Como fazer mais pesquisa publicada verdadeira

sábado, outubro 25, 2014

How to Make More Published Research True

John P. A. Ioannidis mail

Published: October 21, 2014

DOI: 10.1371/journal.pmed.1001747 

Citation: Ioannidis JPA (2014) How to Make More Published Research True. PLoS Med 11(10): e1001747. doi:10.1371/journal.pmed.1001747

Published: October 21, 2014

Copyright: © 2014 John P. A. Ioannidis. 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.

Funding: The Meta-Research Innovation Center at Stanford is funded by the Laura and John Arnold Foundation. The funders had no role in the decision to publish or in the preparation of the manuscript.

Competing interests: JPAI is a member of the Editorial Board of PLOS Medicine. The author has declared that no competing interests exist.

Provenance: Commissioned; externally peer reviewed


Summary Points

Currently, many published research findings are false or exaggerated, and an estimated 85% of research resources are wasted.

To make more published research true, practices that have improved credibility and efficiency in specific fields may be transplanted to others which would benefit from them—possibilities include the adoption of large-scale collaborative research; replication culture; registration; sharing; reproducibility practices; better statistical methods; standardization of definitions and analyses; more appropriate (usually more stringent) statistical thresholds; and improvement in study design standards, peer review, reporting and dissemination of research, and training of the scientific workforce.

Selection of interventions to improve research practices requires rigorous examination and experimental testing whenever feasible.

Optimal interventions need to understand and harness the motives of various stakeholders who operate in scientific research and who differ on the extent to which they are interested in promoting publishable, fundable, translatable, or profitable results.

Modifications need to be made in the reward system for science, affecting the exchange rates for currencies (e.g., publications and grants) and purchased academic goods (e.g., promotion and other academic or administrative power) and introducing currencies that are better aligned with translatable and reproducible research.

FREE PDF GRATIS: PLoS Medicine

10 problemas fundamentais sobre o fato, Fato, FATO da evolução: não é assim uma Brastemp epistêmica!!!

sexta-feira, outubro 24, 2014

10 problemas teóricos fundamentais não resolvidos no contexto de justificação teórica da origem e evolução química e biológica

São os seguintes problemas:

Problema 1: Não há mecanismos viáveis para dar origem à sopa primordial.

Problema 2: Processos químicos não guiados não podem explicar a origem do código genético.

Problema 3: As mutações aleatórias não podem gerar a informação genética necessária para estruturas irredutivelmente complexas.

Problema 4: A seleção natural luta para fixar características vantajosas nas populações.

Problema 5: O surgimento abrupto de espécies no registro fóssil não apoia a evolução darwinista.

Problema 6: A biologia moderna falhou fragorosamente em produzir uma grande “Árvore da Vida”.

Problema 7: A evolução convergente desafia a evolução darwinista e destrói a lógica por trás da hipótese da ancestralidade comum.

Problema 8: As diferenças entre os embriões de vertebrados contradizem as predições da ancestralidade comum.

Problema 9: O neodarwinismo luta para explicar distribuição biogeográfica de muitas espécies.

Problema 10: O neodarwinismo tem uma longa história de predições inacuradas sobre os órgãos vestigiais e o DNA “lixo”.

NOTA DESTE BLOGGER:

Há mais problemas, mas 10 está bom demais da conta para demonstrar que o fato, Fato, FATO da evolução não é assim uma Brastemp no contexto de justificação teórica, e que os cientistas não querem dar o braço a torcer para reconhecer que Darwin está nu, e há algo de podre no reino da Nomenklatura científica na questão de honestidade acadêmica em reconhecer que uma mudança paradigmática está diante de nós.


Ensinem essas coisas aos nossos filhos e nossas filhas!

A meiose é muito mais complexa!!!

Topoisomerase II Is Required for the Proper Separation of Heterochromatic Regions during Drosophila melanogaster Female Meiosis

Stacie E. Hughes mail, R. Scott Hawley mail

Published: October 23, 2014DOI: 10.1371/journal.pgen.1004650

Abstract

Heterochromatic homology ensures the segregation of achiasmate chromosomes during meiosis I in Drosophila melanogaster females, perhaps as a consequence of the heterochromatic threads that connect achiasmate homologs during prometaphase I. Here, we ask how these threads, and other possible heterochromatic entanglements, are resolved prior to anaphase I. We show that the knockdown of Topoisomerase II (Top2) by RNAi in the later stages of meiosis results in a specific defect in the separation of heterochromatic regions after spindle assembly. In Top2 RNAi-expressing oocytes, heterochromatic regions of both achiasmate and chiasmate chromosomes often failed to separate during prometaphase I and metaphase I. Heterochromatic regions were stretched into long, abnormal projections with centromeres localizing near the tips of the projections in some oocytes. Despite these anomalies, we observed bipolar spindles in most Top2 RNAi-expressing oocytes, although the obligately achiasmate 4th chromosomes exhibited a near complete failure to move toward the spindle poles during prometaphase I. Both achiasmate and chiasmate chromosomes displayed defects in biorientation. Given that euchromatic regions separate much earlier in prophase, no defects were expected or observed in the ability of euchromatic regions to separate during late prophase upon knockdown of Top2 at mid-prophase. Finally, embryos from Top2 RNAi-expressing females frequently failed to initiate mitotic divisions. These data suggest both that Topoisomerase II is involved in the resolution of heterochromatic DNA entanglements during meiosis I and that these entanglements must be resolved in order to complete meiosis.

Author Summary

Proper chromosome segregation during egg and sperm development is crucial to prevent birth defects and miscarriage. During chromosome replication, DNA entanglements are created that must be resolved before chromosomes can fully separate. In the oocytes of the fruit fly Drosophila melanogaster, DNA entanglements persist between heterochromatic regions of the chromosomes until after spindle assembly and may facilitate the proper segregation of chromosomes during meiosis. Topoisomerase II enzymes can resolve DNA entanglements by cutting and untwisting tangled DNA. Decreasing Topoisomerase II (Top2) levels in the ovaries of fruit flies led to sterility. RNAi knockdown of the Top2 gene in oocytes resulted in chromosomes that failed to fully separate their heterochromatic regions during meiosis I and caused oocytes to arrest in meiosis I. These studies demonstrate that the Top2 enzyme is required for releasing DNA entanglements between homologous chromosomes before the onset of chromosome segregation during Drosophila female meiosis.

Citation: Hughes SE, Hawley RS (2014) Topoisomerase II Is Required for the Proper Separation of Heterochromatic Regions during Drosophila melanogaster Female Meiosis. 

PLoS Genet 10(10): e1004650. doi:10.1371/journal.pgen.1004650

Editor: Gregory P. Copenhaver, The University of North Carolina at Chapel Hill, United States of America

Received: April 14, 2014; Accepted: July 21, 2014; Published: October 23, 2014

Copyright: © 2014 Hughes, Hawley. 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: The authors confirm that all data underlying the findings are fully available without restriction. The Stowers Institute for Medical Reserach has made all primary data files accessible at the following web page: http://odr.stowers.org/websimr/datasetvi​ew/673/0/.

Funding: RSH is supported by Stowers Institute for Medical Research and is an American Cancer Research Professor supported by the award RP-05-086-06DDC. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

FREE PDF GRATIS: PLoS Genetics

Novos parâmetros para a detecção de vida extraterrestre

Remote life-detection criteria, habitable zone boundaries, and the frequency of Earth-like planets around M and late K stars

James F. Kasting1, Ravikumar Kopparapu, Ramses M. Ramirez, and Chester E. Harman


Author Affiliations

Department of Geosciences, Pennsylvania State University, University Park, PA 16802

Edited by Adam S. Burrows, Princeton University, Princeton, NJ, and accepted by the Editorial Board October 31, 2013 (received for review May 13, 2013)

Abstract Full Text Authors & Info Figures SIMetrics Related Content PDFPDF + SI



Significance

National Aeronautics and Space Administration’s (NASA) Kepler Space Telescope has detected over 3,000 planet candidates, about a dozen of which are probably rocky planets within the liquid-water habitable zones of their parent stars. Climate-modeling calculations discussed here shed light on the width of that zone. Within the next several years, NASA may obtain spectra of nearby transiting Earth-sized planets around M stars, using its James Webb Space Telescope. NASA hopes to build an even more capable space telescope to perform direct imaging of Earth-like exoplanets and take spectra of their atmospheres. Once data are obtained from either of these missions, correct interpretation of possible biomarker gases will become critical. We discuss here how those interpretations might be made.



Abstract

The habitable zone (HZ) around a star is typically defined as the region where a rocky planet can maintain liquid water on its surface. That definition is appropriate, because this allows for the possibility that carbon-based, photosynthetic life exists on the planet in sufficient abundance to modify the planet’s atmosphere in a way that might be remotely detected. Exactly what conditions are needed, however, to maintain liquid water remains a topic for debate. In the past, modelers have restricted themselves to water-rich planets with CO2 and H2O as the only important greenhouse gases. More recently, some researchers have suggested broadening the definition to include arid, “Dune” planets on the inner edge and planets with captured H2 atmospheres on the outer edge, thereby greatly increasing the HZ width. Such planets could exist, but we demonstrate that an inner edge limit of 0.59 AU or less is physically unrealistic. We further argue that conservative HZ definitions should be used for designing future space-based telescopes, but that optimistic definitions may be useful in interpreting the data from such missions. In terms of effective solar flux, Seff, the recently recalculated HZ boundaries are: recent Venus—1.78; runaway greenhouse—1.04; moist greenhouse—1.01; maximum greenhouse—0.35; and early Mars—0.32. Based on a combination of different HZ definitions, the frequency of potentially Earth-like planets around late K and M stars observed by Kepler is in the range of 0.4–0.5.

Footnotes

1To whom correspondence should be addressed. E-mail: jfk4@psu.edu.

Author contributions: J.F.K. designed research; R.K. and R.M.R. performed research; C.E.H. analyzed data; and J.F.K. and R.K. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission. A.S.B. is a guest editor invited by the Editorial Board.

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A desonestidade acadêmica de alguns cientistas quanto ao colapso de seus paradigmas

quarta-feira, outubro 22, 2014

Os cientistas são livres para expressarem suas dúvidas ao saber da existência de problemas fundamentais nos atuais paradigmas vigentes, tal como a biologia evolucionária moderna?



Não pergunte no Posto Ipiranga. Leia o que alguns cientistas e céticos escreveram a respeito:

"Há um sentimento em biologia que os cientistas devem manter escondida sua roupa suja, porque a direita religiosa está sempre procurando qualquer discussão entre os evolucionistas como apoio para suas teorias criacionistas [sic]. Há uma forte escola de pensamento de que nunca ninguém deve questionar Darwin em público." (W. Daniel Hillis, in "Introduction: The Emerging Third Culture," in Third Culture: Beyond the Scientific Revolution, editado por John Brockman, Touchstone, 1995, p. 26.

"There's a feeling in biology that scientists should keep their dirty laundry hidden, because the religious right are always looking for any argument between evolutionists as support for their creationist theories. There's a strong school of thought that one should never question Darwin in public." (W. Daniel Hillis, in "Introduction: The Emerging Third Culture," in Third Culture: Beyond the Scientific Revolution, edited by John Brockman(Touchstone, 1995), p. 26.)

"À primeira vista, é altamente implausível que a vida como nós conhecemos, seja o resultado de uma sequência de acidentes físicos junto com o mecanismo da seleção natural... O meu ceticismo não é baseado em crença religiosa ou em uma crença em qualquer alternativa definitiva. É apenas uma crença de que a evidência científica disponível, apesar do consenso da opinião científica, não nesta questão, racionalmente requeira que nós nos subordinemos à incredulidade do senso comum. Isso é especialmente verdade no que diz respeito à origem da vida... Eu entendo que tais dúvidas podem parecer para muitas pessoas como afrontosas, mas isso é porque quase todo o mundo em nossa cultura secular tem sido intimidado em considerar o programa de pesquisa redutivo como sacrossanto, pelo fato de que qualquer outra coisa não seria ciência. ... Pensando nessas questões, eu tenho sido estimulado pelas críticas da dominante visão científica do mundo... feita pelos defensores do design inteligente. ... Os problemas que esses iconoclastas colocam para o consenso científico ortodoxo devem ser considerados seriamente. Eles não merecem o menosprezo que comumente eles enfrentam. É manifestamente injusto." Thomas Nagel, Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False, Oxford University Press, 2012, p. 6-7, 10.)

"It is prima facie highly implausible that life as we know it is the result of a sequence of physical accidents together with the mechanism of natural selection ... My skepticism is not based on religious belief or on a belief in any definite alternative. It is just a belief that the available scientific evidence, in spite of the consensus of scientific opinion, does not in this matter rationally require us to subordinate the incredulity of common sense. This is especially true with regard to the origin of life ... I realize that such doubts will strike many people as outrageous, but that is because almost everyone in our secular culture has been browbeaten into regarding the reductive research program as sacrosanct, on the ground that anything else would not be science. ... In thinking about these questions I have been stimulated by criticisms of the prevailing scientific world picture... by the defenders of intelligent design. ... [T]he problems that these iconoclasts pose for the orthodox scientific consensus should be taken seriously. They do not deserve the scorn with which they are commonly met. It is manifestly unfair." (Thomas Nagel, Mind and Cosmos: Why the Materialist Neo-Darwinian Conception of Nature Is Almost Certainly False, p. (Oxford University Press, 2012), pp. 6-7, 10.)

"Críticos honestos do modo evolucionário de pensamento que têm enfatizado os problemas com o dogma dos biólogos e seus termos indefiníveis, frequentemente, são desconsiderados como se eles fossem cristãos zelotas fundamentalistas ou racistas preconceituosos. Mas a parte da tese deste livro que insiste que tal terminologia interfere com a ciência verdadeira, exige um debate aberto e ponderado sobre a realidade das afirmações feitas pelos evolucionistas zoocêntricos." Lynn Margulis e Dorion Sagan, Acquiring Genomes: A Theory of the Origins of the Species, Basic Books, 2003, p. 29.

"Honest critics of the evolutionary way of thinking who have emphasized problems with biologists' dogma and their undefinable terms are often dismissed as if they were Christian fundamentalist zealots or racial bigots. But the part of this book's thesis that insists such terminology interferes with real science requires an open and thoughtful debate about the reality of the claims made by zoocentric evolutionists." (Lynn Margulis and Dorion Sagan, Acquiring Genomes: A Theory of the Origins of the Species, (Basic Books, 2003), p. 29).)

"É perigoso despertar a atenção para o fato de que não existe explicação satisfatória para a macroevolução. Alguém facilmente se torna alvo da biologia evolucionária ortodoxa e um falso amigo de proponentes de conceitos não científicos. Conforme a primeira, nós já conhecemos todos os princípios relevantes que explicam a complexidade e a diversidade da vida na Terra; para a última, a ciência e a pesquisa nunca serão capazes de fornecer uma explicação conclusiva, simplesmente porque a vida complexa não tem uma origem natural." Günter Theißen, "The proper place of hopeful monsters in evolutionary biology," Theory in Biosciences, 124: 349-369, 2006.

"It is dangerous to raise attention to the fact that there is no satisfying explanation for macroevolution. One easily becomes a target of orthodox evolutionary biology and a false friend of proponents of non-scientific concepts. According to the former we already know all the relevant principles that explain the complexity and diversity of life on earth; for the latter science and research will never be able to provide a conclusive explanation, simply because complex life does not have a natural origin." (Günter Theißen, "The proper place of hopeful monsters in evolutionary biology," Theory in Biosciences,124: 349-369, 2006.

"Nós temos sido informados por mais de um de nossos colegas que, mesmo que se Darwin estivesse substancialmente errado em afirmar que a seleção natural é o mecanismo da evolução, mesmo assim nós não deveríamos dizer isso. Não, de modo algum, dizer isso em público. Fazer isso, contudo, é se alinhar inadvertidamente, com a Forças do Mal, cujo objetivo é levar a Ciência ao descrédito.. ... O neodarwinismo é aceito axiomaticamente; prossegue, literalmente, sem ser questionado. Uma visão que pareça contradizê-lo é, diretamente ou por implicação, rejeitado, quão plausível possa parecer o contrário. Departmentos completos, publicações científicas e centros de pesquisas operam agora neste princípio." Jerry Fodor e Massimo Piattelli-PalmariniWhat Darwin Got Wrong, Farrar, Straus and Giroux, 2010, p. xx, xvi.

"We've been told by more than one of our colleagues that, even if Darwin was substantially wrong to claim that natural selection is the mechanism of evolution, nonetheless we shouldn't say so. Not, anyhow, in public. To do that is, however inadvertently, to align oneself with the Forces of Darkness, whose goal is to bring Science into disrepute. ... [N]eo-Darwinism is taken as axiomatic; it goes literally unquestioned. A view that looks to contradict it, either directly or by implication is ipso facto rejected, however plausible it may otherwise seem. Entire departments, journals and research centres now work on this principle." (Jerry Fodor and Massimo Piattelli-PalmariniWhat Darwin Got Wrong (Farrar, Straus and Giroux, 2010), pp. xx, xvi.)

Não se percebeu em Altenberg nenhum desejo de atacar a teoria evolucionária a partir da esquerda. Bem ao contrário – a preocupação política dominante foi um medo de ataque por parte dos fundamentalistas. Como Gould descobriu, os criacionistas pegam qualquer sinal de divisões na teoria evolucionária ou uma insatisfação com o Darwinismo. Nas duas últimas décadas, todo mundo tem tomado conhecimento disso, independentemente de sua satisfação ou não com a Síntese Moderna. "Você sempre se sente como se estivesse tentando cobrir sua retaguarda", disse Love. "Se você criticar, é como dar munição a essas pessoas". Assim, não critique de modo arrogante, disse Coyne: "As pessoas não devem suprimir suas diferenças para aplacar os criacionistas, mas para sugerir que o neodarwinismo alcançou algum tipo de ponto de crise nas mãos dos criacionistas", disse ele.

John Whitfield, "Biological theory: Postmodern evolution?," Nature, Vol. 455: 281-284, 7 de setembro de 2008

[T]here was no sense at Altenberg of a desire to attack evolutionary theory from the left. Quite the reverse -- the dominant political concern was a fear of attack from fundamentalists. As Gould discovered, creationists seize on any hint of splits in evolutionary theory or dissatisfaction with Darwinism. In the past couple of decades, everyone has become keenly aware of this, regardless of their satisfaction or otherwise with the modern synthesis. "You always feel like you're trying to cover your rear," says Love. "If you criticize, it's like handing ammunition to these folks." So don't criticize in a grandstanding way, says Coyne: "People shouldn't suppress their differences to placate creationists, but to suggest that neo-Darwinism has reached some kind of crisis point plays into creationists' hands," he says.

John Whitfield, "Biological theory: Postmodern evolution?," Nature, Vol. 455: 281-284, September 17, 2008.

Reconstrução filogenômica indica que o ancestral da mitocôndria era um parasita energético

Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite

Zhang Wang, Martin Wu mail

Published: October 15, 2014DOI: 10.1371/journal.pone.0110685

Abstract

Reconstruction of mitochondrial ancestor has great impact on our understanding of the origin of mitochondria. Previous studies have largely focused on reconstructing the last common ancestor of all contemporary mitochondria (proto-mitochondria), but not on the more informative pre-mitochondria (the last common ancestor of mitochondria and their alphaproteobacterial sister clade). Using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryotic genomes, we reconstructed the metabolisms of both proto-mitochondria and pre-mitochondria. Our reconstruction depicts a more streamlined proto-mitochondrion than these predicted by previous studies, and revealed several novel insights into the mitochondria-derived eukaryotic metabolisms including the lipid metabolism. Most strikingly, pre-mitochondrion was predicted to possess a plastid/parasite type of ATP/ADP translocase that imports ATP from the host, which posits pre-mitochondrion as an energy parasite that directly contrasts with the current role of mitochondria as the cell’s energy producer. In addition, pre-mitochondrion was predicted to encode a large number of flagellar genes and several cytochrome oxidases functioning under low oxygen level, strongly supporting the previous finding that the mitochondrial ancestor was likely motile and capable of oxidative phosphorylation under microoxic condition.

Citation: Wang Z, Wu M (2014) Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite. PLoS ONE 9(10): e110685. doi:10.1371/journal.pone.0110685

Editor: Frank Voncken, University of Hull, United Kingdom

Received: July 14, 2014; Accepted: September 22, 2014; Published: October 15, 2014

Copyright: © 2014 Wang, Wu. 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: The authors confirm that all data underlying the findings are fully available without restriction. All relevant data are within the paper and its Supporting Information files. The genome sequences have been deposited at DDBJ/EMBL/GenBank as follows: endosymbiont of acanthamoeba UWC8 (CP004403), Candidatus Caedibacter acanthamoebae (CP008936-CP008940), Candidatus Paracaedibacter acanthamoebae (CP008941-CP008942), Candidatus Paracaedibacter symbiosus (JQAK00000000) and NHP bacterium (JQAJ00000000).

Funding: This research was funded by an award from Thomas F. & Kate Miller Jeffress Memorial Trust to MW. The funder had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.

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

FREE PDF GRATIS: PLoS One

Poderia ter existido vida 15 milhões de anos após o Big Bang? Loeb, de Harvard, diz que sim.

The Habitable Epoch of the Early Universe

Abraham Loeb (Harvard)

(Submitted on 2 Dec 2013 (v1), last revised 3 Jun 2014 (this version, v3))

Mere illustration/Mera ilustração

(Submitted on 2 Dec 2013 (v1), last revised 3 Jun 2014 (this version, v3))


Abstract


In the redshift range 100≲(1+z)≲137, the cosmic microwave background (CMB) had a temperature of 273–373 K (0–100°C), allowing early rocky planets (if any existed) to have liquid water chemistry on their surface and be habitable, irrespective of their distance from a star. In the standard ΛCDM cosmology, the first star-forming halos within our Hubble volume started collapsing at these redshifts, allowing the chemistry of life to possibly begin when the Universe was merely 10–17 million years old. The possibility of life starting when the average matter density was a million times bigger than it is today is not in agreement with the anthropic explanation for the low value of the cosmological constant.
Comments: 12 pages, accepted for publication in the International Journal of Astrobiology

Subjects: Cosmology and Nongalactic Astrophysics (astro-ph.CO); Earth and Planetary Astrophysics (astro-ph.EP); General Relativity and Quantum Cosmology (gr-qc); High Energy Physics - Phenomenology (hep-ph); High Energy Physics - Theory (hep-th)

Cite as: arXiv:1312.0613 [astro-ph.CO]
  (or arXiv:1312.0613v3 [astro-ph.CO] for this version)

Submission history

From: Avi Loeb [view email] 
[v1] Mon, 2 Dec 2013 21:00:18 GMT (6kb)
[v2] Thu, 16 Jan 2014 16:19:05 GMT (8kb)
[v3] Tue, 3 Jun 2014 20:56:38 GMT (8kb)

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Origem da vida? Nossa ignorância científica acabou - basta fazer uma simulação em computador!

terça-feira, outubro 21, 2014

Issue  EPL 
Volume 107, Number 2, July 2014
Article Number 28004
Number of page(s) 6
Section Interdisciplinary Physics and Related Areas of Science and Technology
DOI http://dx.doi.org/10.1209/0295-5075/107/28004
Published online 15 July 2014

EPL, 107 (2014) 28004

Structure and selection in an autocatalytic binary polymer model

Shinpei Tanaka1, Harold Fellermann2,3 and Steen Rasmussen2,4
1 Graduate School of Integrated Arts and Sciences, Hiroshima University - 1-7-1 Kagamiyama, Higashi-Hiroshima 739-8521, Japan 

2 Center for Fundamental Living Technology (FLinT) Department of Physics, Chemistry and Pharmacy, University of Southern Denmark - Campusvej 55 5230 Odense M, Denmark 

3 School of Computing Science, Newcastle University - Claremont Tower, Newcastle upon Tyne, UK 

4 Santa Fe Institute - 1399 Hyde Park Rd, Santa Fe, NM 87501, USA 

Received: 17 March 2014
Accepted: 20 June 2014

Abstract

An autocatalytic binary polymer system is studied as an abstract model for a chemical reaction network capable to evolve. Due to autocatalysis, long polymers appear spontaneously and their concentration is shown to be maintained at the same level as that of monomers. When the reaction starts from a pool of monomers, highly ordered populations with particular sequence patterns are dynamically selected out of a vast number of possible states. The interplay between the selected microscopic sequence patterns and the macroscopic cooperative structures is examined both analytically and in simulation. Stability, fluctuations, and dynamic selection mechanisms are investigated for the involved self-organizing processes.

PACS: 87.23.Kg – Dynamics of evolution / 05.65.+b – Self-organized systems / 87.23.Cc – Population dynamics and ecological pattern formation

© EPLA, 2014

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James Tour 'falou e disse': sobre a evolução ter dado origem à vida, eles só ficam me olhando!

segunda-feira, outubro 20, 2014

14 de outubro de 2014

Químico de renome: “Eles só ficam me olhando”

“Porque é uma coisa assustadora”

Ontem, James Tour, que em 2009 foi classificado como um dos 10 principais químicos no mundo, explicou que os evolucionistas não entendem como que a evolução poderia ter criado a vida. O que é pior, Tour explica que existe uma falta de clareza sobre este fato científico. Em público, os evolucionistas insistem que a evolução é um fato além de qualquer dúvida razoável. Mas em particular, eles admitem que não existe tal conhecimento científico:

“Deixe-me contar-lhe o que ocorre nos bastidores da ciência — com mebros da Academia Nacional de Ciências [dos Estados Unidos], com ganhadores de prêmio Nobel”, afirmou Tour. “Eu tenho sentado com eles, e quando eles estão sozinhos comigo, não em público — porque é uma coisa assustadora, se alguém disser o que eu acabei de dizer — eu digo, ‘Você entende tudo isso, de onde tudo isso veio, e como que isso acontece?’”

A resposta que ele recebe inevitavelmente, Tour explicou, é: “Não”.

“Todas as vezes que eu me sento com pessoas que são químicos sintéticos, que entendem disso, eles dizem, ‘Ah, de jeito nenhum’”, disse Tour. “E se elas têm medo de dizer ‘sim’, elas nada dizem. Elas simplesmente ficam me olhando, porque, sinceramente, elas não podem dizer isso.”

A verdade é uma coisa assustadora.

Postado por Cornelius Hunter em 14 de outubro de 2014

Darwin kaput e Lamarck redivivus: a epigenética e a evolução dos tentilhões das ilhas Galápagos

sexta-feira, outubro 17, 2014

Genome Biol Evol. Aug 2014; 6(8): 1972–1989.
Published online Jul 24, 2014. doi:  10.1093/gbe/evu158

Epigenetics and the Evolution of Darwin’s Finches

Michael K. Skinner,1,* Carlos Gurerrero-Bosagna,1,3 M. Muksitul Haque,1 Eric E. Nilsson,1 Jennifer A.H. Koop,2,4 Sarah A. Knutie,2 and Dale H. Clayton2

1Center for Reproductive Biology, School of Biological Sciences, Washington State University

2Department of Biology, University of Utah

3Present address: Department of Physics, Biology and Chemistry (IFM), Linköping University, Sweden

4Present address: Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ

*Corresponding author: E-mail: ude.usw@renniks.

Associate editor: Bill Martin

Data deposition: All DMR and CNV genomic data obtained in this study have been deposited in the NCBI public GEO database under the accession (GEO #: GSE58334).



Abstract

The prevailing theory for the molecular basis of evolution involves genetic mutations that ultimately generate the heritable phenotypic variation on which natural selection acts. However, epigenetic transgenerational inheritance of phenotypic variation may also play an important role in evolutionary change. A growing number of studies have demonstrated the presence of epigenetic inheritance in a variety of different organisms that can persist for hundreds of generations. The possibility that epigenetic changes can accumulate over longer periods of evolutionary time has seldom been tested empirically. This study was designed to compare epigenetic changes among several closely related species of Darwin’s finches, a well-known example of adaptive radiation. Erythrocyte DNA was obtained from five species of sympatric Darwin’s finches that vary in phylogenetic relatedness. Genome-wide alterations in genetic mutations using copy number variation (CNV) were compared with epigenetic alterations associated with differential DNA methylation regions (epimutations). Epimutations were more common than genetic CNV mutations among the five species; furthermore, the number of epimutations increased monotonically with phylogenetic distance. Interestingly, the number of genetic CNV mutations did not consistently increase with phylogenetic distance. The number, chromosomal locations, regional clustering, and lack of overlap of epimutations and genetic mutations suggest that epigenetic changes are distinct and that they correlate with the evolutionary history of Darwin’s finches. The potential functional significance of the epimutations was explored by comparing their locations on the genome to the location of evolutionarily important genes and cellular pathways in birds. Specific epimutations were associated with genes related to the bone morphogenic protein, toll receptor, and melanogenesis signaling pathways. Species-specific epimutations were significantly overrepresented in these pathways. As environmental factors are known to result in heritable changes in the epigenome, it is possible that epigenetic changes contribute to the molecular basis of the evolution of Darwin’s finches.

Keywords: epimutations, DNA methylation, copy number variation, phylogeny, adaptive radiation, BMP, toll, melanogenesis

FREE PDF GRATIS: Genome Biol Evol

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Darwin kaput e Lamarck redivivus! A nova teoria geral da evolução - a Síntese Evolutiva Ampliada/Estendida, contrariando Darwin, não selecionista par excellence, e vai incorporar aspectos teóricos neolamarckistas, mas somente será anunciada em 2020.

Enquanto a nova teoria da evolução não vem, estão fazendo biologia sem referencial teórico? Mas, aprendemos nas universidades que a ciência abomina o vácuo epistêmico no contexto de justificação teórica... Abracadabra? Entranhas de galinhas? Búzios? Cartas de tarô? Leitura de mãos? Mágica?

Gente, o fato, Fato, FATO da evolução é ensinado como sendo tão cientificamente comprovado como a lei da gravidade e assim como a Terra gira em torno do Sol. E que não existe crise nenhuma na teoria da evolução. Nada mais falso! Basta ler a literatura científica especializada para ver que existem variações extremas de explicações da história evolucionárias das coisas vivas.

Fui, nem sei por que, rindo da cara de alguns cientistas da Nomenklatura científica que, sabem disso, mas fingem não saber, e da Galera dos meninos e meninas de Darwin, cada vez mais órfã. 

Design inteligente na arquitetura celular: a função da proteína GCP-WD na estrutura organizacional e funcional microtubular central

GCP-WD Mediates γ-TuRC Recruitment and the Geometry of Microtubule Nucleation in Interphase Arrays of Arabidopsis

Ankit Walia, Masayoshi Nakamura, Dorianne Moss, Viktor Kirik, Takashi Hashimoto, David W. Ehrhardt email

DOI: http://dx.doi.org/10.1016/j.cub.2014.09.013

Publication stage: In Press Corrected Proof

Highlights

•GCP-WD labels microtubule nucleation sites

•It is predominantly associated with the core γ-TuRC in interphase arrays

•GCP-WD function governs nucleation position, rate, and geometry in cortical arrays

•These functions are required to build arrays of specialized architecture



Summary

Many differentiated animal cells, and all higher plant cells, build interphase microtubule arrays of specific architectures without benefit of a central organizer, such as a centrosome, to control the location and geometry of microtubule nucleation. These acentrosomal arrays support essential cell functions such as morphogenesis [ 1, 2 ], but the mechanisms by which the new microtubules are positioned and oriented are poorly understood. In higher plants, nucleation of microtubules arises from distributed γ-tubulin ring complexes (γ-TuRCs) at the cell cortex that are associated primarily with existing microtubules [ 3–5 ] and from which new microtubules are nucleated in a geometrically bimodal fashion, either in parallel to the mother microtubule or as a branching event at a mean angle of approximately 40° to the mother microtubule. By imaging the dynamics of individual nucleation events in Arabidopsis, we found that a conserved peripheral protein of the γ-TuRC, GCP-WD/NEDD1 [ 6–8 ], associated with motile γ-TuRCs and localized to nucleation events. Knockdown of this essential protein resulted in reduction of γ-TuRC recruitment to cortical microtubules and total nucleation frequency, showing that GCP-WD controls γ-TuRC positioning and function in these interphase arrays. Further, we discovered an unexpected role for GCP-WD in determining the geometry of microtubule-dependent microtubule nucleation, where it acts to increase the likelihood of branching over parallel nucleation. Cells with normally complex patterns of cortical array organization constructed simpler arrays with cell-wide ordering, suggesting that control of nucleation frequency, positioning, and geometry by GCP-WD allows plant cells to build alternative cortical array architectures.

SOURCE/FONTE: Current Biology

Mudança paradigmática no entendimento dos canais de potássio: mais design inteligente!

Science 17 October 2014: 
Vol. 346 no. 6207 pp. 352-355 
DOI: 10.1126/science.1254840
REPORT
Ion permeation in K+ channels occurs by direct Coulomb knock-on

David A. Köpfer1,†, Chen Song2,*,†, Tim Gruene3, George M. Sheldrick3, Ulrich Zachariae4,5,*,‡, Bert L. de Groot1,*,‡

- Author Affiliations

1Biomolecular Dynamics Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.
2Department of Biochemistry, University of Oxford, Oxford OX1 3QU, UK.
3Department of Structural Chemistry, University of Göttingen, 37077 Göttingen, Germany.
4School of Engineering, Physics and Mathematics, University of Dundee, Dundee DD1 4HN, UK.
5College of Life Sciences, University of Dundee, Dundee DD1 5EH, UK.

↵*Corresponding author. E-mail: sc3210@gmail.com (C.S.); u.zachariae@dundee.ac.uk (U.Z.); bgroot@gwdg.de (B.L.d.G.)

↵† These authors contributed equally to this work.

↵‡ These authors contributed equally to this work.



Abstract

Potassium channels selectively conduct K+ ions across cellular membranes with extraordinary efficiency. Their selectivity filter exhibits four binding sites with approximately equal electron density in crystal structures with high K+ concentrations, previously thought to reflect a superposition of alternating ion- and water-occupied states. Consequently, cotranslocation of ions with water has become a widely accepted ion conduction mechanism for potassium channels. By analyzing more than 1300 permeation events from molecular dynamics simulations at physiological voltages, we observed instead that permeation occurs via ion-ion contacts between neighboring K+ ions. Coulomb repulsion between adjacent ions is found to be the key to high-efficiency K+ conduction. Crystallographic data are consistent with directly neighboring K+ ions in the selectivity filter, and our model offers an intuitive explanation for the high throughput rates of K+ channels.

Received for publication 15 April 2014.

Accepted for publication 27 August 2014.

SOURCE/FONTE: Science

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao site CAPES/Periódicos podem ler gratuitamente este artigo da Science e de mais 22.440 publicações científicas.

Super Homem molecular protege o genoma de danos - 100% design inteligente!

Dicer Promotes Transcription Termination at Sites of Replication Stress to Maintain Genome Stability

Stephane E. Castel4, Jie Ren4, Sonali Bhattacharjee, An-Yun Chang, Mar Sánchez, Alberto Valbuena, Francisco Antequera, Robert A. Martienssen email 4 Co-first author

DOI: http://dx.doi.org/10.1016/j.cell.2014.09.031

Highlights

•Dcr1 has a genome-wide role in terminating Pol II transcription

•Dcr1 termination occurs at highly transcribed protein coding genes, tDNA, and rDNA

•Targets are sites of transcription-replication collisions with DNA damage

•Dcr1 resolves collisions, preventing restart by HR, maintaining genomic stability



Summary

Nuclear RNAi is an important regulator of transcription and epigenetic modification, but the underlying mechanisms remain elusive. Using a genome-wide approach in the fission yeast S. pombe, we have found that Dcr1, but not other components of the canonical RNAi pathway, promotes the release of Pol II from the 3′ end of highly transcribed genes, and, surprisingly, from antisense transcription of rRNA and tRNA genes, which are normally transcribed by Pol I and Pol III. These Dcr1-terminated loci correspond to sites of replication stress and DNA damage, likely resulting from transcription-replication collisions. At the rDNA loci, release of Pol II facilitates DNA replication and prevents homologous recombination, which would otherwise lead to loss of rDNA repeats especially during meiosis. Our results reveal a novel role for Dcr1-mediated transcription termination in genome maintenance and may account for widespread regulation of genome stability by nuclear RNAi in higher eukaryotes.

SOURCE/FONTE: Cell

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Professores, pesquisadores e alunos de universidades públicas e privadas com acesso ao site CAPES/Periódicos podem ler gratuitamente este artigo da Cell e de mais 22.440 publicações científicas.

Pesquisa derruba teoria evolucionária da origem das mitocôndrias: as "usinas de força" celulares já foram parasitas de energia

Phylogenomic Reconstruction Indicates Mitochondrial Ancestor Was an Energy Parasite

Zhang Wang, Martin Wu mail

Published: October 15, 2014DOI: 10.1371/journal.pone.0110685




Abstract

Reconstruction of mitochondrial ancestor has great impact on our understanding of the origin of mitochondria. Previous studies have largely focused on reconstructing the last common ancestor of all contemporary mitochondria (proto-mitochondria), but not on the more informative pre-mitochondria (the last common ancestor of mitochondria and their alphaproteobacterial sister clade). Using a phylogenomic approach and leveraging on the increased taxonomic sampling of alphaproteobacterial and eukaryotic genomes, we reconstructed the metabolisms of both proto-mitochondria and pre-mitochondria. Our reconstruction depicts a more streamlined proto-mitochondrion than these predicted by previous studies, and revealed several novel insights into the mitochondria-derived eukaryotic metabolisms including the lipid metabolism. Most strikingly, pre-mitochondrion was predicted to possess a plastid/parasite type of ATP/ADP translocase that imports ATP from the host, which posits pre-mitochondrion as an energy parasite that directly contrasts with the current role of mitochondria as the cell’s energy producer. In addition, pre-mitochondrion was predicted to encode a large number of flagellar genes and several cytochrome oxidases functioning under low oxygen level, strongly supporting the previous finding that the mitochondrial ancestor was likely motile and capable of oxidative phosphorylation under microoxic condition.

FREE PDF GRATIS: PLoS One

7th International Workshop on Thermodynamics, Disequilibrium and Evolution

quinta-feira, outubro 16, 2014



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Integrantes do grupo focal sobre termodinâmica, desequilíbrio e evolução (TDE) do Nasa Astrobiology Institute, fundado em 2010, reuniram-se pela primeira vez no Brasil, nos dias 24 e 25 de setembro, no Centro Nacional de Pesquisa em Energia e Materiais (CNPEM), em Campinas (SP).

Neddy participou deste workshop. 


Lançado o mais novo livro de Franklin M. Harold - In Search of Cell History

quarta-feira, outubro 15, 2014

In Search of Cell History

THE EVOLUTION OF LIFE'S BUILDING BLOCKS

FRANKLIN M. HAROLD

304 pages | 23 halftones, 12 line drawings | 6 x 9 | © 2014

The origin of cells remains one of the most fundamental problems in biology, one that over the past two decades has spawned a large body of research and debate. With In Search of Cell History, Franklin M. Harold offers a comprehensive, impartial take on that research and the controversies that keep the field in turmoil.

Written in accessible language and complemented by a glossary for easy reference, this book investigates the full scope of cellular history. Assuming only a basic knowledge of cell biology, Harold examines such pivotal subjects as the relationship between cells and genes; the central role of bioenergetics in the origin of life; the status of the universal tree of life with its three stems and viral outliers; and the controversies surrounding the last universal common ancestor. He also delves deeply into the evolution of cellular organization, the origin of complex cells, and the incorporation of symbiotic organelles, and considers the fossil evidence for the earliest life on earth. In Search of Cell History shows us just how far we have come in understanding cell evolution—and the evolution of life in general—and how far we still have to go.


REVIEW QUOTES


Nick Lane | University College London and author of "Life Ascending: The Ten Great Inventions of Evolution"

“This book is a rare pleasure: a beautiful, rational, wise, and eloquent framing of life’s Average mysteries, what remains to be known, and how we might get there. It should be read by anyone who wonders, seriously, how we came to be. If it does not provide all the answers, that is because we honestly do not know.

Moselio Schaechter, Distinguished Professor, emeritus | Tufts University

“When dealing with difficult questions such as the origin of life, one yearns for writing that is both sagacious and readable, two qualities that don’t always go together. Fortunately, we can forego the need for making a choice. Harold’s book provides an account that is both masterful in the pursuit of the very question and in the clarity with which he unravels relevant phenomena. I daresay that few more helpful guides to a complex terrain have come forth since Dante’s Beatrice.”

Mark A. Farmer | University of Georgia

The origin of life is one of the great enigmas yet to yield to modern science. While there are other books that attempt to place their own spin on how life came about, In Search of Cell History stands alone in that it is written not by one of those advocating a particular viewpoint but instead by one who tries to remain a detached, albeit extremely well informed, observer of events. An excellent piece of scholarly work by a suitably unbiased and appropriately skeptical researcher.”

Biological Sciences: Biochemistry | Microbiology


CONTENTS


Contents
Preface
Acknowledgments

Chapter 1: Cells, Genes, and Evolution
(On the Nature and Workings of Life)

Chapter 2: The Tree of Life
(Universal Phylogeny and Its Discontents)

Chapter 3: A World Mostly Made Up of Microbes
(Bacteria, Archaea, and Eukarya)

Chapter 4: The Deep Roots of Cellular Life
(The Common Ancestry of Living Things)

Chapter 5: The Perplexing Chronicles of Bioenergetics
(Making a Living, Now and in the Past)

Chapter 6: Life’s Devices
(On the Evolution of Prokaryotic Cells and Their Parts)

Chapter 7: Emergence of the Eukaryotes
(The Second Mystery in Cell Evolution)

Chapter 8: Symbionts into Organelles
(Mitochondria, Plastids, and Their Kin)

Chapter 9: Reading the Rocks
(What We Can Infer from Geology)

Chapter 10: Ultimate Riddle
(Origin of Cellular Life)

Chapter 11: The Crooked Paths of Cell Evolution
(Cell Evolution Is Special)

Chapter 12: Summing Up: Journey without Maps

Notes
Glossary
References
Index

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