Quem disse que Darwin baniu as essências biológicas - sem as formas platônicas a evolução colapsa!

segunda-feira, setembro 26, 2016

Possible creatures

It seemed Darwin had banished biological essences – yet evolution would fail without nature’s library of Platonic forms

Andreas Wagner is a professor in the Institute of Evolutionary Biology and Environmental Studies at the University of Zurich and at the Santa Fe Institute in New Mexico. His latest book is Arrival of the Fittest: Solving Evolution’s Greatest Puzzle (2014).

Edited by Ed Lake


When it slithers through the grass, the legless glass lizard is indistinguishable from a snake. But harass it and it will perform a very un-snakelike feat. It will leave its tail behind – still wriggling – and slide away. That isn’t the only surprise the glass lizard has in store. A careful look also reveals inflexible jaws, movable eyelids, and ear openings. These are all traits that lizards display but snakes don’t. One way or another, this peculiar creature slithers between the cracks of our familiar categories.

To organise the messy diversity of a million-plus different life forms, we need to sort them into the boxes we call species. And what would be more natural than using visible traits such as legs, jaws or ears for that purpose? About a century before Charles Darwin, the systematist Carl Linnaeus did just that when he created our modern classification of life’s diversity. So did Georges Cuvier, the father of palaeontology, when he classified fossils that had been preserved through the ages.

...

READ MORE HERE/LEIA MAIS AQUI: Aeon

+++++

Saiba mais quem é Andreas Wagner:


Andreas Wagner é professor no Instituto de Biologia Evolucionária na Universidade de Zurique, na Suíça, e Professor Externo no Instituto Santa Fe. Ele palestra pelo mundo inteiro, e é um fellow da American Association for the Advancement of Sciences. Ele reside em Zurique, Suíça.

Andreas Wagner Laboratory, University of Zurich

Fatores genéticos e ambientais são responsáveis pela variação epigenética, mas quanto exatamente?

Genetic and environmental influences interact with age and sex in shaping the human methylome

Jenny van Dongen, Michel G. Nivard, Gonneke Willemsen, Jouke-Jan Hottenga, Quinta Helmer, Conor V. Dolan, Erik A. Ehli, Gareth E. Davies, Maarten van Iterson, Charles E. Breeze, Stephan Beck, BIOS Consortium, H. Eka Suchiman, Rick Jansen, Joyce B. van Meurs, Bastiaan T. Heijmans, P. Eline Slagboom & Dorret I. Boomsma

Nature Communications 7, Article number: 11115 (2016)


Download Citation

DNA methylation Epigenomics

Received: 10 June 2015 Accepted: 23 February 2016 Published online: 07 April 2016



Estimates of DNA methylation heritability from the GRM-based approach in 2,603 individuals. From inside to outside: the most inner circular diagram displays the average methylation level at each site, the second band shows the total heritability of DNA methylation level, the third band shows the SNP heritability of DNA methylation level, and the most outer circle shows the chromosome ideograms. Colours range from dark blue (0%) to dark red (100%).

Abstract

The methylome is subject to genetic and environmental effects. Their impact may depend on sex and age, resulting in sex- and age-related physiological variation and disease susceptibility. Here we estimate the total heritability of DNA methylation levels in whole blood and estimate the variance explained by common single nucleotide polymorphisms at 411,169 sites in 2,603 individuals from twin families, to establish a catalogue of between-individual variation in DNA methylation. Heritability estimates vary across the genome (mean=19%) and interaction analyses reveal thousands of sites with sex-specific heritability as well as sites where the environmental variance increases with age. Integration with previously published data illustrates the impact of genome and environment across the lifespan at methylation sites associated with metabolic traits, smoking and ageing. These findings demonstrate that our catalogue holds valuable information on locations in the genome where methylation variation between people may reflect disease-relevant environmental exposures or genetic variation.


Acknowledgements
We thank the twins and their family members who participate in the studies of the Netherlands Twin Register. This study was funded by: BBRMI-NL-financed BIOS Consortium (NWO 184.021.007), and Genetics of Mental Illness, a lifespan approach to the genetics of childhood and adult neuropsychiatric disorders and comorbid conditions (ERC-230374). JvD is supported by ACTION. ACTION receives funding from the European Union Seventh Framework Program (FP7/2007-2013) under grant agreement no 602768. MV is supported by Royal Netherlands Academy of Science Professor Award (PAH/6635) to DIB. CB was supported by EpiTrain (EU-FP7 316758).

Author information

Author notes
Jenny van Dongen & Michel G. Nivard

These authors contributed equally to this work.
Bastiaan T. Heijmans, P. Eline Slagboom & Dorret I. Boomsma

These authors jointly supervised this work.

Affiliations
Department of Biological Psychology, VU Amsterdam, Van der Boechorststraat 1, 1081BT Amsterdam, The Netherlands
Jenny van Dongen, Michel G. Nivard, Gonneke Willemsen, Jouke-Jan Hottenga, Quinta Helmer, Conor V. Dolan, René Pool & Dorret I. Boomsma
Avera Institute for Human Genetics, 3720 W. 69th Street, Sioux Falls, South Dakota 57108, USA
Erik A. Ehli & Gareth E. Davies
Department of Molecular Epidemiology, Leiden University Medical Center, Postzone S5-P, Postbus 9600, 2300 RC Leiden, The Netherlands
Maarten van Iterson, Marian Beekman, Joris Deelen, Ruud van der Breggen, Nico Lakenberg, Matthijs Moed, René Luijk, H. Eka Suchiman, Bastiaan T. Heijmans & P. Eline Slagboom
UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
Charles E. Breeze & Stephan Beck
Department of Psychiatry, VU University Medical Center, A.J. Ernststraat 1187, 1081 HL Amsterdam, The Netherlands
Rick Jansen
Department of Internal Medicine, Erasmus Medical Center, 's Gravendijkwal 230, 3015 CE Rotterdam, The Netherlands
André G. Uitterlinden, P. Mila Jhamai, Michael Verbiest, Marijn Verkerk, Jeroen van Rooij & Joyce B. van Meurs
Department of Human Genetics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
Peter A.C.’t Hoen, Martijn Vermaat & Michiel van Galen
Department of Internal Medicine and School for Cardiovascular Diseases (CARIM), Maastricht University Medical Center, 6200 MD Maastricht, The Netherlands
Marleen M.J. van Greevenbroek, Coen D.A. Stehouwer, Carla J.H. van der Kallen & Casper G. Schalkwijk
Department of Genetics, University of Groningen, University Medical Centre Groningen, 9700 RB Groningen, The Netherlands
Cisca Wijmenga, Sasha Zhernakova, Ettje F. Tigchelaar, Dasha V. Zhernakova, Patrick Deelen, Marc Jan Bonder & Lude Franke
Department of Gerontology and Geriatrics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
Diana van Heemst
Department of Neurology, Brain Center Rudolf Magnus, University Medical Center Utrecht, 3508 GA Utrecht, The Netherlands
Jan H. Veldink & Leonard H. van den Berg
Department of Genetic Epidemiology, ErasmusMC, 3000 CA Rotterdam, The Netherlands
Cornelia M. van Duijn & Aaron Isaacs
Department of Epidemiology, ErasmusMC, 3000 CA Rotterdam, The Netherlands
Bert A. Hofman
Sequence Analysis Support Core, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
Hailiang Mei, Peter van’t Hof & Wibowo Arindrarto
SURFsara, 1090 GP Amsterdam, The Netherlands
Jan Bot & Irene Nooren
Genomics Coordination Center, University Medical Center Groningen, University of Groningen, 9700 RB Groningen, The Netherlands
Freerk van Dijk & Morris A. Swertz
Medical Statistics Section, Department of Medical Statistics and Bioinformatics, Leiden University Medical Center, 2300 RC Leiden, The Netherlands
Szymon M. Kielbasa & Erik W. van Zwet
Consortia
BIOS Consortium
Peter A.C.’t Hoen, René Pool, Marleen M.J. van Greevenbroek, Coen D.A. Stehouwer, Carla J.H. van der Kallen, Casper G. Schalkwijk, Cisca Wijmenga, Sasha Zhernakova, Ettje F. Tigchelaar, Marian Beekman, Joris Deelen, Diana van Heemst, Jan H. Veldink, Leonard H. van den Berg, Cornelia M. van Duijn, Bert A. Hofman, André G. Uitterlinden, P. Mila Jhamai, Michael Verbiest, Marijn Verkerk, Ruud van der Breggen, Jeroen van Rooij, Nico Lakenberg, Hailiang Mei, Jan Bot, Dasha V. Zhernakova, Peter van’t Hof, Patrick Deelen, Irene Nooren, Matthijs Moed, Martijn Vermaat, René Luijk, Marc Jan Bonder, Freerk van Dijk, Michiel van Galen, Wibowo Arindrarto, Szymon M. Kielbasa, Morris A. Swertz, Erik W. van Zwet, Aaron Isaacs & Lude Franke
Contributions
J.v.D. and M.G.N. contributed equally. B.T.H., G.W., P.E.S. and D.I.B. jointly supervised research. J.v.D., B.T.H., M.G.N., G.W., P.E.S. and D.I.B. conceived and designed the experiments. E.A.E., G.E.D., the BIOS Consortium, H.E.S., and J.B.v.M. performed the experiments. J.v.D., M.G.N. and C.B. performed statistical analysis. J.v.D., B.T.H., M.G.N., J.J.H., Q.H., C.V.D., E.A.E., M.V.I. and the BIOS consortium analysed the data. M.G.N., C.V.D., M.v.I., C.B., S.B. and the BIOS consortium contributed reagents/materials/analysis tools. J.v.D., B.T.H., M.G.N., G.W., E.A.E., G.E.D., R.J., J.B.v.M., P.E.S. and D.I.B. wrote the paper. B.T.H., P.E.S. and D.I.B. contributed equally.

Competing interests
The authors declare no competing financial interests.

Corresponding author
Correspondence to Jenny van Dongen.

Dr. Addy Pross, 'falou e disse': a Biologia e a Física não explicam a origem da vida!

domingo, setembro 25, 2016

“Apesar da opinião generalizada de que a evolução darwinista tem sido capaz de explicar o surgimento da complexidade biológica, isso não é o caso… A teoria darwinista não lida com a questão de como [a vida] foi capaz de passar a existir. A questão problemática ainda em busca de uma resposta é: Como que um sistema capaz de evoluir surgiu originalmente? … A natureza simplesmente não funciona assim! A natureza não faz espontaneamente entidades altamente organizadas… intencionais… E aqui reside exatamente o problema [da origem] da vida… não é apenas o senso comum que nos diz que entidades altamente organizadas simplesmente não surgem espontaneamente. Certas leis básicas de Física acompanhadas de probabilidade matemática] pregam o mesmo sermão – os sistemas tendem para o caos e desordem, não para a ordem e função… A Biologia e a Física parecem contraditórias, bem incompatíveis” – What is Life: How Chemistry Becomes Biology, Oxford University Press, 2012 – Dr. Addy Pross, professor de química, Universidade Ben-Gurion, Israel.

“Despite the widespread view that Darwinian Evolution has been able to explain the emergence of biological complexity that is not the case…Darwinian theory does not deal with the question how [life] was able to come into being. The troublesome question still in search of an answer is: How did a system capable of evolving come about in the first place?…Nature just doesn’t operate like that! Nature doesn’t spontaneously make highly organized…purposeful entities…And here precisely lies the [origin of] life problem…it is not just common sense that tells us that highly organized entities don’t just spontaneously come about. Certain basic laws of physics [coupled with mathematical probability] preach the same sermon – systems tend toward chaos and disorder, not toward order and function… Biology and physics seem contradictory, quite incompatible” – What is Life: How Chemistry Becomes Biology, Oxford University Press, 2012 – Dr. Addy Pross, professor of chemistry, Ben-Gurion University, Israel.

O que há por debaixo da Groenlândia???

sábado, setembro 24, 2016

Geodetic measurements reveal similarities between post–Last Glacial Maximum and present-day mass loss from the Greenland ice sheet

Shfaqat A. Khan1,*, Ingo Sasgen2, Michael Bevis3, Tonie van Dam4, Jonathan L. Bamber5, John Wahr6,†, Michael Willis7, Kurt H. Kjær8, Bert Wouters9, Veit Helm2, Beata Csatho10, Kevin Fleming11, Anders A. Bjørk8, Andy Aschwanden12, Per Knudsen1 and Peter Kuipers Munneke9

- Author Affiliations

1DTU Space, National Space Institute, Department of Geodesy, Technical University of Denmark, Kgs. Lyngby, Denmark.

2Glaciology Section, Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.

3Geodetic Science, Ohio State University, Columbus, OH 43320, USA.

4Faculty of Science, Technology, and Communication, Research Unit of Engineering Sciences, University of Luxembourg, Luxembourg, Luxembourg.

5Bristol Glaciology Centre, University of Bristol, Bristol, U.K.

6Department of Physics and Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, CO 80309, USA.

7Department of Earth and Atmospheric Sciences, Cornell University, Ithaca, NY 14853, USA.

8Centre for GeoGenetics, Natural History Museum of Denmark, University of Copenhagen, Copenhagen, Denmark.

9Institute for Marine and Atmospheric Research Utrecht, Utrecht University, Utrecht, Netherlands.

10Department of Geology, University at Buffalo, Buffalo, NY 14260, USA.

11Centre for Early Warning Systems Helmholtz Centre Potsdam, GFZ German Research Centre for Geosciences, Potsdam, Germany.

12Geophysical Institute, University of Alaska Fairbanks, Fairbanks, AK 99775, USA.

↵*Corresponding author. Email: abbas@space.dtu.dk

↵† Deceased.

Science Advances 21 Sep 2016:

Vol. 2, no. 9, e1600931



Fig. 1 Location map.

Locations of the GNET GPS stations (red dots) and RSL observations (green dots). Black curves denote the major drainage basins numbered from 1 to 7; drainage 3 is separated into subbasins 3A and 3B (inset), the latter representing the near field of the KUAQ glacier. The yellow curve shows a reconstruction of the Iceland hot spot track (57, 58). Bathymetry is shown over the ocean and surface elevation over the land/ice (25).

Abstract

Accurate quantification of the millennial-scale mass balance of the Greenland ice sheet (GrIS) and its contribution to global sea-level rise remain challenging because of sparse in situ observations in key regions. Glacial isostatic adjustment (GIA) is the ongoing response of the solid Earth to ice and ocean load changes occurring since the Last Glacial Maximum (LGM; ~21 thousand years ago) and may be used to constrain the GrIS deglaciation history. We use data from the Greenland Global Positioning System network to directly measure GIA and estimate basin-wide mass changes since the LGM. Unpredicted, large GIA uplift rates of +12 mm/year are found in southeast Greenland. These rates are due to low upper mantle viscosity in the region, from when Greenland passed over the Iceland hot spot about 40 million years ago. This region of concentrated soft rheology has a profound influence on reconstructing the deglaciation history of Greenland. We reevaluate the evolution of the GrIS since LGM and obtain a loss of 1.5-m sea-level equivalent from the northwest and southeast. These same sectors are dominating modern mass loss. We suggest that the present destabilization of these marine-based sectors may increase sea level for centuries to come. Our new deglaciation history and GIA uplift estimates suggest that studies that use the Gravity Recovery and Climate Experiment satellite mission to infer present-day changes in the GrIS may have erroneously corrected for GIA and underestimated the mass loss by about 20 gigatons/year.

Keywords Sea level rise climate change Greenland Ice Sheet GPS glacial isostatic adjustment Last Glacial Maximum

Copyright © 2016, The Authors

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

FREE PDF GRATIS: Science Advances

Vamos poder recriar as cores das penas fossilizadas???

Elemental characterisation of melanin in feathers via synchrotron X-ray imaging and absorption spectroscopy

Nicholas P. Edwards, Arjen van Veelen, Jennifer Anné, Phillip L. Manning, Uwe Bergmann, William I. Sellers, Victoria M. Egerton, Dimosthenis Sokaras, Roberto Alonso-Mori, Kazumasa Wakamatsu, Shosuke Ito & Roy A. Wogelius

Scientific Reports 6, Article number: 34002 (2016)


Download Citation

Analytical chemistry Biochemistry

Received: 15 June 2016 Accepted: 02 September 2016 Published online: 23 September 2016



Abstract

Melanin is a critical component of biological systems, but the exact chemistry of melanin is still imprecisely known. This is partly due to melanin’s complex heterogeneous nature and partly because many studies use synthetic analogues and/or pigments extracted from their natural biological setting, which may display important differences from endogenous pigments. Here we demonstrate how synchrotron X-ray analyses can non-destructively characterise the elements associated with melanin pigment in situ within extant feathers. Elemental imaging shows that the distributions of Ca, Cu and Zn are almost exclusively controlled by melanin pigment distribution. X-ray absorption spectroscopy demonstrates that the atomic coordination of zinc and sulfur is different within eumelanised regions compared to pheomelanised regions. This not only impacts our fundamental understanding of pigmentation in extant organisms but also provides a significant contribution to the evidence-based colour palette available for reconstructing the appearance of fossil organisms.

Acknowledgements

Funding was provided by a UK Natural Environment Research Council grant NE/J023426/1. Portions of this research were carried out at the Stanford Synchrotron Radiation Lightsource (CA, USA), a national user facility operated by Stanford University on behalf of the U.S. Department of Energy, Office of Basic Energy Sciences. Portions of this research were also carried out at Diamond Light Source (UK, allocation SP11865 and SP12948). We thank support staff at SSRL and DLS. PLM thanks the Science and Technology Facilities Council for their support (ST/M001814/1). We also thank the Live Animal Center (LAC) at The Academy of Natural Sciences of Drexel University (Philadelphia, PA, USA) and the Wild Wings Birds of Prey education and rehabilitation centre (UK) for supply of feathers from bird under their care.

Author information

Affiliations

University of Manchester, School of Earth and Environmental Sciences, Williamson Research Centre for Molecular Environmental Science, M13 9PL, UK

Nicholas P. Edwards, Arjen van Veelen, Jennifer Anné, William I. Sellers & Roy A. Wogelius

University of Manchester, School of Earth and Environmental Sciences, Interdisciplinary Centre for Ancient Life, Manchester M13 9PL, UK

Nicholas P. Edwards, Arjen van Veelen, Jennifer Anné, Phillip L. Manning, William I. Sellers, Victoria M. Egerton & Roy A. Wogelius

College of Charleston, Department of Geology and Environmental Geosciences, Charleston, SC, 29424, USA

Phillip L. Manning & Victoria M. Egerton

Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA

Uwe Bergmann

Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA 94025, USA

Dimosthenis Sokaras

Linac Coherent Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, 94025, USA

Roberto Alonso-Mori

Department of Chemistry, Fujita Health University, School of Health Sciences, Toyoake, Aichi 470–1192, Japan

Kazumasa Wakamatsu & Shosuke Ito

Contributions

N.P.E., A.V.V., J.A., P.L.M., U.B., W.I.S., V.M.E., D.S., R.A.-M. and R.A.W. all participated in the synchrotron analyses. N.P.E. and J.A. composed the experimental design with guidance from R.A.W. K.W and S.I. conducted the melanin identification and quantification experiments. N.P.E. processed the synchrotron image, quantitative and sulfur XAS data, created all the figures, and composed the manuscript. A.V.V. processed and fit the Zn EXAFS data. All co-authors gave critical input to the text.

Competing interests

The authors declare no competing financial interests.

Corresponding authors

Correspondence to Nicholas P. Edwards or Roy A. Wogelius.

FREE PDF GRATIS: Scientific Reports Sup Info

Geomitologia: as origens geológicas de mitos e lendas

sexta-feira, setembro 23, 2016

Geomythology: geological origins of myths and legends

Dorothy B. Vitaliano

- Author Affiliations

(e-mail: c/o judy@xylor.com)


Abstract

Myths and geology are related in several ways. Some myths are the result of man's attempts to explain noteworthy features of his environment, such as striking landforms or unusual smaller features, whereas others try to account for conspicuous natural processes, such as earthquakes, volcanic phenomena, and floods. Local myths have sometimes proved helpful in solving geological problems, and even the geological nomenclature is indebted to mythology. Examples of each kind of relationship are given.

© The Geological Society of London 2007

Repensando o Principia de Newton

Rethinking Newton's Principia

Saunders, Simon (2013) Rethinking Newton's Principia. [Preprint]

This is the latest version of this item.


Abstract

It is widely accepted that the notion of an inertial frame is central to Newtonian mechanics and that the correct space-time structure underlying Newton’s methods in Principia is neo-Newtonian or Galilean space-time. I argue to the contrary that inertial frames are not needed in Newton’s theory of motion, and that the right space-time structure for Newton’s Principia requires the notion of parallelism of spatial directions at different times and nothing more.

FREE PDF GRATIS: PhilSci

O agora e o fluir do tempo

Now, and the Flow of Time

Richard A. Muller, a Shaun Maguire b,c

a Department of Physics, University of California, Berkeley, California 94720, USA

Institute for Quantum Information & Matter and Walter Burke Institute for Theoretical Physics,

California Institute of Technology, Pasadena, California 91125, USA

c Department of Mathematics, California Institute of Technology, Pasadena, California 91125, USA

E-mail: ramuller@lbl.gov, smaguire@caltech.edu


Abstract: 

The progression of time can be understood by assuming that the Hubble expansion takes place in 4 dimensions rather than in 3. The flow of time consists of the continuous creation of new moments, new nows, that accompany the creation of new space. This model suggests a modification to the metric tensor of the vacuum that leads to testable consequences. Two cosmological tests are proposed, but they present both experimental and theoretical problems. A more practical and immediate test is based on a predicted lag in the emergence of gravitational radiation when two black holes merge. In such mergers (as recently observed by the LIGO team), a macroscopic volume (millions of cubic kilometers) of space is created in the region in which the gravitational wave is generated; this one-time creation of new space should be accompanied by the creation of detectable level of new time, resulting in a time delay that could be observed as a growing lag in the emission of the wave as the merger takes place.

Keywords: LIGO, gravitational waves, arrow of time

FREE PDF GRATIS: arXiv

Oposição a Galileu não foi somente religiosa, foi também científica

quinta-feira, setembro 22, 2016

Opposition to Galileo was scientific, not just religious

Christopher Graney is a professor of physics at Jefferson Community and Technical College in Louisville, Kentucky. He is interested in the history of astronomy, especially of the late 16th and early 17th centuries. His latest book is Setting Aside All Authority: Giovanni Battista Riccioli and the Science Against Copernicus in the Age of Galileo (2015).



In 1614, when the telescope was new technology, a young man in Germany published a book filled with illustrations of the exciting new things being discovered telescopically: moons circling Jupiter, moon-like phases of Venus, spots on the Sun, the rough and cratered lunar surface. The young man was Johann Georg Locher, and his book was Mathematical Disquisitions Concerning Astronomical Controversies and Novelties. And while Locher heaped praise upon Galileo, he challenged ideas that Galileo championed – on scientific grounds.

You see, Locher was an anti-Copernican, a fan of the ancient astronomer Ptolemy, and a student within the Establishment (his mentor was Christoph Scheiner, a prominent Jesuit astronomer). Locher argued that Copernicus was wrong about Earth circling the Sun, and that Earth was fixed in place, at the centre of the Universe, like Ptolemy said. But Locher was making no religious argument. Yes, he said, a moving Earth messes with certain Biblical passages, like Joshua telling the Sun to stand still. But it also messes with certain astronomical terms, such as sunrise and sunset. Copernicans had work-arounds for all that, Locher said, even though they might be convoluted. What Copernicans could not work around, though, were the scientific arguments against their theory. Indeed, Locher even proposed a mechanism to explain how Earth could orbit the Sun (a sort of perpetual falling – this decades before Isaac Newton would explain orbits by means of perpetual falling), but he said it would not help the Copernicans, on account of the other problems with their theory.

What were those problems? A big one was the size of stars in the Copernican universe. Copernicus proposed that certain oddities observed in the movements of planets through the constellations were due to the fact that Earth itself was moving. Stars show no such oddities, so Copernicus had to theorise that, rather than being just beyond the planets as astronomers had traditionally supposed, stars were so incredibly distant that Earth’s motion was insignificant by comparison. But seen from Earth, stars appear as dots of certain sizes or magnitudes. The only way stars could be so incredibly distant and have such sizes was if they were all incredibly huge, every last one dwarfing the Sun. Tycho Brahe, the most prominent astronomer of the era and a favourite of the Establishment, thought this was absurd, while Peter Crüger, a leading Polish mathematician, wondered how the Copernican system could ever survive in the face of the star-size problem.

Locher thought much was up in the air and ripe for study. In light of the star-size problem, he thought that the Earth clearly did not move; the Sun circled it. But the telescope made it clear that Venus circled the Sun, and that sunspots also went around the Sun. Brahe had theorised that all planets circled the Sun, while it circled Earth. Locher noted that Brahe might be right, but what was clear was that the telescope supported Ptolemy.
...

READ MORE HERE/LEIA MAIS AQUI: Aeon

A seleção natural da má ciência

The natural selection of bad science

Paul E. Smaldino, Richard McElreath

Published 21 September 2016. DOI: 10.1098/rsos.160384


Abstract

Poor research design and data analysis encourage false-positive findings. Such poor methods persist despite perennial calls for improvement, suggesting that they result from something more than just misunderstanding. The persistence of poor methods results partly from incentives that favour them, leading to the natural selection of bad science. This dynamic requires no conscious strategizing—no deliberate cheating nor loafing—by scientists, only that publication is a principal factor for career advancement. Some normative methods of analysis have almost certainly been selected to further publication instead of discovery. In order to improve the culture of science, a shift must be made away from correcting misunderstandings and towards rewarding understanding. We support this argument with empirical evidence and computational modelling. We first present a 60-year meta-analysis of statistical power in the behavioural sciences and show that power has not improved despite repeated demonstrations of the necessity of increasing power. To demonstrate the logical consequences of structural incentives, we then present a dynamic model of scientific communities in which competing laboratories investigate novel or previously published hypotheses using culturally transmitted research methods. As in the real world, successful labs produce more ‘progeny,’ such that their methods are more often copied and their students are more likely to start labs of their own. Selection for high output leads to poorer methods and increasingly high false discovery rates. We additionally show that replication slows but does not stop the process of methodological deterioration. Improving the quality of research requires change at the institutional level.

The more any quantitative social indicator is used for social decision-making, the more subject it will be to corruption pressures and the more apt it will be to distort and corrupt the social processes it is intended to monitor.

Donald T. Campbell (1976, p. 49) [1]

I’ve been on a number of search committees. I don’t remember anybody looking at anybody’s papers. Number and IF [impact factor] of pubs are what counts.

Terry McGlynn (realscientists) (21 October 2015, 4:12 p.m. Tweet.)

FREE PDF GRATIS: Royal Society Open Science

"Escudo de radiação" encontrado no genoma de tardígrados

quarta-feira, setembro 21, 2016

Extremotolerant tardigrade genome and improved radiotolerance of human cultured cells by tardigrade-unique protein

Takuma Hashimoto, Daiki D. Horikawa, Yuki Saito, Hirokazu Kuwahara, Hiroko Kozuka-Hata, Tadasu Shin-I, Yohei Minakuchi, Kazuko Ohishi, Ayuko Motoyama, Tomoyuki Aizu, Atsushi Enomoto, Koyuki Kondo, Sae Tanaka, Yuichiro Hara, Shigeyuki Koshikawa, Hiroshi Sagara, Toru Miura, Shin-ichi Yokobori, Kiyoshi Miyagawa, Yutaka Suzuki et al.

Affiliations Contributions Corresponding authors

Nature Communications 7, Article number: 12808 doi: 10.1038/ncomms12808

Received 21 June 2015 Accepted 03 August 2016 Published 20 September 2016

Fig. 1: The extremotolerant tardigrade R. varieornatus and taxonomic origins of its gene repertoire

Abstract

Tardigrades, also known as water bears, are small aquatic animals. Some tardigrade species tolerate almost complete dehydration and exhibit extraordinary tolerance to various physical extremes in the dehydrated state. Here we determine a high-quality genome sequence of Ramazzottius varieornatus, one of the most stress-tolerant tardigrade species. Precise gene repertoire analyses reveal the presence of a small proportion (1.2% or less) of putative foreign genes, loss of gene pathways that promote stress damage, expansion of gene families related to ameliorating damage, and evolution and high expression of novel tardigrade-unique proteins. Minor changes in the gene expression profiles during dehydration and rehydration suggest constitutive expression of tolerance-related genes. Using human cultured cells, we demonstrate that a tardigrade-unique DNA-associating protein suppresses X-ray-induced DNA damage by ~40% and improves radiotolerance. These findings indicate the relevance of tardigrade-unique proteins to tolerability and tardigrades could be a bountiful source of new protection genes and mechanisms.

FREE PDF GRATIS: Nature Communications Sup Info 1, 2, 3, 4, 5, 6

Variação no relógio molecular dos primatas: divergência entre humanos e chimpanzés ocorreu há 12.1 milhões de anos atrás

terça-feira, setembro 20, 2016

Variation in the molecular clock of primates

Priya Moorjani a,b,1,2, Carlos Eduardo G. Amorim a,1, Peter F. Arndt c, and Molly Przeworski a,d,2

Author Affiliations

aDepartment of Biological Sciences, Columbia University, New York, NY 10027;

bProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142;

cDepartment of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, 14195 Berlin, Germany;

dDepartment of Systems Biology, Columbia University, New York, NY 10027

Edited by David C. Page, Whitehead Institute, Cambridge, MA, and approved July 19, 2016 (received for review January 8, 2016)



Significance

Much of our understanding of the chronology of human evolution relies on a fixed “molecular clock”; that is, a constant rate of substitutions per unit time. To evaluate the validity of this assumption, we analyze whole-genome sequences from 10 primate species. We find that there is substantial variation in the molecular clock between apes and monkeys and that rates even differ within hominines. Importantly, not all mutation types behave similarly; notably, transitions at CpG sites exhibit a more clocklike behavior than other substitutions, presumably because of their nonreplicative origin. Thus, the mutation spectra, and not just the overall substitution rates, are changing across primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions.

Abstract

Events in primate evolution are often dated by assuming a constant rate of substitution per unit time, but the validity of this assumption remains unclear. Among mammals, it is well known that there exists substantial variation in yearly substitution rates. Such variation is to be expected from differences in life history traits, suggesting it should also be found among primates. Motivated by these considerations, we analyze whole genomes from 10 primate species, including Old World Monkeys (OWMs), New World Monkeys (NWMs), and apes, focusing on putatively neutral autosomal sites and controlling for possible effects of biased gene conversion and methylation at CpG sites. We find that substitution rates are up to 64% higher in lineages leading from the hominoid–NWM ancestor to NWMs than to apes. Within apes, rates are ∼2% higher in chimpanzees and ∼7% higher in the gorilla than in humans. Substitution types subject to biased gene conversion show no more variation among species than those not subject to it. Not all mutation types behave similarly, however; in particular, transitions at CpG sites exhibit a more clocklike behavior than do other types, presumably because of their nonreplicative origin. Thus, not only the total rate, but also the mutational spectrum, varies among primates. This finding suggests that events in primate evolution are most reliably dated using CpG transitions. Taking this approach, we estimate the human and chimpanzee divergence time is 12.1 million years,​ and the human and gorilla divergence time is 15.1 million years​.

molecular clock mutation rate primate evolution CpG transition rate human–ape divergence time

Footnotes

1P.M. and C.E.G.A. contributed equally to this work.

2To whom correspondence may be addressed. Email: pm2730@columbia.edu or mp3284@columbia.edu.

Author contributions: P.M., C.E.G.A., and M.P. designed research; P.M., C.E.G.A., and M.P. performed research; P.M. and P.F.A. contributed new reagents/analytic tools; P.M., C.E.G.A., and M.P. analyzed data; and P.M., C.E.G.A., and M.P. wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1600374113/-/DCSupplemental.

Freely available online through the PNAS open access option.

FREE PDF GRATIS: PNAS

Uma abordagem bayesiana para detectar o impacto de eventos de extinção em massa em filogenias moleculares quando varia a taxa de diversificação de linhagem

A Bayesian approach for detecting the impact of mass-extinction events on molecular phylogenies when rates of lineage diversification may vary

Authors: Michael R. May, Sebastian Höhna, Brian R. Moore

First published: 28 May 2016

DOI: 10.1111/2041-210X.12563



Summary


  1. The paleontological record chronicles numerous episodes of mass extinction that severely culled the Tree of Life. Biologists have long sought to assess the extent to which these events may have impacted particular groups. We present a novel method for detecting the impact of mass-extinction events on molecular phylogenies, even in the presence of tree-wide diversification-rate variation and in the absence of additional information from the fossil record.
  2. Our approach is based on an episodic stochastic-branching process model in which rates of speciation and extinction are constant between events. We model three types of events: (i) instantaneous tree-wide shifts in speciation rate; (ii) instantaneous tree-wide shifts in extinction rate and (iii) instantaneous tree-wide mass-extinction events. Each type of event is modelled as an independent compound Poisson process (CPP), where the waiting times between events are exponentially distributed with event-specific rate parameters. The magnitude of each event is drawn from an event-specific prior distribution. Parameters of the model are then estimated in a Bayesian statistical framework using a reversible-jump Markov chain Monte Carlo algorithm. This Bayesian approach enables us to distinguish between tree-wide diversification-rate variation and mass-extinction events by specifying a biologically informed prior on the magnitude of mass-extinction events and empirical hyperpriors on the diversification-rate parameters.
  3. We demonstrate via simulation that this method has substantial power to detect the number of mass-extinction events and provides unbiased estimates of the timing of mass-extinction events, while exhibiting an appropriate (i.e. <5 a.="" a="" an="" approach="" background="" conifers="" demonstration="" diversification="" empirical="" episode="" even="" experienced="" extinction="" false-discovery="" finally="" li="" major="" mass="" nbsp="" of="" provide="" rate="" rates="" reveals="" that="" this="" vary.="" we="" when="" which="">
  4. This new approach – the CPP on Mass-Extinction Times (CoMET) model – provides an effective tool for detecting the impact of mass-extinction events on molecular phylogenies, even when the history of those groups includes temporal variation in diversification rates and when the fossil history of those groups is poorly known.
FREE PDF GRATIS: Methods in Ecology and Evolution Sup. Info.

Rolando grande controvérsia em filogenia: a confiabilidade do BAMM [Bayesian Analysis of Macroevolutionary Mixtures]

Critically evaluating the theory and performance of Bayesian analysis of macroevolutionary mixtures

Brian R. Moore a,1, Sebastian Höhna b,c, Michael R. May a, Bruce Rannala a, and John P. Huelsenbeck b

Author Affiliations

aDepartment of Evolution and Ecology, University of California, Davis, CA 95616;

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

cDepartment of Statistics, University of California, Berkeley, CA 94720

Edited by Michael J. Donoghue, Yale University, New Haven, CT, and approved June 27, 2016 (received for review September 21, 2015)


Significance

We show that Bayesian analysis of macroevolutionary mixtures (BAMM)—a method for identifying lineage-specific diversification rates—is flawed. Exposing the problems with BAMM is important both to empiricists (to avoid making unreliable inferences using this method) and to theoreticians (to focus their efforts on solving the problems that we identify).

Abstract

Bayesian analysis of macroevolutionary mixtures (BAMM) has recently taken the study of lineage diversification by storm. BAMM estimates the diversification-rate parameters (speciation and extinction) for every branch of a study phylogeny and infers the number and location of diversification-rate shifts across branches of a tree. Our evaluation of BAMM reveals two major theoretical errors: (i) the likelihood function (which estimates the model parameters from the data) is incorrect, and (ii) the compound Poisson process prior model (which describes the prior distribution of diversification-rate shifts across branches) is incoherent. Using simulation, we demonstrate that these theoretical issues cause statistical pathologies; posterior estimates of the number of diversification-rate shifts are strongly influenced by the assumed prior, and estimates of diversification-rate parameters are unreliable. Moreover, the inability to correctly compute the likelihood or to correctly specify the prior for rate-variable trees precludes the use of Bayesian approaches for testing hypotheses regarding the number and location of diversification-rate shifts using BAMM.

lineage diversification rates speciation extinction macroevolution phylogeny

Footnotes

1To whom correspondence should be addressed. Email: brianmoore@ucdavis.edu.

Author contributions: B.R.M., S.H., M.R.M., B.R., and J.P.H. designed research, performed research, contributed new reagents/analytic tools, analyzed data, and wrote the paper.

The authors declare no conflict of interest.

This article is a PNAS Direct Submission.

Data deposition: Data from this study have been deposited in the Dryad Digital Repository (doi: 10.5061/dryad.mb0sd).

This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1518659113/-/DCSupplemental.

Freely available online through the PNAS open access option.


FREE PDF GRATIS: PNAS

+++++

NOTA DESTE BLOGGER:

Um dos muitos problemas fundamentais em biologia evolucionária é detectar os padrões de variação em taxas de diversificação de linhagem e trabalhar para entender suas causas. Sugiro acompanhar a controvérsia sobre a confiabilidade do BAMM aqui:

A. Artigo de Daniel L. Rabosky: 
Automatic Detection of Key Innovations, Rate Shifts, and Diversity-Dependence on Phylogenetic Trees

FREE PDF GRATIS: 

http://journals.plos.org/plosone/article/asset?id=10.1371/journal.pone.0089543.PDF

B. Artigo de Wayne P. Maddison et al

Estimating a Binary Character's Effect on Speciation and Extinction

FREE PDF GRATIS: 

http://sysbio.oxfordjournals.org/content/56/5/701.full.pdf+html

+++++

1. Tree thinkers: 

http://treethinkers.org/prior-sensitivity-in-bamm/

2. The BAMM Project:

http://bamm-project.org/replication.html#several-theoretical-concerns-raised-by-mea-cannot-be-evaluated

José Goldemberg, presidente da FAPESP 'falou e disse': A ciência tem que ter critérios mais rígidos!!!

sexta-feira, setembro 16, 2016

Ciência tem que ter critérios mais rígidos, diz presidente da Fapesp
José Goldemberg, presidente da FAPESP, em seu escritório.

Fonte: Adriano Vizoni Folha de São Paulo

+++++

NOTA BENE

Esses critérios mais rígidos são encontrados no contexto de justificação teórica, e certas teorias científicas queridinhas pela Nomenklatura científica e da Galera dos meninos e meninas de Darwin - a origem e evolução do universo e da vida, não estão isentas desse rigor! Entenderam? Ou querem que eu desenhe?

Dr. Goldemberg, esse blogger desde 1998 vem pugnando por esses critérios mais rígidos em ciência. Especialmente quando a questão é Darwin. Ser vindicado por este grande nome na ciência deixou este blogger muito, mas muito envaidecido!!!

Fui, nem sei por que, rindo da cara de alguns cientistas da Nomenklatura científica e da Galera dos meninos e meninas de Darwin que dizem, por tudo que tenho dito aqui, que eu não sei o que é ciência, não faço ciência, sou medieval y otras cositas mais. Dr. Goldemberg, seja bem-vindo!!! 

Computar ancestralidade genética é super exato e confirma o fato, Fato, FATO da evolução???

quinta-feira, setembro 15, 2016

An experimental phylogeny to benchmark ancestral sequence reconstruction

Ryan N. Randall, Caelan E. Radford, Kelsey A. Roof, Divya K. Natarajan & Eric A. Gaucher

Nature Communications 7, Article number: 12847 (2016)


Download Citation

Experimental evolution Phylogenetics

Received 01 April 2016 Accepted 05 August 2016 Published online 15 September 2016


Figure 1: Phylogram of the experimental phylogeny initiated from a single red FP gene.

Abstract

Ancestral sequence reconstruction (ASR) is a still-burgeoning method that has revealed many key mechanisms of molecular evolution. One criticism of the approach is an inability to validate its algorithms within a biological context as opposed to a computer simulation. Here we build an experimental phylogeny using the gene of a single red fluorescent protein to address this criticism. The evolved phylogeny consists of 19 operational taxonomic units (leaves) and 17 ancestral bifurcations (nodes) that display a wide variety of fluorescent phenotypes. The 19 leaves then serve as ‘modern’ sequences that we subject to ASR analyses using various algorithms and to benchmark against the known ancestral genotypes and ancestral phenotypes. We confirm computer simulations that show all algorithms infer ancient sequences with high accuracy, yet we also reveal wide variation in the phenotypes encoded by incorrectly inferred sequences. Specifically, Bayesian methods incorporating rate variation significantly outperform the maximum parsimony criterion in phenotypic accuracy. Subsampling of extant sequences had minor effect on the inference of ancestral sequences.

Acknowledgements

Funding was provided by the Georgia Institute of Technology, NASA (NNX12AI10G to E.A.G.), DuPont (Young Professor Award to E.A.G.) and NSF (grant 1145698 to E.A.G) We thank Andreas S. Bommarius for the mRFP1 gene, Barry G. Hall, Nathan Shaner, Joshua Weitz, and Zihang Yang for scientific discussions, and the following for assistance with building the experimental phylogeny: Kayla Arroyo, Krutika Gaonkar, Kristen Ingram, Penelope Kahn, Mark Leber, Byron Lee, Dione McKenzie, Angeline Pham, Lily Tran, Rebecca Wolf, and Zi-Ming Zhao.

Author information

Affiliations

School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA

Ryan N. Randall, Caelan E. Radford, Kelsey A. Roof, Divya K. Natarajan & Eric A. Gaucher

Institute for Bioengineering and Biosciences, Georgia Institute of Technology, Atlanta, Georgia 30332, USA

Eric A. Gaucher

Contributions

R.N.R. and E.A.G. conceived of the project and wrote the manuscript; R.N.R., C.E.R. and E.A.G. analysed results; R.N.R., C.E.R., K.A.R. and D.K.N performed the experiments.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Eric A. Gaucher.