February 2002

The Budapest Open Access Initiative (BOAI) may not have quite the same historic import as the Theses of Martin Luther or the US Declaration of Independence, but it has the potential to shake up the world of academic publishing in a profound way. The BOAI was proposed at a meeting sponsored by the Open Society Institute in Budapest in December 2001, attended by supporters of open access to researcher-generated literature, and was released in final form on Feb. 14 (www.soros.org/openaccess). The O

Intimidation and bewilderment are but two feelings scientists often confront when facing the ever-expanding published scientific literature. With the birth of any hypothesis, all fantasies of a one-way freeway for a scientific endeavor evaporate when the journey abruptly confronts a forked-road dilemma. One direction, what is known and what was known, leads back in time. A twisted, rutted, convoluted course, it can reveal how, and from where, pioneers from other, unrelated journeys arrived at th

After a year's break as a columnist (erstwhile for Current Biology), I had decided to resume writing several months ago, but my natural tendency to procrastinate and the difficulty in choosing a title for the column have delayed me until now. 

Eugene Garfield's commentary, "Demand Citation Vigilance,"1 particularly the comment "the bibliographic neglect displayed by inventors and patent examiners," struck an all-too-familiar chord. In brief, my group's (which included my mentor, the late Distinguished Professor Ernest Witebsky of autoimmune thyroiditis note) observations of the initial discovery of prostate-specific antigen (PSA) in 19702 were overlooked and misrepresented, including the omission of a key reference, by the patent exam

Regarding the "disregard syndrome,"1 and various opinions expressed thereafter, there is a deliberate disregard for the scientific papers published from India (probably from other developing countries as well). I can quote numerous examples where a paper on a precise topic ignores mentioning related work already done in certain countries, although those papers have appeared in journals that are included in Medline, Current Contents, and other sources. This may partly be due to lack of faith/rega

Reprinted with Permission from Elsevier ScienceDividing by Genotype: Genotype frequencies for the C3435T MDR1 polymorphism among various groups. People with this variant may need higher doses of protease inhibitors. (Image from The Lancet 358:383-4, 2001.)

Humans have long embraced the idea of grouping and naming people who have distinct, genetically determined physical characteristics, like almond-shaped eyes or different skin color. It made sense, from a social standpoint (think safety, politics, and business) to align one's self with kin. However, studying race from a biological point of view, in the hopes of learning about specific diseases or developing new drugs, is a different matter altogether. "Race is generally not a useful consideration

Add this to the pot of stem cell sources creating a political stir: parthenogenesis, creating embryos from unfertilized eggs. Unlike the cloning issue, which has a defined division, the ethical question regarding parthenogenesis may have all the earmarks of being ambivalent. So far, the US government has already placed restrictions on federal funding for new stem cell lines derived from in vitro fertilized embryos, and the Senate is deliberating over a ban on cloning that may block stem cells de

Melvin Silverman, professor of medicine at the University of Toronto, recently got a call from the Canadian Institutes of Health Research. The CIHR surveyor asked the scientist who would benefit from his studies of diabetes and membrane function, and what the intermediate and final outcome of the work would be. To Silverman, the questioner had asked him to justify the funding of basic biomedical research according to its direct community health benefits, rather than its scientific significance.

At the first meeting of the newly assembled President's Council on Bioethics (PCB), Jan. 17-18, members began their consideration of sensitive bioethical issues not with an analysis of the writings of a scientist, nor a bioethicist, nor a legislator, but a novelist. The group discussed Nathaniel Hawthorne's short story The Birthmark, a literary exploration of mankind's apparent aspiration to root out his own imperfections. The story's protagonist, an alchemist named Aylmer, convinces his wife Ge

With a little help from a group of Weddell seals, a team of marine scientists has uncovered new information about the two ecologically most important fish species living far beneath the ice pack in the dark, frigid waters of Antarctica's McMurdo Sound.1 Behavioral ecologist Lee A. Fuiman of the University of Texas, Austin, biologists Randall W. Davis of Texas A&M University, Galveston, and Terrie M. Williams of the University of California, Santa Cruz, and their team at McMurdo equipped each

While the anthrax letters of October 2001 sent microbiologists and geneticists into an unwanted limelight, the chemical community also found itself suddenly grappling with how their field fits into the post-9/11 world. The news from a Jan. 14-16 meeting at the Arnold and Mabel Beckman Center of the National Academies of Science and Engineering in Irvine, California, "National Security and Homeland Defense," was upbeat. The goal of the meeting, the third in a series called Challenges for the Chem

New evidence points to brain trauma as an environmental risk factor for Alzheimer disease (AD). 

Editor's Note: This is the fourth article in a series on sex-based differences in the biology of males and females. Future articles in the series will cover sex-based differences in drug metabolism and in life expectancy. Lisa Damiani In the 1970s, medical textbooks noted that lupus patients should not get pregnant because it could kill them, recalls physician Michael Lockshin. "I was challenged by a medical student, who had lupus, to show the data to prove that. But it didn't exist and it was a

After a three-year effort, scientists have determined the crystal structure of edema factor, a toxic protein secreted by Bacillus anthracis, the bacteria that causes anthrax.1 Edema factor (EF) works in concert with two other anthrax proteins—protective antigen (PA) and lethal factor (LF)—to kill its host cell. PA's crystal structure was reported in 19972 and LF's in November 2001.3 With this three-dimensional map now in hand, researchers are making headway into understanding how the

The Faculty of 1000 is a Web-based literature awareness tool published by BioMed Central. It provides a continuously updated insider's guide to the most important peer-reviewed papers within a range of research fields, based on the recommendations of a faculty of more than 1,400 leading researchers. Each issue, The Scientist will publish a list of the 10 top-rated papers from a specific subject area, as well as a short review of one or more of the listed papers. We will also publish a selection

M.B. Yaffe et al., "A motif-based profile scanning approach for genome-wide prediction of signaling pathways," Nature Biotechnology, 19:348-53, April 2001. F1000 Rating: Recommended "This paper describes a powerful fusion of experimental and computational methods to predict binding motifs in signal transduction pathways. Functional screens of degenerate peptide libraries are used to determine experimentally verified sequence preferences (motifs) that are the basis for a pattern matching approac

For this article, Jim Kling interviewed University of Edinburgh geneticist Adrian Bird and Paul A. Wade, assistant professor in the department of pathology and laboratory medicine at Emory University School of Medicine in Atlanta. Data from the Web of Science (ISI, Philadelphia) show that Hot Papers are cited 50 to 100 times more often than the average paper of the same type and age. H.-H. Ng, Y. Zhang, B. Hendrich, C.A. Johnson et al., "MBD2 is a transcriptional repressor belonging to the MeCP

The ability of cells to degrade and rearrange extracellular matrix proteins is crucial for an organism's growth and development. Nearly 40 years ago, Jerome Gross and Charles Lapiere discovered that when tadpole tail fins resorb, their skin releases an enzyme that degrades native collagen triple helixes in the underlying support matrix.1 This enzyme, called collagenase, is present in a wide variety of vertebrates, invertebrates, and plants. Critical as it is, collagenase is just one member of a

Scientists working with recombinant proteins expressed in Escherichia coli probably use at least one liquid chromatography technique to purify their protein of interest. But liquid chromatography frequently requires a considerable amount of optimization, and usually involves several different chromatographic steps to rid the sample of contaminants.1 The ideal solution would be to create a resin that is completely specific to the target protein, enabling one-step purification. Affinity chromatogr

They say timing is everything, and when it comes to cancer that's especially true. Human cells grow and divide every 24 hours. But in a fraction of a second, an error can occur in the copying of the human genome. Spotting precisely when that error happens is key to understanding, and possibly preventing, the development of cancer. Traditional cell cycle analysis involves staining samples taken at random intervals. But these snapshots don't tell the whole story. To see exactly what takes place ea

Invitrogen Corp. of Carlsbad, Calif., offers TOPO® Tools for those interested in an alternative to conventional, time-consuming cloning techniques. TOPO Tools provide a relatively fast way of joining various sequence elements, such as promoters and tags, to either or both ends of a PCR-amplified product, without traditional cloning procedures such as ligations, vector manipulations, or Escherichia coli transformation. Rather, this method harnesses the dual catalytic activities of Vaccinia t

Confocal microscopes and other related tools allow researchers to take optical sections through a sample to create a three-dimensional picture of that object. But most things worth looking at under a microscope are not static; they move and change shape over time. Coventry, England-based Improvision now offers a software product that allows researchers to study the structure of complex objects over time—that is, in 4D. Company literature describes Volocity as "the first true color 4D rende

Until March 29, 2002, Stratagene of La Jolla, Calif., is offering a 30% discount on the 100-unit size of AccuType DNA polymerase. AccuType DNA polymerase is a high-fidelity PCR enzyme designed for genotyping and mutation detection applications using sensitive DHPLC technologies. The offer is valid for Stratagene direct customers only. Stratagene, +1 (800) 424-5444 www.stratagene.com Mass Spec Time Saver Millipore of Bedford, Mass., has introduced the Montage In-Gel Digest96 Kit for convenient

Good" means average. "Great" means good. "Competent" is a blistering criticism. Welcome to the world of letters of reference, where you never say what you mean, and sometimes what you don't say, says it all. Letters of reference are the dirty work of science—an administrative duty that nobody wants to be bothered with. Yet they are an indisputably important part of being a scientist. In 2000, US universities awarded 25,979 science doctorates, according to a National Science Foundation surv

Call it disease-of-the-month research funding. The US and European practice of earmarking government money to satisfy public demands for new therapies or direct funds to research institutes in parliamentarians' home regions exasperates some scientists working on basic research projects that rarely attract headlines. These scientists complain that earmarking substitutes political decisions for scientific judgments and narrows scientific inquiry. Because politicians, not peers, approve the funding

The Scientist Survey Train Your Staff by Talking There are a total of 282 responses FROM 23-Jan-2002 to 03-Feb-2002.

A principal investigator at a veterinary research institution carpeted her office with the lab technician's reports and refused to sign the technician's time card. When such subtle statements failed to adequately convey the boss's consternation, the PI assigned the technician to work a machine already occupied by a graduate student, forcing the staff member to start her own work after closing time. The PI failed to use the most common technique for influencing the lab tech's working practices: E

Most principal investigators claim their job has nothing to do with the personal lives of lab members. And many lab workers say they would never take personal problems to the head of a lab. But in a place where people are so invested in their work, the definition of a personal problem isn't clear. Relationships, finances, and medical situations would seem to be personal, but all of these can influence work, and the PI or lab member may have to broach a delicate topic. For example, what may seem

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During the height of the national ruckus over anthrax mailings and feared terrorist attacks this past October, the US Senate quietly confirmed John H. Marburger III as scientific adviser to President George W. Bush, and director of the Office of Science and Technology Policy (OSTP). Bush broke records for heel dragging in nominating a candidate and then demoted the position from assistant to the president, granting less face time with the chief of staff.1 Add to this the fact that the OSTP was r