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PubMed unchained. And, Oh, no, not another 'Ome!

By Jeff Perkel | November 1, 2005

I found two cool new tools today. The first, via Sourceforge, is PuMA, a standalone Java front-end to PubMed. PuMA (currently at version 1.0alpha) allows you to view bibliographic search results and abstracts in the same window, visually construct complex Boolean queries, and export data to EndNote, Reference Manager, ProCite, and BibTex. It also offers keyword highlighting, links to Google and Google Scholar (for instance, to find articles citing another's work), and an intuitive user interface

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?Why do people get sick? Science close to answer?

By Tabitha M. Powledge | October 28, 2005

Yeah, right. That?s the assessment on the just-published hapmap papers from a headline writer at, the Web site for several newspapers in the region. And the headline writer is not alone; the story that follows is pretty uncritical too. This reflexive applause?and there were other enthusiastic media reports about this latest analysis of the human genome--generates ridiculous expectations of immediate cures. That?s bad news for scientists who can?t possibly meet them. It?s lou


Cool to some, cruel to others

By Alison McCook | October 28, 2005

It?s important to recognize that consumer-friendly news reports about a promising new technology that?s years away can be somewhat torturous for people with conditions that need that technology now. Case in point: I know someone with a progressive and debilitating neurological disease who asked me the other day to contact a researcher she read about in Newsweek, who implanted a silicon chip into the brain of a person paralyzed from the neck down. The chip enabled the participant to direct a c


Terrorists, Pedophiles, and now Darwin?

By Brendan Maher | October 27, 2005

In a previous post, I said that the Dover school system needs more than a bake sale to get over its issues. I was referring to a fundraiser set up by the political action committee Dover CARES (Citizens Actively Reviewing Educational Strategies). This group is trying to displace the school board that introduced intelligent design into the science curricula thereby dragging the small town through a knock-down, drag-out, First Amendment case ? one that challenges no less than the tenets of scien


Reducto ad absurdum on the LANL ASCI Q?

By Jeff Perkel | October 25, 2005

A research team at Los Alamos National Laboratory has topped a world record for biological simulations, and given us a taste of reducto ad absurdum. As reported in the Nov. 1 issue of PNAS the LANL team, led by Kevin Sanbonmatsu, used 768 of the 8,192 CPUs in LANL's ASCI Q supercomputer to model the motion of 2.64 million atoms in a ribosome complex -- 250,000 in the ribosome itself, and most of the rest from water molecules. The processors chugged away for some 260 days, completing 20 milli


The Dover Downs

By Brendan Maher | October 24, 2005

We?ve finally seen the first full week of witnesses for the defense in Kitzmiller vs. the Dover area school board. Lawyers defending the board called intelligent design shogun, Michael Behe. The biochemist, unsupported by his Lehigh University employers, argued for three days that ID is not creationism ? that ID doesn?t specify a creator, leaving room for a god or gods, past or present, that must have gotten this whole crazy thing started. But oddly enough his ?because-I-said-so,? argument ac


Who teaches us what to eat?

By Alison McCook | October 20, 2005

Everyone?s had the frustration of reading something is good for you one day, then bad for you the next. The same mixed message is now being circulated about fish. On Friday, I participated in a panel discussion in Washington DC hosted by the National Consumer?s League about how to resolve this situation. We, the panelists, were asked to explore the responsibilities of journalists, researchers, and policymakers in disseminating the complex message that fish is very good for you, but some people ?


Discontent at GSAC

By Brendan Maher | October 19, 2005

It should be hard to complain in Hilton Head when the weather?s this nice, but a few folks have found a reason. J. Craig Venter voiced his discontent, yesterday evening at this year?s GSAC (a.k.a. Genomes Medicine and the Environment 2005). Groups aren?t moving fast enough toward the $1000 genome. So, to grease the wheels he?s upping the ante on the $500,000 prize he promised to the first group to achieve a human genome for a grand. In an impromptu announcement, he referred to the logo o


Genomes small, and getting smaller

By Brendan Maher | October 18, 2005

GSAC is back, although the annual genomics meeting this year goes by the name Genomes, Medicine and the Environment Conference 2005. Now under the purview of the J. Craig Venter Institute rather than the institute for genome research (TIGR), it has returned to Hilton Head, and is slightly smaller than it?s been in past years. But that?s not a bad thing. ?It?s good to see things going back to science as usual,? said J. Craig Venter in the opening session yesterday. Sporting a black t-shirt wit


Chris Mooney's "The Republican War on Science" showed up on my desk recently. The book traces the rise of the Republican Party's split with science, from its roots in the supersonic transport debate in the Nixon administration, to George W. Bush's assault on science today, covering science issues from Reagan's "Star Wars" initiative to "intelligent design," global warming to stem cells. From what I read Mooney seems to come across as a bit of a zealot. In the first chapter, for instance, he w


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