July 2006

Volume 20 Issue 7

The Scientist July 2006 Cover




David Baker is professor of biochemistry and an HHMI investigator at the University of Washington. When he started there in 1994, the problem of "computing the structures of naturally occurring proteins and designing brand new ones [was] considered to be almost impossible," he says. His group has since created ROSETTA, a program that searches for lowest energy structures to do just this, and on page 34 he describes how it's being used to design an endonuclease to attack malaria


Zealots for Science

Being mindful of the extremes, science can remain a pursuit of reality.



The future of scientific meetings One of the very wonderful meeting formats, not mentioned in your story on the future of scientific meetings,1 was that of Kroc conferences, sponsored by the Kroc Foundation. The meetings allowed only 24 participants and met in the Double Arches Ranch near Solvang, California. There was a free-flowing bar, and ideal arrangements for continuing discussion between participants. The overall director of the meetings was Bob Kroc, Ray's brother


Proteomics in the kitchen

Credit: © ISTOCK.COMwww.ISTICK.COM" /> Credit: © ISTOCK.COMwww.ISTICK.COM When you're buying fish, you probably look at its color, smell it, and perhaps feel it for texture. If Martine Morzel has her way, you might also perform a mass spectrometry profile. Morzel, of the French National Institute for Agronomic Research, was interested in what effects preslaughter activity have on the quality of resulting fillets. In typical farming practice, trout kept in a large

The Agenda

The Agenda

Credit: © SCIENCE PHOTO LIBRARY" /> Credit: © SCIENCE PHOTO LIBRARY DOLLY TURNS 10 >> Had she lived, Dolly, the sheep cloned from an udder cell's nucleus, would have turned 10 on July 5. After Dolly: The Uses and Misuses of Human Cloning, by lead author on the 1997 announcement of Dolly's birth, Ian Wilmut and journalist Roger Highfield was released last month. BCG VACCINE TURNS 85 >> On July 18, 1921, Albert Calmette and Camille Guerin of the Pasteur Institut


An Archaeal pathogen?

AN ARCHAEAL PATHOGEN? X-ray from a necrotic tooth containing a periapical bone lesion Credit: COURTESY OF MORGANA ELI VIANNA" />AN ARCHAEAL PATHOGEN? X-ray from a necrotic tooth containing a periapical bone lesion Credit: COURTESY OF MORGANA ELI VIANNA The rogue's gallery of human pathogens is filled with members of the Bacteria and Eukaryota domains of life. Notably absent is the third domain: Archaea. According to a recent report in the Journal of Clinical Microbiology, however,

No intelligent design, no $

The last thing McGill University professor Brian Alters expected upon opening a letter late in March was to see his latest $40,000 Canadian ($36,400 US) grant rejected for not providing enough evidence to support a theory he'd made a career of defending: evolution. Alters had applied for funds from Canada's Social Sciences and Humanities Research Council (SSHRC) to study the effect of intelligent design debates in the United States on Canadian students, teachers, administrat

Biology fights computer viruses

Credit: GETTY IMAGES" /> Credit: GETTY IMAGES It's a jungle out there on the Internet. With countless viruses, applets, and attachments on the loose, you might say that the systems designed to protect our computers are facing the kind of challenges that confront animal immune systems in a crowded environment. That's why Stephanie Forrest, a professor of computer science at the University of New Mexico, Albuquerque, calls this "computing in the wild." She argues that c

The death of biology

At Harvard, biology is an endangered species. Next fall's wide-eyed freshmen will have to head down the street to Massachusetts Institute of Technology if they want to concentrate (Harvard-speak for major) in the subject, because it will no longer be offered in Harvard Square. This change was puzzling to my editor, who concentrated in biology at Harvard, and to me, a 2005 graduate with a degree in biochemistry. So I consulted Robert Lue, my former advisor and cochair


'HeLa' Herself

Celebrating the woman who gave the world its first immortalized cell line


The Chief of Bioethics

Why the fact that bioethics is difficult to explain is a positive development.


Proteins by Design

FEATUREProteins by Design New functional proteins are being built on advances in modeling and structure prediction BY DAVID BAKER REPROGRAMMED: This is the structure of the endonuclease I-MsoI computationally redesigned to target a new DNA site. The redesigned enzyme displays altered site specificity with a level of target discrimination comparable to that of wild type (see ref. 8). Such methods are currently being a

A Complementary Pathway

FEATUREComplement How one group of researchers brought a scientific idea to the clinic for a rare diseaseBY ISHANI GANGULI © THOM GRAVES Scott Rollins was starting his graduate thesis at Oklahoma Medical Research Foundation in the late 1980s when he first heard about paroxysmal nocturnal hemoglobinuria (PNH). He learned that in PNH, red blood cells are vulnerable to attack by the complement system's terminal membrane-attack complex. Pat

Margarita Soto: A life with PNH

FEATUREComplement   Margarita Soto: A life with PNH BY ISHANI GANGULI ARTICLE EXTRAS Related Article: A Complement PathwayA Complement RenaissanceInfographics: Interrupting ComplementPaths to Market Margarita Soto had her first blood transfusion to treat her anemia at the age of 16, when she was pregnant with her second child in Puerto Rico. She began to notice her urine was dark soon after, an


Margarita Soto: A life with PNH

FEATUREComplement Margarita Soto: A life with PNH BY ISHANI GANGULI Margarita Soto had her first blood transfusion to treat her anemia at the age of 16, when she was pregnant with her second child in Puerto Rico. She began to notice her urine was dark soon after, and by the age of 18, in the worst of her hemolytic episodes, pain and exhaustion from her anemia kept her from walking up stairs, let alone playing volleybal

A Complement Renaissance

FEATUREComplement A Complement Renaissance  BY M. KATHRYN LISZEWSKI AND JOHN P. ATKINSON ARTICLE EXTRAS Related Article: A Complementary PathwayHow one group of researchers brought a scientific idea to the clinic for a rare diseaseInfographics: Interrupting ComplementPaths to MarketWeb Extra:Margarita Soto: A life with PNH More than 600 million years ago, primitive components of the complement system lik

Living Batteries

FEATUREFuel Cells Using sugars, sludge, and the sea floor, can bacteria power the next green-energy alternative? BY JACK LUCENTINI When Bruce Rittmann got a $100,000 NASA grant two years ago to find ways for converting human excrement and other organic waste into electricity in spacecraft, he prepared to reach for the stars. When the space agency cut research funding, his ambitions became a bit more grounded. Usin

Taming Electricigens

FEATUREFuel Cells Taming Electricigens How electricity-generating microbes can keep going, and going - fasterBY DEREK LOVLEY Electricigens, the microbes that can completely oxidize organic compounds to carbon dioxide and then transfer the electrons derived from that oxidation onto the anode of a microbial fuel cell, are the Energizer Bunnies of the microbe world. They gain energy to support their growth and metabolism from

A Nasty Mother

FEATUREChallenging Nature © Bill Sanderson/Photo Researchers, Inc. Think only the religious right is anti-science? How about the spiritual left? BY LEE M. SILVER To be alive as an organic organism on earth, you must have access to water. On most land areas, water availability varies from month to month and year to year. As a result, the form and number of living things is greatly limited. In the Amazon rainforest, however, getting wate


Farewell to Babel

Will science become monolingual?


The Network Within

Ilya Shmulevich brings creative computation to deciphering gene regulation

Hot Paper

The Big Picture in Microbial Genomics

A revolution aids the study of unculturable microorganisms

Books etc.

Ubiquitin's duality

Ubiquitin does more than mark proteins for degradation. In 2004, Ingrid Wertz, a University of California, Davis graduate student, and advisor Vishva Dixit of Genentech, demonstrated that the protein A20, which was known to downregulate tumor necrosis factor á (TNFá) signaling, has both an ubiquitin ligase domain and a deubiquitinating domain.1 Wertz, now at the University of Washington, St. Louis, says she found the presence of these opposing functions disconcerting: "I was thinking, h

Stem cell woes

Credit: © YORGAS NIKAS/PHOTO RESEARCHERS" /> Credit: © YORGAS NIKAS/PHOTO RESEARCHERS Scientists once believed that human embryonic stem cells were extraordinarily stable in culture. In 2004, Peter Andrews at the University of Sheffield, UK, and colleagues revealed definitive evidence that lines can develop chromosomal abnormalities.1 Sheffield's group discovered three independent human embryonic stem cell lines that gained chromosome 17q on five independent occasions,

Pollutants travel North

Credit: © MATTHEW ANTONINO" /> Credit: © MATTHEW ANTONINO Manufacturers use fluorinated organic chemicals in a variety of coatings on fabrics and paper plates and in fire-fighting foams. Now, these extremely stable compounds are showing up all over the globe. In 2004, Scott Mabury's group from the University of Toronto published a paper demonstrating perfluorinated contaminants in Canadian wildlife, from fish to fowl to fur, with highest concentrations at the top of the food chai


I. Coppens et al.," Toxoplasma gondii sequesters lysosomes from mammalian hosts in the vacuolar space," Cell , 125:261-74, April 21, 2006. This outstanding paper shows that the intracellular protozoan Toxoplasma gondii exploits host microtubules to recruit and sequester host lysosomes into the parasitophorous vacuole. Through this process, the parasite gains access to host organelles that can provide a source of low-molecular-weight nu


Pushing plasticity


Cdk fashions

Books etc.


Katherine Fitzgerald: Waiting, but not in vain

Lab Tools

Give P2P a Chance

Why you should be using peer-to-peer networks to share your data.

Which Transcription Factor Assay Should You Use?

Five ways to match DNA sequences with their cognate binding proteins

How It Works

Atomic Force Microscopy

https://www.the-scientist.com/article/flash/23821/1/ Click to view enlarged diagram Credit: ILLUSTRATION: ANDREW MEEHAN" />https://www.the-scientist.com/article/flash/23821/1/ Click to view enlarged diagram Credit: ILLUSTRATION: ANDREW MEEHAN Invented in 1986 atomic force microscopy (AFM) has become a valuable tool for life scientists, offering the ability to image aqueous biological samples, like membranes, at nanometer resolution. The technique is akin to


The Art of the Tech Transfer Deal

When considering a relationship with industry, anticipate the worst.

An Ideal Balance

One institute's funding formula

Public Concern for Private Funding

The source of research dollars is shifting. Will this affect the direction of academic research?

Patent Peer Review

The US Patent and Trademark Office is evaluating an online peer review initiative that would invite scientists and other outside experts to help evaluate patent applications by advising the PTO about prior art - published literature and other patents - that the patent office's examiners might otherwise overlook. The goal is to improve the quality of patent review and reduce the backlog of applications. "The patent office desperately needs more and better information to make decis

More Drugs Pushed into Trials

Between 2003 and 2005, big pharma companies placed 52% more new drugs into clinical trials per year than in the prior five-year period, according to a study by the Tufts Center for the Study of Drug Development (CSDD). The CSDD included only new entities in clinical trials since 1993 (generics, new formulations of old drugs, or new indications for existing drugs were excluded), as determined according to total drug sales in 2004. The study addressed corporate merger activity by adding d

What's in a Name?

A survey of 1,054 life scientists uncovered a marked affinity for recommending brand names to colleagues rather than competing brands with less market cachet. The study - "Maximizing Market Share Through Brand Differentiation" - focused on differentiating reagents, instruments, and lab supplies by quality, service, or price. Santa Clara, Calif.-based gene chipmaker Affymetrix took top honors as most differentiated brand. New England Biolabs, an Ipswich, Mass.-based maker of

The Scientist

Buyer's Market

Current employment options favor companies as well as less-experienced workers.

Making Your Case

How to avoid the biggest presentations mistakes.


The First Immortal Cell Line

Credit: COURTESY OF TERRY SHARRER (FLASK), GRETCHEN DARLINGTON (INSET)" /> Credit: COURTESY OF TERRY SHARRER (FLASK), GRETCHEN DARLINGTON (INSET) Growing cells outside the body began in 1907 with the work of Ross Harrison at the Johns Hopkins School of Medicine, and continued in the hands of Alexis Carrel and Montrose Burrows at the Rockefeller Institute. These investigators figured out the nutrient solutions that kept cells alive for extended periods of time and allowed them to

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