A vantagem dos abstracts simples de artigos científicos

Journal of Informetrics

Volume 10, Issue 1, February 2016, Pages 1–8

The advantage of simple paper abstracts

Adrian Letchford, , Tobias Preis, Helen Susannah Moat

Data Science Lab, Behavioural Science, Warwick Business School, University of Warwick, CV4 7AL, Coventry, UK

Received 16 June 2015, Revised 1 November 2015, Accepted 1 November 2015, Available online 13 December 2015

doi:10.1016/j.joi.2015.11.001

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Open Access funded by Engineering and Physical Sciences Research Council

Under a Creative Commons license

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Highlights

• We investigate whether or not the style of a scientific paper's abstract bears any relation to the number of times that paper is cited.

• We find that papers whose abstracts contain more frequently used words tend to receive slightly more citations.

• We find that journals which publish papers whose abstracts are shorter and contain more frequently used words receive slightly more citations per paper.

Abstract

Each year, researchers publish an immense number of scientific papers. While some receive many citations, others receive none. Here we investigate whether any of this variance can be explained by the choice of words in a paper's abstract. We find that doubling the word frequency of an average abstract increases citations by 0.70%. We also find that journals which publish papers whose abstracts are shorter and contain more frequently used words receive slightly more citations per paper. Specifically, adding a 5 letter word to an abstract decreases the number of citations by 0.02%. These results are consistent with the hypothesis that the style in which a paper's abstract is written bears some relation to its scientific impact.

Keywords: Citation analysis; Scientific writing; Computational social science; Science of science

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A vantagem dos títulos curtos de artigos científicos

The advantage of short paper titles

Adrian Letchford, Helen Susannah Moat, Tobias Preis

Published 26 August 2015.DOI: 10.1098/rsos.150266

Abstract

Vast numbers of scientific articles are published each year, some of which attract considerable attention, and some of which go almost unnoticed. Here, we investigate whether any of this variance can be explained by a simple metric of one aspect of the paper's presentation: the length of its title. Our analysis provides evidence that journals which publish papers with shorter titles receive more citations per paper. These results are consistent with the intriguing hypothesis that papers with shorter titles may be easier to understand, and hence attract more citations.

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Expressão gênica: aumentando através do ciclo celular

Gene expression: Bursting through the cell cycle

Shani Ben-Moshe Shalev Itzkovitz 

Weizmann Institute of Science, Israel

DOI: http://dx.doi.org/10.7554/eLife.14953

Published March 7, 2016

Cite as eLife 2016;5:e14953

Source/Fonte

Abstract

How are cells able to maintain constant levels of mRNA when the number of genes in a cell doubles ahead of cell division?

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Explorando cérebros miniaturas de insetos utilizando técnicas de exploração micro-CT

Exploring miniature insect brains using micro-CT scanning techniques

Dylan B. Smith, Galina Bernhardt, Nigel E. Raine, Richard L. Abel, Dan Sykes, Farah Ahmed, Inti Pedroso & Richard J. Gill

Scientific Reports 6, Article number: 21768 (2016)

doi:10.1038/srep21768

Download Citation

3-D reconstructionAnimal physiologyX-ray tomography

Received: 20 May 2015 Accepted: 29 January 2016

Published online: 24 February 2016

Abstract

The capacity to explore soft tissue structures in detail is important in understanding animal physiology and how this determines features such as movement, behaviour and the impact of trauma on regular function. Here we use advances in micro-computed tomography (micro-CT) technology to explore the brain of an important insect pollinator and model organism, the bumblebee (Bombus terrestris). Here we present a method for accurate imaging and exploration of insect brains that keeps brain tissue free from trauma and in its natural stereo-geometry, and showcase our 3D reconstructions and analyses of 19 individual brains at high resolution. Development of this protocol allows relatively rapid and cost effective brain reconstructions, making it an accessible methodology to the wider scientific community. The protocol describes the necessary steps for sample preparation, tissue staining, micro-CT scanning and 3D reconstruction, followed by a method for image analysis using the freeware SPIERS. These image analysis methods describe how to virtually extract key composite structures from the insect brain, and we demonstrate the application and precision of this method by calculating structural volumes and investigating the allometric relationships between bumblebee brain structures.

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Evolução inteligente - uma teoria evolucionária alternativa

Intelligent Evolution: An Alternate Theory of Evolution Kindle Edition

by Claire Quinn (Author)

Intelligent design is often depicted as science versus religion but this is not always the case. I have a Ph.D. in molecular biology, don't follow any specific religion, and have come to the conclusion that the complexity of life suggests intelligent design. I believe microbes were designed by an intelligent entity and then released into the cold, vastness of space. Some haphazardly landed on our warm, wet planet and went on to evolve into everything we see here today, including us. This is 'Intelligent Evolution' because we evolved from intelligently designed microbes. Evidence of this and how these microbes took our planet from a barren, wet rock to a thriving, rich ecosystem is outlined in detail, essentially rewriting the entire theory of evolution. 

About the Author: 

I have a B.Sc. in Genetics from the University of Western Ontario, a Masters in Physiology and Pharmacology from the University of Western Ontario, and a Ph.D. in Molecular Biology from the University of Toronto.

Source/Fonte: Amazon

Taxa individual de publicação de pesquisadores não cresceu em um século!!!

Researchers’ Individual Publication Rate Has Not Increased in a Century

Daniele Fanelli , Vincent Larivière

Published: March 9, 2016

DOI: 10.1371/journal.pone.0149504

Source/Fonte

Abstract

Debates over the pros and cons of a “publish or perish” philosophy have inflamed academia for at least half a century. Growing concerns, in particular, are expressed for policies that reward “quantity” at the expense of “quality,” because these might prompt scientists to unduly multiply their publications by fractioning (“salami slicing”), duplicating, rushing, simplifying, or even fabricating their results. To assess the reasonableness of these concerns, we analyzed publication patterns of over 40,000 researchers that, between the years 1900 and 2013, have published two or more papers within 15 years, in any of the disciplines covered by the Web of Science. The total number of papers published by researchers during their early career period (first fifteen years) has increased in recent decades, but so has their average number of co-authors. If we take the latter factor into account, by measuring productivity fractionally or by only counting papers published as first author, we observe no increase in productivity throughout the century. Even after the 1980s, adjusted productivity has not increased for most disciplines and countries. These results are robust to methodological choices and are actually conservative with respect to the hypothesis that publication rates are growing. Therefore, the widespread belief that pressures to publish are causing the scientific literature to be flooded with salami-sliced, trivial, incomplete, duplicated, plagiarized and false results is likely to be incorrect or at least exaggerated.

Citation: Fanelli D, Larivière V (2016) Researchers’ Individual Publication Rate Has Not Increased in a Century. PLoS ONE 11(3): e0149504. 

doi: 10.1371/journal.pone.0149504

Editor: Pablo Dorta-González, Universidad de Las Palmas de Gran Canaria, SPAIN

Received: November 2, 2015; Accepted: January 29, 2016; Published: March 9, 2016

Copyright: © 2016 Fanelli, Larivière. 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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O particionamento da energia elástica na deformação e ligação do DNA às proteínas

Elastic Energy Partitioning in DNA Deformation and Binding to Proteins

Xiaojing Teng† and Wonmuk Hwang*†‡§

† Department of Biomedical Engineering, Texas A&M University, College Station, Texas 77843, United States

‡ Department of Materials Science and Engineering, Texas A&M University, College Station, Texas 77843, United States

§ School of Computational Sciences, Korea Institute for Advanced Study, Seoul, Korea 02455

ACS Nano, 2016, 10 (1), pp 170–180

DOI: 10.1021/acsnano.5b06863

Publication Date (Web): December 05, 2015

Copyright © 2015 American Chemical Society

*E-mail: hwm@tamu.edu.

Abstract

We study the elasticity of DNA based on local principal axes of bending identified from over 0.9-μs all-atom molecular dynamics simulations of DNA oligos. The calculated order parameters describe motion of DNA as an elastic rod. In 10 possible dinucleotide steps, bending about the two principal axes is anisotropic yet linearly elastic. Twist about the centroid axis is largely decoupled from bending, but DNA tends to overtwist for unbending beyond the typical range of thermal motion, which is consistent with experimentally observed twist–stretch coupling. The calculated elastic stiffness of dinucleotide steps yield sequence-dependent persistence lengths consistent with previous single-molecule experiments, which is further analyzed by performing coarse-grained simulations of DNA. Flexibility maps of oligos constructed from simulation also match with those from the precalculated stiffness of dinucleotide steps. These support the premise that base pair interaction at the dinucleotide-level is mainly responsible for the elasticity of DNA. Furthermore, we analyze 1381 crystal structures of protein–DNA complexes. In most structures, DNAs are mildly deformed and twist takes the highest portion of the total elastic energy. By contrast, in structures with the elastic energy per dinucleotide step greater than about 4.16 kBT (kBT: thermal energy), the major bending becomes dominant. The extensional energy of dinucleotide steps takes at most 35% of the total elastic energy except for structures containing highly deformed DNAs where linear elasticity breaks down. Such partitioning between different deformational modes provides quantitative insights into the conformational dynamics of DNA as well as its interaction with other molecules and surfaces.

Keywords: DNA flexibility; DNA−protein complex; DNA nanostructure; principal axis; molecular dynamics; type-II topoisomerase

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Rastreando a transmissão interespécies e a evolução a longo prazo de um retrovírus antigo usando os genomas de mamíferos modernos

Tracking interspecies transmission and long-term evolution of an ancient retrovirus using the genomes of modern mammals

William E Diehl Nirali Patel Kate Halm Welkin E Johnson 

Boston College, United States

DOI: http://dx.doi.org/10.7554/eLife.12704

Published March 8, 2016

Cite as eLife 2016;5:e12704

Source/Fonte

Abstract

Mammalian genomes typically contain hundreds of thousands of endogenous retroviruses (ERVs), derived from ancient retroviral infections. Using this molecular 'fossil' record, we reconstructed the natural history of a specific retrovirus lineage (ERV-Fc) that disseminated widely between ~33 and ~15 million years ago, corresponding to the Oligocene and early Miocene epochs. Intercontinental viral spread, numerous instances of interspecies transmission and emergence in hosts representing at least 11 mammalian orders, and a significant role for recombination in diversification of this viral lineage were also revealed. By reconstructing the canonical retroviral genes, we identified patterns of adaptation consistent with selection to maintain essential viral protein functions. Our results demonstrate the unique potential of the ERV fossil record for studying the processes of viral spread and emergence as they play out across macro-evolutionary timescales, such that looking back in time may prove insightful for predicting the long-term consequences of newly emerging viral infections.

DOI: http://dx.doi.org/10.7554/eLife.12704.001

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A extinção de répteis marinhos em forma de peixe associada a taxas evolutivas reduzidas e a volatilidade ambiental global

Extinction of fish-shaped marine reptiles associated with reduced evolutionary rates and global environmental volatility

Valentin Fischer, Nathalie Bardet, Roger B. J. Benson, Maxim S. Arkhangelsky & Matt Friedman

Affiliations Contributions Corresponding author

Nature Communications 7, Article number: 10825 doi:10.1038/ncomms10825

Received 12 August 2015 Accepted 22 January 2016 Published 08 March 2016

Source/Fonte

Abstract

Despite their profound adaptations to the aquatic realm and their apparent success throughout the Triassic and the Jurassic, ichthyosaurs became extinct roughly 30 million years before the end-Cretaceous mass extinction. Current hypotheses for this early demise involve relatively minor biotic events, but are at odds with recent understanding of the ichthyosaur fossil record. Here, we show that ichthyosaurs maintained high but diminishing richness and disparity throughout the Early Cretaceous. The last ichthyosaurs are characterized by reduced rates of origination and phenotypic evolution and their elevated extinction rates correlate with increased environmental volatility. In addition, we find that ichthyosaurs suffered from a profound Early Cenomanian extinction that reduced their ecological diversity, likely contributing to their final extinction at the end of the Cenomanian. Our results support a growing body of evidence revealing that global environmental change resulted in a major, temporally staggered turnover event that profoundly reorganized marine ecosystems during the Cenomanian.

Subject terms: Biological sciences Evolution Palaeontology

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Desenvolvimento molecular da redução fibular em aves e sua evolução a partir de dinossauros

Molecular development of fibular reduction in birds and its evolution from dinosaurs

João Francisco Botelho1, Daniel Smith-Paredes1, Sergio Soto-Acuña1,2, Jingmai O'Connor3, Verónica Palma4 andAlexander O. Vargas1

Article first published online: 4 MAR 2016

DOI: 10.1111/evo.12882

Source/Fonte: Internet

Abstract

Keywords: Bird–dinosaur transition; fibula, IHH; mesozoic birds; PTHrP; zeugopod

Birds have a distally reduced, splinter-like fibula that is shorter than the tibia. In embryonic development, both skeletal elements start out with similar lengths. We examined molecular markers of cartilage differentiation in chicken embryos. We found that the distal end of the fibula expresses Indian hedgehog (IHH), undergoing terminal cartilage differentiation, and almost no Parathyroid-related protein (PTHrP), which is required to develop a proliferative growth plate (epiphysis). Reduction of the distal fibula may be influenced earlier by its close contact with the nearby fibulare, which strongly expresses PTHrP. The epiphysis-like fibulare however then separates from the fibula, which fails to maintain a distal growth plate, and fibular reduction ensues. Experimental downregulation of IHH signaling at a postmorphogenetic stage led to a tibia and fibula of equal length: The fibula is longer than in controls and fused to the fibulare, whereas the tibia is shorter and bent. We propose that the presence of a distal fibular epiphysis may constrain greater growth in the tibia. Accordingly, many Mesozoic birds show a fibula that has lost its distal epiphysis, but remains almost as long as the tibia, suggesting that loss of the fibulare preceded and allowed subsequent evolution of great fibulo–tibial disparity.

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A plasticidade esqueletal em resposta à atividade muscular embrionária está subjacente ao desenvolvimento e evolução do dígito empoleirador das aves

Skeletal plasticity in response to embryonic muscular activity underlies the development and evolution of the perching digit of birds

João Francisco Botelho, Daniel Smith-Paredes, Sergio Soto-Acuña, Jorge Mpodozis, Verónica Palma & Alexander O. Vargas

Scientific Reports 5, Article number: 9840 (2015)

doi:10.1038/srep09840

Evolutionary developmental biology Palaeontology

Received: 02 November 2014 Accepted: 11 March 2015

Published online: 14 May 2015

Abstract

Most birds have an opposable digit 1 (hallux) allowing the foot to grasp, which evolved from the non-opposable hallux of early theropod dinosaurs. An important morphological difference with early theropods is the twisting of the long axis of its metatarsal. Here, we show how embryonic musculature and the onset of its activity are required for twisting of metatarsal 1 (Mt1) and retroversion of the hallux. Pharmacologically paralyzed embryos do not fully retrovert the hallux and have a straight Mt1 shaft, phenocopying the morphology of early tetanuran dinosaurs. Molecular markers of cartilage maturation and ossification show that differentiation of Mt1 is significantly delayed compared to Mt2-4. We hypothesize on how delayed maturation may have increased plasticity, facilitating muscular twisting. Our experimental results emphasize the importance of embryonic muscular activity in the evolutionary origin of a crucial adaptation.

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Fósseis em âmbar do Cretáceo intermediário ilumina a diversidade passada dos lagartos tropicais

Mid-Cretaceous amber fossils illuminate the past diversity of tropical lizards

Juan D. Daza1,*, Edward L. Stanley2,3, Philipp Wagner4, Aaron M. Bauer5 and David A. Grimaldi6

- Author Affiliations

1Department of Biological Sciences, Sam Houston State University, 1900 Avenue I, Lee Drain Building Suite 300, Huntsville, TX 77341, USA.

2Department of Herpetology, Florida Museum of Natural History, 3215 Hull Road, Gainesville, FL 31611, USA.

3Department of Herpetology, California Academy of Sciences, 55 Music Concourse Drive, San Francisco, CA 94118, USA.

4Zoologische Staatssammlung München, Münchhausenstraße 21, 81247 Munich, Germany.

5Department of Biology, Villanova University, 800 Lancaster Avenue, Villanova, PA 19085, USA.

6Division of Invertebrate Zoology, American Museum of Natural History, Central Park West at 79th Street, New York, NY 10024–5192, USA.

↵*Corresponding author. E-mail: jdd054@shsu.edu

Science Advances 04 Mar 2016:

Vol. 2, no. 3, e1501080 DOI: 10.1126/sciadv.1501080

Abstract

Modern tropical forests harbor an enormous diversity of squamates, but fossilization in such environments is uncommon and little is known about tropical lizard assemblages of the Mesozoic. We report the oldest lizard assemblage preserved in amber, providing insight into the poorly preserved but potentially diverse mid-Cretaceous paleotropics. Twelve specimens from the Albian-Cenomanian boundary of Myanmar (99 Ma) preserve fine details of soft tissue and osteology, and high-resolution x-ray computed tomography permits detailed comparisons to extant and extinct lizards. The extraordinary preservation allows several specimens to be confidently assigned to groups including stem Gekkota and stem Chamaleonidae. Other taxa are assignable to crown clades on the basis of similar traits. The detailed preservation of osteological and soft tissue characters in these specimens may facilitate their precise phylogenetic placement, making them useful calibration points for molecular divergence time estimates and potential keys for resolving conflicts in higher-order squamate relationships.

Keywords Mesozoic period fossils  lizards paleobiology

Copyright © 2016, The Authors

This is an open-access article distributed under the terms of the Creative Commons Attribution-NonCommercial license, which permits use, distribution, and reproduction in any medium, so long as the resultant use is not for commercial advantage and provided the original work is properly cited.

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Avanços nos métodos de cálculo temporal de dados moleculares

Advances in Time Estimation Methods for Molecular Data

Sudhir Kumar*,1,2,3 and S. Blair Hedges1,2,3

- Author Affiliations

1Institute for Genomics and Evolutionary Medicine, Temple University

2Center for Biodiversity, Temple University

3Department of Biology, Temple University

↵*Corresponding author: E-mail: s.kumar@temple.edu

Abstract

Molecular dating has become central to placing a temporal dimension on the tree of life. Methods for estimating divergence times have been developed for over 50 years, beginning with the proposal of molecular clock in 1962. We categorize the chronological development of these methods into four generations based on the timing of their origin. In the first generation approaches (1960s–1980s), a strict molecular clock was assumed to date divergences. In the second generation approaches (1990s), the equality of evolutionary rates between species was first tested and then a strict molecular clock applied to estimate divergence times. The third generation approaches (since ∼2000) account for differences in evolutionary rates across the tree by using a statistical model, obviating the need to assume a clock or to test the equality of evolutionary rates among species. Bayesian methods in the third generation require a specific or uniform prior on the speciation-process and enable the inclusion of uncertainty in clock calibrations. The fourth generation approaches (since 2012) allow rates to vary from branch to branch, but do not need prior selection of a statistical model to describe the rate variation or the specification of speciation model. With high accuracy, comparable to Bayesian approaches, and speeds that are orders of magnitude faster, fourth generation methods are able to produce reliable timetrees of thousands of species using genome scale data. We found that early time estimates from second generation studies are similar to those of third and fourth generation studies, indicating that methodological advances have not fundamentally altered the timetree of life, but rather have facilitated time estimation by enabling the inclusion of more species. Nonetheless, we feel an urgent need for testing the accuracy and precision of third and fourth generation methods, including their robustness to misspecification of priors in the analysis of large phylogenies and data sets.

Key words: molecular clock comparative genomics dating.

© The Author(s) 2016. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com

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A mutação e o excepcionalismo humano: nossa futura carga genética

Mutation and Human Exceptionalism: Our Future Genetic Load

Michael Lynch

GENETICS March 7, 2016 vol. 202 no. 3 869-875; DOI: 10.1534/genetics.115.180471

Abstract

Although the human germline mutation rate is higher than that in any other well-studied species, the rate is not exceptional once the effective genome size and effective population size are taken into consideration. Human somatic mutation rates are substantially elevated above those in the germline, but this is also seen in other species. What is exceptional about humans is the recent detachment from the challenges of the natural environment and the ability to modify phenotypic traits in ways that mitigate the fitness effects of mutations, e.g., precision and personalized medicine. This results in a relaxation of selection against mildly deleterious mutations, including those magnifying the mutation rate itself. The long-term consequence of such effects is an expected genetic deterioration in the baseline human condition, potentially measurable on the timescale of a few generations in westernized societies, and because the brain is a particularly large mutational target, this is of particular concern. Ultimately, the price will have to be covered by further investment in various forms of medical intervention. Resolving the uncertainties of the magnitude and timescale of these effects will require the establishment of stable, standardized, multigenerational measurement procedures for various human traits.

MUTATION, the production of heritable changes in DNA, is one of the most fundamental concepts in genetics. Yet, a broad phylogenetic understanding of the rate and molecular spectrum of mutations and the mechanisms driving the evolution of these key parameters has only recently begun to emerge (Baer et al. 2007; Lynch 2010, 2011). Of special concern is the rate at which mutations are arising in our own lineage and their long-term consequences. In terms of cognitive abilities and proclivity for dominating the global ecosystem, humans are clearly exceptional. But how exceptional are we with respect to the genetic machinery that is the key to long-term genome stability and evolutionary flexibility? And in light of our unusual behavioral features, what are the long-term genetic consequences of being a modern human? Will the miracles of molecular biology and modern medicine reduce the incidence and/or effects of genetic afflictions to negligible levels, or might such applications have the opposite effect?

Two issues are of central relevance here. First, few other species willingly expose themselves to environmental mutagens to the extent that humans do. Presumably, there is some room for reducing the human mutation rate by minimizing negative environmental effects,e.g., through reductions in exposure to smoke from tobacco and other sources, harmful food additives, radon gas, UV irradiation, etc. What, however, is the lower bound to the achievable mutation rate at both the germline and somatic levels? And do factors that influence the somatic mutation rate also have germline effects and vice versa?

Second, owing to the remarkable advances in living conditions and medicine over the past century, and many more likely to come, humans uniquely modify the environment in ways that minimize the consequences of acquired genetic afflictions. Today’s ethical imperative for maximizing individual reproductive potential and longevity independent of genetic background raises significant questions about the future of the human gene pool. Specifically, what are the long-term consequences of the accumulation of mutations whose phenotypic consequences can be transiently minimized through medical intervention and/or a sheltering environment?

It is fitting to review both of these issues in the year 2016, as this would have been the 100th birthday of James Crow, who played a central role in the Genetics Society of America and had a long-standing interest in human mutation (Crow 1993, 1997, 2000, 2006). Many of the issues addressed below were raised by Crow prior to the genomics revolution and can now be evaluated in a more quantitative way.

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Darwin teria seu Origem das Espécies - ideias criacionistas - rejeitado pelo PLoS One!

Perspect Biol Med. 2005 Summer;48(3):362-71.

Was Darwin a creationist?

Cosans C1.

Author information

1Department of Philosophy, Indiana University-Purdue University, Fort Wayne, IN 46805, USA. philoanat@aol.com

Source/Fonte

Abstract

Throughout the Origin of Species, Darwin contrasts his theory of natural selection with the theory that God independently created each species. This makes it seem as though the Origin offers a scientific alternative to a theological worldview. A few months after the Origin appeared, however, the eminent anatomist Richard Owen published a review that pointed out the theological assumptions of Darwin's theory. Owen worked in the tradition of rational morphology, within which one might suggest that evolution occurs by processes that are continuous with those by which life arises from matter; in contrast, Darwin rested his account of life's origins on the notion that God created one or a few life forms upon which natural selection could act. Owen argued that Darwin's reliance on God to explain the origins of life makes his version of evolution no less supernatural than the special creationist that Darwin criticizes: although Darwin limits God to one or a few acts of creation, he still relies upon God to explain life's existence.

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NOTA DESTE BLOGGER:

Para ser lido, tendo por pano de fundo este artigo publicado no PLoS One, que foi retirado após reação da comunidade científica.

Por conter diversas vezes a palavra Criador, o Origem das Espécies de Darwin não seria publicado no PLoS One!!!

Ancestralidade evolutiva das proteínas quinases eucarióticas e colina quinases

Evolutionary Ancestry of Eukaryotic Protein Kinases and Choline Kinases

Shenshen Lai, Javad Safaei and Steven Pelech*

+ Author Affiliations

University of British Columbia, Canada

↵* Corresponding author; email: spelech@kinexus.ca

Author contributions: SP conceived the project. SL and SP designed and performed most of the analyses. JS carried out the pfam domain alignments and kinase domain evolutionary conservation analyses. SL wrote the initial draft of the manuscript and SP completed the final version. SL and SP prepared the figures and tables. All authors analyzed the results and approved the final version of the manuscript.

Abstract

The reversible phosphorylation of proteins catalyzed by protein kinases in eukaryotes supports an important role for eukaryotic protein kinases (ePKs) in the emergence of nucleated cells in the third superkingdom of life. Choline kinases (ChKs) could also be critical in the early evolution of eukaryotes, because of their function in the biosynthesis of phosphatidylcholine, which is unique to eukaryotic membranes. However, the genomic origins of ePKs and ChKs are unclear. The high degeneracy of protein sequences and broad expansion of ePK families have made this fundamental question difficult to answer. In this study, we identified two class-I aminoacyl-tRNA synthetases with high similarities to consensus amino acid sequences of human protein-serine/threonine kinases. Comparisons of primary and tertiary structures supported that ePKs and ChKs evolved from a common ancestor related to glutaminyl aminoacyl-tRNA synthetases, which may have been one of the key factors in the successful of emergence of ancient eukaryotic cells from bacterial colonies.

aminoacyl tRNA synthetase protein evolution protein kinase protein phosphorylation signal transduction choline kinase glutaminyl aminoacyl tRNA synthetase phosphatidylcholine biosynthesis

Received September 10, 2015. Accepted January 7, 2016.

Copyright © 2016, The American Society for Biochemistry and Molecular Biology

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Cromossomo Y de gorila mais semelhante ao humano do que ao de chimpanzé

A time- and cost-effective strategy to sequence mammalian Y Chromosomes: an application to the de novo assembly of gorilla Y

Marta Tomaszkiewicz 1,9, Samarth Rangavittal 1,9, Monika Cechova 1,9, Rebeca Campos Sanchez 2, Howard W. Fescemyer 1, Robert Harris 1, Danling Ye 1, Patricia C.M. O'Brien 3, Rayan Chikhi 4,5,6, Oliver A. Ryder 7, Malcolm A. Ferguson-Smith 3, Paul Medvedev 5,6,8 and Kateryna D. Makova 1

+ Author Affiliations

1Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA;

2Genetics Program, The Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA;

3Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, United Kingdom;

4University of Lille 1/CNRS 59655 Villeneuve d'Ascq, France;

5Department of Computer Science and Engineering, Pennsylvania State University, University Park, Pennsylvania 16802, USA;

6The Genome Sciences Institute of the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802, USA;

7San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA;

8Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802, USA

Corresponding authors: kdm16@psu.edu, pashadag@cse.psu.edu

↵9 These authors contributed equally to this work.

Source/Fonte

Abstract

The mammalian Y Chromosome sequence, critical for studying male fertility and dispersal, is enriched in repeats and palindromes, and thus, is the most difficult component of the genome to assemble. Previously, expensive and labor-intensive BAC-based techniques were used to sequence the Y for a handful of mammalian species. Here, we present a much faster and more affordable strategy for sequencing and assembling mammalian Y Chromosomes of sufficient quality for most comparative genomics analyses and for conservation genetics applications. The strategy combines flow sorting, short- and long-read genome and transcriptome sequencing, and droplet digital PCR with novel and existing computational methods. It can be used to reconstruct sex chromosomes in a heterogametic sex of any species. We applied our strategy to produce a draft of the gorilla Y sequence. The resulting assembly allowed us to refine gene content, evaluate copy number of ampliconic gene families, locate species-specific palindromes, examine the repetitive element content, and produce sequence alignments with human and chimpanzee Y Chromosomes. Our results inform the evolution of the hominine (human, chimpanzee, and gorilla) Y Chromosomes. Surprisingly, we found the gorilla Y Chromosome to be similar to the human Y Chromosome, but not to the chimpanzee Y Chromosome. Moreover, we have utilized the assembled gorilla Y Chromosome sequence to design genetic markers for studying the male-specific dispersal of this endangered species.

Footnotes

[Supplemental material is available for this article.]

Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.199448.115.

Freely available online through the Genome Research Open Access option.

Received September 11, 2015. Accepted January 21, 2016.

© 2016 Tomaszkiewicz et al.; Published by Cold Spring Harbor Laboratory Press

This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.

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O design da mão humana: coisa de profissional.

Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living

Ming-Jin Liu, Cai-Hua Xiong , Le Xiong, Xiao-Lin Huang

Published: January 5, 2016

DOI: 10.1371/journal.pone.0146193

Abstract

Hand coordination can allow humans to have dexterous control with many degrees of freedom to perform various tasks in daily living. An important contributing factor to this important ability is the complex biomechanical architecture of the human hand. However, drawing a clear functional link between biomechanical architecture and hand coordination is challenging. It is not understood which biomechanical characteristics are responsible for hand coordination and what specific effect each biomechanical characteristic has. To explore this link, we first inspected the characteristics of hand coordination during daily tasks through a statistical analysis of the kinematic data, which were collected from thirty right-handed subjects during a multitude of grasping tasks. Then, the functional link between biomechanical architecture and hand coordination was drawn by establishing the clear corresponding causality between the tendinous connective characteristics of the human hand and the coordinated characteristics during daily grasping activities. The explicit functional link indicates that the biomechanical characteristic of tendinous connective architecture between muscles and articulations is the proper design by the Creator to perform a multitude of daily tasks in a comfortable way. The clear link between the structure and the function of the human hand also suggests that the design of a multifunctional robotic hand should be able to better imitate such basic architecture.

Citation: Liu M-J, Xiong C-H, Xiong L, Huang X-L (2016) Biomechanical Characteristics of Hand Coordination in Grasping Activities of Daily Living. PLoS ONE 11(1): e0146193. doi:10.1371/journal.pone.0146193

Editor: Renzhi Han, Ohio State University Medical Center, UNITED STATES

Received: October 28, 2015; Accepted: December 14, 2015; Published: January 5, 2016

Copyright: © 2016 Liu 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: Data are available from the Dryad Digital Repository:http://dx.doi.org/10.5061/dryad.gg8g5.

Funding: This work was partly supported by the National Basic Research Program of China (973 Program, Grant No. 2011CB013301), and National Natural Science Foundation of China (Grant No. 51335004).

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

FREE PDF GRATIS: PLoS One

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NOTA DESTE BLOGGER:

Este é o primeiro abstract que eu vejo a palavra Criador ser mencionada.

Aguardem a reação da Nomenklatura científica e a Galera dos meninos e meninas de Darwin!!!