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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 106 through 120 of 130 found.


Pedia Sapiens: A Genesis Future on Earth and in the Heavens

Future > New Earth > second genesis

Biondi, Elisa and Steven Benner. Artificially Expanded Genetic Information Systems for New Aptamer Technologies. Biomedicines. 6/2, 2018. It is now known that life’s four letter G A T C code, while universally in effect and enough to get us here, is an arbitrary sufficiency. In this MDPI online journal, in an Engineering Aptamers for Biomedical Applications issue, Foundation for Applied Molecular Evolution, Florida bioresearchers (search SB) consider ways to read, expand, enhance and begin to rewrite anew. From our 2020 vista, it might seem that a family genesis ecosmos wants our homo to Anthropo sapience to move from an inefficient stochastic (tinkered) past to an intentional, respectfully guided procreation. See also Aptamer Cell-Based Selection by Silvia Catuogno and Carla Esposito in this issue. A popular review of this work, along with F. Romesberg below, is Life, Rewritten by James Crow in the New Scientist (December 8, 2018).

Directed evolution was first applied to diverse libraries of DNA and RNA molecules a quarter century ago in the hope of gaining technology that would allow the creation of receptors, ligands, and catalysts on demand. Despite isolated successes, the outputs of this technology have been somewhat disappointing, perhaps because the four building blocks of standard DNA and RNA have too little functionality to have versatile binding properties, and offer too little information density to fold unambiguously. This review covers the recent literature that seeks to create an improved platform to support laboratory Darwinism, one based on an artificially expanded genetic information system (AEGIS) that adds independently replicating nucleotide “letters” to the evolving “alphabet”

Aptamers are high affinity single-stranded DNA/RNA molecules, produced by a combinatorial procedure named SELEX (Systematic Evolution of Ligands by Exponential enrichment), that are emerging as promising diagnostic and therapeutic tools.

Future > New Earth > second genesis

Davies, Jamie. Real-World Synthetic Biology. Life. 9/1, 2019. A paper by the University of Edinburgh morphologist (search) for Ricard Sole’s Synthetic Biology from Living Computers to Terraformation issue, see second quote. Similar to Manuel Porcar’s entry herein, at this epic turning point it is vital to get clear on and use consistent life-like metaphors and terms. Thus specific engineering and industrial control methods are not seen as appropriate. Davies proceeds to graphically propose self-organizing organic procedures by way of complex adaptive systems.

Authors often assert that a key feature of 21st-century synthetic biology is its use of an engineering design approach using predictive models, modular architecture, construction using well-characterized parts, and rigorous testing using standard metrics. This article examines whether this is, or even should be, the case. A brief survey of synthetic biology projects that have reached, or are near to, commercial application show very few of these attributes. Instead, they featured much trial and error, and the use of specialized, custom components and assays. I conclude that the engineering approach should not be used to define or constrain synthetic biological endeavour, and that in fact conventional engineering has more to gain by expanding and embracing more biological ways of working. (Davies Abstract excerpts)

Over the last two decades, synthetic biology has emerged as a novel field with major impact on both basic science and biomedical research. By moving beyond the classical approaches of genetic engineering, synthetic circuits implemented within living cells allow to redesign nature from the molecular and cellular levels to multicellular scales. Synthetic microorganisms have been built to explore cooperation and conflict in microbial interactions as well as the rise of multicellularity. Complex computational tasks have also been created de novo and used to expand the cognitive potential of cellular assemblies. In parallel with all these already promising results, synthetic biology is being considered as a potential path to artificially modify microbiomes and even terraform Mars biosphere. (R. Sole proposal)

Future > New Earth > second genesis

Design, Jai and Chaitanya Gokhale.. Synthetic Mutualism and the Intervention Dilemma. Life. 9/1, 2019. Okinawa Institute of Science and Technology, Genomics and Regulatory Systems Unit, and MPI Evolutionary Biology, Theoretical Models of Eco-Evolutionary Dynamics Group researchers extend this nascent endeavor to both gain a better understanding of how life has naturally evolved, developed and emerged, and how our human sapience might begin a intentional procreation by respectful, informed continuance. A working phrase herein is a Synthetic Symbiosis, which could also inspire better human communities.

Ecosystems are complex networks of interacting individuals co-evolving with their environment. As such, changes to an interaction can influence the whole ecosystem. However, to predict the outcome of these changes, considerable understanding of processes driving the system is required. Synthetic biology provides tools to aid this understanding, which then may allow us to change specific interactions. Of particular interest is the ecological importance of mutualism, a subset of cooperative interactions. Mutualism occurs when individuals of different species provide a reciprocal fitness benefit. We review available experimental techniques from the stability of microbial communities in extreme environments to the collapse of ecosystems due to high levels of human intervention. We evaluate the promise of synthetic biology by way of ethics and laws regarding biological alterations, whether on Earth or beyond. (Abstract excerpt)

Future > New Earth > second genesis

Dien, Vivian, et al. Progress Toward a Semi-Synthetic Organism with an Unrestricted Expanded Genetic Alphabet. Journal of the American Chemical Society. 140/47, 2018. A six person team from Floyd Romesberg’s laboratory at the Scripps Research Institute, La Jolla, CA describe a highly technical exercise by which to begin modifications and enhancements of life’s original four letter genomic code. The work was noted in the popular press as Life, Rewritten by James Crow (New Scientist, Dec. 8, 2018), see also the Biondi and Benner entry above.

We have developed a family of unnatural base pairs (UBPs), exemplified by the pair formed between dNaM and dTPT3, for which pairing is mediated not by complementary hydrogen bonding but by hydrophobic and packing forces. These UBPs enabled the creation of the first semisynthetic organisms (SSOs) that store increased genetic information and use it to produce proteins containing noncanonical amino acids. The results demonstrate the importance of evaluating synthetic biology “parts” in their in vivo context and the ability of hydrophobic and packing interactions to replace the complementary hydrogen bonding that underlies the replication of natural base pairs. The identification of dMTMO-dTPT3 and especially dPTMO-dTPT3 represents significant progress toward the development of SSOs able to store and retrieve increased information. (Abstract excerpt)

Future > New Earth > second genesis

Falk, Johannes , et al. Context in Synthetic Biology. Journal of Chemical Physics. 180/024106, 2019. Technical University of Dormstadt biophysicists including Barbara Drossel scope out ways to intentionally carry forth the latest complexity theories so we can proceed to make Earth life better. It might also be noted that a 2001 paper, Biological Evolution and Statistical Physics, by B. Drossel in Advances in Physics (50/2) was one of the first of its integrative kind in a physics journal (second quote) which can show how far and fast this global project has grown and advanced.

Synthetic biology aims at designing modular genetic circuits that can be assembled according to the desired function. When embedded in a cell, a circuit module becomes a small subnetwork within a larger environmental network, and its dynamics is therefore affected by potentially unknown interactions with the environment. It is well-known that the presence of the environment not only causes extrinsic noise but also memory effects, which means that the dynamics of the subnetwork is affected by its past states via a memory function that is characteristic of the environment. We study several generic scenarios for the coupling between a small module and a larger environment, with the environment consisting of a chain of mono-molecular reactions. By mapping the dynamics of this coupled system onto random walks, we are able to give exact analytical expressions for the arising memory functions. Hence, our results give insights into the possible types of memory functions and thereby help to better predict subnetwork dynamics. (Falk Abstract)

This review is an introduction to theoretical models and mathematical calculations for biological evolution, aimed at physicists. The methods in the field are naturally very similar to those used in statistical physics, although the majority of publications have appeared in biology journals. The review has three parts, which can be read independently. The first part deals with evolution in fitness landscapes and includes Fisher's theorem, adaptive walks, quasispecies models, effects of finite population sizes, and neutral evolution. The second part studies models of coevolution, including evolutionary game theory, kin selection, group selection, sexual selection, speciation, and coevolution of hosts and parasites. The third part discusses models for networks of interacting species and their extinction avalanches. (Drossel 2001 Abstract)

Future > New Earth > second genesis

Gilbert, Charles and Tom Ellis. Biological Engineered Living Materials: Growing Functional Materials with Genetically Programmable Properties. ACS Synthetic Biology. 8/1, 2019. As collective human ingenuity initiates a second intentional evolutionary co-creation, Imperial College London bioengineers scope out ways to join microbial, cellular, morphogenetic and more phases into novel, palliative, beneficial ways living systems.

Natural biological materials exhibit remarkable properties: self-assembly from simple raw materials, precise control of morphology, diverse physical and chemical properties, self-repair, and to sense-and-respond to environmental stimuli. But, could it be possible to genetically program microbes to create entirely new and useful biological materials? At the intersection of microbiology, material science, and synthetic biology, an emerging field of biological engineered living materials (ELMs) is underway. Here we review recent efforts to program cells to produce living materials with novel functional properties, focusing on microbial systems that can be engineered to grow materials and on new genetic circuits for pattern formation. (Abstract)

Future > New Earth > second genesis

Hoshika, Shuichi, et al. Hachinoji DNA and RNA: A Genetic System with Eight Building Blocks. Science. 363/884, 2019. A sixteen person collaboration from co-author Steven Benner’s Foundation for Applied Molecular Evolution, Florida, Indiana University, UT Austin, DNA Software, Ann Arbor, and the University of Chicago reports this doubling of the genetic alphabet to show how facile it can be done. The work merited a review DNA Gets a New – Bigger – Genetic Alphabet by Carl Zimmer in the New York Times for February 21, 2019.

We report DNA- and RNA- like systems built from eight nucleotide “letters” (hence the name “hachimoji”) that form four orthogonal pairs. These synthetic systems meet the structural requirements needed to support Darwinian evolution, including a polyelectrolyte backbone, predictable thermodynamic stability, and stereoregular building blocks that fit a Schrödinger aperiodic crystal. Measured thermodynamic parameters predict the stability of hachimoji duplexes, allowing hachimoji DNA to increase the information density of natural terran DNA. These results expand the scope of molecular structures that might support life, including life throughout the cosmos. (Abstract)

Future > New Earth > second genesis

Porcar, Manuel. The Hidden Charm of Life. Life. 9/1, 2019. An entry by a University of Valencia, Spain integrative biologist for a Synthetic Biology from Living Computers to Terraformation issue, see Jamie Davies herein for more. It begins by noting a present metaphor mix of machine and organic analogies and metaphors that it would do well going forward. As an example, “factory” is often applied to cellular metabolism. See also Is Research on Synthetic Cells Moving to the Next Level? by Pasquale Stano in this issue for another take.

Synthetic biology is an engineering view on biotechnology, which has revolutionized genetic engineering. The field has seen a constant development of metaphors that tend to highlight the similarities of cells with machines. I argue here that living organisms, particularly bacterial cells, are not machine-like, engineerable entities, but, instead, factory-like complex systems shaped by evolution. A change of the comparative paradigm in synthetic biology from machines to factories, from hardware to software, and from informatics to economy is discussed. (Abstract)

Future > New Earth > democracy

Abele, Andrea, et al. Facets of the Fundamental Content Dimensions: Agency with Competence and Assertiveness – Communion with Warmth and Morality. Frontiers in Psychology. November, 2016. A. Abele, University of Erlangen (search 2014), Nicole Hauke, University of Queensland, Kim Peters, University of Strasbourg, Eva Louvet, University of Strasbourg, Aleksandra Szymkow, University of Social Sciences, Warsaw, and Yanping Duan, Hong Kong Baptist University contribute to this overdue shift in psychological studies from olden Big Five personality traits to more distinctive Big Two qualities. Their occasion may be traced to Abele, Oscar Ybarra, et al in the 2000s on to Susan Fiske circa 2018, as its validity gains a growing number of colleagues and usages. But it is so curious that as the titles well states, this ultimate pairing is still not realized to be complementary gender archetypes.

Agency (A) and communion (C) are fundamental content dimensions. We propose a facet model that differentiates A into assertiveness (AA) and competence (AC) and C into warmth (CW) and morality (CM). We tested the model in a cross-cultural study by comparing data from Asia, Australia, Europe, and the USA. Both the two-factor model and the four-factor model showed good fit indices across countries. The findings support the model's validity by positioning the traits within a network of self-construal, values, impression management, and the Big Five personality factors. In all countries, A was related to independent self-construal and to agentic values, and C to interdependent self-construal and communal values. Our research shows that (a) the fundamental dimensions of A and C are stable across cultures; and (b) that the here proposed distinction of facets of A and C is fruitful in analyzing self-perception. (Abstract excerpt)

Future > New Earth > democracy

Brijder, Robert, et al. Democratic, Existential, and Consensus-based Output Conventions in Stable Computation by Chemical Reaction Networks.. Natural Computing. 17/1, 2018. Reviewed more in systems Chemistry, RB Hasselt University, Belgium, David Doty UC Davis and David Soloveichik UT Austin metaphorically allude to an electoral polarity of aye and nay options as a good way to explain and represent chemical interactions.

Future > New Earth > democracy

Durante, Federica, et al. Ambivalent Stereotypes Link to Peace, Conflict, and Inequality across 38 Nations. Proceedings of the National Academy of Sciences. 114/669, 2017. Nineteen scholars from the USA, Italy, Turkey, Germany, Norway, Sweden, Jordan, Switzerland, Egypt, Finland and France including Susan Fiske consider how the new Big Two personality model (search SF) might be beneficially applied onto national and cultural phases. It is suggested that the general, malleable agency and communion aspects can contribute vital insights which if appreciated could help mitigate internecine social strife here and everywhere (such as our own polar two party debacle).

Stereotypes reflect a society’s inequality and conflict, providing a diagnostic map of intergroup relations. This map depicts the prime, relative warmth (friendly, sincere) and competence (capable, skilled) behavioral cast of each group. Some societal clusters are high on both (positive “us”) vs. low on both (negative “them”). Other societies, including the United States, have us-them clusters with variance (high on one dimension, low on the other). This cross-national study shows peace-conflict predicts ambivalence. Extremely peaceful and conflictual nations both display unambivalent us-them patterns, whereas intermediate peace-conflict predicts high ambivalence. Inequality and intermediate peace-conflict each use ambivalent stereotypes, explaining complicated intergroup relations and maintaining social system stability. (Significance)

Future > New Earth > democracy

Feng, Michelle and Mason Porter. Persistent Homology of Geospatial Data: A Case Study with Voting. arXiv:1902.05911. UCLA mathematicians first show how this topological method along with simplicial complexes (see below) can help distinguish network phenomena. They proceed to apply this view to actual election patterns and find even such social intensity to take on a typical dynamic network formation.

A crucial step in the analysis of persistent homology is transformation of data into a simplicial complex. We present two new methods for constructing simplicial complexes from two-dimensional geospatial data (such as maps). We apply these methods to a California precinct-level voting data set to show that our new version can capture geometric characteristics that are missed by distance-based constructions and yield more interpretable persistence modules. In particular, they are able to distinguish short-persistence features that occur only for a narrow range of distance scales (local voting behaviors) from short-persistence noise by incorporating information about other spatial relationships between precincts. (Abstract edit)

Although we tailored our methods to yield improvements for the particular problem of detecting voting patterns from Shapefile data, one can use an adjacency construction on data sets with a network structure, and the level-set construction is appropriate for any type of 2D manifold data. More generally, given the ubiquity of 2D spatial data, the insights that we highlighted with the voting application are relevant for a broad range of problems, including transportation networks, spatial demography, granular materials, many structures in biology, and others. (19)

Persistent homology is a method for computing topological features of a space at different spatial resolutions. More persistent features are detected over a wide range of spatial scales and are deemed more likely to represent true features of the underlying space. In mathematics, a simplicial complex is a set composed of points, line segments, triangles, and their n-dimensional counterparts. (Wikipedia)

Future > New Earth > democracy

Fiske, Susan. Political Cognition Helps Explain Social Class Divides: Two Dimensions of Candidate Impressions, Group Stereotypes, and Meritocracy Beliefs. Cognition. Online November, 2018. The Princeton University psychologist and prolific, collegial author and editor contributes to this 21st century shift from Five to Two prime agency/communion personality traits. Indeed, new names and definitions are a work in progress for this major advance, as the first Abstract alludes. See also her companion paper Stereo Content: Warmth and Competence Endure in Current Directions in Psychological Science (27/2, 2018, second Abstract). But as this Organic Democracy section tries to document (Abele, Ybarra, et al), a salutary distinction of complementary bigender archetypes still awaits. See for example Geert Hofstede, et al (2010) for glimpses of a me individual and We group reciprocity.

As a commentary, within our universe to human website compass, similar versions are in current ascent across a wide range such as particle/wave in physics, matter/symbol in neuroscience (Gazzaniga 2018 for both), conserve/create, more/less order cerebral chimeras, self-organized criticalities (Chialvo, Kauffman, et al) and so on. Might our nascent sapiensphere which learns on her/his bicameral own, closing on truth and a hopefully clearer 2020 vision, be at last able to realize nature’s own familial genetic DNA/AND code?

Political cognitions as impressions and stereotypes along two fundamental dimensions of social evaluations play a role in explaining social class divides and resentments. First, the Big Two dimensions (warmth/communion and competence/agency) describe candidate, personal, and group perception. Various evidence from social psychology, political science, and sociology indicates common beliefs that support cross-class dichotomies. Anticipated by systematic theories, these cognitions (impressions, stereotypes, beliefs) help explain the populist and nativist antagonisms in current political discourse which result in polarized, dysfunctional politics. (first Abstract excerpt)

Two dimensions persist in social cognition when people are making sense of individuals or groups. The stereotype content model (SCM) perceives these two basic dimensions as warmth (trustworthiness, friendliness) and competence (capability, assertiveness). Measured reliably and validly, these Big Two modes converge across survey, cultural, laboratory, and biobehavioral approaches. The SCM proposes and tests a comprehensive causal theory: Evident social structure (cooperation, status) predicts stereotypes (warmth, competence), which in turn base emotional prejudices (pride, pity, contempt, envy), and finally, the emotions cast discrimination (active and passive help and harm). (second Abstract)

Future > New Earth > democracy

Galesic, Mirta and Daniel Stein. Statistical Physics Models of Belief Dynamics. arXiv:1706.02287. The Chair of Human Social Dynamics at the Santa Fe Institute and a NYU mathematican discern a novel cross-connection between these disparate domains such that political and cultural conceptions can be quantified as agents which interact in the shape of spin-glass physics, network topologies and more. However a realization awaits, which could not be more obvious, that electoral polarities naturally hold to a particle/ wave, me/We complementarity. This week in February 2019 a senate election in North Carolina was so 50/50 close, and tainted, that it has to be done over.

We build simple computational models of belief dynamics within the framework of discrete-spin statistical physics models, and explore how suitable they are for understanding and predicting real-world belief change on both the individual and group levels. We find that accurate modeling of real-world patterns requires attending to social interaction rules that people use, network structures in which they are embedded, distributions of initial beliefs and intrinsic preferences, and the relative importance of social information and intrinsic preferences. We find that simple statistical physics-based models contain predictive value for real-world belief dynamics and enable empirical tests of different assumptions about the underlying network structure and the social interaction rules.

Future > New Earth > democracy

Hofstede, Geert, et al. Cultures and Organizations: Software of the Mind. New York: McGraw-Hill Education, 2010. The University of Maastricht premier advocate since the 1980s (search) of social dichotomies from families to nations is joined by his son Gert Jan Hofstede, an information biologist at Wageningen University, and Michael Minkow, a global sociologist at the University of Sofia, Bulgaria. This third, 500 page edition of the popular volume continues to articulate a He, She and (S)he and/or an I + We = Us mutual polarity and functional trinity which is seen to recur within every societal phase. These independent/interdependent or individual/collective modes are the basis for our Complementarity of Civilizations section. But it is so obvious that they are not to be opposites locked in battle, as besets political elections which always divide in half. As history closes on 2020, whenever, however, could this iconic yang/yin Tao image become realized as an independent natural genetic source code?

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