Novo ritmo cronobiológico descoberto em mamíferos

quinta-feira, janeiro 07, 2016

The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth

Timothy G. Bromage , Youssef Idaghdour, Rodrigo S. Lacruz, Thomas D. Crenshaw, Olexandra Ovsiy, Björn Rotter, Klaus Hoffmeier, Friedemann Schrenk

Published: January 6, 2016DOI: 10.1371/journal.pone.0145919


Abstract

The paradigm of chronobiology is based almost wholly upon the daily biological clock, or circadian rhythm, which has been the focus of intense molecular, cellular, pharmacological, and behavioral, research. However, the circadian rhythm does not explain biological timings related to fundamental aspects of life history such as rates of tissue/organ/body size development and control of the timing of life stages such as gestation length, age at maturity, and lifespan. This suggests that another biological timing mechanism is at work. Here we focus on a "many days" (multidien) chronobiological period first observed as enigmatic recurring growth lines in developing mammalian tooth enamel that is strongly associate with all adult tissue, organ, and body masses as well as life history attributes such as gestation length, age at maturity, weaning, and lifespan, particularly among the well studied primates. Yet, knowledge of the biological factors regulating the patterning of mammalian life, such as the development of body size and life history structure, does not exist. To identify underlying molecular mechanisms we performed metabolome and genome analyses from blood plasma in domestic pigs. We show that blood plasma metabolites and small non-coding RNA (sncRNA) drawn from 33 domestic pigs over a two-week period strongly oscillate on a 5-day multidien rhythm, as does the pig enamel rhythm. Metabolomics and genomics pathway analyses actually reveal two 5-day rhythms, one related to growth in which biological functions include cell proliferation, apoptosis, and transcription regulation/protein synthesis, and another 5-day rhythm related to degradative pathways that follows three days later. Our results provide experimental confirmation of a 5-day multidien rhythm in the domestic pig linking the periodic growth of enamel with oscillations of the metabolome and genome. This association reveals a new class of chronobiological rhythm and a snapshot of the biological bases that regulate mammalian growth, body size, and life history.

Citation: Bromage TG, Idaghdour Y, Lacruz RS, Crenshaw TD, Ovsiy O, Rotter B, et al. (2016) The Swine Plasma Metabolome Chronicles "Many Days" Biological Timing and Functions Linked to Growth. PLoS ONE 11(1): e0145919. doi:10.1371/journal.pone.0145919

Editor: Shin Yamazaki, University of Texas Southwestern Medical Center, UNITED STATES

Received: September 1, 2015; Accepted: December 10, 2015; Published: January 6, 2016

Copyright: © 2016 Bromage 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: Research support was provided by the 2010 Max Planck Research Award to TGB, endowed by the German Federal Ministry of Education and Research to the Max Planck Society (http://www.mpg.de/en) and the Alexander von Humboldt Foundation (http://www.humboldt-foundation.de/) in respect of the Hard Tissue Research Program in Human Paleobiomics. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Authors BR and KH are employees of the commercial company "GenXPro GmbH", which performed the sncRNA genomics for the study, contributing their expertise as indicated in the Author Contributions.

Competing interests: Authors BR and KH were paid salary by the commercial company "GenXPro GmbH", during which time the funders provided fees for genomics services rendered. They innovated study design and measured concentrations of sncRNA, providing the raw data for analysis by the project team. This competing interest does not alter the authors' adherence to PLOS ONE policies on sharing data and materials.

FREE PDF GRATIS: PLoS One

Uma hélice supramolecular que dispensa a quiralidade

quarta-feira, janeiro 06, 2016

A supramolecular helix that disregards chirality

Cécile Roche, Hao-Jan Sun, Pawaret Leowanawat, Fumito Araoka, Benjamin E. Partridge, Mihai Peterca, Daniela A. Wilson, Margaret E. Prendergast, Paul A. Heiney, Robert Graf, Hans W. Spiess, Xiangbing Zeng, Goran Ungar & Virgil Percec

Affiliations Contributions Corresponding author

Nature Chemistry 8, 80–89 (2016) doi:10.1038/nchem.2397

Received 19 April 2015 Accepted 14 October 2015 Published online 16 November 2015

Source/Fonte: Nature Chemistry


The functions of complex crystalline systems derived from supramolecular biological and non-biological assemblies typically emerge from homochiral programmed primary structures via first principles involving secondary, tertiary and quaternary structures. In contrast, heterochiral and racemic compounds yield disordered crystals, amorphous solids or liquids. Here, we report the self-assembly of perylene bisimide derivatives in a supramolecular helix that in turn self-organizes in columnar hexagonal crystalline domains regardless of the enantiomeric purity of the perylene bisimide. We show that both homochiral and racemic perylene bisimide compounds, including a mixture of 21 diastereomers that cannot be deracemized at the molecular level, self-organize to form single-handed helical assemblies with identical single-crystal-like order. We propose that this high crystalline order is generated via a cogwheel mechanism that disregards the chirality of the self-assembling building blocks. We anticipate that this mechanism will facilitate access to previously inaccessible complex crystalline systems from racemic and homochiral building blocks.

Subject terms: Organic chemistry Self-assembly

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PERGUNTA DESTE BLOGGER:

E agora José, como é que fica aquela história de homoquiralidade sendo um fenômeno especial e coisa e tal???

Epigenética: desembrulhando o genoma e fortalecendo o design inteligente?

Epigenetics: The genome unwrapped

Heidi Ledford

Nature 528, S12–S13 (03 December 2015) doi:10.1038/528S12a

Published online 02 December 2015

Epigeneticists are harnessing genome-editing technologies to tackle a central question hanging over the community — does their field matter?

Source/Fonte: Kyle Bean-Nature

Subject terms: Biological techniques Epigenetics Drug discovery

On 18 February, a consortium of more than 90 laboratories published a landmark catalogue of the chemical changes to DNA that are thought to influence whether and how genes are expressed. Called the Roadmap Epigenomics Project and sponsored by the US National Institutes of Health, the compendium offered an unprecedented look at the layers of coding that exist on top of the genetic code — collectively known as the 'epigenome' — in 127 different human tissues and cell types. The US$154-million project was viewed as a crucial step towards determining how this chemical code contributes to human health and disease. As researchers get to grips with the catalogue's contents, the project is also likely to provide a leap forward in pinning down one of the central mysteries of biology: how do cells with the same genetic instructions take on wildly different identities?

It is still unclear what that epigenetic code actually does, and how it is generated. “I don't think it can be overstated how little we understand about how the epigenome works,” says Charles Gersbach, a biomedical engineer at Duke University in Durham, North Carolina. “There are all of these epigenetic marks and we don't know what they are doing. Are they even necessary?”

After years of wondering, biologists such as Gersbach are now in a position to find out. By harnessing genome-editing technologies, they are able to interrogate the epigenetic control of gene expression with remarkable power and specificity. Researchers can make or delete epigenetic marks at will, and home in on RNAs and proteins that could play a hitherto unrecognized part in directing gene expression. And with these new capabilities, they hope to build an answer to a key question that has plagued the field of epigenetics since its inception — do epigenetic marks alter gene expression or do changes in gene expression alter the marks? “It's an absolutely legitimate question and we need to address it,” says Luca Magnani, a cancer researcher at Imperial College London. “The answer is either going to kill the field, or make it very important.”

...

FULL PDF COMPLETO: Nature

A diversidade estrutural do DNA superenrolado: mero acaso, fortuita necessidade ou design inteligente?

Structural diversity of supercoiled DNA

Rossitza N. Irobalieva, Jonathan M. Fogg, Daniel J. Catanese Jr, Thana Sutthibutpong, Muyuan Chen, Anna K. Barker, Steven J. Ludtke, Sarah A. Harris, Michael F. Schmid, Wah Chiu & Lynn Zechiedrich

Affiliations Contributions Corresponding authors

Nature Communications 6, Article number: 8440 doi:10.1038/ncomms9440

Received 31 January 2015 Accepted 21 August 2015 Published 12 October 2015 Updated online 29 October 2015

Erratum (October, 2015)

Abstract

By regulating access to the genetic code, DNA supercoiling strongly affects DNA metabolism. Despite its importance, however, much about supercoiled DNA (positively supercoiled DNA, in particular) remains unknown. Here we use electron cryo-tomography together with biochemical analyses to investigate structures of individual purified DNA minicircle topoisomers with defined degrees of supercoiling. Our results reveal that each topoisomer, negative or positive, adopts a unique and surprisingly wide distribution of three-dimensional conformations. Moreover, we uncover striking differences in how the topoisomers handle torsional stress. As negative supercoiling increases, bases are increasingly exposed. Beyond a sharp supercoiling threshold, we also detect exposed bases in positively supercoiled DNA. Molecular dynamics simulations independently confirm the conformational heterogeneity and provide atomistic insight into the flexibility of supercoiled DNA. Our integrated approach reveals the three-dimensional structures of DNA that are essential for its function.

Subject terms: Biological sciences Biochemistry Biophysics

FREE PDF GRATIS: Nature Communications
                            Sup. Info. PDF
                                       Sup. Info. 13 videos

Início da vida metazoária: divergência, meio ambiente e ecologia

terça-feira, janeiro 05, 2016

Early metazoan life: divergence, environment and ecology

Douglas H. Erwin

Published 9 November 2015.DOI: 10.1098/rstb.2015.0036


Abstract

Recent molecular clock studies date the origin of Metazoa to 750–800 million years ago (Ma), roughly coinciding with evidence from geochemical proxies that oxygen levels rose from less than 0.1% present atmospheric level (PAL) to perhaps 1–3% PAL O2. A younger origin of Metazoa would require greatly increased substitution rates across many clades and many genes; while not impossible, this is less parsimonious. Yet the first fossil evidence for metazoans (the Doushantuo embryos) about 600 Ma is followed by the Ediacaran fossils after 580 Ma, the earliest undisputed bilaterians at 555 Ma, and an increase in the size and morphologic complexity of bilaterians around 542 Ma. This temporal framework suggests a missing 150–200 Myr of early metazoan history that encompasses many apparent novelties in the early evolution of the nervous system. This span includes two major glaciations, and complex marine geochemical changes including major changes in redox and other environmental changes. One possible resolution is that animals of these still unknown Cryogenian and early Ediacaran ecosystems were relatively simple, with highly conserved developmental genes involved in cell-type specification and simple patterning. In this model, complex nervous systems are a convergent phenomenon in bilaterian clades which occurred close to the time that larger metazoans appeared in the fossil record.

FREE PDF GRATIS: Phil. Trans. R. Soc. B

Falta de transparência na literatura biomédica

Reproducible Research Practices and Transparency across the Biomedical Literature

Shareen A. Iqbal , Joshua D. Wallach , Muin J. Khoury, Sheri D. Schully, John P. A. Ioannidis 

Published: January 4, 2016DOI: 10.1371/journal.pbio.1002333


Abstract

There is a growing movement to encourage reproducibility and transparency practices in the scientific community, including public access to raw data and protocols, the conduct of replication studies, systematic integration of evidence in systematic reviews, and the documentation of funding and potential conflicts of interest. In this survey, we assessed the current status of reproducibility and transparency addressing these indicators in a random sample of 441 biomedical journal articles published in 2000–2014. Only one study provided a full protocol and none made all raw data directly available. Replication studies were rare (n = 4), and only 16 studies had their data included in a subsequent systematic review or meta-analysis. The majority of studies did not mention anything about funding or conflicts of interest. The percentage of articles with no statement of conflict decreased substantially between 2000 and 2014 (94.4% in 2000 to 34.6% in 2014); the percentage of articles reporting statements of conflicts (0% in 2000, 15.4% in 2014) or no conflicts (5.6% in 2000, 50.0% in 2014) increased. Articles published in journals in the clinical medicine category versus other fields were almost twice as likely to not include any information on funding and to have private funding. This study provides baseline data to compare future progress in improving these indicators in the scientific literature.

Author Summary

There is increasing interest in the scientific community about whether published research is transparent and reproducible. Lack of replication and non-transparency decreases the value of research. Several biomedical journals have started to encourage or require authors to submit detailed protocols, full datasets, and disclose information on funding and potential conflicts of interest. In this study, we investigate the reproducibility and transparency practices across the full spectrum of published biomedical literature from 2000–2014. We identify an ongoing lack of access to full datasets and detailed protocols for both clinical and non-clinical biomedical investigation. We also map the availability of information on funding and conflicts of interest in this literature. The results from this study provide baseline data to compare future progress in improving these indicators in the scientific literature. We believe that this information may be essential to sensitize stakeholders in science about the need for improving reproducibility and transparency practices.

Citation: Iqbal SA, Wallach JD, Khoury MJ, Schully SD, Ioannidis JPA (2016) Reproducible Research Practices and Transparency across the Biomedical Literature. PLoS Biol 14(1): e1002333. doi:10.1371/journal.pbio.1002333

Academic Editor: David L. Vaux, Walter and Eliza Hall Institute of Medical Research, AUSTRALIA

Received: October 13, 2015; Accepted: November 19, 2015; Published: January 4, 2016

This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication

Data Availability: All relevant data are within the paper and its Supporting Information files. All authors had full access to all of the data (including statistical reports and tables) in the study and can take responsibility for the integrity of the data and accuracy of the data analysis.

Funding: The authors received no specific funding for this work. The Meta-Research Innovation Center at Stanford (METRICS) is supported by a grant from the Laura and John Arnold Foundation.

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

Abbreviations: ESI, Essential Science Indicators; JCR, Journal Citation Reports; NIH, National Institutes of Health; NSF, National Science Foundation; PMCID, PubMed Central reference number; PMID, PubMed Identification

FREE PDF GRATIS: PLoS Biology

Análises filogenéticas baseadas em distâncias expandidas da evolução do formato de crânio fóssil de Homo

Expanded Distance-based Phylogenetic Analyses of Fossil Homo Skull Shape Evolution

Peter J. Waddell

(Submitted on 30 Dec 2015)

Source/Fonte: John Hawk's blog

Analyses of a set of 47 fossil and 4 modern skulls using phylogenetic geometric morphometric methods corroborate and refine earlier results. These include evidence that the African Iwo Eleru skull, only about 12,000 years old, indeed represents a new species of near human. In contrast, the earliest known anatomically modern human skull, Qafzeh 9, the skull of Eve from Israel/Palestine, is validated as fully modern in form. Analyses clearly show evidence of archaic introgression into Gravettian, pre_Gravettian, Qafzeh, and Upper Cave (China) populations of near modern humans, and in about that order of increasing archaic content. The enigmatic Saldahna (Elandsfontein) skull emerges as a probable first representative of that lineage, which exclusive of Neanderthals that, eventually lead to modern humans. There is also evidence that the poorly dated Kabwe (Broken Hill) skull represents a much earlier distinct lineage. The clarity of the results bode well for quantitative statistical phylogenetic methods making significant inroads in the stalemates of paleoanthropology.

Subjects: Populations and Evolution (q-bio.PE); Genomics (q-bio.GN); Quantitative Methods (q-bio.QM)

Cite as: arXiv:1512.09115 [q-bio.PE]

(or arXiv:1512.09115v1 [q-bio.PE] for this version)

Submission history

From: Peter Waddell [view email

[v1] Wed, 30 Dec 2015 20:45:38 GMT (739kb)

FREE PDF GRATIS: ArXiv

A disseminação de desinformação online

The spreading of misinformation online

Michela Del Vicarioa, Alessandro Bessib, Fabiana Zolloa, Fabio Petronic, Antonio Scalaa,d, Guido Caldarellia,d, H. Eugene Stanleye, and Walter Quattrociocchia,1

aLaboratory of Computational Social Science, Networks Department, IMT Alti Studi Lucca, 55100 Lucca, Italy;

bIUSS Institute for Advanced Study, 27100 Pavia, Italy;

cSapienza University, 00185 Rome, Italy;

dISC-CNR Uos “Sapienza,” 00185 Rome, Italy;

eBoston University, Boston, MA 02115

Edited by Matjaz Perc, University of Maribor, Maribor, Slovenia, and accepted by the Editorial Board December 4, 2015 (received for review September 1, 2015)


Significance

The wide availability of user-provided content in online social media facilitates the aggregation of people around common interests, worldviews, and narratives. However, the World Wide Web is a fruitful environment for the massive diffusion of unverified rumors. In this work, using a massive quantitative analysis of Facebook, we show that information related to distinct narratives––conspiracy theories and scientific news––generates homogeneous and polarized communities (i.e., echo chambers) having similar information consumption patterns. Then, we derive a data-driven percolation model of rumor spreading that demonstrates that homogeneity and polarization are the main determinants for predicting cascades’ size.

Abstract

The wide availability of user-provided content in online social media facilitates the aggregation of people around common interests, worldviews, and narratives. However, the World Wide Web (WWW) also allows for the rapid dissemination of unsubstantiated rumors and conspiracy theories that often elicit rapid, large, but naive social responses such as the recent case of Jade Helm 15––where a simple military exercise turned out to be perceived as the beginning of a new civil war in the United States. In this work, we address the determinants governing misinformation spreading through a thorough quantitative analysis. In particular, we focus on how Facebook users consume information related to two distinct narratives: scientific and conspiracy news. We find that, although consumers of scientific and conspiracy stories present similar consumption patterns with respect to content, cascade dynamics differ. Selective exposure to content is the primary driver of content diffusion and generates the formation of homogeneous clusters, i.e., “echo chambers.” Indeed, homogeneity appears to be the primary driver for the diffusion of contents and each echo chamber has its own cascade dynamics. Finally, we introduce a data-driven percolation model mimicking rumor spreading and we show that homogeneity and polarization are the main determinants for predicting cascades’ size.

misinformation virality Facebook rumor spreading cascades

Footnotes

1To whom correspondence should be addressed. Email: walterquattrociocchi{at}gmail.com.

Author contributions: M.D.V., A.B., F.Z., A.S., G.C., H.E.S., and W.Q. designed research; M.D.V., A.B., F.Z., H.E.S., and W.Q. performed research; M.D.V., A.B., F.Z., F.P., and W.Q. contributed new reagents/analytic tools; M.D.V., A.B., F.Z., A.S., G.C., H.E.S., and W.Q. analyzed data; and M.D.V., A.B., F.Z., A.S., G.C., H.E.S., and W.Q. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission. M.P. is a guest editor invited by the Editorial Board.

FREE PDF GRATIS: PNAS

O mito do consenso científico do esfriamento global dos anos 1970s

Thomas C. Peterson, William M. Connolley, and John Fleck, 2008: The Myth of the 1970s Global Cooling Scientific Consensus. Bull. Amer. Meteor. Soc., 89, 1325–1337.


The Myth of the 1970s Global Cooling Scientific Consensus

Thomas C. Peterson

NOAA/National Climatic Data Center, Asheville, North Carolina

William M. Connolley

British Antarctic Survey, National Environment Research Council, Cambridge, United Kingdom

John Fleck

Albuquerque Journal, Albuquerque, New Mexico


Abstract

Climate science as we know it today did not exist in the 1960s and 1970s. The integrated enterprise embodied in the Nobel Prizewinning work of the Intergovernmental Panel on Climate Change existed then as separate threads of research pursued by isolated groups of scientists. Atmospheric chemists and modelers grappled with the measurement of changes in carbon dioxide and atmospheric gases, and the changes in climate that might result. Meanwhile, geologists and paleoclimate researchers tried to understand when Earth slipped into and out of ice ages, and why. An enduring popular myth suggests that in the 1970s the climate science community was predicting “global cooling” and an “imminent” ice age, an observation frequently used by those who would undermine what climate scientists say today about the prospect of global warming. A review of the literature suggests that, on the contrary, greenhouse warming even then dominated scientists' thinking as being one of the most important forces shaping Earth's climate on human time scales. More importantly than showing the falsehood of the myth, this review describes how scientists of the time built the foundation on which the cohesive enterprise of modern climate science now rests.

FREE PDF GRATIS: Bull. Amer. Meteor. Soc.

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NOTA DESTE BLOGGER:

Consenso é coisa de político, e geralmente com uma agenda ideológica ou pragmática a ser defendida. Em ciência não cabe consenso, mas assentimento transitório ao que as evidências nos oferecem aproximadamente da realidade dos fatos considerados pelos métodos científicos.

Esta pesquisa revela um "consenso" que deu com os burros na água - as evidências não apoiaram os cientistas nas suas afirmações apocalípticas catastróficas de um inverno global.

Este blogger entende que na questão das mudanças climáticas atuais, a questão liderada por Al "Apocalipse" Gore é muito mais político-ideológica do que científica quanto a atribuir o fenômeno dessas mudanças como sendo antropogenicamente provocado. 

Quando é que os cientistas irão aprender que "consenso" é coisa de político e não cabe em ciência? Nesta, o que vale é o debate das ideias e o pesar das evidências. Hoje, as evidências, que se danem as evidências, o que vale é a teoria, oops, o consenso.

Eu penso que este consenso sobre as bruscas mudanças climáticas  é mais um mito científico que irá brevemente para a lata do lixo da História da Ciência.

Porque as publicações científicas deveriam ser anônimas

segunda-feira, janeiro 04, 2016

Why scientific publications should be anonymous

Paul H. P. Hanel

(Submitted on 16 Dec 2015)


Numerous studies have revealed biases within the scientific communication system and across all scientific fields. For example, already prominent researchers receive disproportional credit compared to their (almost) equally qualified colleagues -- because of their prominence. However, none of those studies has offered a solution as to how to decrease the incidence of these biases. In this paper I argue that by publishing anonymously, we can decrease the incidence of inaccurate heuristics in the current scientific communication system. Specific suggestions are made as to how to implement the changes.

Subjects: Digital Libraries (cs.DL)

Cite as: arXiv:1512.05382 [cs.DL]

(or arXiv:1512.05382v1 [cs.DL] for this version)

Submission history

From: Paul Hanel [view email

[v1] Wed, 16 Dec 2015 21:39:55 GMT (75kb)

Which authors of this paper are endorsers? | Disable MathJax (What is MathJax?)

Link back to: arXiv, form interface, contact.

FREE PDEF GRATIS: ArXiv

Transferência horizontal de gene entre bactérias e seu papel na evolução biológica

Life 2014, 4(2), 217-224; doi:10.3390/life4020217

Review

Horizontal Gene Transfer among Bacteria and Its Role in Biological Evolution


Biozentrum, University of Basel, Klingelbergstr. 50/70, CH-4056 Basel, Switzerland

Received: 19 February 2014 / Revised: 22 April 2014 / Accepted: 23 April 2014 / Published: 16 May 2014

(This article belongs to the Special Issue Horizontal Gene Transfer and the Last Universal Common Ancestor)

Abstract

This is a contribution to the history of scientific advance in the past 70 years concerning the identification of genetic information, its molecular structure, the identification of its functions and the molecular mechanisms of its evolution. Particular attention is thereby given to horizontal gene transfer among microorganisms, as well as to biosafety considerations with regard to beneficial applications of acquired scientific knowledge.


This is an open access article distributed under the Creative Commons Attribution License (CC BY) which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

FREE PDF GRATIS: Life

O modelo do Big Bang não é assim uma Brastemp epistêmica

Paul J. Steinhardt

Albert Einstein Professor in Science, Departments of Physics and Astrophysical Sciences, Princeton University; coauthor: Endless Universe




The Big Bang Cannot Be What We Thought It Was

A year and half ago, the scientific community and the press trumpeted the claim by a team of scientists that they had found definitive proof that the universe began with a Big Bang followed by a period of accelerated expansion, known as inflation. Their proof was that the light produced in the infant universe and collected by their detectors exhibited a distinctive pattern of polarization that could only be explained if the large scale structure of the universe was set when the temperature and density of the universe were extraordinarily high, just as posited in the Big Bang inflationary picture.

Over the ensuing year, though, it became clear that the claim was a blunder: in searching for a cosmic signal from the distant universe, the team had not taken proper account of the polarization of light that occurred nearby when it passed through the dust in our Milky Way on the way to their detectors. The new claim from the team, published in recent months, is that there is no sign of the cosmic polarization they had been seeking despite an extensive search with extraordinarily sensitive detectors.

The retraction received considerable attention but the full import of the news has not been appreciated: we now know that the Big Bang cannot be what we thought it was.

The prevailing view has been that the Big Bang was a violent high-energy event during which space, time, matter and energy were suddenly created from nothing in a distorted, non-uniform distribution. To account for the undistorted nearly uniform universe we actually observe, many cosmologists hypothesize a period of rapid stretching (inflation) just after the bang when the concentration of energy and matter was still very high. If there were inflationary stretching only, the universe would become perfectly smooth, but there is always quantum physics in addition to stretching and quantum physics resists perfect smoothness.

At the high concentrations of energy required for inflation, random quantum fluctuations keep generating bumps and wiggles in the shape of space and the distribution of matter and energy that should remain when inflation ends. The quantum-generated irregularities should appear today as hot spots and cold spots in the pattern of light emanating from the early universe, the so-called cosmic background radiation. Indeed, the hot and cold spots have been observed and mapped in numerous experiments since the COBE satellite detected the first spatial variations in the cosmic background radiation temperature in 1992.

The problem is that, when the concentration of energy is high, the quantum-generated distortions in space should modify the way light scatters from matter in the early universe and imprint a spiraling pattern of polarization across the cosmos. It was the detection of this spiraling pattern (referred to as B-mode) that was claimed as proof of the Big Bang inflationary picture, and then retracted. The failure to detect the B-mode pattern means that there is something very wrong with the picture of a violent Big Bang followed by a period of high energy-driven inflation. Whatever processes set the large-scale structure of the universe had a to be a gentler, lower-energy process than has been supposed.

Simply lowering the energy concentration at which inflation starts, as some theorists have suggested, only leads to more trouble. This leaves more time after the Big Bang for the non-uniform distribution of matter and energy to drive the universe away from inflation. Starting inflation after the Big Bang and having enough inflation to smooth the universe becomes exponentially less likely as the energy concentration is lowered. The universe is more likely to emerge as too rough, too curved, too inhomogeneous compared to what we observe.

Something more radical is called for. * Perhaps an improved understanding of quantum gravity will enable us to understand how the Big Bang and inflation can be discarded in favor of gentler beginning. Or perhaps the Big Bang was actually a gentle bounce from a previous period of contraction to the current period of expansion. During a period of slow contraction, it is possible to smooth the distribution of space, matter and energy and to create hot spots and cold spots without creating any B-modes at all.

As the news sinks in, scientists will need to rethink depending on whether forthcoming, more sensitive efforts to detect a B-mode pattern find anything at all. Whatever is found, our view of the Big Bang will be changed, and that is newsworthy.

Source/Fonte: Edge

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NOTA DESTE BLOGGER:

O que Steinhardt quis dizer? Que o modelo inflacionário estava errado desde sua criação vinte anos atrás. E não passou no teste mais importante em ciência: o observacional.

Alô MEC/SEMTEC/PNLEM: hora de revisar e atualizar o conteúdo da origem e evolução do universo, pois o modelo do Big Bang "explodiu" (este blogger não se conteve!). 

O número Pi encontrado escondido no átomo de hidrogênio?

domingo, janeiro 03, 2016

Quantum mechanical derivation of the Wallis formula for π

Tamar Friedmann 1,a) and C. R. Hagen 2,b)

1 Department of Mathematics and Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, USA

2 Department of Physics and Astronomy, University of Rochester, Rochester, New York 14627, USA

a) Email address: tfriedma@ur.rochester.edu

b) Email address: hagen@pas.rochester.edu

J. Math. Phys. 56, 112101 (2015);


Abstract

A famous pre-Newtonian formula for π is obtained directly from the variational approach to the spectrum of the hydrogen atom in spaces of arbitrary dimensions greater than one, including the physical three dimensions.

Epigenética do RNA

sábado, janeiro 02, 2016

RNA Epigenetics

DNA isn’t the only decorated nucleic acid in the cell. Modifications to RNA molecules are much more common and are critical for regulating diverse biological processes.


By Dan Dominissini, Chuan He and Gidi Rechavi | January 1, 2016

For years, researchers described DNA and RNA as linear chains of four building blocks—the nucleotides A, G, C, and T for DNA; and A, G, C, and U for RNA. But these information molecules are much more than their core sequences. A variety of chemical modifications decorate the nucleic acids, increasing the alphabet of DNA to about a dozen known nucleotide variants. The alphabet of RNA is even more impressive, consisting of at least 140 alternative nucleotide forms. The different building blocks can affect the complementarity of the RNA molecules, alter their structure, and enable the binding of specific proteins that mediate various biochemical and cellular outcomes.

The large size of RNA’s vocabulary relative to that of DNA’s is not surprising. DNA is involved mainly with genetic information storage, while RNA molecules—mRNA, rRNA, tRNA, miRNA, and others—are engaged in diverse structural, catalytic, and regulatory activities, in addition to translating genes into proteins. RNA’s multitasking prowess, at the heart of the RNA World hypothesis implicating RNA as the first molecule of life, likely spurred the evolution of numerous modified nucleotides. This enabled the diversified complementarity and secondary structures that allow RNA species to specifically interact with other components of the cellular machinery such as DNA and proteins.

Methylating RNA

The nucleotide building blocks of RNA contain pyrimidine or purine rings, and each position of these rings can be chemically altered by the addition of various chemical groups. Most frequently, a methyl (–CH3) group is tacked on to the outside of the ring. Other chemical additions such as acetyl, isopentenyl, and threonylcarbamoyl are also found added to RNA bases.

Among the 140 modified RNA nucleotide variants identified, methylation of adenosine at the N6 position (m6A) is the most prevalent epigenetic mark in eukaryotic mRNA. Identified in bacterial rRNAs and tRNAs as early as the 1950s, this type of methylation was subsequently found in other RNA molecules, including mRNA, in animal and plant cells as well. In 1984, researchers identified a site that was specifically methylated—the 3′ untranslated region (UTR) of bovine prolactin mRNA. 1 As more sites of m6A modification were identified, a consistent pattern emerged: the methylated A is preceded by A or G and followed by C (A/G—methylated A—C).

Although the identification of m6A in RNA is 40 years old, until recently researchers lacked efficient molecular mapping and quantification methods to fully understand the functional implications of the modification. In 2012, we (D.D. and G.R.) combined the power of next-generation sequencing (NGS) with traditional antibody-mediated capture techniques to perform high-resolution transcriptome-wide mapping of m6A, an approach we termed m6A-seq. 2 Briefly, the transcriptome is randomly fragmented and an anti-m6A antibody is used to fish out the methylated RNA fragments; the m6A-containing fragments are then sequenced and aligned to the genome, thus allowing us to locate the positions of methylation marks.

Analyzing the human transcriptome in this way, we identified more than 12,000 methylated sites in mRNA molecules derived from approximately 7,000 protein-coding genes. The transcripts of most expressed genes, in a variety of cell types, were shown to be methylated, indicating that m6A modifications are widespread. In addition, about 250 noncoding RNA sequences—including well-characterized long noncoding RNAs (lncRNAs), such as the XIST transcripts that have a key role in X-chromosome inactivation—are decorated by m6A. In almost all cases, the epigenetic mark was found on adenosines embedded in the predicted A/G—methylated A—C sequence. We found that this pattern was consistently preceded by an additional purine (A or G) and followed by a uracil (U), extending the known consensus sequence to A/G—A/G—methylated A—C—U. 2

At the macro level, we found that m6A methylation sites were enriched at two distinct landmarks. The highest relative representation of m6A was found in the stop codon–3′ UTR segment of the RNA, with nearly a third of such methylation found in this sequence just beyond a gene’s coding region. Within the coding regions of the RNA molecules, m6A enrichment mapped to unusually long internal exons; 87 percent of the exonic methylation peaks were found in exons longer than 400 nucleotides. (The average human exon is only 145 nucleotides in length). This pattern of decoration of transcribed RNA suggests that m6A is involved in the mediation of splicing of long-exon transcripts. RNAs transcribed from single­-isoform genes were found to be relatively undermethylated, while transcripts that are known to have multiple isoforms, determined by alternative splicing patterns, were hypermethylated. 2 Moreover, specific alternative splicing types, such as intron retention, exon skipping, and alternative first or last exon usage, were highly correlated with m6A decoration. And silencing the m6A methylating protein METTL3 affected global gene expression and alternative splicing patterns in both human and mouse cells. 2

These findings clearly indicate the importance of m6A decoration in regulating the expression of diverse transcripts. Moreover, our parallel study of the human and mouse methylome by m6A-seq has uncovered a remarkable degree of conservation in both consensus sequence and areas of enrichment, further supporting the importance of m6A function. 2 But research into understanding how m6A marks themselves are regulated, and how this affects various cellular processes, is only just beginning.
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Read more here/Leia mais aqui: The Scientist

No princípio... Kaput cosmologia???

sexta-feira, janeiro 01, 2016

In the beginning

Cosmology has been on a long, hot streak, racking up one imaginative and scientific triumph after another. Is it over?

Source/Fonte: Aeon

by Ross Andersen

Ross Andersen is a senior editor at The Atlantic where he oversees the Science, Health and Technology sections. He was formerly the deputy editor of Aeon.

9,500 words

Edited by Brigid Hains

One crisp day last March, Harvard professor John Kovac walked out of his office and into a taxicab that whisked him across town, to a building on the edge of the MIT campus. People were paying attention to Kovac’s comings and goings that week. He was the subject of a fast-spreading rumour. Kovac is an experimental cosmologist midway through the prime of a charmed career. He did his doctoral work at the University of Chicago and a postdoc at Caltech before landing a professorship at Harvard. He is a blue chip. And since 2009, he has been principal investigator of BICEP2, an ingenious scientific experiment at the South Pole.

Kovac had come to MIT to visit Alan Guth, a world-renowned theoretical cosmologist, who made his name more than 30 years ago when he devised the theory of inflation. Guth told Kovac to take the back steps up to his office, to avoid being seen. If Guth’s colleagues caught a glimpse of the two men talking, the whispers swirling around Kovac would have swelled to a roar.

The science of cosmology has achieved wonders in recent centuries. It has enlarged the world we can see and think about by ontological orders of magnitude. Cosmology wrenched the Earth from the centre of the Universe, and heaved it, like a discus, into its whirling orbit around one unremarkable star among the billions that speed around the black-hole centre of our galaxy, a galaxy that floats in deep space with billions of others, all of them colliding and combining, before they fly apart from each other for all eternity. Art, literature, religion and philosophy ignore cosmology at their peril.

But cosmology’s hot streak has stalled. Cosmologists have looked deep into time, almost all the way back to the Big Bang itself, but they don’t know what came before it. They don’t know whether the Big Bang was the beginning, or merely one of many beginnings. Something entirely unimaginable might have preceded it. Cosmologists don’t know if the world we see around us is spatially infinite, or if there are other kinds of worlds beyond our horizon, or in other dimensions. And then the big mystery, the one that keeps the priests and the physicists up at night: no cosmologist has a clue why there is something rather than nothing.

To solve these mysteries, cosmologists must make guesses about events that are absurdly remote from us. Guth’s theory of inflation is one such guess. It tells us that our Universe expanded, exponentially, a trillionth of a trillionth of a trillionth of a second after the Big Bang. In most models of this process, inflation’s expansive kick is eternal. It might cease in particular parts of the cosmos, as it did in our region, after only a fraction of a second, when inflation’s energy transformed into ordinary matter and radiation, which time would sculpt into galaxies. But somewhere outside our region, inflation continued, generating an infinite number of new regions, including those that are roaring into existence at this very moment.

Not all these regions are alike. Quantum mechanics puts a slot-machine spin on the cosmic conditions of every region, so that each has its own physical peculiarities. Some contain galaxies, stars, planets, and maybe even people. Others are entirely devoid of complex structures. Many are too alien to imagine. The slice of space and time we can see from Earth is 90 billion light years across. Today’s inflationary models tell us that this enormous expanse is only one small section of one tiny bubble that floats along in a frothy sea whose proportions defy comprehension. This vision of the world is wondrous, in its vastness and variety, in the sheer range of possibilities it suggests to the mind. But could it ever be proved?

John Kovac had come to MIT to deliver good news. In 2009, Kovac and colleagues installed a telescope at the bottom of the Earth, and with it caught some of the oldest light in the Universe. He’d come to tell Guth that this light bore scars from time’s violent beginning, scars that strongly suggested the theory of inflation is true.

If the BICEP2 discovery held up, it would mint Nobel Prizes, and his would be the first

That same week, Chao-Lin Kuo, one of Kovac’s collaborators, paid a similar visit to Andrei Linde, another pioneer of inflationary theory. Kuo surprised Linde at his home, not far from Stanford’s sunny Silicon Valley campus. He brought a cameraman to record the moment for posterity, and a bottle of Champagne. When he knocked on Linde’s door, Linde and his wife answered. ‘I have a surprise for you,’ Kuo said. Linde’s wife, Renata Kallosh, who is also a physicist, was the first to react. She closed her eyes and hugged Kuo. Linde was stunned. ‘What?!’ he said, before asking Kuo to repeat the data. Soon, they were drinking Champagne, and Linde was effusive. ‘If this is true,’ he said, ‘this is a moment of understanding of nature of such magnitude, it just overwhelms.’

Back at MIT, Guth grilled Kovac with question after question, feeling around for weaknesses in the data. Guth would want to be sure. If the BICEP2 discovery held up, it would mint Nobel Prizes, and his would be the first. It would mean that an extraordinary idea entered human culture by way of his imagination. After more than an hour of interrogation, Guth relented. He could find no fault with the data.

A week later, the BICEP2 team went public, sparking a rare media event for the cerebral science of cosmology. In a front-page story for The New York Times Magazine, Kovac was quoted saying there was a one-in-10-million chance that the result was a fluke. The MIT physicist Max Tegmark told the Times that Kovac’s work would be one of the greatest discoveries in the history of science, ‘if [it] stays true’. For a time, it seemed as though cosmology had once again delivered a new cosmos.

When you read that word cosmos, you might begin to imagine the most expansive physical world your mind can build. Deep fields of glittering, star-filled galaxies stretching out in every direction, and maybe into forever. But even that image represents only the barest sliver of what is meant by ‘cosmos’. To build a cosmos, you have to extend your imagination to all of space and all of time. Only one of Earth’s creatures can pull off that cognitive trick. All living things are attuned to their environment: bacteria can sense chemical shifts in their immediate surroundings; migrating birds know our planet well enough to wing annually across its whole face; dung beetles navigate by the light of the Milky Way. But only the human being lives inside a cosmos, and only recently.

By the end of the last Ice Age, humans had travelled to every continent on Earth except Antarctica. At some point during these prehistoric wanderings, we began to pay close attention to the celestial realm. There are hints of this in Paleolithic cave art, where we find the first etchings of the Moon and its phases, its cycling from silver sliver to illuminated whole, and back again. We see it in the stone pillars that humans hauled across landscapes, to form rings that tracked the Sun’s seasonal arcs through the sky.

But these clues are few and far between. They aren’t enough for us to sketch the wider cosmos that the prehistoric mind inhabited. The first cosmos we can confidently describe comes down to us from the Bronze Age, whose belief systems were caught and preserved, in a newly invented cultural amber called writing. Even these, we know only crudely. Just well enough to identify a few of their common elements.

The ancient cosmos was not a complex mathematical structure. It was a sensory world, stitched together from people’s everyday experiences, people who had never seen Earth’s curves from orbit, or the night sky as magnified by a telescope. The ancient cosmos had a beginning, a birth out of a formless state, usually an infinite liquid realm, or a chaotic void that would suddenly separate into opposites, like light and darkness, or fire and ice, or earth and sky. This separation concept is still with us today in scientific creation stories, which often invoke a primordial splitting of symmetries. But the ancient versions were much more vivid. In the sacred Sanskrit text the Rig Veda, the universe begins as a symmetrical orb of pure potential, an egg surrounded by an infinite amniotic sea, which splits into two bowls of earth and sky, with the yolk-like sun hovering somewhere in the middle.

The earth that emerged from this primordial separation was usually a flat, round disc, wrinkled by mountains, cut through with rivers, and surrounded by ocean on every side. Above this disc was the closed dome of the sky, and below it was an underground realm of equivalent size. Together, they formed a sphere. Every night, the sun would travel through the invisible underworld after teetering over the horizon’s edge. The ancients knew this because the sun reappeared at dawn on the earth’s opposite side.
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Read more here/Leia mais aqui: Aeon

A epigenética forçando a evolução ir além de Darwin: Lamarck, você está sendo chamado!!!

EPIGENETICS: SCOPE AND MECHANISMS

Evolution beyond neo-Darwinism: a new conceptual framework

Denis Noble

Journal of Experimental Biology 2015 218: 7-13; doi: 10.1242/jeb.106310


Abstract

Experimental results in epigenetics and related fields of biological research show that the Modern Synthesis (neo-Darwinist) theory of evolution requires either extension or replacement. This article examines the conceptual framework of neo-Darwinism, including the concepts of ‘gene’, ‘selfish’, ‘code’, ‘program’, ‘blueprint’, ‘book of life’, ‘replicator’ and ‘vehicle’. This form of representation is a barrier to extending or replacing existing theory as it confuses conceptual and empirical matters. These need to be clearly distinguished. In the case of the central concept of ‘gene’, the definition has moved all the way from describing a necessary cause (defined in terms of the inheritable phenotype itself) to an empirically testable hypothesis (in terms of causation by DNA sequences). Neo-Darwinism also privileges ‘genes’ in causation, whereas in multi-way networks of interactions there can be no privileged cause. An alternative conceptual framework is proposed that avoids these problems, and which is more favourable to an integrated systems view of evolution.

Origin of this article

This paper represents the culmination of ideas previously developed in a book, The Music of Life (Noble, 2006), and four related articles (Noble, 2011b; Noble, 2012; Noble, 2013; Noble et al., 2014). Those publications raised many questions from readers in response to which the ‘Answers’ pages (http://musicoflife.co.uk/Answers-menu.html) of The Music of Life website were drafted. Those pages, in particular the page entitled The language of Neo-Darwinism, were written in preparation for the present article. The ideas have been extensively honed in response to further questions and comments.

                            Sup. Info - Video

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NOTA DESTE BLOGGER:


Este blogger está muito feliz - mais uma vez vindicado por cientistas evolucionistas honestos. Explico. Em 1998, após ler o livro A Caixa Preta de Darwin, de Michael Behe, fiquei convencido de que a atual teoria geral da evolução - Síntese Evolutiva Moderna, não explicava mais questões evolucionárias fundamentais, e que uma mudança paradigmática se fazia necessária.

Contactei e notifiquei vários editores de ciência - Folha de São Paulo, Galileu, VEJA, SuperInteressante, Época e até o Observatório da Imprensa (que acolheu nossos artigos) sobre a crise na teoria da evolução de Darwin através da seleção natural e n mecanismos evolucionários, crise esta profunda verificada no contexto de justificação teórica. 

Resposta da maioria dos editores científicos e da Nomenklatura científica? Não existe crise epistêmica! E que a teoria proposta - teoria do Design Inteligente, era pseudociência e criacionismo disfarçado. Nada mais falso.

Depois vieram os 16 de Altenberg, Austria, que se reuniram de 11-13 de julho de 2008, no Instituto Konrad Lorenz para Evolução e Pesquisa da Cognição, naquela cidade, propondo uma nova teoria geral da evolução: a Síntese Evolutiva Ampliada/Estendida (SEA). Este blogger esperava que ela fosse anunciada ao mundo em 2010. Não foi. Ficou para 2020, e agora a grata surpresa de ver qual é a sua estrutura, pressupostos e predições.

Por que este blogger ficou alegre? Porque foi vindicado nas suas afirmações por evolucionistas sérios e respeitados nas suas especialidades, e por ter visto a Grande Mídia ter sido mais uma vez desnudada na sua relação incestuosa com a Nomenklatura científica - não existe nenhuma crise na evolução, pois é uma teoria científica tão certa quanto a lei da gravidade, que a Terra é redonda e gira em torno do Sol, de que não estamos no centro do universo y otras cositas mais!

Chupem essa manga epistêmica - vem aí a nova teoria geral da evolução - a Síntese Evolutiva Ampliada/Estendida que 11 entre 10 evolucionistas da Nomenklatura científica e da Galera dos meninos e meninas de Darwin ficaram sabendo aqui por este blogger!

Darwin kaput, pois a SEA não incorporou a origem da informação genética. Ah, a teoria do Design Inteligente é uma teoria de informação...