December 2003

To Toss or to Archive I enjoyed reading Jill Adams' article1 and it brought up a dilemma all researchers face: whether to save or throw away old data? In my opinion, the value of old data cannot be neglected; they are important for future research. Considering the consistency and integrity of the research, it is always good to save old data. The general composition of a research team involves technicians, graduate students, and postdocs, who come and go. Newcomers can follow well-kept

Plagiarism or Plain Survival? The undersigned have read with interest the excellent article on plagiarism by Sudip K. Das.1 Although the article deals with the incidence of plagiarism in higher education* that has recently set off some empathetic alarm bells throughout the academic community, its content can undoubtedly be applied to another related problem, that is, plagiarism among non-native English-speaking scientists while writing papers. For a non-native English-speaking scientis

Of the 393 readers of The Scientist who answered our recent survey, 95% spend one-half hour or more visiting Web sites every day, and 63% browse for more than an hour. Some 70% use more than half of their Web-cruising time visiting sites relating to their work. Echoing many of our respondents, one reader comments, "The Web has revolutionized how I get scientific information. I hardly ever go to the library any more!" Another warns, "I have come to realize that visiting Web sites is becoming

Frontlines | Trilobites: Living on the Edge Courtesy of The Yoho-Burgess Shale Foundation The most familiar and abundant species of trilobites in North America may have followed an exotic survival strategy. Elrathia kingii, found in Middle Cambrian formations in Utah, lived exclusively in low-oxygen environments, according to geologist Robert Gaines of Pomona College, Claremont, Calif.1 "Elrathia occurs typically in monospecific communities, with as many as 500 individuals per square

Frontlines | Selling Directly to the Mind Erica P. Johnson You see a sweater for sale and think, "I have to have that!" Clint Kilts wants to know why. Kilts, a professor of psychiatry and behavioral sciences at Emory University in Atlanta, is investigating the underlying neural organization that governs personal preferences and the decision-making process. Regarding a product, there's not a lot of conscious deliberation, he says. People decide quickly whether they like something. Kil

Foundations | The Boron Connection Click for larger version of measurements (35K) In 1999 we discovered LuxS, an enzyme needed for making a signal molecule (AI-2) that bacteria use for interspecies communication.1 X-ray crystallography allowed us to see that AI-2 is composed of two, five-membered rings. The challenge was to determine which atoms composed the rings. Our initial guess, a mixture of carbons and oxygens, appalled our chemist friends: we had drawn a carbon atom covalently

First Person | Marc Vidal Courtesy of The Marc Vidal Lab In 1996, Marc Vidal, proteomic cartographer and coinventor of the reverse two-hybrid system, couldn't find work that paid more than a postdoc's salary. He survived on a National Institutes of Health grant and the good graces (if not the prescience) of Harvard University cell biologist Ed Harlow, who believed in Vidal's vision to map protein to protein and let the young Belgian work in his lab. The ideas weren't fashionable, Vida

5-Prime| Bacteria--109 Tough Cookies Courtesy of CDC Is there any place where bacteria can't be found? Pick an environment, a temperature, an elevation, a climate, and a bacterial species calls it home. Scientists have found bacteria in every exotic habitat in the biosphere, says Thomas Whittam, a microbiologist at Michigan State University, East Lansing. Why are they so ubiquitous? One ecosystem can't supply enough resources for the more than 109 bacterial species1 that exist, so t

Off The Cuff | What Is It About Research That Makes You Smile? Knowing that for every answer you find, 10 more questions are revealed. Now that's job security. --Heather Kiefer, Intelligent Medical Devices, Cambridge, Mass. Every action has an equal and opposite reaction--the third law of physics. As it applies to research: For every brilliant discovery there's an equally stupid mistake. For example, one can spend months purifying a protein, only to spill it on the floor looking at one's

Science Seen | Jelly Belly Courtesy of Claudia Mills, University of Washington, Friday Harbor Laboratories  Most molecular biologists use GFP today. Likewise, most of them know that the original source of the green fluorescent protein is a jellyfish. But how many are aware that the Aequorea victoria really is a beautiful creature? function sendData() { document.frm.pathName.value = location.pathname; result = false if (document.frm.score[0].checked) result = true; if (docum

Click to view enlarged diagrams (172K) Cell-cycle cameras recently recorded a troubling scene. Investigators had taken away genes thought to control cell-cycle progression, a central force in growth and development and cancer, but some mice and cell lines grew anyway (see A Cell-Cycle Couple Loses Its Luster). At the perceived time of the incident--the mitotic transition from G1 to S phase-- putative primary players such as cyclin-dependent kinase 2 (CDK2) were not at the scene. Now, private

Courtesy of Philipp Kaldis, © 2003 Elsevier  THE UNEXPECTED SURVIVOR: Mice that lack the CDK2 protein (-/-) survive to adulthood but are slightly smaller than their wild-type littermates (+/+). The knockouts are also sterile. After several groups reported discovering cyclin E and cyclin-dependent kinase 2 (CDK2) in 1991, a consensus emerged. It held that these protein partners are crucial in promoting the cell cycle's G1- to S-phase transition and driving cancer-cell proliferation.

Courtesy of Preston Huey, © 2003 AAAS  LIFE IN THE HOT SEAT: In one hypothetical model, an alkaline hydrothermal solution of constant temperature and pH may have convectively pumped through a confining porous mound of precipitated clays, hydroxides such as Mg(OH)2, and iron nickel sulfides into a cool and acidulous ocean. In 1953 a University of Chicago graduate student, Stanley Miller, shot electric sparks into an apparatus that circulated water, methane, ammonia, and hydrogen in a

Courtesy of Zachary Knight  BEAUTIFUL CLEAVAGE: Trypsin cleaving a hypothetical protein into smaller fragments with C-terminal phosphorylated residues--a basis for phosphorylation mapping techniques. Proteins communicate with each other through posttranslational modifications, and locating modified sites is a key challenge in proteomics. Phosphorylation, the most common modification by far, is central to cell signaling, and knowledge of where and when proteins are phosphorylated could he

© 2003 Nature Publishing Group  CROSS TALKING PATHWAYS: Schematic depicting the TNF-R1-induced pathways modulating apoptosis. Blocking the NF-kB-dependent pathway leads to sustained JNK activation and apoptosis. Conversely, blocking the TNF-a induced JNK pathway promotes cell survival. JNK may induce death by triggering mitochondrial events, either directly or indirectly, but its targets remain unknown. (From G. Franzoso et al., Cell Death Differ, 10:13-15. doi: 10.1038/sj.cdd4401154)

Research Briefs Cancer Cook-Off; Faculty of 1000 | Interdisciplinary Research; Sir2, In Flagrante Delicto Cancer Cook-Off © 2003 National Academy of Sciences, USA In a departure from traditional Texas barbecue, researchers at Rice University and the University of Texas MD Anderson Cancer Center, both in Houston, recently showed that they could literally cook cancer cells to death, using nanotechnology. Rice bioengineer Jennifer West and colleagues demonstrated that an injection of so

Front Page Bibliographies for the Penguin Faithful; Legible Lab Labels; High-Power Proteomic Fractionation SOFTWARE WATCH | Bibliographies for the Penguin Faithful Courtesy of Larry Ewing EndNote, the commercial bibliographic management program, has been a godsend to scientists, provided they work on PCs or Macs. Those who depend on Linux are out of luck--or at least, they were. Now Pybliographer (www.pybliographer.org), from French programmer Frederic Gobry, is trying to fill the void. Th

Michel Tcherevkoff Ltd. Grid computing is hot these days. With high-profile projects ranging from a search for extraterrestrial intelligence to a search for smallpox therapeutics, many researchers are looking to the grid as a way to get supercomputing power without dishing out supercomputing prices. The Grid Computing Info Centre defines a grid as "a type of parallel and distributed system that enables the sharing, selection, and aggregation of geographically distributed 'autonomous' resourc

Courtesy of AfCS-Nature Signaling Gateway (www.signaling-gateway.org)  A WORK IN PROGRESS Complex as it is, this cell signaling map isn't finished. But since every interaction shown is a potential point for therapeutic intervention, understanding the wiring of these messaging systems could deliver new drugs to the clinic. Signal transduction wasn't exactly the first thing that came to mind when my mother told me that she had medullary thyroid cancer. Thoughts of not having my mother aroun

Courtesy of NextGen Sciences As a company that develops breast cancer protein chips, Cambridge, UK-based NextGen Sciences experiences the pitfalls of proteomics research on a daily basis. One of the bottlenecks at the moment, says CEO Kevin Auton, is the need to produce enough different proteins to meet the demands of therapeutic groups both internally and for corporate clients. Resolving complex protein mixtures into their component parts is another ongoing problem. In September, NextGen Sci

Courtesy of Vitra Bioscience The unprecedented number of promising new drug candidates coming out of drug-discovery efforts has not translated into a commensurate increase in new drugs available at the pharmacy. Drug development backlogs arise, in part, because compounds are tested sequentially, one variable at a time, says Andrew Whiteley, CEO of Vitra Bioscience, Mountain View, Calif. What's needed, he says, is a more streamlined approach that allows scientists to look at the effects of dru

Courtesy of Ambion Isolating RNA and proteins from crude lysates is no longer a painstaking task, thanks to the myriad kits available. But isolating both from the same sample? Sacre bleu! This can be tricky, as most methods for extracting RNA are phenol-based and yield denatured protein. Now, Austin, Texas-based Ambion offers the PARIS (Protein and RNA Isolation System) kit, which extracts RNA and protein from a single sample using completely aqueous technology. The PARIS protocol can be use

A Duke University report adds to the growing consensus that a climate of exclusion persists despite women's advancement into academic positions. More women may be getting science degrees today than 40 years ago, but that fact has not translated to gender equity in the academic workplace. Duke's study indicates that lower salaries, fewer leadership positions, and slower promotion rates are not alone in creating barriers that discourage women from continuing in the science career pipeline.1 "We

Oxford drawing (1731) courtesy of Marc Edwards Oxford and Cambridge Universities continue to top UK rankings for research and academic attainment, yet despite a recent streamlining, both are under strong pressure from the government to make further changes in management structures that until recently had survived almost unchanged for centuries. The universities enjoy considerable self-rule, and individual colleges have autonomy over aspects of teaching and the ability to fund some of their ow

dimpleart.com Art Caplan Terri Schaivo lies on life support in a Florida hospital and Art Caplan has work to do: an appearance on CNN's Wolfe Blitzer Reports and telephone interviews with reporters from Time magazine and US News and World Report. A driver awaits Caplan in an immaculate blue Cadillac parked in front of Montreal's Ritz Carlton Hotel. Caplan is attending the annual meeting of the American Society for Bioethics and Humanities (ASBH) in Montreal, and the cable news network ha

Courtesy of University of Texas M.D. Anderson Cancer Center Roy Herbst In those rare moments when Roy Herbst isn't seeing a patient or assessing the results of his research, he's aware of the quickening pace of time. So much of his time has been absorbed with education, training, mulling choices, and making hard decisions, each with potential to twist his life in a new direction. Somewhere in between the classes, the residency, the research, and the promotions, 22 years have slipped by.

Anne MacNamara For years, when neuroscientists who study taste and smell submitted research grant proposals to the National Institutes of Health, half of the reviewers were not experts in the subspecialty. Instead, they studied language. Likewise, when language neuroscientists submitted proposals, their fates lay partly in the hands of people whose main interest in the human head started at the mouth and nose and ended in parts of the brain unrelated to language. "Historically, we had been pl

File photo Scientists are debating the implications of a proposed new set of rules requiring federal agencies to consult outside scientists systematically when revising regulations. The White House Office of Management and Budget (OMB) says that the "peer-review" requirements are meant to "further engage the scientific community in the regulatory process." Under the draft rules, independent scientists must review significant amendments to any federal agency rule, which includes amendments tha

File photo My family holds firmly to the belief that my husband and I are keeping something from them, something imminent and important. My current appointment is nearly up, I need a new job, and thus we need to move. My parents have been persistent, and for months my response has been, "We don't know where we are moving. We just know we are going to move." They feel excluded, yet I do, too. I am not privy to something important that is happening in my life. And so continues my tenure-track qu

No Sex Research Please, We're American By Richard Gallagher During a budget debate in the US House of Representatives on July 10, Rep. Patrick Toomey (R-Pa.) proposed an amendment to defund five NIH grants,1 four of which would examine aspects of human sexuality. "Who thinks this stuff up?" Toomey asked. His amendment was barely defeated, 210 to 212. Combined, the threatened studies will receive $1.5 million (US) next year. Specifically, the money will be spent on studying American Indian a

The English language, with its rich vocabulary and means of expression, has emerged as the lingua franca of scientific communication, prompting the thought that perhaps the term should be replaced with lingua anglica. Yet, that wouldn't be quite accurate, because many scientists claim that the true language of scientific meetings and manuscripts is "broken English." Latin, which provides considerable insight into scientific terminology, was a compulsory requirement for university studies in

Since The Institute for Genomic Research first decoded the complete genetic material of a free-living organism (Haemophilus influenzae) in 1995,1 we have seen an explosion in the number of completed genomes. The total completed genome count is about 150, a number that is likely to double in 2004. Next year, we will experience a greater shift in genomics, from simply obtaining the genetic code of organisms to comparing and interpreting them, eventually understanding how the four-letter (ACGT)