Web da velocidade cósmica

segunda-feira, agosto 21, 2017

The Cosmic V-Web

Daniel Pomarède1, Yehuda Hoffman2, Hélène M. Courtois3, and R. Brent Tully4

Published 2017 August 10 • © 2017. The American Astronomical Society. All rights reserved.

The Astrophysical Journal, Volume 845, Number 1


Abstract

The network of filaments with embedded clusters surrounding voids, which has been seen in maps derived from redshift surveys and reproduced in simulations, has been referred to as the cosmic web. A complementary description is provided by considering the shear in the velocity field of galaxies. The eigenvalues of the shear provide information regarding whether or not a region is collapsing in three dimensions, which is the condition for a knot, expanding in three dimensions, which is the condition for a void, or in the intermediate condition of a filament or sheet. The structures that are quantitatively defined by the eigenvalues can be approximated by iso-contours that provide a visual representation of the cosmic velocity (V) web. The current application is based on radial peculiar velocities from the Cosmicflows-2 collection of distances. The three-dimensional velocity field is constructed using the Wiener filter methodology in the linear approximation. Eigenvalues of the velocity shear are calculated at each point on a grid. Here, knots and filaments are visualized across a local domain of diameter.

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Compreendendo a resistência a antibióticos usando métodos experimentais e computacionais

Antibiotics Disrupt Coordination between Transcriptional and Phenotypic Stress Responses in Pathogenic Bacteria

Paul A. Jensen 2,3, Zeyu Zhu 3, Tim van Opijnen 4,

2Present address: Department of Bioengineering and Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, IL, USA

3These authors contributed equally

4Lead Contact

Open Access


Article Info

Publication History

Published: August 15, 2017 Accepted: July 23, 2017

Received in revised form: June 28, 2017 Received: March 10, 2017

User License

Creative Commons Attribution – NonCommercial – NoDerivs (CC BY-NC-ND 4.0) 


Highlights

Phenotypic and transcriptional stress responses consist of distinct gene sets

• Metabolic network modeling reveals co-localization of stress-response gene sets

• Different stressors trigger responses indicative of their evolutionary history

• Separating expression and phenotype protects from erratic transcriptional behavior

Summary

Bacterial genes that change in expression upon environmental disturbance have commonly been seen as those that must also phenotypically matter. However, several studies suggest that differentially expressed genes are rarely phenotypically important. We demonstrate, for Gram-positive and Gram-negative bacteria, that these seemingly uncoordinated gene sets are involved in responses that can be linked through topological network analysis. However, the level of coordination is stress dependent. While a well-coordinated response is triggered in response to nutrient stress, antibiotics trigger an uncoordinated response in which transcriptionally and phenotypically important genes are neither linked spatially nor in their magnitude. Moreover, a gene expression meta-analysis reveals that genes with large fitness changes during stress have low transcriptional variation across hundreds of other conditions, and vice versa. Our work suggests that cellular responses can be understood through network models that incorporate regulatory and genetic relationships, which could aid drug target predictions and genetic network engineering.

FREE PDF GRATIS: Cell Reports

A tribo esquecida: cientistas como escritores

sábado, agosto 19, 2017

The Forgotten Tribe: Scientists as Writers

By Lisa Emerson

Copy edited by Julia Smith. Designed by Mike Palmquist.

In The Forgotten Tribe: Scientists as Writers, Lisa Emerson offers an important corrective to the view that scientists are "poor writers, unnecessarily opaque, not interested in writing, and in need of remediation." She argues that scientists are among "the most sophisticated and flexible writers in the academy, often writing for a wider range of audiences (their immediate disciplinary peers, peers in adjacent fields, a broad scientific audience, industry, and a range of public audiences including social media) than most other faculty." Moreover, she notes, the often collaborative and multidisciplinary nature of their work results in writing practices that "may be more socially complex, and require more articulation, mediation, and interpersonal communication, and more use of advanced media and technology than those of faculty in other disciplines."

Drawing on extensive interviews with scientists, Emerson argues that writing scholars have "engaged in a form of cultural appropriation" that has worked against a deeper understanding of the contexts in which scientists work and the considerations they bring to their writing. Emerson grounds her analysis in the voices of scientists in a way that allows us to understand not only how they approach writing but also how we might usefully teach writing in the sciences. The Forgotten Tribe offers a valuable contribution to our understanding of scientific writing, allowing us to hear voices that are seldom included in our discussions of this critical area.

About the Author

Lisa Emerson is Associate Professor in the School of English and Media Studies at Massey University. Her scholarly interests include science writing, scientists as writers, academic writing, plagiarism, and transitions to academic literacy. Her work has appeared in Double Helix, Curriculum Matters, and Higher Education Research and Development as well as in edited collections.

Publication Information: Emerson, Lisa. (2016). The Forgotten Tribe: Scientists as Writers. Perspectives on Writing. Fort Collins, Colorado: The WAC Clearinghouse and University Press of Colorado. Available at https://wac.colostate.edu/books/emerson/

Online Publication Date: June 18, 2016.

Print Publication Date: March 1, 2017.

Contact Information:

Lisa Emerson: L.Emerson@massey.ac.nz

FREE PDF GRATIS: The WAC Clearinghouse 

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Superfície ácida em Marte: inabitável

Perchlorates on Mars enhance the bacteriocidal effects of UV light

Jennifer Wadsworth & Charles S. Cockell

Scientific Reports 7, Article number: 4662 (2017)


Download Citation

Astrobiology Soil microbiology

Received: 15 February 2017 Accepted: 22 May 2017

Published online: 06 July 2017

Source/Fonte: NASA

Abstract

Perchlorates have been identified on the surface of Mars. This has prompted speculation of what their influence would be on habitability. We show that when irradiated with a simulated Martian UV flux, perchlorates become bacteriocidal. At concentrations associated with Martian surface regolith, vegetative cells of Bacillus subtilis in Martian analogue environments lost viability within minutes. Two other components of the Martian surface, iron oxides and hydrogen peroxide, act in synergy with irradiated perchlorates to cause a 10.8-fold increase in cell death when compared to cells exposed to UV radiation after 60 seconds of exposure. These data show that the combined effects of at least three components of the Martian surface, activated by surface photochemistry, render the present-day surface more uninhabitable than previously thought, and demonstrate the low probability of survival of biological contaminants released from robotic and human exploration missions.

Acknowledgements

We acknowledge support from the UK Space Agency for this work under the Aurora program and support for the PhD funding for J. Wadsworth. Support was also provided by Science and Technology Facilities Council (STFC) Grant no. ST/M001261/1.

Author information

Affiliations

UK Centre for Astrobiology, School of Physics and Astronomy, University of Edinburgh, Edinburgh, EH10 4EP, UK

Jennifer Wadsworth & Charles S. Cockell

Contributions

C.S.C. & J.W. designed the project; J.W. performed the research and wrote the manuscript.

Competing Interests

The authors declare that they have no competing interests.

Corresponding author

Correspondence to Jennifer Wadsworth.

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Por que a Terra é especial e o que isso significa para a vida no universo?

‘Lucky Planet: Why Earth is Exceptional, and What That Means for Life in the Universe’ by Dave Waltham
Posted on Jan 27, 2015 in Book reviews 

In Lucky Planet, David Waltham argues that Earth’s teeming, complex biosphere is a rare anomaly in an almost sterile cosmos. From the start, he acknowledges that many of us have strong intuitions to the contrary: isn’t Earth just another planet orbiting just another star? There are trillions of stars; most have planets, many of them in the so-called habitable zone. Why should the one planet on which we happen to find ourselves be special? The answer to this, Waltham explains, is that we find ourselves on it. Wherever intelligent observers arise, they will necessarily find conditions just right for their having arisen, even if those conditions are vanishingly rare. This “anthropic selection effect” pre-determines the kind of world we look out on, giving us the “most severe case of observational bias in the history of science”.
This book shows that Earth has indeed been blessed with a highly stable and clement climate over billions of years despite regular geological and biological upheavals and the steady brightening of the sun. This is a remarkable fact; “a warming trend as small as 1 °C every 100 million years would have been enough to make our world uninhabitable by now.” The conventional explanation (“Gaia theory”) is that Earth naturally self-regulates: changes in the sun’s brightness or Earth’s albedo are automatically compensated by negative feedback mechanisms, working like a thermostat. When global temperatures increase, for example, so does the rate at which volcanic rocks are weathered, a process that pulls CO2 out of the atmosphere, diminishing the greenhouse effect and minimising the change in temperature. The result is a dynamic equilibrium.
Waltham agrees that such “Gaian processes must have played a substantial role” in Earth’s history. But he points out that any planet capable of producing observers like us must turn out to have been climatically stable over the several-billion-year timescale required for our evolution, even if purely by coincidence. The anthropic selection effect negates the need to invoke a strong Gaian thermostat. It may be that oxygenic photosynthesis evolved and spread at just the right time and rate to cancel the effect of a rising solar heat flux by removing methane from the atmosphere. Likewise, a steady increase in biological weathering may have drawn down just the right amount of CO2. Earth’s long-term habitability may have been sustained by nothing more than a series of fortunate coincidences like these.
Waltham draws on a wide range of evidence from geology, astronomy and climate modeling to substantiate this claim. The chapter on the Moon’s role in Earth’s habitability—based on Waltham’s own research—is particularly intriguing, and shows that far from stabilizing the Earth’s axis of rotation (as often claimed), our Moon is almost large enough to destabilize it. On the other hand, if the Moon had been much smaller (or absent), Earth could have been cooler and more prone to ice ages. It seems that we have a “Goldilocks” Moon, a coincidence neatly explained by anthropic selection.
Those who claim that the Earth is special are sometimes accused of anthropocentric arrogance. One could, of course, throw the same accusation back at those who expect to find Earth-like planets throughout the universe—as Waltham points out, there are many different ways to build a planet. But the tone of this book is measured, cautious, philosophical and pleasantly light-hearted. Waltham is respectful of his scientific opponents, and even humorously self-deprecating at times.
For the sake of balance, I would like to offer a few small criticisms. It is occasionally unclear whether Waltham’s anthropic arguments concern the rareness of life itself, of complex multicellular life, or of humanly intelligent observers. The long discussion of the cosmological version of the anthropic principle seems a little digressive, and the omission of any reference to the Fermi Paradox or to Nick Bostrom’s related and important work on “great filters” looks like an oversight. These are minor and somewhat academic complaints, however. Lucky Planetis a persuasive and pleasurable read.
Icon Books, May 2014 / £11.99 (hardcover) / More details
Reviewed by: Sean McMahon, Yale University

O mito da evolução - genes cantando: "O sr. Darwin entendeu errado"

quinta-feira, agosto 17, 2017



The Evolution Myth 

OR, THE GENES CRY OUT THEIR URGENT SONG, MISTER DARWIN GOT IT WRONG

The Evolution Myth

JIRÍ A. MEJSNAR

Distributed for Karolinum Press, Charles University

116 pages | 20 halftones, 8 charts | 5 x 8 | © 2014



The origins of life, species, and man continue to interest scientists and stir debate among the general public more than one hundred and fifty years after Charles Darwin published On the Origin of Species. The Evolution Myth approaches the subject with two intertwined objectives. Jirí A. Mejsnar first sets out to convey the advances made in cosmology, molecular biology, genetics, and other sciences that have enabled us to change our views on our origins and our relationship with the universe. Scientific advances now allow us to calculate, for example, the age of the universe, the period in which biblical Eve lived, and, with good justification, to reconsider the possibility that the Neanderthals and primates might be our ancestors.

The author’s second objective is to use biology to explain why evolution cannot have taken place in the way that is most commonly assumed. Mejsnar builds his case around gene stability and on the sophisticated modern techniques for gene manipulation, the complexity of which make these modified genes inaccessible to nature. Development of life on Earth is a discontinuous, saltatory progression that results in stages following from preceding latent periods in which new forms suddenly appear and possess new types of genome. This, the author argues, is difficult to reconcile with the hypothesis of continuous biological evolution based on the natural selection of random variations.

Taking a new approach to a much-debated subject, Mejsnar distills complex information into a readable style. The result is a book that is sure to get readers talking.

+++++


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NOTA CAUSTICANTE DESTE BLOGGER:

Gente, alguém me belisque - a renomada University of Chicago Press publicou este livro? Mas não tem um mantra que diz: nada em biologia faz sentido a não ser à luz da evolução? E a evolução é um mito? Pode isso, Arnaldo? A regra é clara: a publicação de um livro polêmico e controverso desse, indica que a teoria da evolução já não é assim uma Brastemp no contexto de justificação teórica!

Darwin kaput! Darwin morreu! Viva Darwin!!!

Pano rápido!!!

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

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£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

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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.