The Nutshell

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Hollywood Science

By | October 10, 2005

What if the 20-somethings on Friends were scientists? Columbia biology professor Darcy Kelley insists it could work. ?We?re just like regular people,? added Nobel laureate and Memorial Sloan Kettering director Harold Varmus. But does the rest of the country, perspectives shaped largely by the lenses of filmmakers, see scientists this way? Or are we pegged as either absent-minded superheroes or evil manipulators of human fate? Such was the topic of debate this week at the 20

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In Dover: what she said, and what he wanted to say

By | October 6, 2005

Barbara Forrest, Southeastern Louisiana University philosophy professor testified in the case against Dover?s school board adding intelligent design to the science curriculum yesterday and today. School district attorneys had opposed the testimony, and possibly for good reason. She outlined the Discovery Institute?s ?wedge strategy? and presented a substantial smoking gun in early versions of the book Of Pandas and People to which Dover students are referred to in the paragraph teachers must r

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Bringing Biology to the Office

By | October 5, 2005

The latest e-TOC from the journal Bioinformatics contains an application note on a really cool tool. ProTag is a Microsoft Office extension that uses biological name and markup services called ProThesaurus and LiMB to find protein names and database identifiers in Word, Excel, and Powerpoint documents. From there, you can perform a range of actions on that text, all without ever leaving the Office. So, for instance, if you type the phrase ?TIM4_HUMAN is the SwissProt identifier for tissu

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End of Week One

By | October 1, 2005

Yesterday marked the conclusion of the first full week of trials over the Dover, PA School Board?s decision to include intelligent design in the science curriculum. This week was devoted to the plaintiffs? witnesses. Lawyers questioned Drs. Kenneth Miller, a Brown University cell and molecular biologist, Robert Pennock, professor of science and philosophy at Michigan State, and Jack Haught, professor of theology at Georgetown University. The professors ? presumably picked from hundreds of scien

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ERCC Issues a Call to Arms

By | September 30, 2005

Microarray data quality is an issue that has been covered extensively in The Scientist (see, for instance, here and here). The basic issue is this: how reliable are the sometimes-subtle changes in gene expression levels these experiments yield, and how reproducible are they. The External RNA Controls Consortium, an ad-hoc group with approximately 70 members from private, public, and academic organizations formed in 2003, is one of several groups working to address these questions. The Consort

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ID Crushes First Amendment Rights, Again!

By | September 28, 2005

A second first amendments rights case broke out amidst the brouhaha over the legality of teaching intelligent design in a Dover school district. But this battle, over the freedom of the press, is nearing a denouement that?s left me a bit ambivalent. The Thomas More Law Center, which has been defending the Dover school district had subpoenaed two freelance reporters, Joseph Maldonado for the York Daily Record and Heidi Bernhard-Bubb for the York Dispatch, to question them regarding the details of

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No United Front for Intelligent Design

By | September 28, 2005

In the weeks before the battle over first amendment rights ramped up in Dover, the Discovery Institute folks said they didn?t support intelligent design mandates in science curricula, saying that such cases will only be politically divisive. Now, lawyers representing the school board are apparently happy to hear it. The York Daily Record, which has nicely covered some of the dismay experienced by a small town under the media heat lamp and now listed as the Number One Island of Ignorance by on

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The Human Interactome, Take 2

By | September 28, 2005

Four weeks after Erich Wanker?s team published its human interactome paper, Marc Vidal?s group at the Dana-Farber Cancer Institute in Boston has followed suit. In today?s (Sept. 28) online edition of Nature Vidal?s team reports its analysis of interactions between 8,100 or so human open reading frames corresponding to some 7,200 protein-coding genes. From that ?search space? of 7,200 x 7,200, or nearly 52 million combinations, the group used a high-throughput yeast two-hybrid approach to ide

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Intelligent design in thirty minutes or less

By | September 26, 2005

Looks like I can harden my reserve to never again eat Domino?s pizza ? not that I liked it much anyway. The Thomas Moore Law Center, founded by ?za magnate Thomas Monaghan, is representing the defending Dover school board that tried passing off intelligent design as real science. As a card carrying Pennsylvanian, I?ll be closely watching the proceedings in our neighbor county. But I actually have little faith that the A.C.L.U. will be able to successfully convince district judge John E. Jones

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Plague in New Jersey?

By | September 17, 2005

On Thursday, the Associated Press reported that mice carrying Yersinia pestis ? the bacteria that cause bubonic plague -- had disappeared from a laboratory at the Public Health Research Institute, part of the campus of the University of Medicine and Dentistry of New Jersey. The university says it does not know what happened to the mice, first discovered missing two weeks ago. According to the AP, health experts reassured that there was ?scant public risk.? That?s not what Robert Brubaker,

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