February 2003

Volume 17 Issue 4

The Scientist February 2003 Cover

Departments

Frontlines

What Does the Manatee Say to the Aardvark? Ancient Auntie.

Frontlines | What Does the Manatee Say to the Aardvark? Ancient Auntie. The aardvark or "earth pig" may be the closest living relative to the ancestral placental mammal, a new chromosomal comparison suggests. Molecular sequence analyses group it with tenrecs, hyraxes, elephant shrews, manatees, elephants, and golden moles as "Afrotheria," the oldest of four groups of placental mammals that originated, according to fossil evidence, on the supercontinent Gondwana 105 million years ago. Terr

Snapshot

How Scientists Get Their News

The Scientist surveyed 485 readers to find out how they keep up with the (nonscientific) news. More than 98% of readers stay abreast of current events, and more than 70% use three or more media. Most popular is television news, with 71.1% watching regularly, closely followed by news Web sites (68.8%). Daily newspapers and Sunday newspapers follow with 57.2% and 47.9%, respectively. About 2% admit to not keeping up with the news. CNN is the overwhelming favorite among the more than 70 TV channel

First Person

Josef Penninger

First Person | Josef Penninger Courtesy of Josef Penninger  Angelica and Gabriel with Josef He eschews awards, readily changes his baby's diapers, and still dreams of playing in the World Cup. Molecular geneticist Josef Penninger, 38, who likens cellular parts to Lego pieces, believes that science is simple because, he has said, its "pieces are always the same." Lured away from the University of Toronto last year to direct the Austrian Academy of Sciences' Institute of Molecular Biote

Foundations

The First Polymerase Chain Reaction

Foundations | The First Polymerase Chain Reaction This page from my notebook lists the chemicals which I put together into a single, purple-capped tube on September 8th, 1983, in a reaction I labeled PCR01. No cycling, only one tube, no variations, no controls, and anyone familiar with PCR conditions used today will recognize very little here, except the idea. I wasn't positive that the reaction would not cycle itself. I knew that any chemical equilibrium had some finite value, meaning that

Frontlines

Better Rap for Bilirubin

Frontlines | Better Rap for Bilirubin Erica P. Johnson The yellow bile pigment bilirubin has a bad reputation. The normal end-product of hemoglobin breakdown, in excess it causes jaundice, lethargy, seizures, and death. Yet, people with only slightly elevated levels are less prone to heart disease. Neuroscientist Solomon Snyder and colleagues at Johns Hopkins Medical School in Baltimore discovered why the body makes bilirubin at all, when its immediate precursor, biliverdin, is easily excr

5-Prime

Ribozymes

5-Prime | Ribozymes 1. What's a ribozyme? It is a catalytic RNA molecule. That discovery won the 1989 Nobel Prize in Chemistry for Tom Cech and Sidney Altman. Eight classes of ribozymes have now been identified, including seven that modify the nucleic acid backbone: hammerhead, hairpin, HDV (hepatitis delta virus), ribonuclease P, group I intron, group II intron, and VS ribozyme. The eighth type, the ribosome's peptidyl transferase center, builds peptide bonds. 2. What's all the fuss ab

Frontlines

Collaborations Become Innate

Frontlines | Collaborations Become Innate Courtesy of The Scripps Research Institute A five-year, $24 million National Institutes of Health grant to study innate immunity could supply a bounty of new reagents and animal models as well as a free database of experimental information to immunologists. Innate immunity, the once unappreciated first-line defense against infections, has recently been implicated in sepsis and inflammatory disorders such as Crohn disease. As more scientists got hook

So They Say

So They Say

So They Say "I have never been as worried for space shuttle safety as I am now. ... One of the roots of my concern is that nobody will know for sure when the safety margin has been eroded too far." --Richard D. Bloomberg, testifying before Congress in April 2002 as chairman of NASA's Aerospace Safety Advisory Panel. From The New York Times.   "America's journey into space will go on." --US President George W. Bush, on Feb. 3, two days after the space shuttle Columbia exploded, kill

Editorial

Postdocs: Truly, Les Miserables

There comes an hour when protest no longer suffices; after philosophy there must be action; the strong hand finishes what the idea has sketched. --Victor Hugo, Les Miserables, Saint Denis in book 13, ch. 3 In the Feb. 10 issue, after polling 2,800 postdocs, we highlighted the best places to work and the factors that contribute to job satisfaction. But in the box for free-text comments, quite a different set of verdicts was being delivered. Most of the 600 comments were shrieks of protest, f

Opinion

Keep Philanthropic Funding Distinct

The biomedical and pharmaceutical powerhouses of North America and Europe disproportionately focus their resources on the mostly chronic diseases affecting the relatively well-to-do. Of the $70 billion (US) the international health community spends on research, only 10% goes toward diseases responsible for 90% of the international health burden; it's called the 10/90 gap1 and it's deadly for poor countries. So, when an American private foundation announces a major investment in global health

Letter

Mechanisms of HIV Infection

Mechanisms of HIV Infection Regarding your article, "Researchers Dissect the Mechanisms of HIV Infection,"1 in my opinion, DC-SIGN researchers have neglected an important means of HIV-1 and dendrite attachment important to the HIV-1 infection process. As HIV-1 buds from the host cell of replication membrane during its budding maturation process, many different host cell molecules are incorporated into the HIV-1 viral envelope. Among these budding acquired molecules (BAMs) are functional ICA

A Lesson from Enron

A Lesson from Enron Nicholas Wade's article, "Fraud Happens: What to Do About It,"1 touches on several aspects of the phenomenon of scientific fraud in the wake of Jan Henrik Schon's scandal at Bell Labs. However, I found myself a bit disappointed reading about actions and checkpoints that do not work in curbing fraud in science and not much in terms of "what to do about it." Although an attempt was made to shift the responsibility of fraud detection to the lab chief, in many cases the chie

Letter

Keep on Going

Keep on Going Regarding your article on the history of immunology,1 why stop at the 1970s? Why not go back to the 1920s--Metalnikov's work on conditioned responses of the immune system, à la Pavlov, at the Pasteur Institute, and Hans Selye's initial ideas on the "syndrome of just being sick." One of the great problems in immunology research in the 20th century was its almost total domination by medical infectious disease specialists looking into clonal immunity. In some ways this is

Feature

Putting Humpty Dumpty Back Together Again

Corbis For 50 years, biologists have focused on reducing life to its constituent parts, first focusing on the cell, then working their way down to the genome itself. However, such achievements created a new challenge--making sense of the huge amounts of data produced. As professor Denis Noble, Oxford University, puts it: "It took Humpty Dumpty apart but left the challenge of putting him back together again." Systems biology attempts to reconstruct Humpty Dumpty as a series of overlapping math

The People's Biology

Erica P. Johnson Systems biologists envision a hulking database where all biological knowledge can be stored, freely accessed, and designed to interact. From it, researchers could easily extract data to construct virtual molecular pathway models working in their respective networks and in dynamic contexts of time, space, and various environmental cues. Hypotheses could be plucked like apples from the electronic tree of knowledge, and drug targets would fall like leaves. Some want to play out

The Alpha Project

One day, genomic data will be translated into language that can be used to find new diagnostic and therapeutic targets for disease. Computers will mine DNA codes to build nanomachines, and "smart fabrics" will contain sensing capabilities modeled on living things. So says Shankar Shastry, chairman of electrical engineering and computer sciences at the University of California at Berkeley. "Bio is my bet on where the new set of glamour technologies will be," he predicts. But even the small step

Research Front Page

New Lead for Sporadic CJD Cause; Enlisting Evolutionary Help; Science Seen

Front Page | New Lead for Sporadic CJD Cause; Enlisting Evolutionary Help; Science Seen Courtesy of Astrid & Hanns-Frieder Michler/Science, Photo Library  SCIENCE SEENA cross section of a madonna lily anther shows four pollen sacs filled with pollen grains (blue dots with red nuclei). Some of the pollen grains of this Lilium candidum are undergoing meiosis, the process whereby a normal diploid cell divides to form four haploid cells, called gametes.   Courtesy of Keith Welle

Research

RNA Calls the Shots

Courtesy of Vasudeva Mahavisno  CANCER CARTOGRAPHY: Metastatic prostate cancer from a tissue array stained for EZH2 protein. The background represents gene expression signatures of prostate cancer as a heat map, which lead to the discovery of EZH2 as a prostate cancer biomarker. As soon as Watson and Crick deduced DNA's structure half a century ago, their thoughts turned to RNA. Arguably the most important molecule in the living world, RNA not only connects gene to protein, but its catal

Special Delivery

Courtesy of Nadine Barrie Smith  PATCHING THROUGH: The ultrasound patch, weighing less than 22 grams, is an array made from up to four cymbal transducers, encased in a flexible polymer. This array's dimensions are 37 x 37 x 7 mm. It can be made thinner. Proteins represent the largest class of biotech drug ap-provals, and the numbers will continue to rise as work with the human genome sequence proceeds. Figures from 2000 show that 86% of 77 approved biotech medicines are proteins, with hu

Building an 'EvoBank'

Courtesy of Gerhard W. Weber  MEET MRS. PLES: Found in South Africa, this 2.5 million-year-old fossil graces the cover of a CD-ROM that contains digital 3-D data from CT scans in different formats. Paleoanthropologists are reputedly a passionate bunch, which is not surprising for a discipline that asks questions that hit close to home and relies heavily on interpreting differences among hard-won, unique specimens to provide answers. With a mixture of frustration and pride, they regularly

Hot Paper

Arabidopsis thaliana, Meet Microarray Technology

Courtesy of Steve Kay Data derived from the Science Watch/Hot Papers database and 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. P. Schenk et al., "Coordinated plant defense responses in Arabidopsis revealed by microarray analysis," Proc Natl Acad Sci, 97:11655-60, 2000. (Cited in 118 papers) S. Harmer et al., "Orchestrated transcription of key pathways in Arabidopsis by the circadian clock," S

Technology Front Page

Golden Electroporation; Reduce, Reuse, Recycle; Rad! Volocity Goes Modular

Front Page | Golden Electroporation; Recyclable Microarrays?; Rad! Volocity Goes Modular Courtesy of BTX GADGET WATCH | Golden Electroporation Scientists in high-throughput labs are no longer limited to chemical transfection technologies; thanks to BTX, they can opt to electroporate, instead. The San Diego-based company (www.btxonline.com) recently released a 96-well, gold-plated, disposable electroporation microplate--a high-throughput alternative to single-use cuvettes. Now, rather than

Technology Profile

A Rosy Forecast for Precast Gels

Images Courtesy of Genomic Solutions Product literature for Invitrogen's E-gels®, a precast agarose gel system, neatly summarizes the purported advantages of such products: "E-gels make agarose electrophoresis as easy as Plug & Play." The vast majority of researchers are perfectly capable of pouring their own gels, of course--the process is certainly not difficult. It may, however, be tedious. It can also be tricky; leaks are a constant bugaboo, and gel-to-gel variation can be a probl

Toward a Paperless Lab?

Courtesy of Thermo Lab Systems Data management in the lab can be dizzying: Where is that clone? Which samples still need to be tested? Has anyone in the lab ever tried this experiment? Which batch of reagent did we use in that trial? As a laboratory grows, the inability to access and process data quickly can become a nightmare. Many research labs track samples, reagents, and experiments using paper records or even simple electronic spreadsheets. But as the amount and complexity of data grow,

Technology

Microarrays in a Microtube

Image courtesy of CLONDIAG Companies in the microarray sector are trying to take the technology out of core facilities and put it into the hands of individual researchers by developing technologies such as smaller, less-costly scanners and more streamlined software for array analysis. These improvements could make microarray technology more attractive to labs that lack the large budgets required for sophisticated biochip-related equipment. CLONDIAG® Chip Technologies of Jena, Germany, has

The Incredible Shrinking Scanner

Courtesy of Affymetrix Instrument manufacturers, recognizing that bench space is at a premium, are downsizing their products, and Santa Clara, Calif.-based Affymetrix is no exception. The company's new GeneChip® Scanner 3000, a PC-sized scanner that requires neither external laser power supplies nor special ventilation systems, is one-third the size of the company's current system, according to Chip Leveille, senior director of corporate marketing and instrumentation. Leveille says the Ge

A Quantum Leap for Fluorescence

Courtesy of Quantum Dot Corp. Fluorescent reporter molecules are used for microscopy, real-time PCR, microarrays, and other applications. Yet most fluorescent dyes share some fundamental flaws: They are subject to photobleaching, are not very bright, and have overlapping emission and absorption spectra. Some nanotechnologists are betting that quantum dots (QDs) will eliminate these problems. QDs consist of a nanometer-scale crystalline core of semiconductor material; biologically active versi

Profession

Don't Leave it, Love it; Gene Grounding; Watson's Words: Advice to Young Scientists

Front Page | Gene Grounding; Tip Trove; Watson's Own Words Courtesy of Joel Garfinkle TIP TROVE | Don't Leave it, Love it 1. Expand what you love. Identify the most enjoyable activities or projects of your job and fully incorporate them into your daily responsibilities. 2. Prioritize your most important activities. Work smarter, not harder. 3. Create a professional support team. Ask a helpful coworker, an inspiring mentor, a member of management, and a bright junior employee to be a p

Biotechs Change to Stay Alive

Anne Macnamara Like the life systems it studies, the biotechnology industry evolves to survive. Today, companies founded and generously funded in the 1990s are scrambling to transform themselves from suppliers of technology, data, or discovery targets into full-fledged drug development firms that make products for patients. Those that fail to make the transformation face the future as low-profit providers of biotech building blocks, or as acquisitions in the business world's equivalent of exti

The NIH: A Budget Appraisal

Digital Vision President George W. Bush's decision to halt historic increases in the National Institutes of Health budget in fiscal year 2004 raises questions about how much the agency and the researchers it funds should expect to receive in the coming years. With a possible war on the horizon, the economy in a slump, and dreams of future federal surpluses fading, policymakers and scientists suggest that funding other science-related agencies may be a higher priority. Beltway observers also q

UK Scientists Assess Planned Salary Raises

Anne Macnamara Declining salary levels and a withering laboratory infrastructure have long threatened the United Kingdom's status as a major world research center. The Ministry of Education had a golden opportunity to reverse this continuing decline as part of a major higher education funding shakeup over the past few months. But senior scientists and lobbying groups charge that the government has failed to back up fine words with the necessary funding commitment. "I think it's pretty poor a

Systems Biology: A Pale Beacon For Biotechs

Systems biology, a siren in a sea of dark prospects, has lured investors frustrated with low returns in biotechnology and anxious to set a new course of drug discovery. Institutions have also geared up training programs, but the excitement in the new field has failed to arrest downsizing in the biotech industry. Major research institutions and pharmaceutical companies, including AstraZeneca, Novartis, and Eli Lilly and Company, are implementing systems biology in the hopes of slashing drug di

Fine Tuning

Start a Business, Don't Sell Out

Courtesy of Simon Portman Many scientists offered the opportunity of doing industrially sponsored work would be glad for the cash. But they also face the prospect with a certain amount of nervousness. Will their academic integrity be compromised? Will they be shackled by a complicated legal document, which they do not understand until, months later, they find themselves targeted in a lawsuit because they have unwittingly breached one of its contractual terms? The problem is that industry and

How I Got This Job

Cyber Scientist Ciphers Biology

How I Got This Job | Cyber Scientist Ciphers Biology Courtesy of Terry Gaasterland  Terry GaasterlandAssociate professor, Head, Laboratory of Computational Genomics, Rockefeller University Early Indications: I always wanted to be a scientist, the question was, what kind? For a long time in high school I saw myself becoming a medical doctor, but when I wrote my first computer program as a college freshman I got hooked on computer science. Pivotal Paper: My most thrilling, accepted pap

Closing Bell

Wriggling on a Pin

For young journalists, interviewing a scientific expert can be a queasy experience. This feeling doesn't arise directly from relative ignorance, to which the interviewer may be modestly resigned. It stems from uncertainty about how that ignorance might be perceived and tolerated. The patience of some scientists can be short, although many are receptive and responsive to the media. Those differences not only show the danger in generalizing about personalities, but also point out the real sourc

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