Peer review

If so, big problem for starter physicists From Nature: The site – where physicists, mathematicians and other researchers routinely post their articles before peer review — has previously been accused of bias for filtering out some of the wilder ideas it receives. But in a December blogpost that is now provoking debate, Nicolas Gisin, a quantum physicist at the University of Geneva, Switzerland, suggests that arXiv moderators wrongly blacklisted two of his students from posting their work. Gisin notes that being unable to post to arXiv has a detrimental effect on young researchers’ careers, because it is so influential — the preprint server holds more than 1.1 million papers and receives well over 9,000 submissions each month. He is concerned Read More ›

From a recent article in Molecular Phylogenetics and Evolution: In summary, the long c-genes that are required for accurate reconstruction of species trees using shortcut coalescence methods do not exist and are a delusion. Coalescence approaches based on SNPs that are widely spaced in the genome avoid problems with the recombination ratchet and merit further pursuit in both empirical systematic research and simulations. A delusion? Wow. Story: Well, here’s a ScienceDirect abstract, and you decide: Higher-level relationships among placental mammals are mostly resolved, but several polytomies remain contentious. Song et al. (2012) claimed to have resolved three of these using shortcut coalescence methods (MP-EST, STAR) and further concluded that these methods, which assume no within-locus recombination, are required to unravel Read More ›

From Slate: Amy Cuddy’s famous finding is the latest example of scientific overreach. Consider the case of Amy Cuddy. The Harvard Business School social psychologist is famous for a TED talk, which is among the most popular of all time, and now a book promoting the idea that “a person can, by assuming two simple one-minute poses, embody power and instantly become more powerful.” The so-called “power pose” is characterized by “open, expansive postures”—Slate’s Katy Waldman described it as akin to “a cobra rearing and spreading its hood to the sun, or Wonder Woman with her legs apart and her hands on her hips.” In a published paper from 2010, Cuddy and her collaborators Dana Carney and Andy Yap report Read More ›

Geek Psychologist wonders: At a time when more research studies are being published than ever before and vast quantities of information are available on the internet to be mined, synthesized, and analyzed, we need to implement changes to popular science communication – changes that emphasize a data-driven approach to communicating research and that make it easier for members of the general public to synthesize a large volume of research findings. After all, most people understand that no scientific study is without limitations, and that each individual finding must be taken with a grain of salt. Therefore, focusing exclusively on new individual research findings likely does little to change minds, aid decision-making, and support scientific literacy in the general public. If Read More ›

This row has been going on for twelve years. From Nature: The saga began when the paper described a method for using RNA sequences to grow tiny hexagonal crystals of palladium metal. The work hinted that RNA might have a role in producing inorganic materials in the environment. It has been cited more than 135 times. But Stefan Franzen, another chemist at NCSU, soon raised questions about the work. In a series of publications, he challenged whether the team had really seen RNA-driven action or stable palladium crystals. Franzen filed a formal complaint to NCSU, which kicked off a series of investigations. In the 2013 report, the NSF inspector-general found that the researchers had omitted experimental details and overstated the Read More ›

From Nature: Work that describes harm from crops was cited in Italian Senate hearing. The papers’ findings run counter to those of numerous safety tests carried out by food and drug agencies around the world, which indicate that there are no dangers associated with eating GM food. But the work has been widely cited on anti-GM websites — and results of the experiments that the papers describe were referenced in an Italian Senate hearing last July on whether the country should allow cultivation of safety-approved GM crops. … Cattaneo noted what looked like problems in all three papers: sections of images of electrophoresis gels appeared to have been obliterated, and some of the images in different papers appeared to be Read More ›

Focus on supporting stable, long term gains. From editor Jonathan Gitlin at Ars Technica, responding to the recent U.S. State of the Union (SOTU) address: Science needs steady sustainable boring growth, not flashy ill-formed initiatives. Done correctly, history shows that lofty scientific and engineering challenges can work. The actual moonshot for example, or the Human Genome Project. Both of those had one thing in common: a clear and well-defined goal at the beginning. “Before 1970, fly someone to the Moon and return them safely.” “Sequence the entire human genome.” But Nebulous concepts like “end all cancer” get good applause—curing all cancers is right up there with sunshine and puppies. But such concepts are effectively meaningless. Hey, reality check: There isn’t Read More ›

From The Scientist: Of 441 randomly selected biomedical research papers analyzed in a new study, none provided access to all the authors’ data. And only one of these papers shared a complete protocol. The results of this analysis, which could shed light on science’s reproducibility problem, were published today (January 4) in PLOS Biology. “What was most surprising to me was the complete lack of data-sharing and protocol availability,” said study coauthor John Ioannidis, a professor of medicine and health research and policy at the Stanford University School of Medicine. “That was worse than I would have predicted.” “This study confirms what most of us already know—that the current clinical research enterprise is set up in a way that researchers Read More ›

Not only are mouse data often meaningless for humans, but according to a recent piece by Monya Baker in Nature News: Reports of hundreds of biomedical experiments lack essential information. Whereas reports of clinical trials in major medical journals routinely state how many patients die or drop out of analysis during the course of a study, animal studies generally fail to report this figure — or drop animals without saying why, according to a team led by Ulrich Dirnagl at the Charité Medical University in Berlin. That lapse could significantly bias results, the team reports in the journal PLoS Biology. … Dirnagl’s team reviewed 100 reports published between 2000 and 2013 describing 522 experiments that used rodents to test cancer Read More ›

From RealClearScience: “Animal models are limited in their ability to mimic the extremely complex process of human carcinogenesis, physiology and progression,” McMaster University scientists Isabella Mak, Nathan Evaniew, and Michelle Ghert, wrote in 2014. “Therefore the safety and efficacy identified in animal studies is generally not translated to human trials.” While the systems that regulate gene activity are generally the same in mice and humans, there are key biological differences in other areas that prevent successful results from applying to humans. Transcription factor binding sites, where information is passed on, differ for between 41 and 89 percent of the genes that our species share. Moreover, unlike humans, mice used in studies are often highly inbred. The mouse immune system is Read More ›

From The Scientist: A lack of jobs leaves postdocs without a future in academia in the United States. Meanwhile, other challenges threaten the postdoc community abroad. Postdoctoral fellows play a critical role in the research productivity of any country. Currently, the United States has a relatively strong postdoc infrastructure, offering higher salaries and more benefits than most other countries. Postdocs also have support from the National Postdoctoral Association (NPA) and postdoc offices in most American universities. However, limited growth in federal research funding during the last decade has made it increasingly hard for postdocs to find permanent jobs. The limited funding has also created a highly competitive environment for those who do find positions as principal investigators (PIs). Under constant Read More ›

Structures were fabricated. From The Scientist: Neither Nature nor the paper’s authors have fully explained why it took so long to retract the study. “This is a pretty old story, I don’t know why Nature took so long,” coauthor Narayana Sthanam from the University of Alabama at Birmingham (UAB) told Retraction Watch. “Nature asked us maybe two months back, do I have any comment or objection for retracting.” Apparently, two authors did not agree to retraction. One of the coauthors who did not agree with the retraction, former UAB researcher M. Krishna Murthy, was found “solely responsible for the fraudulent data” by the UAB investigation. More. Note: Allegations of fraud may involve legal as well as career issues; it would Read More ›

Asks Stat News, offering a roundup of notable views in support: Hanel, a psychologist at Cardiff University in the United Kingdom, posted a manuscript recently calling for anonymity in science articles. More than that, Hanel suggests stripping identifiers from virtually all academic output: doing away with name-based citations, CVs on researchers’ web sites, author names on book chapters, titles on academic journals, and more. The immodest proposal — made available on arXiv, a preprint server, before peer review — is akin to destroying the academic village in order to rid it of pests. But while some of what Hanel recommends is impossible at best, and perhaps even counterproductive, his overarching point seems pretty solid. When it comes to protecting the Read More ›

From Matters: Your submission enters a triple-blind peer review process, meaning that the handling editors have no personal information on the authors and assign the observations to reviewers solely on the basis of the content. The reviewers also do not know who you are, where you live or the institution where you work. Also: We believe in free access to scientific data. Hence, all articles published in Matters are, of course, freely available to everyone through our Open Access Creative Commons licence. We also allow publishing of the raw and unprocessed data linked to the article, thus promoting Open Data and Science. Matters charges $150/submission for non-profit entities, $300/submission for for-profit entities, though the first 500 submissions are free of Read More ›

But there doesn’t seem to be anyone to punch it down*. From Vox: “Unprecedented!” “Amazing!” “Novel!” Punch. Punch. Punch. A team of researchers from the Netherlands tried to quantify the rise in hype by studying the titles and abstracts of scientific papers published in the PubMed database between 1974 and 2014. They wanted to see how often adjectives such as “unprecedented,” “amazing,” “groundbreaking,” and “promising” were used. They found a ninefold increase in frequency during the period — and published their results in BMJ. … In half the cases, terms like “breakthrough,” “miracle,” and “cure” were used to describe medicines that hadn’t even been approved yet by regulators. More. Punch. Punch. Punch. See also: Fleming’s penicillin find couldn’t be published Read More ›