Issue | March 2004 | March 2004 | The Scientist Magazine®

Feature

Stuart Blackman | Mar 1, 2004 | 10+ min read

Digital VisionIn April 2003, the UK's Medical Research Council established a task force to assess possible future research models for the council's National Institute of Medical Research. "We've been looking ... for any hard data that helps us look at the relative merits of different models," says MRC task force secretary David Smith, "and we're not finding it." While the council gathered lots of anecdotal material, Smith continues, "I don't think it obviously leads to any clear conclusion.No wo

Editorial

Make Way for the Robot Scientist

"[The VK is] a very advanced form of lie detector that measures contractions of the iris muscle and the presence of invisible airborne particles emitted from the body. The bellows were designed for the latter function and give the machine the menacing air of a sinister insect. The VK is used primarily by Blade Runners to determine if a suspect is truly human by measuring the degree of his empathic response through carefully worded questions and statements."- 1982 Blade Runner presskit definition

Opinion

The InterAcademy Council: Inventing a New Global Organization

Brad FitzpatrickLast month, UN Secretary General Kofi Annan presided over the launch of a report by the InterAcademy Council, Inventing a Better Future: A Strategy for Building Worldwide Capacities in Science and Technology.1 The report is a call for action to strengthen national scientific capabilities throughout the world and to foster new opportunities for cooperation among the world's scientific and technological communities.This is the first report issued by the InterAcademy Council,2 an or

Letter

A Modest and Smart Proposal

I congratulate Professor Potts for his Opinion – "A Modest Financial Proposal".1 His proposal, if used effectively, could help people who make health policy decisions obtain the very information they need to design cost-effective research and delivery of health care. At a time when healthcare budgets are spiraling out of control, tough decisions will need to be made about where the money will be allocated. The sort of information Dr. Potts is advocating to be disclosed is precisely the typ

Benefits of Archiving

Publishing research in a journal usually archives minimal qualitative and quantitative amounts of an experimental record. Yan Sun emphasized the importance of keeping research data for future personal discoveries.1 These behaviors limit access to research data. The following experiences illustrate the societal needs for permanent institutional archiving.A report2 of ultraviolet (UV)-A protection of 18 UV-A light sensitive patients2 and a review of its unpublished study records revealed an unreco

Enzymatic Origins

The article by Mark Greener1 and commentary by the Editor2 give us a superb view of the present and future of enzymology, but there are also lessons to be learned by revisiting its past that suggest how enzymes came into being and how they relate to the origin of life.3Enzymes accelerate biochemical processes by factors ranging up to a billion billion (1018) fold.4 A reasonable speculation is that the first evolutionary structure contained one protein molecule that replicated with extreme slowne

5-Prime

IP for the PI

What is intellectual property?It's any product of the human mind that has commercial value. This can include literary works or a concept for a new tool; for life scientists, this may mean a lab technique or a new small molecule. The courts protect intellectual property with patents and copyrights.If I'm listed as the inventor on a patent, does that mean I own it?No, in most cases the inventor's institution – be it a private company, university, or government-run organization – keeps

Snapshot

D Expenditures as a Percentage of Gross Domestic Product

- Christine Bahls

Frontlines

Nails and Hooves: Designed for Wear and Tears

At first glance, it seems like a paper worthy of an Ig Nobel Prize. Roland Ennos, University of Manchester, has examined why fingernails, when nibbled or torn, tend to rip in a transverse direction, not longitudinally toward the nail bed.1 Using 3 mm-long snippets of undergraduates' nails, he found that it took twice the energy (6kJm-2) to cut them lengthwise as crosswise (3kJm-2). "And that's a good thing," he says. "Otherwise, we would be in agony throughout our lives, because every tear would

More Predators, Healthier Prey

Courtesy of Jon Eisenback, NemaPixA new mathematical model is turning the conventional notion of predator-prey relationships on its head. David Brown and colleagues at the University of California, Davis, have shown that prey populations can benefit from a high predator density.1Ecologists previously have shown that predators can have indirect positive effects on their prey through nutrient cycling and mineralization. Brown's group, however, modeled predators' direct positive effects on the prey

Foundations

Climbing the Molecular Stairway

Courtesy of Steven BlockIt had long been assumed that motor proteins would advance in discrete steps. However, the steps posed a challenge for measurement because they were small enough to be comparable to the background noise due to the Brownian (thermal) motion. During 1993, together with graduate student Karel Svoboda, postdoc Christoph Schmidt, and kinesin codiscoverer Bruce Schnapp, I set out to show that kinesin moved in a stepwise fashion along microtubules, and to measure the size of tho

First Person

Mario R. Capecchi

How did you survive as a child?Courtesy of Mario R. CapecchiPart luck, part [ly being] resourceful, you had to get food by stealing. I became fairly good with it.... Once you are operating in a particular area, and your cover is blown, then you move on.What scars remain? What strengths did you gain?The easiest way is not even to think about it. The strengths are self-reliance. There are different ways of doing science. What we like to do [at this lab] is do it all ourselves.... To me, it's impor

Research

Rice of Life

Compiled by Brendan MaherWhen the United Nation's Food and Agriculture Organization chose to dedicate 2004 as the International Year of Rice, it set as a theme, "rice is life," and with good reason. Rice supplies 20% of the world's nutritional energy and is a staple food for more than half the population. In some Southeast Asian countries, it contributes more than 50% of dietary energy. Nearly 1 billion households in Asia, Africa and the Americas depend on rice for employment and livelihood; and

CHARTING THE GENOMIC LANDSCAPE

To appreciate a natural wonder such as a mountain range or a canal system on Mars, an observer must stand back. So it is with the human genome. As annotation progresses, some researchers are stepping back to better see patterns within the sequence. In addition to offering clues about humanity's biology and origins, the research generates positive feedback where discoveries fueled by the sequence enable researchers to refine annotation.The human genome sequence is providing a broader, aerial view

The Adaptive Gap

AFFILIATION RELATION© Newsquest Media GroupJoining the crowd may be an evolutionarily productive practice. And people will often band together by whatever means available. In a 2001 study, for example, John Tooby and colleagues concluded that no part of the human cognition is designed to encode race as a group identifier (not the case with age or gender). During humans' evolutionary history, the researchers reasoned, people did not often encounter other races. As they showed using team jers

Inside Two Brains at Once

THINKING ABOUT ROLESCourtesy P. Read MontagueThe brain images show activity for two subjects engaged in a social exchange. The difference in activity may be a result of their different roles in the context of the task.Today's imaging technology can practically gauge brain activity in real time. But scans of a single brain don't offer much information about real life, according to P. Read Montague. "There's a reason that you don't have a cocktail party one person at a time," says Montague, profes

Hot Paper

RICE GENOME RISING

David Nance ARS Image GalleryMore than half of the world's population depends on rice as a principal source of calories and nutrition. And from a scientific perspective, the genome of this prolific grain offers clues for others, including corn, wheat, and barley. While its cereal cousins dwarf rice's 400-Mb genome, nearly all of the proteins found in these other staples have homologs in rice. As such, rice serves as a model for all cereal agriculture. Unraveling its code may enable scientists to

Briefs

Lost in Division

Courtesy of Steve Scadding and Sandra AckerleyResearchers aren't sure whether chromosomes maintain their place in the nucleus through mitosis or get lost in the shuffle. Biochemist Wendy Bickmore says it's the latter. Last March, two German research teams reached opposite conclusions about the heritability of chromatin organization – where chromosomes are within the nucleus and in relation to each other.1 Now Bickmore and colleagues in the Medical Research Council's Human Genetics Unit, Ed

Journal Entries From the Heart

Courtesy of Chrissa KioussiLike ants marching to an unspoken command, embryonic heart cells follow distinct orders for organ formation, according to a group at the Pasteur Institute. Although many cardiac regulator genes have been isolated, researchers do not understand the cellular mechanisms that form a four-chambered heart from a simple tube. To track dividing cells in an embryonic mouse heart, researchers in Margaret Buckingham's lab created a transgenic line harboring an inactivated reporte

Neurons

The copiousness of the Drosophila Down Syndrome cell adhesion molecule (Dscam), puzzles geneticists. Through alternative splicing, Dscam can produce 38,016 unique protein isoforms. Yet, no one has discerned a reason for such bounty. Andrew Chess and postdoc Guilherme Neves, at the Whitehead Institute for Biomedical Research, suggest that Dscam variants may serve as identity signatures to help individual neurons discern self from non-self.1In the study, microarray data revealed temporal and spati

Software Watch

Bioperl Unveils Version 1.4

Most bioinformatics programs churn out raw text files bursting with data, but devoid of interpretation. Programmers spend much of their time slogging through these files-computationally speaking – to extract useful information. For nearly 10 years, the bioperl project http://www.bioperl.org has labored to relieve bioinformaticians of this burden, building an object-oriented toolkit that handles the nitty gritty of data format and access so that developers can concentrate on their bioinform

Patent Watch

Prion-Detection System Patented

One of the problems in detecting prions is that the infectious agent is just a conformational isomer of a normal "self" protein. Typical diagnostic approaches, such as looking for tell-tale antibodies or nucleic acids, therefore won't work. The successful approach exploits conformational differences between the two protein variants, says Jiri Safar of the Institute for Neurodegenerative Diseases at the University of California, San Francisco. Safar and Stanley Prusiner, who won a Nobel Prize for

Gadget Watch

And They Even Tell Time!

Courtesy of ThinkGeek, Inc.This week's Gadget Watch features ... watch gadgets. The Antidote Watch, manufactured by Android, features a pill-sized "secret" compartment for storing pharmacologics, breath mints, small insects, or whatever suits your fancy. As an added plus, this analog time piece's face changes color according to body temperature, offering a convenient alternative to bulky, uncomfortable mood rings. A great gift for a tense coworker: an accessory that diagnoses anxiety and treats

Technology

Desktop Drug Discovery

Erica P. JohnsonImagine being able to discover the latest blockbuster drug using nothing but a PC and some highly sophisticated software. It's not as far-fetched as it sounds. A growing number of labs – both industrial and academic – are going "in silico," simulating everything from cells to clinical trials. The result is a sea change in pharmaceutical research, with resources once earmarked for bench work now being shunted into central processing unit clock cycles.This shift in focu

Cell Culture Automation

READY WHEN YOU ARECourtesy of The Automation PartnershipAutomated tissue culture systems, like the SelecT automated mammalian cell culture system shown here, provide a level of plate-to-plate uniformity that can be difficult to achieve manually. And because the systems work 24/7, they can have assay-ready plates available early on a Monday morning.Much has been written of how robots have been used to streamline drug development efforts. Robots never vary their routines, never tire, and never mak

Tools and Technology

New Hydrogel Aids Protein Chip Development

ANATOMY OF A HYDROGELReprinted with permissions from Nature MaterialsA top and side view of the crystal lattices of the hydrogel shows the interdigitated biomolecular structure. Grey: carbon; red: oxygen; light blue: nitrogen; dark blue: oxygen of water molecules. The red dashed lines represent hydrogen-bonding networks.Put a piece of DNA on a clean, DNAase-free piece of glass, and it will probably still be there in its original state hours later. Proteins, though, are much less forgiving. They

A Springboard to Easier Bioassays

Courtesy of ProtiverisSurface plasmon resonance (SPR), today's dominant bioassay technology, abolishes the need for chemical tags to identify targeted molecules. But the technique is gaining some competition. Rockville, Md.-based Protiveris's new VeriScan 3000 bioassay reader offers a cost-competitive alternative using microcantilevers that not only may be easier to use but also can read as many as 64 different samples at once.One edge of a 25-millimeter chip bears a series of silicon filaments,

High-Throughput Cell Motion Detector

Courtesy of ReifyHigh-content imaging systems for cell-based assays have proliferated in the past year, but so far none of the systems available allows users to directly quantify dynamic processes such as muscle contraction or cellular migration. To analyze these events, users generally have to monitor the cells throughout the course of the experiment. But a new imaging system developed by Cambridge, Mass.-based Reify http://www.reifycorp.com promises to change all that."The approaches that are

Data Points

Innovation's Rewards

Patent PowerhousesCompiled by Francesco FiondellaInstitutions that received the most license income in fiscal-year 2002Banking on InventionInstitutions which got back the highest percentage of their research spending as license income in fiscal-year 2002. Pies are proportional to the institution's research expenditures.Science by the People, for the PeopleResearch expenditures for US universities, hospitals, and institutes equaled $37 billion in fiscal year 2002; most of the money came from fede

Profession

Stealth Stipulation Shadows Stem Cell Research

A mid the flurry that followed the United States Congressional winter 2003 recess, the presidential primaries, and the debate over this year's budget, lawmakers gave final approval to 30 words that could have far-reaching consequences for the scientific community. With few hearings, and scant review or debate, Congress sanctioned a plan that forbids the US Patent and Trade Office (PTO) to issue patents on human organisms.1While seemingly innocuous – after all, the federal government has lo

Butler's Last Stand

On Wednesday, March 10, Thomas Butler, the Texas Tech University researcher convicted last December of fraud and improperly shipping plague samples, is scheduled to be sentenced in a US District Court in Lubbock, Texas.Found guilty on 47 counts, Butler, a plague expert, faces sentences that when added together, total 315 years, and he may be ordered to pay more than $100,000 (US) in fines. "[He] took extraordinary steps to conceal contracts from his employer, pocketed the proceeds from those con

Arm and Wrist Injuries Teach Scientists to Accept Limits

Courtesy of VistaLab TechnologiesMatthew Springer learned to take breaks and rest his hands after suffering two repetitive-motion injuries. "I ended up with two basically useless arms." In constant pain, he says, he could not type for more than a few seconds or do simple tasks like grasp a steering wheel.The injury sent him to physical therapy and he followed a prescribed regimen for a full year. He also practiced yoga, and learned to manage stress. With help from colleagues, who took over his m

Postdoc Talk

Three-Minute Activism

My foray into political activism began after reading a letter from The Scientist that responded to an article extolling the wealth of knowledge available to postdocs and implying that poor postdocs should be happy that we have been provided opportunities to learn interesting things.1 That article hit a raw nerve. Written by a fellow postdoc, it made me realize that we have been bred to be compliant, nonconfrontational, and abuse friendly. Wealth in knowledge indeed!Weeks after my response letter

Science Rules

Fight About Fees Unites Foes

File PhotoAboycott over the high price of online access to scientific journals has turned into a rolling protest with faculty and administrators, for once, on the same side of a budget battle.By last month, Harvard University, Cornell University, Duke University, North Carolina State University, and the University of North Carolina at Chapel Hill had all joined the movement that started in 2003 at the University of California, San Francisco. The schools' faculty took a hard line in contract nego

Closing Bell

Your Robot is Ready!

As your sales rep for US Lab Robotics Inc., here's an update about our most recent models. We've come a long way since UK researchers built the first science robot. In hindsight, that first model was rather primitive. To quote its designers, it "automatically originates hypotheses to explain observations, devises experiments to test these hypotheses, physically runs the experiments using a laboratory robot, interprets the results to falsify hypotheses inconsistent with the data, and then repeats