Ten Simple Rules for the Care and Feeding of Scientific Data Citation: Goodman A, Pepe A, Blocker AW, Borgman CL, Cranmer K, Crosas M, et al. (2014) Ten Simple Rules for the Care and Feeding of Scientific Data. PLoS Comput Biol 10(4): e1003542. Editor: Philip E. Bourne, University of California San Diego, United States of America Published: April 24, 2014 Copyright: © 2014 Goodman et al. Funding: The authors received no specific funding for writing this manuscript. Competing interests: The authors have declared that no competing interests exist. Introduction In the early 1600s, Galileo Galilei turned a telescope toward Jupiter. Figure 1. On these pages, Galilei combines data (drawings of Jupiter and its moons), key metadata (timing of each observation, weather, and telescope properties), and text (descriptions of methods, analysis, and conclusions). So how do we go about caring for and feeding data? Rule 1. Data management is a repeat-play game. Rule 2.
Nautilus Three Sentence Science The Earthquake That Will Devastate Seattle When the 2011 earthquake and tsunami struck Tohoku, Japan, Chris Goldfinger was two hundred miles away, in the city of Kashiwa, at an international meeting on seismology. As the shaking started, everyone in the room began to laugh. Earthquakes are common in Japan—that one was the third of the week—and the participants were, after all, at a seismology conference. Seismologists know that how long an earthquake lasts is a decent proxy for its magnitude. When Goldfinger looked at his watch, it was quarter to three. It was March. Oh, shit, Goldfinger thought, although not in dread, at first: in amazement. For a moment, that was pretty cool: a real-time revolution in earthquake science. In the end, the magnitude-9.0 Tohoku earthquake and subsequent tsunami killed more than eighteen thousand people, devastated northeast Japan, triggered the meltdown at the Fukushima power plant, and cost an estimated two hundred and twenty billion dollars. The first clue came from geography. But it did not.
Public-Friendly Open Science Previous “A “Modern Scientist” Manifesto” In the 21st century science is growing more technical and complex, as we gaze further and further while standing on the shoulders of many generations of giants. The public has often a hard time understanding research and its relevance to society. One of the reasons for this is that scientists do not spend enough time communicating their findings outside their own scientific community. Obviously there are some exceptions, but the rule is that scientists write content for scientists. Academia is often perceived as an ivory tower, and when new findings are shared with the outside world, this is not done by scientists, but by the media or even the political class. At the same time transparency and reproducibility are at stake in the increasingly complex world of research, which is still using old-fashioned tools when packaging and sharing content. Action Items. 21st century scientists need to produce “Public-Friendly Open Science” (PFOS).
PLOS Genetics: Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation Abstract An outstanding question in human genetics has been the degree to which adaptation occurs from standing genetic variation or from de novo mutations. Here, we combine several common statistics used to detect selection in an Approximate Bayesian Computation (ABC) framework, with the goal of discriminating between models of selection and providing estimates of the age of selected alleles and the selection coefficients acting on them. Author Summary Considerable effort has been devoted to detecting genes that are under natural selection, and hundreds of such genes have been identified in previous studies. Citation: Peter BM, Huerta-Sanchez E, Nielsen R (2012) Distinguishing between Selective Sweeps from Standing Variation and from a De Novo Mutation. Editor: Mikkel H. Received: December 17, 2011; Accepted: August 20, 2012; Published: October 11, 2012 Competing interests: The authors have declared that no competing interests exist. Introduction Statistics affected by selection Results
GIP 58: The Geologic Time Spiral, A Path to the Past The Earth is very old—4.5 billion years or more according to scientific estimates. Most of the evidence for an ancient Earth is contained in the rocks that form the Earth's crust. The rock layers themselves—like pages in a long and complicated history—record the events of the past, and buried within them are the remains of life—the plants and animals that evolved from organic structures that existed 3 billion years ago. Also contained in rocks once molten are radioactive elements whose isotopes provide Earth with an atomic clock. Within these rocks, "parent" isotopes decay at a predictable rate to form "daughter" isotopes. By determining the relative amounts of parent and daughter isotopes, the age of these rocks can be calculated. Thus, the scientific evidence from rock layers, from fossils, and from the ages of rocks as measured by atomic clocks attests to a very old Earth. See USGS Fact Sheet 2007-3015 at for ages of geologic time periods.
Science of 'the Dress': Why We Confuse White & Gold with Blue & Black Remember "The Dress" — the photograph that sparked an online firestorm about whether the garment was white and gold or blue and black? Now, researchers have studied the phenomenon scientifically. It's been well-documented that people can see shapes and colors differently, but "the dress" is perhaps one of the most dramatic examples of a difference in color perception, the researchers said. [Eye Tricks: A Gallery of Visual Illusions] "By studying the pair of colors in 'The Dress,' we can answer the age-old question: Do you see colors the way that I see them? But until now, the effect had not been documented scientifically. Color constancy In one study, Conway and his colleagues asked 1,401 people (313 of whom had never seen the image of the dress before) what color they thought the garment was. People who saw the dress as a white-gold color probably assumed it was lit by daylight, so their brains ignored shorter, bluer wavelengths. Daylight vs. artificial light A new property of color
Steven Weinberg: the 13 best science books for the general reader If you had a chance to ask Aristotle what he thought of the idea of writing about physical science for general readers, he would not have understood what you meant. All of his own writing, on physics and astronomy as well as on politics and aesthetics, was accessible to any educated Greek of his time. This is not evidence so much of Aristotle’s skills as a writer, or of the excellence of Greek education, as it is of the primitive state of Hellenic physical science, which made no effective use of mathematics. It is mathematics above all that presents an obstacle to communication between professional scientists and the general educated public. The development of pure mathematics was already well under way in Aristotle’s day, but its use in science by Plato and the Pythagoreans had been childish, and Aristotle himself had little interest in the use of mathematics in science. It was not long before writers called “commentators” began to try to fill this gap.
Anthropocene: The human age Illustration by Jessica Fortner Almost all the dinosaurs have vanished from the National Museum of Natural History in Washington DC. The fossil hall is now mostly empty and painted in deep shadows as palaeobiologist Scott Wing wanders through the cavernous room. Wing is part of a team carrying out a radical, US$45-million redesign of the exhibition space, which is part of the Smithsonian Institution. And when it opens again in 2019, the hall will do more than revisit Earth's distant past. Alongside the typical displays of Tyrannosaurus rex and Triceratops, there will be a new section that forces visitors to consider the species that is currently dominating the planet. “We want to help people imagine their role in the world, which is maybe more important than many of them realize,” says Wing. Simon Lewis discusses the best candidate dates to define the beginning of the Anthropocene The greeting was a tad premature. Written in stone Walker's work sits at the top of the timescale.
The top ten myths about evolution For those of you who are not familiar Cameron Smith's The Top Ten Myths About Evolution, it is an excellent book. Like the best works of popular science, it guides the reader without expecting them to already know anything about the subject. While its main purpose is to rebut the most popular misconceptions about the theory of evolution, it also teaches the science needed to fill the void that abandoning creationism leaves. In this post, I am going to provide my own rebuttals to Cameron's "top ten myths." 1: Survival of the fittest. A common misunderstanding about evolution is that "survival of the fittest" means only the strong and ruthless survive. It should also be noted that many of the best strategies for passing on ones genes often have nothing to do with strength or ruthlessness. 2: Its just a theory A common objection made to evolution is that the science must be still out because it is "only a theory." 3: The ladder of progress 4: The missing link 5: Evolution is random Conclusion
Why Isn't the Sky Blue? What is the color of honey, and "faces pale with fear"? If you're Homer--one of the most influential poets in human history--that color is green. And the sea is "wine-dark," just like oxen...though sheep are violet. Which all sounds...well, really off. Read more: Guy Deutscher, Through the Language Glass: Why the World Looks Different in Other Languages Homer, The Odyssey: The Fitzgerald Translation virology blog — About viruses and viral disease The top 100 papers The discovery of high-temperature superconductors, the determination of DNA’s double-helix structure, the first observations that the expansion of the Universe is accelerating — all of these breakthroughs won Nobel prizes and international acclaim. Yet none of the papers that announced them comes anywhere close to ranking among the 100 most highly cited papers of all time. Citations, in which one paper refers to earlier works, are the standard means by which authors acknowledge the source of their methods, ideas and findings, and are often used as a rough measure of a paper’s importance. Fifty years ago, Eugene Garfield published the Science Citation Index (SCI), the first systematic effort to track citations in the scientific literature. To mark the anniversary, Nature asked Thomson Reuters, which now owns the SCI, to list the 100 most highly cited papers of all time. Richard van Noorden discusses what makes it to the top of the citation-count charts. Biological techniques Bioinformatics