This Week in PLoS

In PLoS Genetics this week, McGill University's Brent Richards and his colleagues report on their analysis of data derived from 1,998 individuals they Sanger-sequenced at seven genes, which "provide guidance in the analysis and interpretation of the role of rare base-pair variation in the etiology of complex traits and diseases," the authors write. "These findings provide guidance in the analysis and interpretation of the role of rare base-pair variation in the etiology of complex traits and diseases," Richards et al. add.

Over in PLoS One, researchers in France identify the gene encoding S100 calcium binding protein A11 as a potential diagnostic biomarker of infective endocarditis. The team also identified the aquaporin-9 gene as a potential prognostic factor.

In a PLoS Computational Biology paper published this week, a public-private team led by investigators at the Rockville, Md.-based Ariadne Genomics presents an approach to the meta-analysis of microarray datasets that "relies on aggregation of individual profiling experiments combined with leave-one-dataset-out validation approach." Using the Sub-Network Enrichment Analysis algorithm, the team studied aggregated publicly available human muscle gene expression profiling datasets related to Duchenne muscular dystrophy, identifying potential "muscle remodeling-related drug targets and biomarkers" of the disease.

Finally, in PLoS Neglected Tropical Diseases, researchers at the Max Planck Institute for Evolutionary Biology in Germany, and Imperial College London's John Mumford discuss the regulation of genetically modified insects on an international scale.

No Lab Coats Here

Allie Wilkinson's new blog, This Is What a Scientist Looks Like, asks readers to "change the perception of who and what a scientist is or isn't" through personal photo and story submissions. "There is no single clear-cut path to becoming a scientist. A scientist can come from any background," Wilkinson says.

On Twitter, GeneNomad's K. Thomas Pickard links to Wilkinson's blog, saying: "Scientists come in all shapes, sizes, and ages." Matt Shipman at First Step Project, a charitable organization, tweets: "Love the 'Looks Like Science' site, but would love to see more not-white scientists on there."

In a related discussion, researchers on Twitter are sharing stories on how they came to be scientists, using the hashtag #iamscience. Simon Trevino jokes: "When somebody asks where the negative control is, I just point to the unloaded lane on the gel."

Pretty Pictures and Science, Too

Science and the US National Science Foundation announced the winners of their annual International Science and Engineering Visualization Challenge. "The aim is to promote cutting-edge efforts to visualize scientific data, principles, and ideas—skills that are critical for communication among scientists and between scientists and the general public, especially students," writes Colin Norman, Science's news editor.

Bryan William Jones from the University of Utah Moran Eye Center won for his Metabolomic Eye photograph in which he used computational molecular phenotyping to define the different tissues of the eye. In the informational posters and graphics category, Johns Hopkins University's Miguel Angel Aragon-Calvo and Julieta Aguilera and Mark Subbarao from Adler Planetarium won for their representation of the growth of galaxies. TSRI's Graham Johnson, NCMIR's Andrew Noske, and IMB's Bradley Marsh's video of a pancreatic cell won in that category. Finally, the top prize in the games category went to the creators of Foldit, Seth Cooper, David Baker, Zoran Popović, Firas Khatib, and Jeff Flatten at the University of Washington.

The Guardian also picked its favorites, which it highlights here.

In Control

Scripp's Eric Topol "wants to digitize you by collecting streams of your anatomical, physiological, and biological data and uploading them to your iPhone (or PC) for easy and constant accessibility," says Future Tense, a collaboration between Arizona State University, the New America Foundation, and Slate. Topol's new book, The Creative Destruction of Medicine: How the Digital Revolution Will Create Better Health Care, calls for patients to take control of their healthcare and advocate for personalized medicine. "We've got to get the consumers to drive this thing," Topol says.

More Jobs

The healthcare sector in the US added just more than 30,000 jobs last month, reports The Wall Street Journal's Health Blog. The overall economy added 243,000 jobs. However, the blog notes that the data from the Bureau of Labor Statistics breaks the numbers down by facility type, not job description. "For example, the report shows that hospitals added 12,700 jobs, but doesn't say whether those were nursing, IT, or cafeteria positions," it says.

A 'Science Groupie' Sings

Icelandic singer Bjork released an album in October called Biophilia, and Bjork appeared as a guest on The Colbert Report this week to promote the album, which she says is an exploration of science and nature, reports the Huffington Post. She performed a song from the album, Cosmology — a song that centers around the creation of life and explores both creation myths and the big bang theory.

When the album was released in October, MTV's Rob Mitchum wrote that this was her most "scientifically-influenced" album yet, "with songs based around biology, physics, astronomy, and geology, a tour that will incorporate educational lectures and nature footage, and a publicity campaign that included unusual stops such as National Geographic and the scientific journal Nature Medicine." In a Nature podcast about Biophilia, Bjork calls herself "a science groupie."

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Hold the Arsenic

When NASA astrobiologist Felisa Wolfe-Simon released a study in December 2010 that described a bacterium that seemed to grow on arsenic and incorporate it into its DNA, researchers were at first amazed. Some, however, were skeptical, and tried to replicate Wolfe-Simon's work. University of British Columbia microbiologist Rosemary Redfield has posted a paper on ArXiv that refutes Wolfe-Simon's conclusions, reports ScienceInsider's Elizabeth Pennisi. "Redfield … has grown the bacterium in the presence of arsenic and found no evidence of its uptake in the microbe's genetic material," Pennisi says. Redfield says she doesn't plan to do anymore follow-up research at this point, and adds that the "burden of proof" is back on Wolfe-Simon and her colleagues to show "better data than they did in their paper."

Wolfe-Simon and her group tell ScienceInsider their work is just beginning, but they don't plan on commenting on Redfield's work until it has been peer-reviewed and published.

Cuts at AstraZeneca

AstraZeneca announced that it will be eliminating 7,300 jobs, reports The Wall Street Journal. The Journal adds that these cuts, which are to be made by the end of 2014, will bring the company's total jobs cuts during the past five years to about 30,000. This round includes 2,200 cuts to R&D, 1,350 to manufacturing and operations, and 3,750 to administration and sales, and the closure of two neuroscience labs, one in Sweden and the other in Montreal. "AstraZeneca is ripping up some of its research roots in Europe and North America and forging more virtual research alliances with academic institutions and small biotech companies," the Journal notes.

This Week in Science

In a report published online in advance in Science this week, Duke University's Robin Hopkins and Mark Rausher discuss the strength of reinforcing selection in nature "by demonstrating strong selection favoring an allele conferring increased pigment intensity in the plant Phlox drummondii in areas of sympatry with the closely related species P. cuspidata," they write. Hopkins and Rausher also say non-random pollinator movement is behind such reinforcing selection in P. drummondii and P. cuspidata.

Over in this week's issue, researchers at the University of Washington in Seattle report "a genome representing the as-yet uncultured marine group II Euryarchaeota, assembled de novo from 1.7 percent of a metagenome sequenced from surface seawater." The team says its study demonstrates that high-coverage mate-paired sequence "can overcome assembly difficulties caused by inter-strain variation in complex microbial communities, enabling inference of ecosystem functions for uncultured members."

And in Science Signaling, researchers at the University of Utah School of Medicine and the University of Basel show that in Saccharomyces cerevisiae, "PAS kinase promotes cell survival and growth through activation of Rho1." Upon isolating PSK1 and PSK2 in a suppressor screen of a temperature-sensitive mutant of target of rapamycin 2, or TOR2, the team found that "post-translational activation of yPASK, either by cell integrity stress or by growth on nonfermentative carbon sources, also suppressed the growth defect resulting from tor2 mutation," it writes.

Trouble for Elsevier?

Nearly 3,000 researchers, including several winners of the Fields Medal, have signed a petition to boycott scientific publisher Elsevier because of its stance on open-access publishing and journal pricing model, reports ScienceInsider's Jop de Vrieze. The petitioners have pledged not to publish papers in any Elsevier journals, nor do any editorial work or peer review for the company. "The petition, which has created a buzz on researchers' blogs and Twitter, isn't just an attack on Elsevier, its organizers say, but also an attempt to show the scientific community that it can help change the publishing business themselves to increase access to their studies," de Vrieze says. "Many scientists and librarians consider Amsterdam-based Elsevier … one of the villains in the scientific publishing industry; its journals can cost up to $20,000 a year, while the company's profit margin in 2010 was 36%." The company has also received a lot of heat from the scientific community over its support of the Research Works Act, which seeks to limit public access to scientific research.

In a statement to ScienceInsider, Elsevier says its price increases over the past decade have been "among the industry's lowest," and that it has made several attempts to increase access to the studies in its journals.

'Mediocre to Awful'

"Mediocre to awful" is not the description most people want to hear about the quality of science education in the US. But a new report from the Thomas B. Fordham Institute shows that many state standards for science education are worthy of a failing grade, reports Scientific American's Anna Kuchment at the Budding Scientist blog. "Standards are the foundation upon which educators build curricula, write textbooks and train teachers," Kuchment says. "They often take the form of a list of facts and skills that students must master at each grade level. Each state is free to formulate its own standards, and numerous studies have found that high standards are a first step on the road to high student achievement." Only California and the District of Columbia were awarded As. Indiana, Massachusetts, South Carolina, and Virginia scored A-minuses, while Oregon, Idaho, Montana, Nebraska, and several others scored Fs.

The study's lead authors found four factors that contribute to the quality of standards, Kuchment says — "an undermining of evolution, vague goals, not enough guidance for teachers on how to integrate the history of science and the concept of scientific inquiry into their lessons, and not enough math instruction." For example, eight anti-evolution bills were introduced in six states in 2011, she adds, and in some states, standards for introducing science into the classroom are "vague to the point of uselessness."

There is some good news, however. Twenty-six states have agreed to write new standards that will be "more rigorous and specific" than what they currently have, Kuchment says.

The Bully Pulpit of Peer Review?

The Scholarly Kitchen's Tim Vines notes that "the opinions of highly respected senior scientists tend to get a lot of attention, and a number have lamented the state of peer review." Because of this, he asks: "What if the reviewer experience for high-profile researchers is the exception and not the rule?"

Touching on an oft-expressed gripe about peer review — that "the rapid growth in the number of papers submitted to journals has led to a massive increase in the demands on the reviewer community," he says — Vines digs into data on reviewer invitations by rank and prestige. In the context of the journal Molecular Ecology, Vines found that "the main predictor of how often someone was invited was how much they published" there. So, contrary to popular thought, " the data … actually suggest that being famous generally makes you less likely to be invited. … However, as a researcher you can only be central to one field, and peripheral to lots of others, and hence being famous may mean you attract review invitations from many different disciplines," Vines says.

Overall, he adds, "the big picture here is that senior academics are being bombarded with requests to review papers. … There's little evidence above that junior researchers are overburdened." And that, Vines says, is perhaps why some senior scientists might have a biased view on the state of peer review.

Philip Lawley Dies

Philip Lawley, who was a chemist at the Chester Beatty Research Institute in the UK, has died, reports Nature. Lawley studied how mutagens and carcinogens bind to and affect DNA, and was among the first to link DNA damage to cancer. Lawley and Peter Brookes, his colleague at Chester Beatty, which is now the Institute of Cancer Research, reported that mustard gas forms adducts with guanine in DNA, and those adducts then affect DNA replication and cell division. Further, they found that how frequently polycyclic aromatic hydrocarbons bind to DNA increases their carcinogenic strength. "This discovery overturned the prevailing view that proteins were the critical cellular targets for carcinogens and it changed the course of cancer research," Nature says.