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A Sourcebook for the Worldwide Discovery of a Creative Organic Universe
Table of Contents
Genesis Vision
Learning Planet
Organic Universe
Earth Life Emerge
Genesis Future
Recent Additions

Recent Additions: New and Updated Entries in the Past 60 Days
Displaying entries 31 through 45 of 86 found.

Systems Evolution: A 21st Century Genesis Synthesis

Quickening Evolution

Koonin, Eugene. CRISPR: A New Principle of Genome Engineering Linked to Conceptual Shifts in Evolutionary Biology. Biology & Philosophy. 34/9, 2019. The National Center for Biotechnology Information, Bethesda biotheorist and author writes an invited paper for a special issue to broadly appreciate these multi-faceted genetic advances and abilities. In so doing, it is broached that biomolecular mechanisms for actual Lamarckian epigenetic effects seem to be evident. After an introduction Philosophy of CRISPR-Cas by Thomas Pradeau, the edition adds commentaries such as by Eva Jablonka who leavens with a “quasi” Lamarckian model. Other entries cite its potential for easy palliative editing, the specter of Jean Baptiste is opposed by Ford Dollitle, Emily Parke, Sam Woolley, et al. A balanced view may be Sophie Veigl’s paper A Use/Disuse Paradigm.

The CRISPR-Cas systems of bacterial and archaeal adaptive immunity have become a household name among biologists and the general public by the unprecedented success of new generation of genome editing tools utilizing Cas proteins. However, the fundamental biological features of CRISPR-Cas are of no lesser interest and have major impacts on our understanding of the evolution of antivirus defense, host-parasite coevolution, self versus non-self discrimination and mechanisms of adaptation. CRISPR-Cas systems present the best known case in point for Lamarckian evolution, i.e. generation of heritable, adaptive genomic changes in response to encounters with external factors, in this case, foreign nucleic acids.

CRISPR-Cas systems employ multiple mechanisms of self versus non-self discrimination but, as is the case with immune systems, are costly because autoimmunity cannot be eliminated completely. Analysis of the evolutionary connections of Cas proteins reveals multiple contributions of mobile genetic elements (MGE) to the origin of various components of CRISPR-Cas systems, The shared features of adaptive defense systems and MGE, namely the ability to recognize and cleave unique sites in genomes, make them ideal candidates for genome editing and engineering tools. (Abridged Abstract)

Quickening Evolution > Biosemiotics

Witzany, Guenther. Communication as the Main Characteristic of Life. Vera Kolb, ed. . Handbook of Astrobiology, 2019. The Austrian philosopher (search) continues his emphasis that cross-information and sign-sharing amongst and across all manner of fauna and flora from life’s cellular advent is a vital, definitive characteristic. The medium is the message from chemical and electro-sensory modes to gestures and grunts on to our loquacious language. The chapter courses through fungi, plants, genomes, bacteria, eukaryotes, viruses, insects, while finally reaching we peoples. Within this subject book, this essence of an animate semiotic ecosmos is suggested as a good guide for astrobiological surveys going forward.

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

Earth Life > Nest > Geological

Lofta, Nastaran, et al. Centrality in Earthquake Multiplex Networks. Chaos. 28/063113, 2018. University of Zanjan, Iran and University of Sao Paulo physicists achieve a detailed global complex systems analysis of these spurious geological calamities. To reflect, out of this arduous planetary evolution and human history a collective, cumulative knowledge at last arises which then might be fed back to give better warnings, and maybe mitigate. What could its cosmic identity and purpose be?

Seismic time series has been mapped as a complex network, where a geographical region is divided into square cells that represent the nodes and connections are defined according to the sequence of earthquakes. In this paper, we map a seismic time series to a multiplex network, and characterize the evolution of the network structure in terms of the eigenvector centrality measure. We generalize previous works that considered the single layer representation of earthquake networks. Our results suggest that the multiplex representation captures better earthquake activity than methods based on single layer networks. We also verify that the regions with highest seismological activities in Iran and California can be identified from the network centrality analysis. The temporal modeling of seismic data provided here may open new possibilities for a better comprehension of the physics of earthquakes. (Abstract)

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 > 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 > 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 > DNA word

Searls, David. A Primer in Macromolecular Linguistics. Biopolymers. 99/3, 2013. The philosophical geneticist (bio below) has been a prescient observer (search) that nature’s dual domains of informational nucleotides and literary discourse are innately similar in kind. This entry describes via graphic, evidential visuals their parallel, self-similar essence. The import is that if the relation could move from metaphor to analogy to factual, both the genetics and linguistics endeavors could much benefit from cross-applications of methods and analytic techniques.

Polymeric macromolecules, when viewed abstractly as strings of symbols, can be treated in terms of formal language theory, providing a mathematical foundation for characterizing such strings both as collections and in terms of their individual structures. In addition this approach offers a framework for analysis of macromolecules by tools and conventions widely used in computational linguistics. This article introduces the ways that linguistics can be and has been applied to molecular biology, covering the relevant formal language theory at a relatively nontechnical level. Analogies between macromolecules and human natural language are used to provide intuitive insights into the relevance of grammars, parsing, and analysis of language complexity to biology. (Abstract)

David A. Searls received degrees in Philosophy and Life Sciences from MIT and a PhD in Biology from Johns Hopkins University. Following a postdoctoral fellowship at the Wistar Institute in Philadelphia he completed a Master's in Computer and Information Science at the University of Pennsylvania. He went on to co-found the Computational Biology and Informatics Laboratory at UP. He then spent 13 years at SmithKline Beecham and GlaxoSmithKline Pharmaceuticals, where he was Senior Vice-President of Bioinformatics. He left GSK in 2008 and is now an independent consultant.

Earth Life > Genetic Info > DNA word

Wu, Yanying and Quanlong Wang. A Categorical Compositional Distributional Modelling for the Language of Life. arXiv:1902.09303. Oxford University computer neuroscientists are able to treat and parse protein biology in a linguistic manner by use of this title computational insight achieved by the Oxford computer science group, search Bob Coecke. We log in amongst concurrent papers which establish this deep affinity between genetic and literary domains, broadly conceived, as a later evolutionary stage of one, same natural script.

The Categorical Compositional Distributional (DisCoCat) Model is a powerful mathematical method for composing the meaning of sentences in natural languages. Since we can think of biological sequences as the "language of life", here we apply this model to see if we can obtain new insights and a better understanding of life’s language. We choose to focus on proteins as their linguistic features are more prominent as compared with other macromolecules such as DNA or RNA. Thus, we treat each protein as a sentence and its constituent domains as words. The meaning of a word or the sentence is its biological function, and the arrangement of protein domains corresponds to the syntax. Putting all those into the DisCoCat frame, we can "compute" the function of a protein with grammar rules that combine them together. (Abstract excerpts)

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