Nature: hora de remodelar o fator de impacto das publicações científicas

sexta-feira, julho 29, 2016

Time to remodel the journal impact factor

Nature and the Nature journals are diversifying their presentation of performance indicators.

27 July 2016

Source/Fonte: Journal Metrics

Metrics are intrinsically reductive and, as such, can be dangerous. Relying on them as a yardstick of performance, rather than as a pointer to underlying achievements and challenges, usually leads to pathological behaviour. The journal impact factor is just such a metric.

During a talk just over a decade ago, its co-creator, Eugene Garfield, compared his invention to nuclear energy. “I expected it to be used constructively while recognizing that in the wrong hands it might be abused,” he said. “It did not occur to me that ‘impact’ would one day become so controversial.”

As readers of Nature probably know, journal impact factors measure the average number of citations, per published article, for papers published over a two-year period. Journals do not calculate their impact factor directly — it is calculated and published by Thomson Reuters.

Publishers have long celebrated strong impact factors. It is, after all, one of the measures of their output’s significance — as far as it goes.

But the impact factor is crude and also misleading. It effectively undervalues papers in disciplines that are slow-burning or have lower characteristic citation rates. Being an arith­metic mean, it gives disproportionate significance to a few very highly cited papers, and it falsely implies that papers with only a few citations are relatively unimportant.

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FREE PDF GRATIS: Natur

Darwin, lascou-se, mano: o problema difícil da origem da vida não é redutível a princípios físicos conhecidos!

quinta-feira, julho 28, 2016

The "Hard Problem" of Life

Sara Imari Walker, Paul C.W. Davies

(Submitted on 23 Jun 2016)



Chalmer's famously identified pinpointing an explanation for our subjective experience as the "hard problem of consciousness". He argued that subjective experience constitutes a "hard problem" in the sense that its explanation will ultimately require new physical laws or principles. Here, we propose a corresponding "hard problem of life" as the problem of how `information' can affect the world. In this essay we motivate both why the problem of information as a causal agent is central to explaining life, and why it is hard - that is, why we suspect that a full resolution of the hard problem of life will, similar to as has been proposed for the hard problem of consciousness, ultimately not be reducible to known physical principles.

Comments: To appear in "From Matter to Life: Information and Causality". S.I. Walker, P.C.W. Davies and G.F.R. Ellis (eds). Cambridge University Press

Subjects: Other Quantitative Biology (q-bio.OT)

Cite as: arXiv:1606.07184 [q-bio.OT]

(or arXiv:1606.07184v1 [q-bio.OT] for this version)

Submission history

From: Sara Walker [view email

[v1] Thu, 23 Jun 2016 04:50:44 GMT (111kb,D)

FREE PDF GRATIS: arXiv

A multicelularidade faz a diferenciação somática estável

quarta-feira, julho 27, 2016

Multicellularity makes somatic differentiation evolutionarily stable

Mary E. Wahl a,b,1 and Andrew W. Murray a,b,2

Author Affiliations

aDepartment of Molecular and Cellular Biology, Harvard University, Cambridge, MA 02138;

bFAS Center for Systems Biology, Harvard University, Cambridge, MA 02138

Contributed by Andrew W. Murray, June 15, 2016 (sent for review September 13, 2015; reviewed by Harmit S. Malik and Boris I. Shraiman)

Source/Fonte: Nature

Significance

Unicellular species lack the nonreproductive somatic cell types that characterize complex multicellular organisms. We consider two alternative explanations: first, that the costs of lost reproductive potential never exceed the benefits of somatic cells in unicellular organisms; and second, that somatic cells may profit a unicellular population but leave it vulnerable to invasion by common mutants. We test these hypotheses using engineered yeast strains that permit direct comparisons of fitness and evolutionary stability between lifestyles. We find that the benefits of somatic cell production can exceed the costs in unicellular strains. Multicellular, soma-producing strains resist invasion by nondifferentiating mutants that overtake unicellular populations, supporting the theory that somatic differentiation is stabilized by population structure imposed by multicellularity.

Abstract

Many multicellular organisms produce two cell lineages: germ cells, whose descendants produce the next generation, and somatic cells, which support, protect, and disperse the germ cells. This germ-soma demarcation has evolved independently in dozens of multicellular taxa but is absent in unicellular species. A common explanation holds that in these organisms, inefficient intercellular nutrient exchange compels the fitness cost of producing nonreproductive somatic cells to outweigh any potential benefits. We propose instead that the absence of unicellular, soma-producing populations reflects their susceptibility to invasion by nondifferentiating mutants that ultimately eradicate the soma-producing lineage. We argue that multicellularity can prevent the victory of such mutants by giving germ cells preferential access to the benefits conferred by somatic cells. The absence of natural unicellular, soma-producing species previously prevented these hypotheses from being directly tested in vivo: to overcome this obstacle, we engineered strains of the budding yeast Saccharomyces cerevisiae that differ only in the presence or absence of multicellularity and somatic differentiation, permitting direct comparisons between organisms with different lifestyles. Our strains implement the essential features of irreversible conversion from germ line to soma, reproductive division of labor, and clonal multicellularity while maintaining sufficient generality to permit broad extension of our conclusions. Our somatic cells can provide fitness benefits that exceed the reproductive costs of their production, even in unicellular strains. We find that nondifferentiating mutants overtake unicellular populations but are outcompeted by multicellular, soma-producing strains, suggesting that multicellularity confers evolutionary stability to somatic differentiation.

evolution multicellularity differentiation synthetic biology yeast

Footnotes

1Present address: Microsoft New England Research and Development Center, Cambridge, MA 02142.

2To whom correspondence should be addressed. Email: awm@mcb.harvard.edu.

This contribution is part of the special series of Inaugural Articles by members of the National Academy of Sciences elected in 2014.

Author contributions: M.E.W. and A.W.M. designed research; M.E.W. performed research; M.E.W. analyzed data; and M.E.W. and A.W.M. wrote the paper.

Reviewers: H.S.M., Fred Hutchinson Cancer Research Center; and B.I.S., University of California, Santa Barbara.

The authors declare no conflict of interest.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1608278113/-/DCSupplemental.

FREE PDF GRATIS: PNAS

A evolução não pode explicar como funciona a mente, Dobzhansky???

Behavioural Processes

Volume 117, August 2015, Pages 82–91

Cause and Function in Behavioral Biology: A tribute to Jerry Hogan

Evolution cannot explain how minds work

Johan J. Bolhuis a, b, , 

a Cognitive Neurobiology and Helmholtz Institute, Departments of Psychology and Biology, Utrecht University, Utrecht, The Netherlands

b Department of Zoology and Sidney Sussex College, University of Cambridge, UK

Available online 16 June 2015


Abstract

Following Jerry Hogan, I argue that questions of function and evolution, and questions of mechanism should be seen as logically distinct. Evolution is concerned with a historical reconstruction of traits, while the actual underlying mechanisms are the domain of cognitive neuroscience and psychology. Functional and evolutionary considerations may be used to generate hypotheses regarding the underlying mechanisms. But these hypotheses may be false and should always be tested empirically. Many researchers still hold that common descent implies cognitive closeness. Studies on birds suggest that evolutionary convergence may be the rule rather than the exception in animal cognition. Neurocognitive differences between classes of individuals are often thought to be the result of adaptive specialisation. In the case of learning and memory, however, empirical results are more consistent with a ‘general process’ interpretation, without qualitative differences between different taxa. Evolutionary psychology (EP) argues that the mind of modern humans was formed as a result of selection pressures in the Stone Age. The empirical data are often overinterpreted, and EP is mostly based upon an outdated view of evolutionary biology. In human speech and language, both neurogenetic homology and evolutionary convergence are involved regarding speech, but human language has a unique combinatorial complexity.

This article is part of a Special Issue entitled: In Honor of Jerry Hogan.

Keywords Evolution; Cognition; Learning; Memory; Birdsong; Songbirds; Birdsong learning; Speech; Language

Correspondence to: Cognitive Neurobiology and Helmholtz Institute, Departments of Psychology and Biology, Utrecht University, Padualaan 8, 3584CH Utrecht, The Netherlands.

Copyright © 2015 Elsevier B.V. All rights reserved.

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Subscription or payment needed/Requer assinatura ou pagamento:



Descoberta a fisiologia e o habitat do LUCA???

terça-feira, julho 26, 2016

The physiology and habitat of the last universal common ancestor

Madeline C. Weiss, Filipa L. Sousa, Natalia Mrnjavac, Sinje Neukirchen, Mayo Roettger, Shijulal Nelson-Sathi & William F. Martin

Nature Microbiology 1, Article number: 16116 (2016)


Download Citation

BacteriaEvolutionary ecologyPhylogenetics

Received: 19 April 2016 Accepted: 21 June 2016 Published online: 25 July 2016

Source/Fonte: RealClearScience

Abstract

The concept of a last universal common ancestor of all cells (LUCA, or the progenote) is central to the study of early evolution and life's origin, yet information about how and where LUCA lived is lacking. We investigated all clusters and phylogenetic trees for 6.1 million protein coding genes from sequenced prokaryotic genomes in order to reconstruct the microbial ecology of LUCA. Among 286,514 protein clusters, we identified 355 protein families (∼0.1%) that trace to LUCA by phylogenetic criteria. Because these proteins are not universally distributed, they can shed light on LUCA's physiology. Their functions, properties and prosthetic groups depict LUCA as anaerobic, CO2-fixing, H2-dependent with a Wood–Ljungdahl pathway, N2-fixing and thermophilic. LUCA's biochemistry was replete with FeS clusters and radical reaction mechanisms. Its cofactors reveal dependence upon transition metals, flavins, S-adenosyl methionine, coenzyme A, ferredoxin, molybdopterin, corrins and selenium. Its genetic code required nucleoside modifications and S-adenosyl methionine-dependent methylations. The 355 phylogenies identify clostridia and methanogens, whose modern lifestyles resemble that of LUCA, as basal among their respective domains. LUCA inhabited a geochemically active environment rich in H2, CO2 and iron. The data support the theory of an autotrophic origin of life involving the Wood–Ljungdahl pathway in a hydrothermal setting.

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Subscription or payment needed/Requer assinatura ou pagamento: Nature Microbiology

Mudança paradigmática na determinação do oxigênio atmosférico do Neoproterozóico

segunda-feira, julho 25, 2016

Paradigm shift in determining Neoproterozoic atmospheric oxygen

Nigel J.F. Blamey 1,2,3, Uwe Brand 1, John Parnell 3, Natalie Spear 4, Christophe Lécuyer 5, Kathleen Benison 6, Fanwei Meng 7 and Pei Ni 8

- Author Affiliations

1Department of Earth Sciences, Brock University, 1812 Sir Isaac Brock Way, St Catharines, Ontario L2S 3A1, Canada

2Department of Earth and Environmental Science, New Mexico Tech, 801 Leroy Place, Socorro, New Mexico 87801, USA

3Department of Geology and Petroleum Geology, University of Aberdeen, AB24 3Ue Aberdeen, Scotland

4Department of Earth and Environmental Science, University of Pennsylvania, Philadelphia, Pennsylvania 19014, USA

5Laboratoire de Géologie de Lyon, UMR CNRS 5276, University of Lyon and Institut Universitaire de France, 69622 Villeurbanne, France

6Department of Geology and Geography, University West Virginia, Morgantown, West Virginia 26506, USA

7Nanjing Institute of Geology and Palaeontology, Chinese Academy of Sciences, #39 East Beijing Road, Nanjing 210008, China

8School of Earth Sciences and Engineering, Nanjing University, Nanjing 210093, China


Abstract

We present a new and innovative way of determining the oxygen level of Earth's past atmosphere by directly measuring inclusion gases trapped in halite. After intensive screening using multiple depositional, textural/fabric, and geochemical parameters, we determined that tectonically undisturbed cumulate, chevron, and cornet halite inclusions may retain atmospheric gas during crystallization from shallow saline, lagoonal, and/or saltpan brine. These are the first measurements of inclusion gas for the Neoproterozoic obtained from 815 ± 15–m.y.–old Browne Formation chevron halite of the Officer Basin, southwest Australia. The 31 gas measurements afford us a direct glimpse of the composition of the mid- to late Neoproterozoic atmosphere and register an average oxygen content of 10.9%. The measured pO2 puts oxygenation of Earth's paleoatmosphere ∼100–200 m.y. ahead of current models and proxy studies. It also puts oxygenation of the Neoproterozoic atmosphere in agreement with time of diversification of eukaryotes and in advance of the emergence of marine animal life.

Received 28 March 2016. Revision received 7 June 2016. Accepted 9 June 2016.

©The Authors

Gold Open Access: This paper is published under the terms of the CC-BY license.

FREE PDF GRATIS: Geology

Maurício Tuffani, o cético seletivo, está equivocado em relação à Teoria do Design Inteligente

Maurício Tuffani, o cético seletivo, está equivocado em relação à cientificidade da teoria do Design Inteligente: "a chamada teoria do design inteligente (TDI), que é uma versão sofisticada do criacionismo."

Esta é a posição oficial do Discovery Institute sobre a definição do Design Inteligente, e esta tem sido a única definição há décadas:

"The theory of Intelligent Design holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection." 

[A teoria do Design Inteligente afirma que determinadas características do universo e das coisas vivas são melhor explicadas por uma causa inteligente, e não por um processo não guiado como a seleção natural."


Tuffani, esse corolário é uma hipótese testável e falseável. Ou uma causa inteligente provoca mudanças nas frequências de alelos das populações biológica, ou não provoca. Ou existem outros processos não randômicos que conduzem as mudanças morfológicas nos sistemas biológicos, além da seleção natural, ou não existem. Tais predições, Tuffani, não é questão de ceticismo localizado, mas de verificar se são testáveis e falseáveis. Ao incluir características não vivas, a TDI pode ser aplicada à Química e à Física sobre o surgimento da vida.

Esses sinais de inteligência são empiricamente detectados na natureza todas as vezes que encontrarmos complexidade irredutível de sistemas biológicos e informação complexa especificada como a informação digital encontrada no DNA. 

Nós sabemos que esses corolários não são derivados de relatos sagrados de criação, tipo Gênesis, mas de evidências encontradas na natureza. Tuffani sabe disso.

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O texto de Maurício Tuffani, o cético nada cético, que motivou a resposta acima, foi este:

Amit Goswami diz ser criador de ‘novo paradigma da física’, mas não debate com cientistas

MAURÍCIO TUFFANI,

Editor

Um dos grandes legados do pensamento de Paul Feyerabend (1924-1994) é o ensinamento de que os avanços da ciência muitas vezes ocorrem graças às transgressões dos preceitos rígidos do conhecimento. Autor de importantes obras da filosofia da ciência, entre elas “Contra o método” e “Adeus à razão”, o pensador austríaco tem sido frequentemente citado por aqueles que propõem novas interpretações das teorias científicas.

O mesmo acontece com a obra do físico teórico e historiador da ciência norte-americano Thomas Kuhn (1922-1996), autor de “A estrutura das revoluções científicas”. Esse livro, que define o conceito de “paradigma” como um conjunto de compromissos conceituais, metodológicos e instrumentais compartilhados pelos membros de uma especialidade científica durante um determinado período, tem sido amplamente invocado para justificar toda e qualquer proposta para a ciência como “novo paradigma”.

O apelo a interpretações distorcidas de obras como as de Feyerabend, Kuhn e de outros pensadores têm sido frequente para “justificar”, por exemplo, desde a negação dos fatores antropogênicos — ou seja, gerados pela humanidade — no aquecimento global à recusa da seleção natural das espécies proposta por Charles Darwin, propondo, ao mesmo tempo, a chamada teoria do design inteligente (TDI), que é uma versão sofisticada do criacionismo.

Infelizmente uma outra distorção da ciência também tem se apoiado indevidamente no pensamento desses pensadores, seja por seu formulador, seja por seus defensores. Trata-se da obra do físico indiano Amit Goswami, que em novembro, no Brasil, será uma das principais atrações do 1º Congresso Internacional: Felicidade, Prosperidade, Abundância e Física Quântica.

Fonte: Direto da Ciência Análise, Opinião e Jornalismo Investigativo

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Tuffani, aproveitando o gancho de seu blog ser de jornalismo investigativo, pode dizer por que do seu silêncio sobre os estertores epistêmicos da Síntese Evolutiva Moderna que se transformou em Síntese Evolutiva Ampliada/Estendida em agosto de 2015, e que a Royal Society vai ter uma conferência em 7-9 de novembro de 2016 sobre como - em outras palavras - se desapegar do Darwinismo em favor de uma teoria científica mais baseada em evidências?

Deixemos que a Royal Society fale:


Overview

Scientific discussion meeting organised in partnership with the British Academy by Professor Denis Noble CBE FMedSci FRS, Professor Nancy Cartwright, Professor Sir Patrick Bateson FRS, Professor John Dupré and Professor Kevin Laland.

Developments in evolutionary biology and adjacent fields have produced calls for revision of the standard theory of evolution, although the issues involved remain hotly contested. This meeting will present these developments and arguments in a form that will encourage cross-disciplinary discussion and, in particular, involve the humanities and social sciences in order to provide further analytical perspectives and explore the social and philosophical implications.

The schedule of talks, and biographies of the organisers and speakers are available below. Alternatively you can download the draft programme (PDF). Speaker abstracts will be available closer to the meeting date. Recorded audio of the talks will be available on this page after the event has taken place.

...

Tuffani, cientistas de renome irão participar, inclusive gente do Third Way que, assim como os proponentes e defensores da TDI expressam ceticismo localizado sobre o poder criativo da seleção natural na história evolutiva das coisas bióticas:

Below, you will find a list of researchers and authors who have, in one way or another, expressed their concerns regarding natural selection’s scope and who believe that other mechanisms are essential for a comprehensive understanding of evolutionary processes. (See/Vide)

Esse tipo de jornalismo investigativo quando a questão é Darwin está faltando no Direto da Ciência, Tuffani, mas é preciso ter cojones para tal!

(Foto)

Proteção XX contra as mutações relacionadas com a idade

quinta-feira, julho 21, 2016

Inbreeding removes sex differences in lifespan in a population of Drosophila melanogaster

Pau Carazo, Jared Green, Irem Sepil, Tommaso Pizzari, Stuart Wigby

Published 28 June 2016.DOI: 10.1098/rsbl.2016.0337

Source/Fonte: The Conversation

Abstract

Sex differences in ageing rates and lifespan are common in nature, and an enduring puzzle for evolutionary biology. One possibility is that sex-specific mortality rates may result from recessive deleterious alleles in ‘unguarded’ heterogametic X or Z sex chromosomes (the unguarded X hypothesis). Empirical evidence for this is, however, limited. Here, we test a fundamental prediction of the unguarded X hypothesis in Drosophila melanogaster, namely that inbreeding shortens lifespan more in females (the homogametic sex in Drosophila) than in males. To test for additional sex-specific social effects, we studied the lifespan of males and females kept in isolation, in related same-sex groups, and in unrelated same-sex groups. As expected, outbred females outlived outbred males and inbreeding shortened lifespan. However, inbreeding-mediated reductions in lifespan were stronger for females, such that lifespan was similar in inbred females and males. We also show that the social environment, independent of inbreeding, affected male, but not female lifespan. In conjunction with recent studies, the present results suggest that asymmetric inheritance mechanisms may play an important role in the evolution of sex-specific lifespan and that social effects must be considered explicitly when studying these fundamental patterns.

Ethics

The research conducted (under project numbers: PIEF-GA-2010-273010 and CGL2014-58722-P) complies with the ASAB/ABS ethical guidelines and with all applicable national and international legislation.

Data accessibility

Data are available from the Dryad digital repository: http://dx.doi.org/10.5061/dryad.pp6k7.

Authors' contributions

P.C. and T.P. conceived the study; P.C., T.P. and S.W. designed the study; P.C., J.G., I.S. and S.W. carried out the laboratory work; P.C. and J.G. analysed the data; P.C., J.G., T.P., I.S. and S.W. drafted the manuscript or revised it critically. All authors approve the final form of manuscript and agree to be held accountable for its content.

Competing interests

The authors declare that they have no competing interests.

Funding

This work was supported by the Marie Curie FP7 programme (PIEF-GA-2010-273010 to P.C.), by the Spanish Government (CGL2014-58722-P to P.C.) and by the Biological Sciences Research Council (BBSRC; BB/K014544/1 to S.W.).

Received April 22, 2016. Accepted June 8, 2016. 

© 2016 The Authors.

Creative Commons logo

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

FREE PDF GRATIS: Biology Letters

À luz da evolução X: filogeografia comparativa

quarta-feira, julho 20, 2016

In the light of evolution X: Comparative phylogeography
John C. Avisea,1, Brian W. Bowenb, and Francisco J. Ayalaa
Author Affiliations

aDepartment of Ecology and Evolutionary Biology, University of California, Irvine, CA 92697-2525;

bHawai’i Institute of Marine Biology, Kane’ohe, HI 96744

Source/Fonte: Diversity

Phylogeography is the study of the spatial arrangement of genealogical lineages, especially within and among conspecific populations and closely related species (10). Ever since its inception in the late 1970s (11, 12) and mid-1980s (13), the field has sought to extend phylogenetic reasoning to the intraspecific level, and thereby build empirical and conceptual bridges between the formerly separate disciplines of microevolutionary population genetics and macroevolutionary phylogenetics. In the early years, phylogeographers relied on data from restriction-site surveys of mitochondrial (mt) DNA to draw inferences about population structure and historical demography, but stunning improvements in molecular techniques (14, 15) and extensions of coalescent theory and other analytical methods (16) later broadened the field’s scope dramatically (17). Phylogeographic perspectives have transformed aspects of population biology, biogeography, systematics, ecology, genetics, and biodiversity conservation. One aim of this colloquium was to bring together leading scientists to address the current state of phylogeography as the discipline enters its fourth decade. The broader goal was to update a wide audience on recent developments in phylogeographic research and their relevance to past accomplishments and future research directions.
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FREE PDF GRATIS: PNAS

Cientistas cortaram o "Nó Górdio" do genoma humano???

Deletion of DXZ4 on the human inactive X chromosome alters higher-order genome architecture

Emily M. Darrowa,1, Miriam H. Huntleyb,c,d,e,1, Olga Dudchenkob,c,f, Elena K. Stamenovab,c,e, Neva C. Durandb,c, Zhuo Suna, Su-Chen Huangb,c, Adrian L. Sanbornb,f,g, Ido Macholb,c, Muhammad Shamimb,c, Andrew P. Seberga, Eric S. Landere,h,i,2, Brian P. Chadwicka,2, and Erez Lieberman Aidenb,c,e,f,j,k,2

Author Affiliations

aDepartment of Biological Science, Florida State University, Tallahassee, FL 32306;

bThe Center for Genome Architecture, Baylor College of Medicine, Houston, TX 77030;

cDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030;

dJohn A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, MA 02138;

eBroad Institute of MIT and Harvard, Cambridge, MA 02139;

fCenter for Theoretical Biological Physics, Rice University, Houston, TX 77030;

gDepartment of Computer Science, Stanford University, Stanford, CA 94305;

hDepartment of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139;

iDepartment of Systems Biology, Harvard Medical School, Boston, MA 02115;

jDepartment of Computer Science, Rice University, Houston, TX 77005;

kDepartment of Computational and Applied Mathematics, Rice University, Houston, TX 77005

Contributed by Eric S. Lander, June 24, 2016 (sent for review May 8, 2016; reviewed by Frank Alber, Marisa S. Bartolomei, Uta Francke, and Sundeep Kalantry)


Significance

In human females, one of the two X chromosomes is inactive (Xi) and adopts an unusual 3D conformation. The Xi chromosome contains superloops, large chromatin loops that are often anchored at the macrosatellite repeat DXZ4, and is partitioned into two large intervals, called superdomains, whose boundary lies at DXZ4. Here, we use spatial proximity mapping, microscopy, and genome editing to study the Xi. We find that superloops and superdomains are conserved across humans, macaque, and mouse. By mapping proximity between three or more loci, we show that superloops tend to occur simultaneously. Deletion of DXZ4 from the human Xi disrupts superloops, eliminates superdomains, and alters chromatin modifications. Finally, we show that a model in which CCCTC-binding factor (CTCF) and cohesin extrude chromatin can explain the formation of superloops and superdomains.

 
Next Section
Abstract
During interphase, the inactive X chromosome (Xi) is largely transcriptionally silent and adopts an unusual 3D configuration known as the “Barr body.” Despite the importance of X chromosome inactivation, little is known about this 3D conformation. We recently showed that in humans the Xi chromosome exhibits three structural features, two of which are not shared by other chromosomes. First, like the chromosomes of many species, Xi forms compartments. Second, Xi is partitioned into two huge intervals, called “superdomains,” such that pairs of loci in the same superdomain tend to colocalize. The boundary between the superdomains lies near DXZ4, a macrosatellite repeat whose Xi allele extensively binds the protein CCCTC-binding factor. Third, Xi exhibits extremely large loops, up to 77 megabases long, called “superloops.” DXZ4 lies at the anchor of several superloops. Here, we combine 3D mapping, microscopy, and genome editing to study the structure of Xi, focusing on the role of DXZ4. We show that superloops and superdomains are conserved across eutherian mammals. By analyzing ligation events involving three or more loci, we demonstrate that DXZ4 and other superloop anchors tend to colocate simultaneously. Finally, we show that deleting DXZ4 on Xi leads to the disappearance of superdomains and superloops, changes in compartmentalization patterns, and changes in the distribution of chromatin marks. Thus, DXZ4 is essential for proper Xi packaging.

X chromosome inactivation inactive X chromosome Hi‐C CTCF genome engineering

FREE PDF GRATIS: PNAS

A dinâmica da rede turbulenta da evolução microbiana e a Árvore da Vida estatística

J Mol Evol (2015) 80:244–250


The Turbulent Network Dynamics of Microbial Evolution and the Statistical Tree of Life

Eugene V. Koonin 1

Received: 18 March 2015 / Accepted: 8 April 2015 / Published online: 18 April 2015

The Author(s) 2015. This article is published with open access at Springerlink.com

Source/Fonte: Seed

Abstract 

The wide spread and high rate of gene exchange and loss in the prokaryotic world translate into ‘‘network genomics’’. The rates of gene gain and loss are comparable with the rate of point mutations but are substantially greater than the duplication rate. Thus, evolution of prokaryotes is primarily shaped by gene gain and loss. These processes are essential to prevent mutational meltdown of microbial populations by stopping Muller’s ratchet and appear to trigger emergence of major novel clades by opening up new ecological niches. At least some bacteria and archaea seem to have evolved dedicated devices for gene transfer. Despite the dominance of gene gain and loss, evolution of genes is intrinsically tree-like. The significant coherence between the topologies of numerous gene trees, particularly those for (nearly) universal genes, is compatible with the concept of a statistical tree of life, which forms the framework for reconstruction of the evolutionary processes in the prokaryotic world.

Keywords Microbial evolution Phylogenetic trees Horizontal gene transfer Muller’s ratchet Evolvability

Como os genes são regulados - fatores de transcrição. Mero acaso, fortuita necessidade ou design inteligente?

terça-feira, julho 19, 2016

Uma nova pesquisa rastreia "a ascensão dos gigantes do oceano."

The rise of ocean giants: maximum body size in Cenozoic marine mammals as an indicator for productivity in the Pacific and Atlantic Oceans

Nicholas D. Pyenson, Geerat J. Vermeij

Published 5 July 2016.DOI: 10.1098/rsbl.2016.0186

Fig. 1. (a,b) Maximal body size in North Pacific and North Atlantic marine mammal herbivores, and (c,d) similarly for mammalian filter-feeders, during the Cenozoic. PhyloPics of herbivores, except Hydrodamalis, by Steven Traver.


Abstract

Large consumers have ecological influence disproportionate to their abundance, although this influence in food webs depends directly on productivity. Evolutionary patterns at geologic timescales inform expectations about the relationship between consumers and productivity, but it is very difficult to track productivity through time with direct, quantitative measures. Based on previous work that used the maximum body size of Cenozoic marine invertebrate assemblages as a proxy for benthic productivity, we investigated how the maximum body size of Cenozoic marine mammals, in two feeding guilds, evolved over comparable temporal and geographical scales. First, maximal size in marine herbivores remains mostly stable and occupied by two different groups (desmostylians and sirenians) over separate timeframes in the North Pacific Ocean, while sirenians exclusively dominated this ecological mode in the North Atlantic. Second, mysticete whales, which are the largest Cenozoic consumers in the filter-feeding guild, remained in the same size range until a Mio-Pliocene onset of cetacean gigantism. Both vertebrate guilds achieved very large size only recently, suggesting that different trophic mechanisms promoting gigantism in the oceans have operated in the Cenozoic than in previous eras.

Data accessibility

All additional data are in the electronic supplementary material file.

Authors' contributions

N.D.P collected the data. N.D.P. and G.J.V. analysed the data, wrote the manuscript, approved the final draft of the manuscript and agree to be held accountable for the content herein.

Competing interests

We have no competing interests.

Funding

N.D.P. is supported by the Smithsonian Institution, its Remington Kellogg Fund, and the Basis Foundation. All figures are our own.

Acknowledgements

We thank J. Vélez-Juarbe for help with data collection and four anonymous reviewers along with A. H. Fleming, J. A. Goldbogen, A. O'Dea, J. F. Parham, C. M. Peredo and J. Vélez-Juarbe for helpful comments.

Received March 3, 2016. Accepted June 13, 2016.

© 2016 The Authors.

Published by the Royal Society under the terms of the Creative Commons Attribution License http://creativecommons.org/licenses/by/4.0/, which permits unrestricted use, provided the original author and source are credited.

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Nova pesquisa desafia hipótese evolucionista antiga sobre o voo das aves

The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents

Evolutionary Studies Paleontology

T. Alexander Dececchi​1, Hans C.E. Larsson2, Michael B. Habib3,4

July 7, 2016

Source/Fonte:
“Dinosaur into Bird” artwork by paleoartist Mark Hallett, part of “The Dinosaur Postcard Book” (1987) from Running Press.

Abstract

Background: Powered flight is implicated as a major driver for the success of birds. Here we examine the effectiveness of three hypothesized pathways for the evolution of the flight stroke, the forelimb motion that powers aerial locomotion, in a terrestrial setting across a range of stem and basal avians: flap running, Wing Assisted Incline Running (WAIR), and wing-assisted leaping.

Methods: Using biomechanical mathematical models based on known aerodynamic principals and in vivo experiments and ground truthed using extant avians we seek to test if an incipient flight stroke may have contributed sufficient force to permit flap running, WAIR, or leaping takeoff along the phylogenetic lineage from Coelurosauria to birds.

Results: None of these behaviours were found to meet the biomechanical threshold requirements before Paraves. Neither was there a continuous trend of refinement for any of these biomechanical performances across phylogeny nor a signal of universal applicability near the origin of birds. None of these flap-based locomotory models appear to have been a major influence on pre-flight character acquisition such as pennaceous feathers, suggesting non-locomotory behaviours, and less stringent locomotory behaviours such as balancing and braking, played a role in the evolution of the maniraptoran wing and nascent flight stroke. We find no support for widespread prevalence of WAIR in non-avian theropods, but can’t reject its presence in large winged, small-bodied taxa like Microraptor and Archaeopteryx.

Discussion: Using our first principles approach we find that “near flight” locomotor behaviors are most sensitive to wing area, and that non-locomotory related selection regimes likely expanded wing area well before WAIR and other such behaviors were possible in derived avians. These results suggest that investigations of the drivers for wing expansion and feather elongation in theropods need not be intrinsically linked to locomotory adaptations, and this separation is critical for our understanding of the origin of powered flight and avian evolution.

Cite this as

Dececchi TA, Larsson HCE, Habib MB. (2016) The wings before the bird: an evaluation of flapping-based locomotory hypotheses in bird antecedents. PeerJ 4:e2159 https://doi.org/10.7717/peerj.2159

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Base de dados de literatura de Física de Alta Energia

segunda-feira, julho 18, 2016


Sobre a estratégia da natureza em atribuir multiplicidade ao código genético

On Nature’s Strategy for Assigning Genetic Code Multiplicity

Simone Gardini, Sara Cheli, Silvia Baroni, Gabriele Di Lascio, Guido Mangiavacchi, Nicholas Micheletti, Carmen Luigia Monaco, Lorenzo Savini, Davide Alocci, Stefano Mangani, Neri Niccolai 



Abstract

Genetic code redundancy would yield, on the average, the assignment of three codons for each of the natural amino acids. The fact that this number is observed only for incorporating Ile and to stop RNA translation still waits for an overall explanation. Through a Structural Bioinformatics approach, the wealth of information stored in the Protein Data Bank has been used here to look for unambiguous clues to decipher the rationale of standard genetic code (SGC) in assigning from one to six different codons for amino acid translation. Leu and Arg, both protected from translational errors by six codons, offer the clearest clue by appearing as the most abundant amino acids in protein-protein and protein-nucleic acid interfaces. Other SGC hidden messages have been sought by analyzing, in a protein structure framework, the roles of over- and under-protected amino acids.

Citation: Gardini S, Cheli S, Baroni S, Di Lascio G, Mangiavacchi G, Micheletti N, et al. (2016) On Nature’s Strategy for Assigning Genetic Code Multiplicity. PLoS ONE 11(2): e0148174. doi:10.1371/journal.pone.0148174

Editor: Denis Dupuy, Inserm U869, FRANCE

Received: October 7, 2015; Accepted: January 13, 2016; Published: February 5, 2016

Copyright: © 2016 Gardini et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

Data Availability: All relevant data are within the paper and its Supporting Information files.

Funding: The authors have no support or funding to report.

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

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A distinção espectral em animais daltônicos através de aberração cromática e formato de pupila

domingo, julho 17, 2016

Spectral discrimination in color blind animals via chromatic aberration and pupil shape

Alexander L. Stubbs a,b,1,2 and Christopher W. Stubbs c,d,2

Author Affiliations

aMuseum of Vertebrate Zoology, University of California, Berkeley, CA 94720;

bDepartment of Integrative Biology, University of California, Berkeley, CA 94720;

cDepartment of Physics, Harvard University, Cambridge, MA 02138;

dDepartment of Astronomy, Harvard University, Cambridge, MA 02138

Edited by John Mollon, University of Cambridge, Cambridge, United Kingdom, and accepted by Editorial Board Member Jeremy Nathans May 23, 2016 (received for review December 13, 2015)


Significance

We describe a means of obtaining spectral information using the principles of physical optics and an off-axis pupil shape without requiring spectrally distinct photoreceptor classes. The mechanism described here offers a possible solution to a long-standing puzzle in marine animals: cephalopods dramatically change color for both producing chromatically matched camouflage and signaling to conspecifics, despite having a single photoreceptor channel. The ability of these animals to achieve such excellent color matching to their surroundings, despite being “color blind” in the traditional sense, can be understood if they exploit chromatic aberration to deduce spectral information. The bizarre off-axis pupils of these animals can be understood as an adaptation that maximizes spectral information, even at the expense of image acuity.

Abstract

We present a mechanism by which organisms with only a single photoreceptor, which have a monochromatic view of the world, can achieve color discrimination. An off-axis pupil and the principle of chromatic aberration (where different wavelengths come to focus at different distances behind a lens) can combine to provide “color-blind” animals with a way to distinguish colors. As a specific example, we constructed a computer model of the visual system of cephalopods (octopus, squid, and cuttlefish) that have a single unfiltered photoreceptor type. We compute a quantitative image quality budget for this visual system and show how chromatic blurring dominates the visual acuity in these animals in shallow water. We quantitatively show, through numerical simulations, how chromatic aberration can be exploited to obtain spectral information, especially through nonaxial pupils that are characteristic of coleoid cephalopods. We have also assessed the inherent ambiguity between range and color that is a consequence of the chromatic variation of best focus with wavelength. This proposed mechanism is consistent with the extensive suite of visual/behavioral and physiological data that has been obtained from cephalopod studies and offers a possible solution to the apparent paradox of vivid chromatic behaviors in color blind animals. Moreover, this proposed mechanism has potential applicability in organisms with limited photoreceptor complements, such as spiders and dolphins.

spectral discrimination chromatic aberration color vision pupil shape cephalopod

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Espaço, Tempo e Matéria (e como eles importam): discussão sobre alguns insights metafísicos fornecidos por nossas melhores teorias físicas


Space, Time, and (how they) Matter: a Discussion about some Metaphysical Insights Provided by our Best Fundamental Physical Theories

Allori, Valia (2017) Space, Time, and (how they) Matter: a Discussion about some Metaphysical Insights Provided by our Best Fundamental Physical Theories. [Preprint]


Abstract

This paper is a brief (and hopelessly incomplete) non-standard introduction to the philosophy of space and time. It is an introduction because I plan to give an overview of what I consider some of the main questions about space and time: Is space a substance over and above matter? How many dimensions does it have? Is space-time fundamental or emergent? Does time have a direction? Does time even exist? Nonetheless, this introduction is not standard because I conclude the discussion by presenting the material with an original spin, guided by a particular understanding of fundamental physical theories, the so-called primitive ontology approach.

Keywords: space, time, space-time, substantivalism, relationism, wave function realism, primitive ontology,string theory, dualities, quantum gravity, emergence, unreality of time

Allori, Valia vallori@niu.edu 

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