This is shocking, indeed. Here are some thoughts: 1. Geoffrey Chang (or anyone else in his lab) did not catch these mistakes at an earlier point in time, or he would have fixed the problem or told us. 2. The reviewers did not catch the problem! They most likely did not have enough information to do so. And this opens up a good discussion point how this information could be provided. Here is a problem to ponder: if you are a reviewer (or other 'quality assurance' person), would you essentially redo the structure determination to check for things like this? With what data do you then start? In case of MAD phasing, will you request all the original data to do local scaling yourself, etc? I think that recalculating maps is useful, but to reprocess data to catch mistakes like this, that would be a HUGE effort on behalf of the reviewers. 3. It is a great idea to demand a good 'methods' section. Science (and even more so) Nature have traditionally done a very poor job at carrying those. And it isn't the case that the authors don't want to provide this information, there is no *space* for this information in these high-profile journals. 4. Very low resolution and difficult structures (like the ABC transporters covered) are particularly difficult to judge, you are (among many other things) fighting a poor ratio of observed data points/refined parameters. If you go back to the pdb file (1z2r) - I just have done so, you don't see anything out of the ordinary and yet it's wrong. 5. Here is a confession. At the time when Geoffrey Chang was doing this work, it was my job to monitor his work on behalf of one of the funding agencies that supported his work. This monitoring consists minimally on reporting to 'management' (which usually does not understand science in general and crystallography in particular) if the PI is indeed doing the job they have proposed. Therefore my review of the work published was (I would hope) a bit better than a casual reading of a publication. I never read or saw anything that triggered an alarm. And I am absolutely convinced that this was/is an honest mistake. 6. Yes, if you use 'homemade' programs, they need to be thoroughly tested and the test(s) probably need
to be published for review. I personally do not like to use programs that have not passed such a test (or worse, to use programs that HAVE passed the test, but were subsequently 'amended' by someone else). I don't think this is what happened here, but there are some pretty good examples out there where such things did happen. I wonder what Geoffrey's thoughts would be on 'how to avoid this' from a reviewer perspective. He (unfortunately) eminently qualifies to have an opinion about this. Mark Mark van der Woerd Dept. of Biochemistry and Molecular Biology Colorado State University Fort Collins, CO 80523 -----Original Message----- From: [EMAIL PROTECTED] To: [email protected] Sent: Sat, 23 Dec 2006 11:32 AM Subject: [ccp4bb]: Retraction of ABC transporter structures - were there warning signs? *** For details on how to be removed from this list visit the *** *** CCP4 home page http://www.ccp4.ac.uk *** I was shocked to see the retraction in yesterday's issue of Science (Dec 22, 2006) of several ABC transporter structures and papers from the Chang lab, including three published in Science. The retraction says that the structures have the wrong hand and topology due to an "in-house" program that inverted the signs on the anomalous pairs. I have no expertise in ABC transporters, but were there warning signs in the structures? Were red flags raised by PDB or the other servers such as EDI, EDS, etc.? Looking at some of these papers, these are low resolution structure and I see very high R/Rfree, but there must have been other signs of problems as well. In the past few years, there have been almost no structures retracted due to gross errors and the checks being used by structural biology community seemed to working quite well - what can we learn from this tragic and sad error ? -- Arun Malhotra Phone: (305) 243-2826 Associate Professor Lab: (305) 243-2890 Dept. of Biochemistry & Molecular Biology Fax: (305) 243-3955 University of Miami School of Medicine PO Box 016129 E-Mail: [EMAIL PROTECTED] Miami, FL 33101 Web: http://structure.med.miami.edu ________________________________________________________________________ Check Out the new free AIM(R) Mail -- 2 GB of storage and industry-leading spam and email virus protection.
