Biocurious is a weblog about biology, quantified.

Reciprocal space-cadets in Science

by PhilipJ on 26 January 2007

We didn’t blog about this when it happened (perhaps part of me felt bad for the poor graduate student or postdoc that missed this bug in the code of a homebrewed x-ray diffraction analysis program). To bring everyone up to speed, from the 2006 December 22 issue of Science, crystallographer Geoffrey Chang retracted five papers in total, three of which from Science:

In September, Swiss researchers published a paper in Nature that cast serious doubt on a protein structure Chang’s group had described in a 2001 Science paper. When he investigated, Chang was horrified to discover that a homemade data-analysis program had flipped two columns of data, inverting the electron-density map from which his team had derived the final protein structure. Unfortunately, his group had used the program to analyze data for other proteins. As a result, on page 1875, Chang and his colleagues retract three Science papers and report that two papers in other journals also contain erroneous structures.

Entirely by accident, a significant amount of time and effort has been wasted by these erroneous structures. It became difficult for people doing less flashy work on these molecules to get papers published when their results were incompatible assuming the structure originally published by Cheng’s lab was correct.

Regarding this mix up, a scathing letter was published in this week’s Science, reminding everyone not to ignore good old fashioned biochemistry, particularly in the face of pretty pictures:

The mistake so clearly illustrates two lessons that we aging baby boomer professors ram down the throats of our proteomically aroused graduate students: (i) that those lovely colored ribbons festooning the covers and pages of journals are just models, not data, and (ii) that you invite disaster if you don’t know what your software is actually doing down there in the computational trenches. Students have a hard time subsuming these dicta into their souls for two reasons: the tyranny of authority (the vanity journals occupying the vanguard) and the inherent beauty of the macromolecular models that emerge, as if by magic, from the user-friendly crystallographic software accumulated over decades through the generous labor of the field’s talented reciprocal space-cadets. This case highlights the dangers of ignoring biochemical results, conventional but logically solid, as was done in the original papers and as is now outlined in the politely flaccid news report published along with the retractions.

I particularly like the swipe at Science as a vanity journal.

  1. Mark Adams    3683 days ago    #

    Yikes! And Bill Tozier was just going on the other day about the need for unit testing in scientific computing.

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