August 2010

Many say the peer review system is broken. Here’s how some journals are trying to fix it.

Contributors William J. Pearce is head of the Genito-Urinary & Reproductive Pharmacology section of the Faculty of Pharmacology & Drug Discovery at F1000, and a professor of physiology at Loma Linda University School of Medicine. He writes in this issue about the inappropriate use of citations in science papers, a subject with which he is very familiar—he published his first peer-reviewed paper 30 years ago, has served on dozens of study sections

By Sarah Greene Peer Review and the Age of Aquarius It’s time to reinvent the system that validates scientific discovery The most wonderous disruption of all: the idea that papers and data have lives beyond their original posting. This month our new column, Thought Experiment, considers whether mathematics can answer the deepest perplexities of science, such as evolution and consciousness. Here’s a corollary: Can metrics point to the great

Mail Earmark Science The practice of funding science with congressional earmarks1 is just the tip of the iceberg. I fear that we are experiencing a general disintegration of the quality and integrity of American science and engineering. From fundamental research to operating decisions like the ones made on the Deepwater Horizon that led to the disaster in the Gulf, bad technical decisions are being made—more often than not driven by politicians, lawye

Eavesdroppings Science Quotations of the Month © João Fazenda “Even the crustiest editors have been known to turn giddy when new light is shed on [gerontology] and take to blowing raspberries at the Reaper with headlines suggesting immortality elixirs are just around the corner.” —Author David Stipp writing on thescientist.com about science’s quest for the fountain of youth. © João Fazenda &

By Aaron Rowe Shoestring gene therapy An RNA synthesizer Courtesy of Alnylam, photography by J. Earle On a frigid weekend in the winter of 2004, a medical charity held a meeting at the Yarrow Hotel in Park City, Utah, to discuss a problem. It had been nearly ten years since geneticists Irwin McLean and Frances Smith had discovered the genetic underpinnings of pachyonychia congenita, a rare and extremely painful skin disorder. But a cure was nowhere in sight.

By Richard P. Grant Creative madness Consider a brick. What can you do with it? Your answer to that question can be a measure of how creative you are. Örjan de Manzano, a PhD student at the Karolinska Institutet in Stockholm, is using the query to explore the potential neurological link between creativity and psychoses. Highly creative people and those with mental disorders are usually better at seeing novel connections between ideas or objects—at t

Top 7 From F1000 © SERCOMI / Photo Researchers, Inc. 1. Piston proton pump » The X-ray structure of a membrane complex involved in aerobic respiration (and implicated in neurodegeneration) reveals an unusual piston-like mechanism for pumping protons across the mitochondrial membrane, and provides clues for developing drugs against Parkinson’s and other related diseases. R.G. Efremov et al., Nature, 2010 May 27, 465(7297):441–4

Jo Handelsman discusses a paper that found gut microbiota can influence sexual fitness in an invasive pest.

By William J. PearceCitations: Too Many, or Not Enough? We are citing too many papers inappropriately.Students, colleagues and coauthors must critically read each paper cited in its entirety.For more than 100 years, before PubMed was freely accessible via the Internet, the medical literature was commonly accessed via Index Medicus, the first comprehensive index of journal articles available through the Library of Medicine. Finding the perfect reference often necess

By Mark E Hay and Douglas B Rasher Corals in Crisis Marine protected areas reduce coral loss, but they are not enough. © Ken Lucas / Visuals Unlimited The world’s coral reefs are rapidly disappearing due to cascades of interacting stresses ranging from global warming, pollution, overfishing and ocean acidification to catastrophic events like the oil spill in the Gulf of Mexico. One of the world’s most productive,

By Karen Hopkin Strength in Numbers A mathematical mind has helped Leonid Kruglyak scan millions of yeast for the secrets of genetic complexity. © Denise Applewhite for Princeton University Leonid Kruglyak did his graduate work in physics, but when he dove into biology, he jumped with both feet. “The first thing I wrote about genetics was an eight-line letter to Nature,” he says. In it, he defend

Mohamed-Ali Hakimi and Robert Ménard RNA Arms Race Do parasites use their own microRNAs to hijack host cell pathways? Red blood cells infected with the Plasmodium falciparum parasite. GARY D. GAUGLER / PHOTO RESEARCHERS, INC. RNA silencing, which fine tunes up to 30% of genome during development,1 also plays a major role in innate antiviral and antibacterial defenses in plants, insects, and animals. But

By Richard GrantCodon clusters © Alfred Pasieka / Photo Researchers, Inc.The paper G. Cannarozzi et al., “A role for codon order in translation dynamics,” Cell, 141:355-67, 2010.http://bit.ly/codonorder The finding For more than 8 years, Yves Barral’s group at the ETH in Zürich has puzzled over this question: When the same amino acid is repeated several times in a protein, why is it often specified by the same codon? His group used a

By Richard GrantNetworked genes From M. Costanzo et al., “The genetic landscape of a cell,” Science, 327:425–31, 2010. reprinted with permission from aaas.The paper M. Costanzo et al., “The genetic landscape of a cell,” Science, 327:425–31, 2010.http://bit.ly/genlandscape The finding Knocking out a single gene in yeast often has little effect; yeast can survive with only about 20% of their 6,000 genes intact and researcher

By Richard GrantInflammation amplification Steven Moskowitz / Advanced Medical GraphicsThe paper E. Boilard et al., “Platelets amplify inflammation in arthritis via collagen-dependent microparticle production,” Science, 327:580–83, 2010. http://bit.ly/plateletRA The finding An international team led by David Lee at the Brigham and Women’s Hospital was surprised to find cell-surface markers from platelets in the fluid of inflamed join

By Jeffrey M. Perkel Probing Proteins How to make sense of proliferating proteomics data…even if you’re not a proteomicist. Pity the poor protein biologist. DNA sequence gurus have GenBank, structural biologists, PDB. But those looking to data-mine the spectral peaks and valleys of today’s burgeoning proteomics literature are out of luck. Or are they? Several freely available databases are dedicated to the

By Brendan Borrell Bio Island Dream For 40 years, Puerto Rico has been a pharmaceutical manufacturing powerhouse, but is it ready to finally edge its way into research and development? Conceptual rendering of Science City Courtesy of Puerto Rico Science, Technology and Research Trust Ignacio “Nacho” Pino opens up another bottle of red wine as the sun sets over the city of Mayagüez on

By Megan Scudellari Skipping Retirement Scientists nearing forced retirement age in Europe and Japan find more welcoming laboratories abroad. Learn the secrets to their success. Jan-Åke Gustafsson never got an official retirement notice from the University. But that’s because the 63-year-old chairman of the Department of Biosciences and Nutrition at the Karolinska Institutet didn’t wait around for it. When a

By The Scientist Staff Breakthroughs from the Second Tier Peer review isn’t perfect— meet 5 high-impact papers that should have ended up in bigger journals. © Pedro Scassa / Corbis Often the exalted scientific and medical journals sitting atop the impact factor pyramid are considered the only publications that offer legitimate breakthroughs in basic and clinical research. But some of the most important findings have been published in considera