Quem sabe, entende e faz ciência polariza mais sobre tópicos científicos controversos!!!

quarta-feira, agosto 23, 2017

Individuals with greater science literacy and education have more polarized beliefs on controversial science topics

Caitlin Drummond a,1 and Baruch Fischhoff b,c  

Author Affiliations

aDepartment of Social and Decision Sciences, Carnegie Mellon University, Pittsburgh, PA 15213;

bDepartment of Engineering and Public Policy, Carnegie Mellon University, Pittsburgh, PA 15213;

cInstitute for Politics and Strategy, Carnegie Mellon University, Pittsburgh, PA 15213

Edited by Roger E. Kasperson, Clark University, Worcester, MA, and approved July 19, 2017 (received for review March 23, 2017)

Edited by Roger E. Kasperson, Clark University, Worcester, MA, and approved July 19, 2017 (received for review March 23, 2017)



Significance

Public opinion toward some science and technology issues is polarized along religious and political lines. We investigate whether people with more education and greater science knowledge tend to express beliefs that are more (or less) polarized. Using data from the nationally representative General Social Survey, we find that more knowledgeable individuals are more likely to express beliefs consistent with their religious or political identities for issues that have become polarized along those lines (e.g., stem cell research, human evolution), but not for issues that are controversial on other grounds (e.g., genetically modified foods). These patterns suggest that scientific knowledge may facilitate defending positions motivated by nonscientific concerns.

Abstract

Although Americans generally hold science in high regard and respect its findings, for some contested issues, such as the existence of anthropogenic climate change, public opinion is polarized along religious and political lines. We ask whether individuals with more general education and greater science knowledge, measured in terms of science education and science literacy, display more (or less) polarized beliefs on several such issues. We report secondary analyses of a nationally representative dataset (the General Social Survey), examining the predictors of beliefs regarding six potentially controversial issues. We find that beliefs are correlated with both political and religious identity for stem cell research, the Big Bang, and human evolution, and with political identity alone on climate change. Individuals with greater education, science education, and science literacy display more polarized beliefs on these issues. We find little evidence of political or religious polarization regarding nanotechnology and genetically modified foods. On all six topics, people who trust the scientific enterprise more are also more likely to accept its findings. We discuss the causal mechanisms that might underlie the correlation between education and identity-based polarization.

science literacy polarization science communication science education trust

Footnotes

1To whom correspondence should be addressed. Email: cdrummon@andrew.cmu.edu.

Author contributions: C.D. and B.F. designed research; C.D. performed research; C.D. analyzed data; and C.D. and B.F. 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.1704882114/-/DCSupplemental.

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Epigenômica de plantas - decifrando os mecanismos da herança epigenética e plasticidade em plantas

Plant epigenomics—deciphering the mechanisms of epigenetic inheritance and plasticity in plants

Claudia Köhler and Nathan Springer

Genome Biology 201718:132



Source/Fonte: The Scientist

EDITORIAL

Published: 6 July 2017

It is an exciting time to study plant epigenetics. Technological advances are providing unprecedented opportunities to monitor chromatin modifications, gene expression, and genome structure. Many classical epigenetic phenomena (transposable element inactivation, imprinting, paramutation, transgene silencing, and co-suppression) were first documented in plants. Combined with classical genetic studies, newly available sequencing technologies are facilitating the study of these and other epigenetic phenomena at a level of detail that was unthinkable only a few years ago. Studies of epigenetics in plants are of great importance. Plants are heavily dependent upon changes in gene expression in order to respond to environmental stimuli, and chromatin-based regulation of gene expression is likely crucial for these responses. Furthermore, the level of chromatin ‘resetting’ during sexual reproduction appears to be lower in plants in comparison with animal species [1, 2], potentially allowing inheritance of epimutations acquired during plant life. In addition, many plant species can propagate asexually and produce vegetative clones, providing opportunities for mitotic inheritance of epigenetic states leading to important traits. This issue of Genome Biology highlights exciting progress in many areas of plant epigenetics and epigenomics.

DNA methylation is a well-studied chromatin modification in animals and plants that can be stably inherited, both following cell divisions and, to some extent, across generations. DNA methylation can be monitored at high resolution by using sodium bisulfite treatment of DNA, followed by next-generation sequencing. Cytosines in different sequence contexts (CG, CHG, and CHH (where H is any base other than G)) and at different types of loci in plant genomes can be targeted by DNA methylation. This modification has likely evolved as a mechanism to silence transposons, which are ‘genomic parasites’ invading the genome of their hosts. The vast majority of transposons are highly methylated and are likely a primary target for epigenetic silencing. However, the repetitive nature of transposons and the fact that they generate large insertion/deletion polymorphisms among genotypes has led to difficulties in monitoring the link between transposon polymorphism and DNA methylation variation. Daron and Slotkin describe a new tool to study the interactions between transposon methylation and transposon insertions using whole-genome bisulfite sequencing datasets [3]. This type of analysis is expected to be very useful in documenting the role of genetic and epigenetic variation in DNA methylation among individuals of the same species.

The RNA-dependent DNA methylation (RdDM) pathway is crucial for maintenance of CHH methylation and requires the plant-specific RNA polymerases IV and V (Pol IV and V, respectively). Pol IV generates precursor transcripts of 24-nt small RNAs (sRNAs) that target scaffold transcripts from Pol V by sequence complementarity and recruit the domains rearranged methyltransferase 2 [4]. A rather unexpected link between RdDM and the chromatin remodeling factor PICKLE (PKL) is revealed by Zhang and colleagues, who report that PKL is required for the accumulation of transcripts generated by Pol V and for the positioning of Pol V-stabilized nucleosomes at a subset of RdDM target loci [5]. These findings link nucleosome positioning with the initiation of RdDM, consistent with the previously proposed role of SWI/SNF chromatin remodeling complexes in establishing positioned nucleosomes on specific loci primed for RdDM [6]. It is well established that PKL regulates plant development and, in particular, regulates the access of Polycomb-group proteins to its targets [7]. Likewise, SWI/SNF complexes have well-described roles in plant development [7], extended by the study of Benhamed and colleagues in this issue showing that the SWI/SNF complex core subunit BAF60 regulates access of the Phytochrome Interacting Factor 4 (PIF4) to nucleosome-free regions [8]. The dual functional role of chromatin-remodeling factors in regulating plant development and RdDM suggests that both processes are more closely connected than is widely appreciated.
...

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Hierarquias na organização do genoma eucariótico: insights da teoria de polímeros e simulações

Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations

Balaji VS Iyer, Martin Kenward and Gaurav AryaEmail author

BMC Biophysics20114:8

https://doi.org/10.1186/2046-1682-4-8 © Iyer et al; licensee BioMed Central Ltd. 2011 ReadCube 

Received: 7 January 2011Accepted: 15 April 2011Published: 15 April 2011

Source/Fonte: BuhrooZafar 

Abstract

Eukaryotic genomes possess an elaborate and dynamic higher-order structure within the limiting confines of the cell nucleus. Knowledge of the physical principles and the molecular machinery that govern the 3D organization of this structure and its regulation are key to understanding the relationship between genome structure and function. Elegant microscopy and chromosome conformation capture techniques supported by analysis based on polymer models are important steps in this direction. Here, we review results from these efforts and provide some additional insights that elucidate the relationship between structure and function at different hierarchical levels of genome organization.

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A organização tridimensional do genoma de Drosophila melanogaster através da integração de dados

The three-dimensional genome organization of Drosophila melanogaster through data integration

Qingjiao Li†, Harianto Tjong†, Xiao Li, Ke Gong, Xianghong Jasmine Zhou, Irene Chiolo and Frank Alber

†Contributed equally

Genome Biology201718:145

https://doi.org/10.1186/s13059-017-1264-5 ©  The Author(s). 2017 ReadCube

Received: 26 December 2016Accepted: 26 June 2017Published: 31 July 2017



Abstract

Background

Genome structures are dynamic and non-randomly organized in the nucleus of higher eukaryotes. To maximize the accuracy and coverage of three-dimensional genome structural models, it is important to integrate all available sources of experimental information about a genome’s organization. It remains a major challenge to integrate such data from various complementary experimental methods. Here, we present an approach for data integration to determine a population of complete three-dimensional genome structures that are statistically consistent with data from both genome-wide chromosome conformation capture (Hi-C) and lamina-DamID experiments.

Results

Our structures resolve the genome at the resolution of topological domains, and reproduce simultaneously both sets of experimental data. Importantly, this data deconvolution framework allows for structural heterogeneity between cells, and hence accounts for the expected plasticity of genome structures. As a case study we choose Drosophila melanogaster embryonic cells, for which both data types are available. Our three-dimensional genome structures have strong predictive power for structural features not directly visible in the initial data sets, and reproduce experimental hallmarks of the D. melanogaster genome organization from independent and our own imaging experiments. Also they reveal a number of new insights about genome organization and its functional relevance, including the preferred locations of heterochromatic satellites of different chromosomes, and observations about homologous pairing that cannot be directly observed in the original Hi-C or lamina-DamID data.

Conclusions

Our approach allows systematic integration of Hi-C and lamina-DamID data for complete three-dimensional genome structure calculation, while also explicitly considering genome structural variability.

Keywords

3D genome structure Higher order genome organization Population-based modeling Data integration Hi-C Lamina-DamID Homologous pairing Drosophila melanogaster Heterochromatin

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Pesquisa revela que dormir pode ajudar a memória

Formation and suppression of acoustic memories during human sleep

Thomas Andrillon, Daniel Pressnitzer, Damien Léger & Sid Kouider

Nature Communications 8, Article number: 179 (2017)

doi:10.1038/s41467-017-00071-z 

Human behaviour Perception Sleep

Received: 13 April 2016

Accepted: 30 May 2017

Published online: 08 August 2017



Abstract

Sleep and memory are deeply related, but the nature of the neuroplastic processes induced by sleep remains unclear. Here, we report that memory traces can be both formed or suppressed during sleep, depending on sleep phase. We played samples of acoustic noise to sleeping human listeners. Repeated exposure to a novel noise during Rapid Eye Movements (REM) or light non-REM (NREM) sleep leads to improvements in behavioral performance upon awakening. Strikingly, the same exposure during deep NREM sleep leads to impaired performance upon awakening. Electroencephalographic markers of learning extracted during sleep confirm a dissociation between sleep facilitating memory formation (light NREM and REM sleep) and sleep suppressing learning (deep NREM sleep). We can trace these neural changes back to transient sleep events, such as spindles for memory facilitation and slow waves for suppression. Thus, highly selective memory processes are active during human sleep, with intertwined episodes of facilitative and suppressive plasticity.

Acknowledgements

This research was supported by ANR grants (ANR-10-LABX-0087 and ANR-10-IDEX-0001-02), by the European Research Council (ERC project METAWARE to S.K. and ERC project ADAM to D.P.), by the EU H2020 program (COCOHA #644732 to DP), and by the Ministère de la Recherche and the Société Française de Recherche et Médecine du Sommeil (T.A.). We thank V. Bayon, A. Dalbin, L. de Sanctis, M. Elbaz, S. Rio, and C. Varazzani for their help.

Author information

Affiliations

Brain and Consciousness Group (ENS, EHESS, CNRS), Département d’Études Cognitives, École Normale Supérieure-PSL Research University, Paris, 75005, France

Thomas Andrillon & Sid Kouider

École Doctorale Cerveau Cognition Comportement, Université Pierre et Marie Curie, Paris, 75005, France

Thomas Andrillon

Laboratoire des Systèmes Perceptifs, CNRS UMR 8248, Département d’Études Cognitives, École Normale Supérieure-PSL Research University, Paris, 75005, France

Daniel Pressnitzer

Université Paris Descartes, Sorbonne Paris Cité, APHP, Hôtel Dieu, Centre du Sommeil et de la Vigilance et EA 7330 VIFASOM, Paris, 75006, France

Damien Léger

Contributions

T.A., D.P., D.L., and S.K. designed the study. T.A. collected and analyzed the data. T.A., D.P., D.L., and S.K. wrote the paper.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Thomas Andrillon or Sid Kouider.

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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.

FREE PDF GRATIS: Preprint ArXiv

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

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