Issue | November 2004 | November 2004 | The Scientist Magazine®

Editorial

Dateline: 8 November 2004. In a few days time we will proudly launch our upgraded Web site and with it the first daily online newspaper for the life sciences, The Scientist Daily. Simply register your preferences at http://www.the-scientist.com and enjoy The Scientist Daily every working day, delivered electronically to your mailbox completely free of charge.As you'd expect from your favorite newspaper, The Scientist Daily will include:• Breaking news. Our extensive network of contributors

Opinion

Downsizing the Status of Science

Contemporary Western society has a love-hate relationship with scientific knowledge. We pursue it and celebrate it, employing people to gain knowledge of our genetic makeup, market conditions, or the nation's mood. Often we complain that we lack sufficient knowledge to find a cure for AIDS or for minimizing the consequences of global warming. Outwardly we take knowledge very seriously, with expressions like 'knowledge is power.'Yet, society is uncomfortable with the pursuit of knowledge, and oft

Letter

Organic Food Placebo: Three Take Issue

The issues surrounding conventional versus organic farming are many and complex, encompassing environmental protection and biodiversity, animal welfare, sustainable development in poorer countries, and the avoidance of risks to human health such as those presented by antibiotic resistance.Each of these questions has both scientific and political dimensions, and all of them are areas of incomplete knowledge and ongoing debate and research.In an ideal world, we could pick and choose the properties

The Ultracentrifuge

You really do not get to appreciate the engineering that goes into the ultracentrifuge1 until you have a rotor failure. While I was a grad student at UT Austin, our SW-65 Ti rotor spilt apart at 65K. It powdered the refrigeration can, pretzeled the stabilizer bar, trashed the temperature probe and speed control, bent the top chamber cover, and put a 3/8-inch gouge in the chamber armor. Yet all that flying metal was contained in the rotor chamber. Five days of labor by the Beckman service rep, an

Notebook

Egging on the flu vaccine

The October 5 announcement by the Chiron Corporation that it could not ship nearly half the US supply of influenza vaccine has trained a spotlight on the vaccine production process. The ensuing public frenzy was abetted by a frightening flu season last year, stronger CDC recommendations on infant immunization, the looming threat of avian flu, and a harder push from public health groups for vulnerable populations to get immunized.The shortage, say experts, illustrates the drawbacks of relying on

Tales from the cryptozoologists

The Loch Ness monster and the Sasquatch are as elusive as ever, but rumors of cryptozoology's demise may be exaggerated.French zoologist Bernard Heuvelmans coined the term cryptozoology in the late 1950s to describe the study of unverified animals that turn up in sighting reports, explorers' accounts, archeological artifacts, and folklore. Back in 1993, The Scientist reported that cryptozoologists, the scientists who try to track down previously undescribed animals, were becoming an endangered s

Research

Structured Water Is Changing Models

Courtesy of Martin ChaplinWater molecules cluster to form hydrogen-bonded bicyclo-octamers (H2O)8 (top left) that can link together into larger structures (top right). Ideally they form 280-member icosahedral clusters, (H2O)280, (below), shown looking down the two-fold, three-fold, and five-fold axes of symmetry. Only the oxygen atoms of the constituent water molecules are shown (except at top left).Researchers are beginning to glimpse water's secret social life. Evidence is mounting that water

"Big Cross" Lands Sticklebacks in the Spotlight

Marine threespine sticklebacks haven't morphologically changed in an estimated 10 million years, but their freshwater offshoots show no signs of slowing down. These 5-cm-long, freshwater fish have undergone a recent evolutionary change, variably losing their calcified body armor and retractable pelvic and dorsal spines. Remarkably, isolated marine and freshwater sticklebacks can be hybridized in the laboratory, a fact that is allowing researchers to analyze the genetics behind their natural dive

Hot Paper

Turning the Tuberculosis Bacterium Lineage on its Head

Courtesy of Roland BroschThe regions absent from the attenuated vaccine strain Mycobacterium bovis BCG Pasteur relative to the M. tuberculosis H37Rv genome are shown as gray boxes. Open reading frames (ORFs) are represented as pointed boxes showing the direction of transcription, with colors reflecting the functional classification of the ORFs similar to the ones on the TubercuList server http://genolist.pasteur.fr/TubercuList/.Not long after the genome sequence of Mycobacterium tuberculosis was

Vision

A Battle Cry to Decipher Immunity

Courtesy of Luke A. O'NeillLuke A. O'NeillThe march to demystify mammalian immunity has been long and arduous. At the frontlines we face a dizzying array of biochemicals and interactions between multiple cell types aimed at detecting, eliminating, and remembering intruders. The regulation of this system often appears impenetrable.But recent advances in our understanding of innate immunity – that hard-wired, first line of defense that doesn't appear to adapt during infection – have se

How to Launch a Biotech Success

Christoph H. WestphalCourtesy of David Shopper PhotographyMost people say this is an industry driven by how much money a drug, such as Lipitor, can bring in. I would argue that Lipitor is a great molecule, but it's the people who made the molecule the number-one selling drug on the planet. It took a talented team of chemists, clinicians, marketing executives, and regulatory experts to drive it to $4 billion in sales. The original discovery of a target is a small part of the value chain; you need

Briefs

Inclusion Bodies Acquitted

Courtesy of Steven FinkbeinerInclusion bodies play a protective, not pathogenic, role in Huntington disease, according to a recent study by Steven Finkbeiner of the Gladstone Institute of Neurological Disease at the University of California, San Francisco.1 The paper contributes to an ongoing debate about the role of inclusion bodies – intracellular clumps of mutant huntingtin (Htt) protein – in the pathology of diseases such as Huntington and spinocerebellar ataxia.Finkbeiner and co

Edging Closer to a Malaria Vaccine

Scientists frustrated with the lack of progress toward a useful malaria vaccine may have edged a step closer to that goal with the announcement by a public-private partnership that it has created a promising candidate. GlaxoSmithKline's RTS,S/AS02A is a fusion of immunogenic components of the circumsporozoite protein with hepatitis B surface antigen, plus a proprietary adjuvant. The compound achieved a 58% efficacy against severe disease in 1- to 5-year-old children in a Phase IIb trial in Mozam

Hitchhiker's Guide to the New World

Courtesy of CDCUS researchers are looking to otherwise unwanted guests to piece together humans' evolutionary past: lice. They suggest that modern Homo sapiens may have had direct physical contact with Homo erectus in Asia before crossing over to the New World.Florida Museum of Natural History's David Reed and colleagues present evidence that the New World lineage of head and body lice coevolved with H. erectus, but switched hosts to H. sapiens around 25,000 years ago.1 The effective isolation o

Technology

Linux in the Lab

WHAT COMMAND LINE?Left: Courtesy of Pratul K. Agarwal; Right: Courtesy of High Performance Computing Facility, University of Puerto RicoUsers no longer need remember arcane command-line incantations with Linux; the OS hides its complexities beneath a snazzy user interface. Here, Linux versions of ImageJ, an image manipulation suite (top) and PyMOL, a biomolecular structure visualizer (left) are shown.On August 25, 1991, a student named Linus Torvalds at the University of Helsinki posted an innoc

Phospho-Mania

ERK1/2 ACTIVATIONCourtesy of Biosource Internationalis plainly visible in heart tissue from an MHC-Rac1 transgenic mouse (right), compared with its normal counterpart (left). Green, pERK 1/2 (pTEpY185/187); blue, actin; red, nuclei.Protein phosphorylation is one of the most widely studied posttranslational modifications, with good reason. Many cellular signaling events rely on the addition or subtraction of phosphate groups (by kinases and phosphatases, respectively) to serine, threonine, and ty

Tools and Technology

Transcription by Design

UPS AND DOWNS OF TRANSCRIPTION:© 2002 Elsevier ScienceGenomic DNA is wrapped around histone octamers to provide nucleosomes that are further compacted in chromatin fibers. To up-regulate a gene (a), the activator binds to a specific sequence and recruits various cellular machines that permit RNA polymerase and its associated proteins to bind and transcribe. During transcriptional repression (b), the repressor binds to a specific DNA site and recruits protein complexes that modify the histon

Want a Jolt of Literature? Try Textpresso!

Few research tasks are as time-consuming and tedious as scouring the scientific literature. The searcher might need only one nugget of information, yet it can take hours or days to slog through hundreds of papers before that one fact is found. Now, a new open-source tool called Textpresso http://www.textpresso.org can find a single fact just by typing in a quick search entry.Paul Sternberg's lab at the California Institute of Technology designed Textpresso to organize papers on Caenorhabditis el

Force-detection Microscopy Takes Big Steps Forward

A SINGLE-SPIN MRFM EXPERIMENT© 2004 Nature Publishing Groupcan probe spins as deep as 100 nm below the sample surface. The magnetic tip at the end of an ultrasensitive silicon cantilever is positioned 125 nm above a polished SiO2 sample containing a low density of unpaired electron spins. The resonant slice represents those points in the sample where the field from the magnetic tip (plus an external field) matches the condition for magnetic resonance. (Reprinted with permission from Nature,

High-Carb Science with Sugarcoated Arrays

© Bob CrimiComplex carbohydrates play crucial roles in biological processes as diverse as development, infection, and immunity. So naturally, the field has gone 'omic, at least in theory.1 In practice, good tools have been hard to come by.Stanford University biologist Denong Wang, formerly of the Columbia University Genome Center, set out to give glycomicists the chip capacity and manufacturing prowess that have transformed genomics. Like proteins, carbohydrates must maintain a specific thr

Scientists Get a "Do Not Call" List

Scientists are not known for staying put. With as much as 20% of the life sciences workforce switching labs each year, product manufacturers' mailing lists are as labile as proteins at room temperature.Enter i-kode http://www.i-kode.com, a new service from Nottingham, UK-based Ikon Informatix. I-kode helps scientists keep their contact information and research interests up-to-date, select vendors from which they want mailings, and gain control over their junk mail."It really puts them in control

Speeding up Real-Time PCR

Courtesy of ExiqonWith the launch of its new ProbeLibrary kits, Danish biotech firm Exiqon http://www.exiqon.com seeks to simplify real-time PCR. Typically 30 to 35 bases long, PCR probes must be ordered individually from their manufacturers. Exiqon's kits, however, based on locked nucleic acid (LNA) technology, give researchers a ready-to-use library that they can keep in their freezers. (LNAs are bicyclic DNA analogs that exhibit high thermal stability and affinity towards complementary sequen

BioBusiness

Dodging Patent Perils in Collaborations

Research collaborations often form the bedrock of truly great science. Scientific alliances can also help businesses commercialize their basic research or reveal the next blockbuster drug. In recent years, economic and competitive pressures have encouraged research collaborations between universities and industry, and between small biotech companies and Big Pharma. While these associations frequently prove to be beneficial for all parties, research collaborations can sometimes trap the unwary, c

The Process of Patenting

The cost of obtaining a patent in the life sciences is high and likely to get higher, even as a growing legal complexity and regulatory logjam lengthen the amount of time it takes to get the patent in hand."Most people don't like to hear it, but they know it is going to cost quite a bit," says Robert Hunter, a registered patent agent who practices out of Kamuela, Hawaii. "Quite a bit" generally means more than the price of a minivan but less than the sticker on a Hummer, or somewhere in the neig

NIH Proposes a One-Year Ban on Consulting

Getty ImagesA proposed ban on consulting at the National Institutes of Health might make it more difficult to translate basic research findings into new drugs and therapies, according to pharmaceutical and biotech companies, who say they will need to tap new sources to provide expert help in ongoing research. The NIH announced in September that it would seek to ban its scientists from all outside paid consulting activities with drug and biotech companies for at least one year, while the agency r

Update

Bovine Genome Map May Change Dairy/Livestock Industry

An international consortium of scientists reported the completion of a first draft of the bovine genome sequence in October. In a separate announcement, New Zealand-based BoviQuest reported it has sold the first license for two genes linked to milk production to Merial, a multinational company that produces vaccines and pharmaceuticals for livestock and pets. The two genes will be used in tests to screen dairy cows for potential milk production.The mapping of the bovine genome is poised to revol

France OKs Stem Cell Research

Two leading members of France's largest biotech trade organization, France Biotech, say the country's recent decision to allow human embryonic stem cell research moves the industry forward, but not far or fast enough to catch up with the United States and Great Britain.Alain Guedon, vice president of Paris-based France Biotech, says moral and ethical concerns will continue to hamper research despite the new law. His organization represents about 150 biotech companies. "France is pretending to be

Best Places to Work

The Best Places to Work in Academia, 2004

There are more work-related factors that unite scientists than divide them, according to The Scientist's 2004 survey on the Best Places to Work in Academia. Across the world, scientists are surprisingly uniform in their needs. Adequate laboratory and research facilities for themselves and their coworkers topped the list in just about every country. A desire for good working relationships with peers also holds a high place in the ranking.Institutions that ranked favorably in this year's survey sc

Scientists Select the Best Places in the US

The US institutions that made the top 10 list in The Scientist's 2004 Best Places to Work in Academia survey represent an interesting mix of small and large academic and private research centers from across the country. The characteristics that make them great places to work, however, are surprisingly similar.Many respondents from these campuses noted support for interdisciplinary research as one of their institution's strengths. Top-ranked California Institute of Technology in Pasadena, with on

Oh, Canada!

Canada has been putting the pieces of the puzzle together in recent years, and a pretty picture is emerging for scientists. A new focus on innovative programs and increased funding for scientists suggests that it's no fluke that for the first time, five Canadian universities are in the top 10 of The Scientist's 2004 survey of the Best Places to Work in Academia.Since the late 1990s, the research environment in Canada has witnessed "a virtual revolution," says Bruce McManus, a professor of pathol

What's Important to the Academic Scientist?

Top Factors by US & Non-US ResearchersMy institution provides adequate laboratory and research facilities for me and my coworkersI maintain good working relationships with my peersMy institution provides an adequate research funding package for new faculty membersMy institution has the resources to supply basic research infrastructure needs not covered by grantsMy institution fosters collaboration among facultyTop Factors by US Researchers OnlyMy institution provides adequate health coverage

Reverse Transcript

Think Big, Dress Casual

Mike SnyderCourtesy of Michael Marsland"We couldn't get that project funded for the life of us," says Yale University's Mike Snyder of the experiment that, in his opinion, launched the functional genomics era. It was the late 1980s, years before the dawn of DNA microarrays, and Snyder and his colleagues were proposing to use epitope-bearing transposons to tag every protein in yeast. With this collection, the scientists planned to track the positions of all 6,000 yeast proteins, information that