings and many others are filling in a embryonic gestation of cerebral capacities from life’s earliest advent to our collective abilities to learn all this.

Various forms of elementary learning have recently been discovered in organisms lacking a nervous system, such as protists, fungi and plants. This finding has fundamental implications for how we view the role of convergent evolution in biological cognition. In this article, I first review the evidence for basic forms of learning in aneural organisms, focusing particularly on habituation and classical conditioning. Next, I examine the possible role of convergent evolution regarding these basic learning abilities during the early evolution of nervous systems. This sets the stage for at least two major events relevant to convergent evolution that are central to biological cognition: (i) nervous systems evolved, perhaps more than once, because of strong selection pressures for sustaining sensorimotor strategies in increasingly larger multicellular organisms and (ii) associative learning was a subsequent adaptation that evolved multiple times within the neuralia. (Abstract excerpt)

Earth Life > Genetic Info

Zimmer, Carl. She Has Her Mother’s Laugh: The Powers, Perversions, and Potential of Heredity. New York: Dutton, 2018. We record this 650 page volume by the popular science writer and New York Times columnist because it covers every copious aspect of genetic phenomena via personal and social vignettes as this generative source continues to expand its influence.

Earth Life > Genetic Info

Zou, James, et al. A Primer on Deep Learning in Genomics. Nature Genetics. 51/1, 2019. Stanford University, Karolinska Institute, Sweden, and Scripps Translational Research Institute, CA genoinformaticians introduce how these neural net methods can apply to and serve genetic studies. See also A Guide to Deep Learning in Healthcare in Nature Medicine by Andre Esteva, et al (25/1, 2019).

Deep learning methods are a class of machine learning techniques capable of identifying highly complex patterns in large datasets. Here, we provide a perspective and primer on deep learning applications for genome analysis. We discuss successful applications in the fields of regulatory genomics, variant calling and pathogenicity scores. We include general guidance for how to effectively use deep learning methods as well as a practical guide to tools and resources. This primer is accompanied by an interactive online tutorial.

Earth Life > Genetic Info > Paleo/Cosmo

Allaga, Benoit, et al. Universality of the DNA Methylation Codes in Eucaryotes. Nature Scientific Reports. 9/173, 2019. Five University of Montpelli biogeneticists make a strong case to date that “epigenetic” aspects, much a work in progress, have a major part to play along with the nucleotide contribution. A graphic representation of 147 species from insects to us illustrates how often this methylation feature occurs across life’s evolutionary scale. See also Epigenetics: A Way to Bridge the Gap between Biological Fields by Antoine Nicoglou and Francesca Merlin in Studies in History and Philosophy of Biological and Biomedical Sciences (66/73, 2017).

Genetics and epigenetics are tightly linked heritable information classes. Question arises if epigenetics provides just a set of environment dependent instructions, or whether it is integral part of an inheritance system. We argued that in the latter case the epigenetic code should share the universality quality of the genetic code. We focused on DNA methylation. Since availability of DNA methylation data is biased towards model organisms we developed a method that uses kernel density estimations of CpG observed/expected ratios to infer DNA methylation types in any genome. Our analysis indicates that there are only four gene body methylation types. We conclude that the gene body DNA methylation codes have universality similar to the universality of the genetic code and should consequently be considered as part of the inheritance system. (Abstract excerpt)

DNA methylation is an epigenetic mechanism that occurs by the addition of a methyl (CH3) group to DNA, thereby often modifying the function of the genes and affecting gene expression. The most widely characterized DNA methylation process is the covalent addition of the methyl group at the 5-carbon of the cytosine ring resulting in 5-methylcytosine (5-mC), also informally known as the “fifth base” of DNA. These methyl groups project into the major groove of DNA and inhibit transcription. (whatisepigenetics.com)

Earth Life > Genetic Info > Paleo/Cosmo

Henn, Brenna and Lluis Quintana-Murci. The History, Geography and Adaptation of Human Genes: A Tribute to Luca Cavalli-Sforza. Current Opinion in Genetics & Development. 53/iii, 2018. An introduction to this special issue by a UC Davis anthropologist and a Pasteur Institute, Paris evolutionary geneticist about the lifetime contributions (1922-2018) of the University of Parma, Pavia and Stanford population geneticist, who first realized and pursued historic parallels between genomes and languages. Among the 26 entries, e.g., are Admixture and Adaptation in Human Evolution by Michael Dannemann and Fernando Racimo, Insights from Epigenetic Studies on Human Health by Connie Mulligan, Clarify Distince Models of Modern Human Origins in Africa by B. Henn, et al, and Fine-Tuning of Approximate Bayesian Computation for Human Population Genomics by Niall Cooke and Shigeki Nakagome.

This special issue on the Genetics of Human Origins is dedicated to Luigi Luca Cavalli-Sforza who passed away last August 2018. Luca — “please, call me Luca” he always said whoever he was talking to — was the grandfather of the field of human population genetics , and influenced many of the perspectives we review here in foundational ways. His interests in human prehistory cut across several disciplines, as he worked to compare patterns from linguistic, cultural and archaeological data with emerging protein polymorphism, mitochondrial and Y-chromosomal data. His cross-disciplinary thinking opened new avenues of research, including that of how cultural evolution may impact biological evolution: “If there's any interaction between genes and languages, it is often languages that influence genes, since linguistic differences between populations lessen the chance of genetic exchange between them”.

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