Re: [ccp4bb] pdb-l: Retraction of 12 Structures....
From a statistical point of view, there could be a rare bad apple reviewer as well as a rare bad apple (fraud intending) author. Life is inherently risky but we still cross streets. More important, science is based on accessibility of primary data and reproducibility of results. Without primary data (in the normal case SFs) the results are not falsifiable and in Poppers sense en par with quackery. Most editors and authors should be susceptible to that argument. BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Dyda Sent: Saturday, December 12, 2009 8:33 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] pdb-l: Retraction of 12 Structures On Sat, 12 Dec 2009 11:58:27 +0530 Dr. Anthony Addlagatta wrote: Bernhard, I would be worried about sending the structure factors and the coordinates along with the manuscript. I wonder why? Cheers Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] pdb-l: Retraction of 12 Structures....
A number of years ago - we were asked to setup an ftp site a particular reviewer could see the coordinates... I could have looked at the logs to figure out where they were coming in from but chose not to. Some journals also allow the author to upload additional info - that would be available to the reviewer - but not included in the publication (I think Biochemistry is one of them)... Authors could then upload SF's and coordinates... If the reviewer wants to look - he/she then has the option - while still maintaining the anonymity of the review process... Ezra Dyda wrote: On Sat, 12 Dec 2009 11:58:27 +0530 Dr. Anthony Addlagatta wrote: Bernhard, I would be worried about sending the structure factors and the coordinates along with the manuscript. I wonder why? Cheers Fred [32m*** Fred Dyda, Ph.D. Phone:301-402-4496 Laboratory of Molecular BiologyFax: 301-496-0201 DHHS/NIH/NIDDK e-mail:fred.d...@nih.gov Bldg. 5. Room 303 Bethesda, MD 20892-0560 URGENT message e-mail: 2022476...@mms.att.net Google maps coords: 39.000597, -77.102102 http://www2.niddk.nih.gov/NIDDKLabs/IntramuralFaculty/DydaFred ***[m
Re: [ccp4bb] pdb-l: Retraction of 12 Structures
After a thorough examination of the available data, which included a re-analysis of each structure alleged to have been fabricated, the committee found a preponderance of evidence that structures 1BEF, 1CMW, 1DF9/2QID, 1G40, 1G44, 1L6L, 2OU1, 1RID, 1Y8E, 2A01, and 2HR0 were more likely than not falsified and/or fabricated and recommended that they be removed from the public record, the university said in its statement this week. I think it's worth pointing out, as I did when this came up last time, that one needs to read this list of PDB codes very carefully, and in a font that distinguishes 0 from O, and 1 from I. It would be very unfortunate, for example, if an innocent bacterial enzyme structure (2HRO) was called into question in some people's minds because of the apparent fabrication of the structure 2HR0. Once again, I'd like to get the community's thoughts: should we ask the PDB to stop using 0 and 1 in its IDs? I'll get off the soapbox now. - Matt (who has nothing to do with any of these structures...) -- Matthew Franklin , Ph.D. Senior Scientist, ImClone Systems, a wholly owned subsidiary of Eli Lilly Company 180 Varick Street, 6th floor New York, NY 10014 phone:(917)606-4116 fax:(212)645-2054 Confidentiality Note: This e-mail, and any attachment to it, contains privileged and confidential information intended only for the use of the individual(s) or entity named on the e-mail. If the reader of this e-mail is not the intended recipient, or the employee or agent responsible for delivering it to the intended recipient, you are hereby notified that reading it is strictly prohibited. If you have received this e-mail in error, please immediately return it to the sender and delete it from your system. Thank you.
Re: [ccp4bb] pdb-l: Retraction of 12 Structures
Matthew Franklin wrote: Once again, I'd like to get the community's thoughts: should we ask the PDB to stop using 0 and 1 in its IDs? I'll get off the soapbox now. I would be all for it... Having tried to downloade 1o08 and gotten it screwed up Especially when journals use a sans-serif font - things get interesting Ezra
