A origem da vida: um problema complicadíssimo para a Física.

quarta-feira, agosto 16, 2017

Origins of Life: A Problem for Physics

Sara Imari Walker

School of Earth and Space Exploration and Beyond Center for Fundamental

Concepts in Science, Arizona State University, Tempe AZ USA; Blue Marble Space

Institute of Science, Seattle WA USA

E-mail: sara.i.walker@asu.edu


Abstract. The origins of life stands among the great open scientific questions of our time. While a number of proposals exist for possible starting points in the pathway from non-living to living matter, these have so far not achieved states of complexity that are anywhere near that of even the simplest living systems. A key challenge is identifying the properties of living matter that might distinguish living and non-living physical systems such that we might build new life in the lab. This review is geared towards covering major viewpoints on the origin of life for those new to the origin of life field, with a forward look towards considering what it might take for a physical theory that universally explains the phenomenon of life to arise from the seemingly disconnected array of ideas proposed thus far. The hope is that a theory akin to our other theories in fundamental physics might one day emerge to explain the phenomenon of life, and in turn finally permit solving its origins.

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INTERESTING EXCERPT/EXCERTO INTERESSANTE:

All else being equal, the thermodynamic benefits of self-replication quantified by Eq. 8 seem to favor the simplest replicators (i.e. the shortest replicators which can replicate and degrade the fastest and therefore maximize entropy production). However, this misses a critical point about information and its role in selection of replicators – all else is not equal. Physical systems encoding the information necessary to replicate fast will do so at an exponential rate [130], whereas sequences of similar length that contain no fitness-relevant information will die. That information and selection matter to life has been one of the most challenging aspects of understanding life as a physical process, and nonequilibrium approaches have yet to address this issue – even if we could identify natural or “intrinsic” macrostates. The forgoing demonstrates that selection for systems that dissipate energy at a fast rate will yield simple replicators. Dissipation is a consequence of selection of information, not a driver of it. Co-polymerization provides one explicit example where dissipation is closely related to information [131]. It seems likely that in the absence of appealing to informational principles, discussions of dissipation and entropy-production alone cannot explain the origins of life (hence Schrödinger’s original appeal to “other laws”).

FREE PDF GRATIS: arXiv

Dois lados da mesma moeda: uma perspectiva de genética populacional sobre mutagênese letal e colapso mutacional

terça-feira, agosto 15, 2017

Two sides of the same coin: A population genetics perspective on lethal mutagenesis and mutational meltdown 

Sebastian Matuszewski Louise Ormond Claudia Bank Jeffrey D. Jensen

Virus Evolution, Volume 3, Issue 1, 1 January 2017, vex004, https://doi.org/10.1093/ve/vex004

Published: 02 March 2017



Abstract

The extinction of RNA virus populations upon application of a mutagenic drug is frequently referred to as evidence for the existence of an error threshold, above which the population cannot sustain the mutational load. To explain the extinction process after reaching this threshold, models of lethal mutagenesis have been proposed, in which extinction is described as a deterministic (and thus population size-independent) process. As a separate body of literature, the population genetics community has developed models of mutational meltdown, which focus on the stochastic (and thus population-size dependent) processes governing extinction. However, recent extensions of both models have blurred these boundaries. Here, we first clarify definitions in terms of assumptions, expectations, and relevant parameter spaces, and then assess similarities and differences. As concepts from both fields converge, we argue for a unified theoretical framework that is focused on the evolutionary processes at play, rather than dispute over terminology.

lethal mutagenesis, mutational meltdown, Hill–Robertson interference, Muller's Ratchet.

Issue Section: Reflections

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Onde estão os extraterrestres? As implicações do silêncio cósmico

domingo, agosto 13, 2017

Implication of our technological species being first and early

Daniel P. Whitmire (a1) 

(a1)

Department of Mathematics, The University of Arkansas, Fayetteville, AR, USA


Published online: 03 August 2017


Abstract

According to the Principle of Mediocrity, a cornerstone of modern cosmology, in the absence of any evidence to the contrary, we should believe that we are a typical member of an appropriately chosen reference class. If we assume that this principle applies to the reference class of all extant technological species, then it follows that other technological species will, like us, typically find that they are both the first such species to evolve on their planet and also that they are early in their potential technological evolution. Here we argue that this suggests that the typical technological species becomes extinct soon after attaining a modern technology and that this event results in the extinction of the planet's global biosphere.

Copyright

COPYRIGHT: © Cambridge University Press 2017 

Corresponding author

e-mail: dpwhitmi@uark.edu

Cientistas da Universidade de Washington descobrem que o DNA sequenciado pode hackear computadores

quinta-feira, agosto 10, 2017

Published at the 2017 USENIX Security Symposium; addition information at https://dnasec.cs.washington.edu/.

Computer Security, Privacy, and DNA Sequencing: Compromising Computers with Synthesized DNA, Privacy Leaks, and More

Peter Ney, Karl Koscher, Lee Organick, Luis Ceze, Tadayoshi Kohno

University of Washington

{neyp,supersat,leeorg,luisceze,yoshi}@cs.washington.edu


Abstract

The rapid improvement in DNA sequencing has sparked a big data revolution in genomic sciences, which has in turn led to a proliferation of bioinformatics tools. To date, these tools have encountered little adversarial pressure. This paper evaluates the robustness of such tools if (or when) adversarial attacks manifest. We demonstrate, for the first time, the synthesis of DNA which — when sequenced and processed— gives an attacker arbitrary remote code execution. To study the feasibility of creating and synthesizing a DNA-based exploit, we performed our attack on a modified downstream sequencing utility with a deliberately introduced vulnerability. After sequencing, we observed information leakage in our data due to sample bleeding. While this phenomena is known to the sequencing community, we provide the first discussion of how this leakage channel could be used adversarially to inject data or reveal sensitive information. We then evaluate the general security hygiene of common DNA processing programs, and unfortunately, find concrete evidence of poor security practices used throughout the field. Informed by our experiments and results, we develop a broad framework and guidelines to safeguard security and privacy in DNA synthesis, sequencing, and processing.

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O maior de todos os mitos da ciência: não tem preconceitos e se autocorrige!



“O maior de todos os mitos de ciência é que ela não codifica preconceito e está sempre se autocorrigindo. Na verdade, a ciência frequentemente tem feito de sua existência o codificar e justificar preconceito, e se recusar fazer qualquer coisa sobre o fato de que os dados dizem que algo está errado.”

“Science’s greatest myth is that it doesn’t encode bias and is always self-correcting. In fact, science has often made its living from encoding and justifying bias, and refusing to do anything about the fact that the data says something’s wrong.”


Chanda Prescod-Weinstein é uma física de partículas, filósofa de ciência na Universidade de Washington/Chanda Prescod-Weinstein is a particle physicist, philosopher of science at the University of Washington.

Slate Stop Equating “Science” With Truth

Nova visão sobre o DNA arcaico reescreve a história da evolução humana

terça-feira, agosto 08, 2017

Early history of Neanderthals and Denisovans

Alan R. Rogers a,1, Ryan J. Bohlender b, and Chad D. Huff b 

Author Affiliations

aDepartment of Anthropology, University of Utah, Salt Lake City, UT 84112;

bDepartment of Epidemiology, MD Anderson Cancer Center, Houston, TX 77030

Edited by Richard G. Klein, Stanford University, Stanford, CA, and approved July 7, 2017 (received for review April 18, 2017)

These population trees with embedded gene trees show how mutations can generate nucleotide site patterns. The four branch tips of each gene tree represent genetic samples from four populations: modern Africans, modern Eurasians, Neanderthals, and Denisovans. In the left tree, the mutation (shown in blue) is shared by the Eurasian, Neanderthal and Denisovan genomes. In the right tree, the mutation (shown in red) is shared by the Eurasian and Neanderthal genomes. Credit: Alan Rogers, University of Utah

Significance

Neanderthals and Denisovans were human populations that separated from the modern lineage early in the Middle Pleistocene. Many modern humans carry DNA derived from these archaic populations by interbreeding during the Late Pleistocene. We develop a statistical method to study the early history of these archaic populations. We show that the archaic lineage was very small during the 10,000 y that followed its separation from the modern lineage. It then split into two regional populations, the Neanderthals and the Denisovans. The Neanderthal population grew large and separated into largely isolated local groups.

Abstract

Extensive DNA sequence data have made it possible to reconstruct human evolutionary history in unprecedented detail. We introduce a method to study the past several hundred thousand years. Our results show that (i) the Neanderthal–Denisovan lineage declined to a small size just after separating from the modern lineage, (ii) Neanderthals and Denisovans separated soon thereafter, and (iii) the subsequent Neanderthal population was large and deeply subdivided. They also (iv) support previous estimates of gene flow from Neanderthals into modern Eurasians. These results suggest an archaic human diaspora early in the Middle Pleistocene.

human evolution archaic admixture introgression Neanderthals Denisovans

Footnotes

1To whom correspondence should be addressed. Email: rogers@anthro.utah.edu.

Author contributions: A.R.R. and C.D.H. designed research; A.R.R. and R.J.B. performed research; A.R.R. and R.J.B. analyzed data; and A.R.R. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1706426114/-/DCSupplemental.

Freely available online through the PNAS open access option.

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O desafio imprevisível - do genótipo ao fenótipo em populações celulares

Reports on Progress in Physics

REVIEW ARTICLE

The unforeseen challenge: from genotype-to-phenotype in cell populations

Erez Braun

Published 26 February 2015 • © 2015 IOP Publishing Ltd 

Reports on Progress in Physics, Volume 78, Number 3

Article information

Author e-mails

Erez@physics.technion.ac.il

Author affiliations

Department of Physics and Network Biology Research Laboratories, Technion, Haifa 32000, Israel

Dates

Received 27 June 2014 Accepted 18 December 2014 Published 26 February 2015 

REVIEW ARTICLE

The unforeseen challenge: from genotype-to-phenotype in cell populations

Erez Braun

Published 26 February 2015 • © 2015 IOP Publishing Ltd 

Erez Braun 2015 Rep. Prog. Phys. 78 036602

DOI https://doi.org/10.1088/0034-4885/78/3/036602


Abstract

Biological cells present a paradox, in that they show simultaneous stability and flexibility, allowing them to adapt to new environments and to evolve over time. The emergence of stable cell states depends on genotype-to-phenotype associations, which essentially reflect the organization of gene regulatory modes. The view taken here is that cell-state organization is a dynamical process in which the molecular disorder manifests itself in a macroscopic order. The genome does not determine the ordered cell state; rather, it participates in this process by providing a set of constraints on the spectrum of regulatory modes, analogous to boundary conditions in physical dynamical systems. We have developed an experimental framework, in which cell populations are exposed to unforeseen challenges; novel perturbations they had not encountered before along their evolutionary history. This approach allows an unbiased view of cell dynamics, uncovering the potential of cells to evolve and develop adapted stable states. In the last decade, our experiments have revealed a coherent set of observations within this framework, painting a picture of the living cell that in many ways is not aligned with the conventional one. Of particular importance here, is our finding that adaptation of cell-state organization is essentially an efficient exploratory dynamical process rather than one founded on random mutations. Based on our framework, a set of concepts underlying cell-state organization—exploration evolving by global, non-specific, dynamics of gene activity—is presented here. These concepts have significant consequences for our understanding of the emergence and stabilization of a cell phenotype in diverse biological contexts. Their implications are discussed for three major areas of biological inquiry: evolution, cell differentiation and cancer. There is currently no unified theoretical framework encompassing the emergence of order, a stable state, in the living cell. Hopefully, the integrated picture described here will provide a modest contribution towards a physics theory of the cell.

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A formalização e o significado de "teoria" nas ciências biológicas inexatas

Biological Theory

June 2013, Volume 7, Issue 4, pp 298–310

Formalization and the Meaning of “Theory” in the Inexact Biological Sciences

Authors Authors and affiliations

James Griesemer1

Email author

1.Department of PhilosophyUniversity of California, DavisDavisUSA

Thematic Issue Article: The Meaning of "Theory" in Biology

First Online: 18 September 2012

Citations

Source/Fonte: Adaptive Landscapes

Abstract

Exact sciences are described as sciences whose theories are formalized. These are contrasted to inexact sciences, whose theories are not formalized. Formalization is described as a broader category than mathematization, involving any form/content distinction allowing forms, e.g., as represented in theoretical models, to be studied independently of the empirical content of a subject-matter domain. Exactness is a practice depending on the use of theories to control subject-matter domains and to align theoretical with empirical models and not merely a state of a science. Inexact biological sciences tolerate a degree of “mismatch” between theoretical and empirical models and concepts. Three illustrations from biological sciences are discussed in which formalization is achieved by various means: Mendelism, Weismannism, and Darwinism. Frege’s idea of a “conceptual notation” is used to further characterize the notion of a form/content distinction.

Keywords

Darwin Exact and inexact science Formalization Mendel, model Theory Weismann

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Abordagens à macroevolução - conceitos gerais e origem da variação

Evolutionary Biology

pp 1–24

Approaches to Macroevolution: 1. General Concepts and Origin of Variation

Authors Authors and affiliations

David Jablonski1

Email author

View author's OrcID profile

1.Department of Geophysical SciencesUniversity of ChicagoChicagoUSA

Open Access Synthesis Paper

First Online: 03 June 2017

Source/Fonte: Nature

Abstract

Approaches to macroevolution require integration of its two fundamental components, i.e. the origin and the sorting of variation, in a hierarchical framework. Macroevolution occurs in multiple currencies that are only loosely correlated, notably taxonomic diversity, morphological disparity, and functional variety. The origin of variation within this conceptual framework is increasingly understood in developmental terms, with the semi-hierarchical structure of gene regulatory networks (GRNs, used here in a broad sense incorporating not just the genetic circuitry per se but the factors controlling the timing and location of gene expression and repression), the non-linear relation between magnitude of genetic change and the phenotypic results, the evolutionary potential of co-opting existing GRNs, and developmental responsiveness to nongenetic signals (i.e. epigenetics and plasticity), all requiring modification of standard microevolutionary models, and rendering difficult any simple definition of evolutionary novelty. The developmental factors underlying macroevolution create anisotropic probabilities—i.e., an uneven density distribution—of evolutionary change around any given phenotypic starting point, and the potential for coordinated changes among traits that can accommodate change via epigenetic mechanisms. From this standpoint, “punctuated equilibrium” and “phyletic gradualism” simply represent two cells in a matrix of evolutionary models of phenotypic change, and the origin of trends and evolutionary novelty are not simply functions of ecological opportunity. Over long timescales, contingency becomes especially important, and can be viewed in terms of macroevolutionary lags (the temporal separation between the origin of a trait or clade and subsequent diversification); such lags can arise by several mechanisms: as geological or phylogenetic artifacts, or when diversifications require synergistic interactions among traits, or between traits and external events. The temporal and spatial patterns of the origins of evolutionary novelties are a challenge to macroevolutionary theory; individual events can be described retrospectively, but a general model relating development, genetics, and ecology is needed. An accompanying paper (Jablonski in Evol Biol 2017) reviews diversity dynamics and the sorting of variation, with some general conclusions.

Keywords Evolutionary developmental biology Contingency Hierarchy Diversification Disparity Evolutionary novelty Paleobiology

FREE PDF GRATIS: Evol. Biol.

Seleção natural cosmológica???

Complexity

Volume 2017 (2017), Article ID 4745379, 4 pages


Research Article

Entropy and Selection: Life as an Adaptation for Universe Replication

Michael E. Price

Department of Life Sciences, Brunel University, London, UK

Correspondence should be addressed to Michael E. Price

Received 21 February 2017; Accepted 28 May 2017; Published 20 June 2017

Academic Editor: Carlos Gershenson

Copyright © 2017 Michael E. Price. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Abstract

Natural selection is the strongest known antientropic process in the universe when operating at the biological level and may also operate at the cosmological level. Consideration of how biological natural selection creates adaptations may illuminate the consequences and significance of cosmological natural selection. An organismal trait is more likely to constitute an adaptation if characterized by more improbable complex order, and such order is the hallmark of biological selection. If the same is true of traits created by selection in general, then the more improbably ordered something is (i.e., the lower its entropy), the more likely it is to be a biological or cosmological adaptation. By this logic, intelligent life (as the least-entropic known entity) is more likely than black holes or anything else to be an adaptation designed by cosmological natural selection. This view contrasts with Smolin’s suggestion that black holes are an adaptation designed by cosmological natural selection and that life is the by-product of selection for black holes. Selection may be the main or only ultimate antientropic process in the universe/multiverse; that is, much or all observed order may ultimately be the product or by-product of biological and cosmological selection.

“Another, related meaning of entropy is that it is a measure of disorganization. The atoms in a gas are disordered to the extent that there is no way to tell one from another. In equilibrium there is maximal disorder, because every atom moves randomly, with the same average energy as any other atom. A living system, on the contrary, continually creates an enormous number of different kind of molecules, each of which generally perform a unique function. The entropy of a living thing is consequently much lower, atom for atom, than anything else in the world.”

Smolin (1997), The Life of the Cosmos, p. 28.

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A matemática não é a única linguagem da natureza

segunda-feira, agosto 07, 2017

Mathematics is not the only language in the book of nature

Nguyen, James and Frigg, Roman (2017) Mathematics is not the only language in the book of nature. [Preprint]


Abstract

How does mathematics apply to something non-mathematical? We distinguish between a general application problem and a special application problem. A critical examination of the answer that structural mapping accounts offer to the former problem leads us to identify a lacuna in these accounts: they have to presuppose that target systems are structured and yet leave this presupposition unexplained. We propose to fill this gap with an account that attributes structures to targets through structure generating descriptions. These descriptions are physical descriptions and so there is no such thing as a solely mathematical account of a target system.

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Charles Darwin: o fabricante de mito vitoriano

sábado, agosto 05, 2017

Charles Darwin: Victorian Mythmaker

By A N Wilson

Coming Soon Add to wishlist Hardback

£25.00

A radical reappraisal of Charles Darwin from the bestselling author of Victoria: A Life

Charles Darwin: the man who discovered evolution? The man who killed off God? Or a flawed man of his age, part genius, part ruthless careerist who would not acknowledge his debts to other thinkers?

In this bold new life - the first single volume biography in twenty-five years - A. N. Wilson, the acclaimed author of The Victorians and God's Funeral, goes in search of the celebrated but contradictory figure Charles Darwin.

Darwin was described by his friend and champion, Thomas Huxley, as a 'symbol'. But what did he symbolize? In Wilson's portrait, both sympathetic and critical, Darwin was two men. On the one hand, he was a naturalist of genius, a patient and precise collector and curator who greatly expanded the possibilities of taxonomy and geology. On the other hand, Darwin, a seemingly diffident man who appeared gentle and even lazy, hid a burning ambition to be a universal genius. He longed to have a theory which explained everything.

But was Darwin's 1859 master work, On the Origin of Species, really what it seemed, a work about natural history? Or was it in fact a consolation myth for the Victorian middle classes, reassuring them that the selfishness and indifference to the poor were part of nature's grand plan?

Charles Darwin: Victorian Mythmaker is a radical reappraisal of one of the great Victorians, a book which isn't afraid to challenge the Darwinian orthodoxy while bringing us closer to the man, his revolutionary idea and the wider Victorian age.

Biographical Notes 

A. N. Wilson was born in North Staffordshire, and taught literature for seven years at New College Oxford, where he won the Chancellor's English Essay Prize and the Ellerton Prize. He is the author of over twenty novels, and as many works of non-fiction. His biography of Tolstoy won the Whitbread Prize in 1988. His biography of Queen Victoria was published to critical acclaim. He is also the author of The Victorians and of God's Funeral, an account of how the Victorians lost their faith. He is a Fellow of the Royal Society of Literature, and a Member of the American Academy and Institute of Arts and Letters. He lives in London, and is the father of three daughters.

Other details

ISBN: 9781444794885 Publication date: 07 Sep 2017 Page count: 448 Imprint: John Murray

A book to treasure. A. N Wilson throws down the gauntlet on the very first line, 'Darwin was wrong' he begins. What follows is a sharply observed and wonderfully compelling analysis which evokes the Victorian titan brilliantly and challenges received wisdom. A work of scholarship that is hard to put down. — Deborah Cadbury

Publisher: Hodder & Stoughton

Etiquetagem eletrônica de células

sexta-feira, agosto 04, 2017

Micrometer-Scale Magnetic-Resonance-Coupled Radio-Frequency Identification and Transceivers for Wireless Sensors in Cells

Xiaolin Hu, Kamal Aggarwal, Mimi X. Yang, Kokab B. Parizi, Xiaoqing Xu, Demir Akin, Ada S. Y. Poon, and H.-S. Philip Wong

Phys. Rev. Applied 8, 014031 – Published 26 July 2017

We report the design, analysis, and characterization of a three-inductor radio-frequency identification (RFID) and transceiver system for potential applications in individual cell tracking and monitoring. The RFID diameter is 22μm and can be naturally internalized by living cells. Using magnetic resonance coupling, the system shows resonance shifts when the RFID is present and also when the RFID loading capacitance changes. It operates at 60 GHz with a high signal magnitude up to − 50 dB and a sensitivity of 0.2. This miniaturized RFID with a high signal magnitude is a promising step toward continuous, real-time monitoring of activities at cellular levels.

Received 6 March 2017

© 2017 American Physical Society

Subscription or payment needed/Requer assinatura our pagamento:

Physical Review Applied

Como a novidade deve ser avaliada em ciência?

Point of View: How should novelty be valued in science?

Barak A Cohen Is a corresponding author

Washington University School of Medicine, United States


Abstract

Scientists are under increasing pressure to do "novel" research. Here I explore whether there are risks to overemphasizing novelty when deciding what constitutes good science. I review studies from the philosophy of science to help understand how important an explicit emphasis on novelty might be for scientific progress. I also review studies from the sociology of science to anticipate how emphasizing novelty might impact the structure and function of the scientific community. I conclude that placing too much value on novelty could have counterproductive effects on both the rate of progress in science and the organization of the scientific community. I finish by recommending that our current emphasis on novelty be replaced by a renewed emphasis on predictive power as a characteristic of good science.


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Recombinação meiótica: nascimento e morte de uma proteína

eLIFE
Meiotic Recombination: Birth and death of a protein

Julie Clément Bernard de Massy Is a corresponding author

CNRS-Université de Montpellier, France

INSIGHT Jul 20, 2017


Abstract

The ways in which recombination sites are determined during meiosis are becoming clearer following a phylogenomic analysis for 225 different species.

Main text

Each of our cells carry two almost identical copies of each of our chromosomes, one copy inherited from each parent. These small differences, which are mainly caused by mutations, make an important contribution to the genetic diversity observed in humans and other species. During meiosis, the chromosomes from each parent pair up and then swap segments of DNA: this process, which is known as meiotic recombination, is important for diversity and is essential for fertility (Hunter, 2015). An important scientific goal is to understand where recombination occurs on chromosomes, what molecular processes are involved, and how meiotic recombination affects the evolution of the genome.

Many components of the molecular machinery involved in meiotic recombination are similar in fungi, plants and animals. However, some features of meiotic recombination have not been conserved across species. For example, in all yeast, plant and vertebrate species studied to date, meiotic recombination happens at specific regions within the chromosomes known as hotspots. In flies and worms, on the other hand, it happens at many more locations within the chromosomes. Moreover, there are two main pathways that direct meiotic recombination to hotspots.
...

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Novas pistas do que pode ter provocado a extinção mais catastrófica mundial há aproximadamente 252 milhões de anos atrás

quinta-feira, agosto 03, 2017

Initial pulse of Siberian Traps sills as the trigger of the end-Permian mass extinction

S. D. Burgess, J. D. Muirhead & S. A. Bowring

Nature Communications 8, Article number: 164 (2017)


Download Citation

Geology Natural hazards Palaeoclimate Volcanology

Received: 31 October 2016 Accepted: 31 May 2017

Published online: 31 July 2017

Source/Fonte: YouTube

Abstract

Mass extinction events are short-lived and characterized by catastrophic biosphere collapse and subsequent reorganization. Their abrupt nature necessitates a similarly short-lived trigger, and large igneous province magmatism is often implicated. However, large igneous provinces are long-lived compared to mass extinctions. Therefore, if large igneous provinces are an effective trigger, a subinterval of magmatism must be responsible for driving deleterious environmental effects. The onset of Earth’s most severe extinction, the end-Permian, coincided with an abrupt change in the emplacement style of the contemporaneous Siberian Traps large igneous province, from dominantly flood lavas to sill intrusions. Here we identify the initial emplacement pulse of laterally extensive sills as the critical deadly interval. Heat from these sills exposed untapped volatile-fertile sediments to contact metamorphism, likely liberating the massive greenhouse gas volumes needed to drive extinction. These observations suggest that large igneous provinces characterized by sill complexes are more likely to trigger catastrophic global environmental change than their flood basalt- and/or dike-dominated counterparts.

Acknowledgements

The authors would like to acknowledge J.T. Hagstrum and B. Schoene for thoughtful comments, and A.R. Van Eaton, A.T. Calvert, M.A. Coble, D.T. Downs, J.A. Vazquez, and C.R. Bacon for discussion during development of this manuscript. S.D.B. would like to acknowledge the USGS Mendenhall postdoctoral program.

Author information

Affiliations

U.S. Geological Survey, Volcano Science Center, 345 Middlefield Road, Mail Stop 910, Menlo Park, CA, 94025, USA

S. D. Burgess

Department of Earth Sciences Syracuse University, 204 Heroy Geology Laboratory, Syracuse, NY, 13244, USA

J. D. Muirhead

Earth, Atmospheric, and Planetary Sciences Department Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA, 02139, USA

S. A. Bowring

Contributions

S.D.B. wrote the manuscript. J.D.M. and S.A.B. contributed intellectual and editorial advisement.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to S. D. Burgess.

Tabela Cronoestratigráfica Internacional v. 2017

quarta-feira, agosto 02, 2017

Como as células humanas mantêm o número correto de cromossomos: mero acaso, fortuita necessidade ou design inteligente?

Aurora-B kinase pathway controls the lateral to end-on conversion of kinetochore-microtubule attachments in human cells

Roshan L. Shrestha, Duccio Conti, Naoka Tamura, Dominique Braun, Revathy A. Ramalingam, Konstanty Cieslinski, Jonas Ries & Viji M. Draviam

Nature Communications 8, Article number: 150 (2017)


Download Citation

Chromosome segregation Mitosis

Received: 19 August 2016 Accepted: 12 June 2017

Published online: 28 July 2017

Source/Fonte: PMG Biology

Abstract

Human chromosomes are captured along microtubule walls (lateral attachment) and then tethered to microtubule-ends (end-on attachment) through a multi-step end-on conversion process. Upstream regulators that orchestrate this remarkable change in the plane of kinetochore-microtubule attachment in human cells are not known. By tracking kinetochore movements and using kinetochore markers specific to attachment status, we reveal a spatially defined role for Aurora-B kinase in retarding the end-on conversion process. To understand how Aurora-B activity is counteracted, we compare the roles of two outer-kinetochore bound phosphatases and find that BubR1-associated PP2A, unlike KNL1-associated PP1, plays a significant role in end-on conversion. Finally, we uncover a novel role for Aurora-B regulated Astrin-SKAP complex in ensuring the correct plane of kinetochore-microtubule attachment. Thus, we identify Aurora-B as a key upstream regulator of end-on conversion in human cells and establish a late role for Astrin-SKAP complex in the end-on conversion process.

Acknowledgements

We thank J. DeLuca for phospho-specific HEC1 antibodies, S. Lens for Mis12-INCENP-GFP and CenpB-INCENP-GFP expression vectors, A. Saurin for KNL1 expression vectors and J. Nilsson for BubR1-expressing cell lines. We thank the Draviam group members and in particular Madeleine Hart for comments on the manuscript. We also thank S. Court, P. Ungerer, U. Matti and A. Sossick for technical and infrastructural support. D.C. is supported through an MRC studentship award (MR/K50127X/1; RG70550) and Cambridge Commonwealth, European and International Trust. This work was supported by research funding from Cancer Research UK Career (C28598/A9787), MRC (MR/K50127X/1; RG70550), Royal Society (JP100104) and QMUL laboratory startup grant.

Author information

Author notes

Roshan L. Shrestha

Present address: Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, 20892, USA

Naoka Tamura

Present address: Barts Cancer Institute, Queen Mary University of London, London, EC1M 6BQ, UK

Roshan L. Shrestha and Duccio Conti contributed equally to this work.

Affiliations

Department of Genetics, University of Cambridge, Cambridge, CB2 3EH, UK

Roshan L. Shrestha, Duccio Conti, Naoka Tamura, Dominique Braun & Viji M. Draviam

School of Biological and Chemical Sciences, Queen Mary University of London, London, E1 4NS, UK

Duccio Conti, Revathy A. Ramalingam & Viji M. Draviam

European Molecular Biology Laboratory, Cell Biology and Biophysics Unit, Meyerhofstrasse 1, Heidelberg, Germany

Konstanty Cieslinski & Jonas Ries

Contributions

D.C. contributed to data in Fig. 4, Supplementary Figs. 5, 6 and 7, and the illustration of model in Fig. 6. R.A.R. and N.T. contributed to Supplementary Fig. 1A and reagents in Supplementary Fig. 8B, respectively. J.R., D.C. and K.C. contributed to super-resolution images in Supplementary Fig. 7B. R.L.S. contributed to data in all other figures. Manuscript text was written by V.M.D. and revised together with R.L.S., D.C. and N.T.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Viji M. Draviam.

Encontrando a estrutura causal na tabela representativa dos elementos químicos

Finding causal structure

Ross, Lauren N. (2017) Finding causal structure. [Preprint]

rossl@uci.edu

Source/Fonte: Manual de Química

Abstract

The periodic table of elements represents and organizes all known chemical elements on the basis of their properties. While the importance of this table in chemistry is uncontroversial the role that it plays in scientific reasoning remains heavily disputed. Many philosophers deny the explanatory role of the periodic table, while insisting that it is "merely" classificatory (Shapere 1977, 534-5; Scerri 1997a, 239). In particular, it has been claimed that the table doesn’t figure in causal explanation because it "does not reveal causal structure" (Woody 2014, 143). This paper argues that the modern periodic table does reveal causal structure in the sense of containing causal information that figures in explanations in chemistry. However, this analysis suggests that the earliest versions of the table did serve more of a classificatory role, as they lack the causal structure present in modern versions.

FREE PDF GRATIS: PhilSci

Quer analisar milhões de artigos científicos de uma vez? Seus problemas acabaram!!!

terça-feira, agosto 01, 2017


Text mining of 15 million full-text scientific articles

David Westergaard, Hans-Henrik Stærfeldt, Christian Tønsberg, Lars Juhl Jensen,  Søren Brunak

doi: https://doi.org/10.1101/162099

This article is a preprint and has not been peer-reviewed [what does this mean?].


Abstract

Across academia and industry, text mining has become a popular strategy for keeping up with the rapid growth of the scientific literature. Text mining of the scientific literature has mostly been carried out on collections of abstracts, due to their availability. Here we present an analysis of 15 million English scientific full-text articles published during the period 1823-2016. We describe the development in article length and publication sub-topics during these nearly 250 years. We showcase the potential of text mining by extracting published protein-protein, disease-gene, and protein subcellular associations using a named entity recognition system, and quantitatively report on their accuracy using gold standard benchmark data sets. We subsequently compare the findings to corresponding results obtained on 16.5 million abstracts included in MEDLINE and show that text mining of full-text articles consistently outperforms using abstracts only.

Copyright 
The copyright holder for this preprint is the author/funder. It is made available under a CC-BY 4.0 International license.

FREE PDF GRATIS: bioRxiv

Sequenciamento de genomas de tardígrados revela sinais conflitantes de relação evolucionária

Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus

Yuki Yoshida , Georgios Koutsovoulos , Dominik R. Laetsch, Lewis Stevens, Sujai Kumar, Daiki D. Horikawa, Kyoko Ishino, Shiori Komine, Takekazu Kunieda, Masaru Tomita, Mark Blaxter , Kazuharu Arakawa 



Abstract

Tardigrada, a phylum of meiofaunal organisms, have been at the center of discussions of the evolution of Metazoa, the biology of survival in extreme environments, and the role of horizontal gene transfer in animal evolution. Tardigrada are placed as sisters to Arthropoda and Onychophora (velvet worms) in the superphylum Panarthropoda by morphological analyses, but many molecular phylogenies fail to recover this relationship. This tension between molecular and morphological understanding may be very revealing of the mode and patterns of evolution of major groups. Limnoterrestrial tardigrades display extreme cryptobiotic abilities, including anhydrobiosis and cryobiosis, as do bdelloid rotifers, nematodes, and other animals of the water film. These extremophile behaviors challenge understanding of normal, aqueous physiology: how does a multicellular organism avoid lethal cellular collapse in the absence of liquid water? Meiofaunal species have been reported to have elevated levels of horizontal gene transfer (HGT) events, but how important this is in evolution, and particularly in the evolution of extremophile physiology, is unclear. To address these questions, we resequenced and reassembled the genome of H. dujardini, a limnoterrestrial tardigrade that can undergo anhydrobiosis only after extensive pre-exposure to drying conditions, and compared it to the genome of R. varieornatus, a related species with tolerance to rapid desiccation. The 2 species had contrasting gene expression responses to anhydrobiosis, with major transcriptional change in H. dujardini but limited regulation in R. varieornatus. We identified few horizontally transferred genes, but some of these were shown to be involved in entry into anhydrobiosis. Whole-genome molecular phylogenies supported a Tardigrada+Nematoda relationship over Tardigrada+Arthropoda, but rare genomic changes tended to support Tardigrada+Arthropoda.

Author summary

Tardigrades are justly famous for their abilities to withstand environmental extremes. Many freshwater and terrestrial species can undergo anhydrobiosis—life without water—and thereby withstand desiccation, freezing, and other insults. We explored the comparative biology of anhydrobiosis in 2 species of tardigrade that differ in the mechanisms they use to enter anhydrobiosis. Using newly assembled and improved genomes, we find that Ramazzottius varieornatus, a species that can withstand rapid desiccation, differs from Hypsibius dujardini, a species that requires extended preconditioning, in not showing a major transcriptional response to anhydrobiosis induction. We identified a number of genetic systems in the tardigrades that likely play conserved, central roles in anhydrobiosis as well as species-unique components. Compared to previous estimates, our improved genomes show much reduced levels of horizontal gene transfer into tardigrade genomes, but some of the identified horizontal gene transfer (HGT) genes appear to be involved in anhydrobiosis. Using the improved genomes, we explored the evolutionary relationships of tardigrades and other molting animals, particularly nematodes and arthropods. We identified conflicting signals between sequence-based analyses, which found a relationship between tardigrades and nematodes, and analyses based on rare genomic changes, which tended to support the traditional tardigrade-arthropod link.

Citation: Yoshida Y, Koutsovoulos G, Laetsch DR, Stevens L, Kumar S, Horikawa DD, et al. (2017) Comparative genomics of the tardigrades Hypsibius dujardini and Ramazzottius varieornatus. PLoS Biol 15(7): e2002266. https://doi.org/10.1371/journal.pbio.2002266

Academic Editor: Chris Tyler-Smith, The Wellcome Trust Sanger Institute, United Kingdom of Great Britain and Northern Ireland

Received: February 20, 2017; Accepted: June 23, 2017; Published: July 27, 2017

Copyright: © 2017 Yoshida et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All raw data have been deposited in the relevant INSDC databases. The H. dujardini assembly (nHd3.1) has been deposited at DDBJ/ENA/GenBank under the accession MTYJ00000000. All mRNA-Seq data have been uploaded to GEO and SRA under the accession IDs GSE94295 and SRP098585, and the PacBio raw reads and miRNA-Seq data into SRA under the accession IDs SRX2495681 and SRX2495676. Accession IDs for each individual sequence file are given in Supplementary S1 Table. We have established a dedicated Ensembl genome browser (version 85) using the EasyImport pipeline and imported the H. dujardini genome and annotations described in this paper and the new gene predictions for R. varieornatus. These data are available to browse, query, and download at http://www.tardigrades.org.

Funding: University of Edinburgh. Baillie Gifford Studentship for LS. James Hutton Institute/School of Biological Sciences University of Edinburgh. Studentship for DRL. Japan Society for the Promotion of Science (JSPS) https://www.jsps.go.jp (grant number 22681029). Grant-in-Aid for Young Scientists for KA. BBSRC (grant number BB/K020161/1). Award for SK. Tomy Digital Biology Co., Ltd. Sequencing Grant Program For PacBio sequencing for KA. The Sumitomo Foundation http://www.sumitomo.or.jp (grant number 140340). Grant for Basic Science Research Projects for KA. Yamagata Prefectural Government and Tsuruoka City, Japan. Funding for KA and MT. BBSRC (grant number COD17089). PhD studentship for GK. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

Competing interests: The authors have declared that no competing interests exist.

Abbreviations: AMPK, 5' adenosine monophosphate-activated protein kinase; API, application-programming interface; ATM, ataxia-telangiectasia mutated; ATR, ataxia telangiectasia and Rad3-related protein; BER, base excision repair; BLAST, Basic Local Alignment Search Tool; BSC1, bypass of stop codon protein 1; BUSCO, Benchmarking Universal Single-Copy Orthologs; CAHS, cytosolic abundant heat soluble; CaM, calmodulin; CASP, caspase; CATE, catalase; CBF, C-repeat-binding factor; CDS, coding sequence; CEGMA, Core Eukaryotic Genes Mapping Approach; CHK, checkpoint kinase; CNG, cyclic nucleotide-gated channel; Dsup, damage suppressor; EGF, epidermal growth factor; GPCR, G-protein-coupled receptor; GST, glutathione S-transferase; GTP, guanosine-5'-triphosphate; GTR+G, General Time Reversible model with Gamma distribution of rates model; GTR-CAT+G, GTR plus rate categories model; HGT, horizontal gene transfer; HR, homologous recombination; HSP, heat shock protein; INSDC, International Nucleotide Sequence Database Collaboration; IPR, InterPro domain identifier; KAAS, KEGG Automatic Annotation Server; KEGG, Kyoto Encyclopedia of Genes and Genomes; LDL, low-density lipoprotein; MAHS, mitochondrial abundant heat soluble protein; MCL, Markov Cluster Algorithm; miRNA-Seq, microRNA sequencing; MMR, mismatch repair; mTOR, mechanistic target of rapamycin; NER, nucleotide excision repair; NHEJ, nonhomologous end joining; PacBio, Pacific Biosciences; PARP, poly(ADP-ribose) polymerase; PF, PFam identifier; PHD, plant homeodomain; RAxML, Randomized Axelerated Maximum Likelihood; RH, relative humidity; RNAi, RNA interference; RNA-Seq, RNA sequencing; ROS, reactive oxygen species; RyLEAM, late embryogenesis abundant protein mitochondrial; SAHS, secretory abundant heat soluble; SIRT1, sirtuin 1; SOD, superoxide dismutase; SRA, Sequence Read Archive; TPM, transcript(s) per million; TPS, trehalose-6-phosphatase synthase; TSC1/2, tuberous sclerosis 1/2; UDP, uridine diphosphate; UGT, UDP-glucuronosyltransferase; VHL, von Hippel-Lindau tumor suppressor

FREE PDF GRATIS: PLoS Biology

A origem microscópica da termodinâmica: o papel da entropia em um sistema quântico

segunda-feira, julho 31, 2017


Vincenzo Alba a,1 and Pasquale Calabrese a  

Author Affiliations

a International School for Advanced Studies, Istituto Nazionale di Fisica Nucleare, Sezione di Trieste, 34136 Trieste, Italy

Edited by Subir Sachdev, Harvard University, Cambridge, MA, and approved June 6, 2017 (received for review March 3, 2017)


Significance

Understanding how statistical ensembles arise from the out-of-equilibrium dynamics of isolated pure systems has been a fascinating question since the early days of quantum mechanics. Recently, it has been proposed that the thermodynamic entropy of the long-time statistical ensemble is the stationary entanglement of a large subsystem in an infinite system. Here, we combine this concept with the quasiparticle picture of the entanglement evolution and integrability-based knowledge of the steady state to obtain exact analytical predictions for the time evolution of the entanglement in arbitrary 1D integrable models. These results explicitly show the transformation between the entanglement and thermodynamic entropy during the time evolution. Thus, entanglement is the natural witness for the generalized microcanonical principle underlying relaxation in integrable models.

Abstract

Entanglement and entropy are key concepts standing at the foundations of quantum and statistical mechanics. Recently, the study of quantum quenches revealed that these concepts are intricately intertwined. Although the unitary time evolution ensuing from a pure state maintains the system at zero entropy, local properties at long times are captured by a statistical ensemble with nonzero thermodynamic entropy, which is the entanglement accumulated during the dynamics. Therefore, understanding the entanglement evolution unveils how thermodynamics emerges in isolated systems. Alas, an exact computation of the entanglement dynamics was available so far only for noninteracting systems, whereas it was deemed unfeasible for interacting ones. Here, we show that the standard quasiparticle picture of the entanglement evolution, complemented with integrability-based knowledge of the steady state and its excitations, leads to a complete understanding of the entanglement dynamics in the space–time scaling limit. We thoroughly check our result for the paradigmatic Heisenberg chain.

entanglement quantum quench integrability thermodynamics

Footnotes

1 To whom correspondence should be addressed. Email: valba@sissa.it.

Author contributions: V.A. and P.C. designed research, performed research, analyzed data, and wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1703516114/-/DCSupplemental.

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E os cananeus não foram totalmente destruídos conforme afirmado em texto oriental milenar

sexta-feira, julho 28, 2017

Continuity and Admixture in the Last Five Millennia of Levantine History from Ancient Canaanite and Present-Day Lebanese Genome Sequences

Marc Haber9,Claude Doumet-Serhal9, Christiana Scheib9, Yali Xue, Petr Danecek, Massimo Mezzavilla, Sonia Youhanna, Rui Martiniano, Javier Prado-Martinez, Michał Szpak, Elizabeth Matisoo-Smith, Holger Schutkowski, Richard Mikulski, Pierre Zalloua, Toomas Kivisild, Chris Tyler-Smith

9These authors contributed equally to this work

Published Online: July 27, 2017

Publication stage: In Press Corrected Proof

Open Access


Open access funded by Wellcome Trust

Article Info

Publication History

Published: July 27, 2017 Accepted: June 27, 2017

Received: May 25, 2017

User License

Creative Commons Attribution (CC BY 4.0)

Source/Fonte: The New York Times

The Canaanites inhabited the Levant region during the Bronze Age and established a culture that became influential in the Near East and beyond. However, the Canaanites, unlike most other ancient Near Easterners of this period, left few surviving textual records and thus their origin and relationship to ancient and present-day populations remain unclear. In this study, we sequenced five whole genomes from ∼3,700-year-old individuals from the city of Sidon, a major Canaanite city-state on the Eastern Mediterranean coast. We also sequenced the genomes of 99 individuals from present-day Lebanon to catalog modern Levantine genetic diversity. We find that a Bronze Age Canaanite-related ancestry was widespread in the region, shared among urban populations inhabiting the coast (Sidon) and inland populations (Jordan) who likely lived in farming societies or were pastoral nomads. This Canaanite-related ancestry derived from mixture between local Neolithic populations and eastern migrants genetically related to Chalcolithic Iranians. We estimate, using linkage-disequilibrium decay patterns, that admixture occurred 6,600–3,550 years ago, coinciding with recorded massive population movements in Mesopotamia during the mid-Holocene. We show that present-day Lebanese derive most of their ancestry from a Canaanite-related population, which therefore implies substantial genetic continuity in the Levant since at least the Bronze Age. In addition, we find Eurasian ancestry in the Lebanese not present in Bronze Age or earlier Levantines. We estimate that this Eurasian ancestry arrived in the Levant around 3,750–2,170 years ago during a period of successive conquests by distant populations.