Pretty Structures, But What About the Data?

The “Great pentaretraction” (“A scientist's nightmare: software problem leads to five retractions,” G. Miller, News of the Week, 22 Dec. 2006, p. [1856][1]; “Retraction,” G. Chang et al. , 22 Dec. 2006, p. [1875][2]) in the wake of one of protein crystallography's greatest blunders, while an embarrassment to the authors, nevertheless provides the rest of the field with some small measure of comfort beyond mere schadenfreude. 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. Schuldiner's group, for instance, had shown in careful studies published in unglamorous workaday journals that the upside-down topology asserted from the erroneous structures of the multidrug resistance pump emrE could not possibly apply to the protein in its membrane home [e.g., ([1][3])]. It's too bad these results were dismissed as just old-fashioned biochemistry. 1. 1.[↵][4] 1. S. Ninio, 2. Y. Elbaz, 3. S. Schuldiner , FEBS Lett. 562, 193 (2004). [OpenUrl][5][CrossRef][6][PubMed][7][Web of Science][8] [1]: /lookup/doi/10.1126/science.314.5807.1856 [2]: /lookup/doi/10.1126/science.314.5807.1875b [3]: #ref-1 [4]: #xref-ref-1-1 "View reference 1. in text" [5]: {openurl}?query=rft.jtitle%253DFEBS%2BLetters%26rft.stitle%253DFEBS%2BLetters%26rft.aulast%253DNinio%26rft.auinit1%253DS.%26rft.volume%253D562%26rft.issue%253D1-3%26rft.spage%253D193%26rft.epage%253D196%26rft.atitle%253DThe%2Bmembrane%2Btopology%2Bof%2BEmrE%2B-%2Ba%2Bsmall%2Bmultidrug%2Btransporter%2Bfrom%2BEscherichia%2Bcoli.%26rft_id%253Dinfo%253Adoi%252F10.1016%252FS0014-5793%252804%252900240-6%26rft_id%253Dinfo%253Apmid%252F15044024%26rft.genre%253Darticle%26rft_val_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Ajournal%26ctx_ver%253DZ39.88-2004%26url_ver%253DZ39.88-2004%26url_ctx_fmt%253Dinfo%253Aofi%252Ffmt%253Akev%253Amtx%253Actx [6]: /lookup/external-ref?access_num=10.1016/S0014-5793(04)00240-6&link_type=DOI [7]: /lookup/external-ref?access_num=15044024&link_type=MED&atom=%2Fsci%2F315%2F5811%2F459.2.atom [8]: /lookup/external-ref?access_num=000220553000033&link_type=ISI