Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
I didn't think I had anything to say on this, but following an interesting discussion on a non-science based forum, I'd like to expand on a point that both Dale and Felix made in different ways. In the retraction of these 12 structures (and the 6 structures last year), we are not seeing the failure of the scientific method, rather we are seeing the scientific method working as it should. More specifically, we are seeing peer review at work. I that the implementation of peer review as part of the publication has perhaps lead us to forget that peer review is a longer term, ongoing process, conducted by the whole scientific community. In fact, although I haven't looked into this, I would hesitate a guess that formalised peer review for publication is perhaps a recent innovation, an anomaly rather than the norm in the history of science? (Think of Darwin, for example.) The problem is not then in the failings of the journal peer review process, but rather in our failure to maintain an appropriate level of doubt concerning anything we read in a paper or download from a database - a complacency which may be built on an unrealistic idealisation of the journals' peer review process, which has lead us to neglect the real meaning of peer review. Given that the databases are used by people who are not specialists in our discipline, a very appropriate response is for us to work with the database curators to try and present indications of the level of doubt along with the structure - which is exactly what is now happening. Kevin Dale Tronrud wrote: There are reasons for optimism. The self-correcting nature of the scientific method worked in this case. Kudos to the University of Alabama at Birmingham for facing this problem and following through with their investigation of earlier allegations.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
How very correct. And if anyone is doubt, remember the fiasco of the 'memory of water', published in Nature. To borrow the title of DVD's talks, Just because its in Nature, it does not mean its true. More specifically, we are seeing peer review at work. I that the implementation of peer review as part of the publication has perhaps lead us to forget that peer review is a longer term, ongoing process, conducted by the whole scientific community. A.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
On Dec 16, 2009, at 7:40 AM, Anastassis Perrakis wrote: How very correct. And if anyone is doubt, remember the fiasco of the 'memory of water', published in Nature. To borrow the title of DVD's talks, Just because its in Nature, it does not mean its true. Or, as one of my colleagues is known to say: It's in Nature, and it's even right! More specifically, we are seeing peer review at work. I that the implementation of peer review as part of the publication has perhaps lead us to forget that peer review is a longer term, ongoing process, conducted by the whole scientific community. A.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...
Dear Robbie, List, This thread is steadily diverging. Apologies for my contribution to its diversification. snip Who knows what they did to the maps in terms of (unwarrented) density modefication to make them look cleaner? The advantage of the EDS is that it is impartial and uniform. The maps are generated in a clear and well-described way. /snip I agree with you that map deposition is probably a waste of resources. I strongly disagree, though, with the existence of validation tools that have strong views about how best I should do science. For example, your sentence above imply that the validation tool is more fit (than myself) to decide which maps I should be looking at. Which means that if I chose to calculate (and view) not the simple FFT-derived map, but its maximum entropy estimate, I am in danger of being accused that 'I did something to the maps to make them look cleaner', where in fact, I'm just doing a better job out of the existing data than the validation tool (which probably generate maps in a clear, well-described and wrong way :-) The take home message of what I'm saying is this: We should not be deterred from practising our craft as best as we could, even if that implies that our models contain information that a validation tool can not reproduce. It is only fair that a well-informed and well-educated human being can do a better job than a fixed-frozen automated procedure. Fraud is a moral issue, and can not (and should not) be used as an excuse for converting validation tools to the sacred holders of scientific standards. My twocents, Nicholas -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...
I just scrapped most of my answer, Robbie was quicker, and I guess Gerard is on holiday ;-) As 'honorary Dutch' though here are my two cents. It is only fair that a well-informed and well-educated human being can do a better job than a fixed-frozen automated procedure. This is exactly the whole problem Niko. I must say that a certain proportion of the PDB depositors, are neither well-informed nor well-educated. Else, I cannot see why anyone in his right mind would put 'waters' 1.8 A from a Ca in 2009 (see Robbie's email) or create O-O clashes of 2.4 A in 2008 (where a simple peptide flip would make two perfect hydrogen bonds), etc etc. Would be easy to blame it to students that spend three or four years cloning before they get a structure that ends up with many mistakes in the PDB. PIs here carry most (if not all) of the blame: many are simply not competent to supervise crystallographic projects (see some CCP4 questions to see what I mean ...), a few are too busy (thus they should not be supervising PhD students if they lack the time), some make honest mistakes (ehm ... just in case somebody finds any errors in my lab's structures ...), and many do a good job and educate good students. But errors in the PDB accumulate. Recently, I had a look, together with Robbie, at my good-old chitinase (1994). Thats a pre-likelihood structure. Simple re-refinement with Robbie's tools (and some new tricks, also automated) and the script does in this 2.3 A structure a better job than I did as a PhD student, pushing it from the 48% of MolProbity to 98%. And I dont think that me or my supervisors could had done a better job at that time, sharing night shifts in an Indy and an ESV, with PROLSQ/PROTIN. So, I am more than happy if an automated procedure in 2009 can tell me that this job can be done better with new tools. Finally, validation tools are not there to pass judgement. They are tools to be used by depositors, referees, and users alike, to help them make a better informed interpretation of crystallographic *models*. Servers like EDS and PDB_REDO must be seen in that light, Take care - A.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...
Not sure if in any of the 112 posts regarding either the retraction theme or 'was 12 retraction' theme did mention, that after all despite good or as good as possible refinement of the structure, the goal is still to describe as accurately as possible the biological system using crystallography as a tool. If you can't confirm your structure by solid biochemical or biophysical methods what conclusions should you draw ? Sure faking data is not the default and looking at the ratio of suspected faked structures / deposited structures I do believe we are doing much better than other researchers e.g. in medical science. I agree that validation tools are very helpful and everybody should use them prior to deposition of your structure to ensure good standards and if you are not happy with the result of those validation tools e.g. Procheck, Molprobity well then change something - re-refine your structure and fix it prior to deposition. Regarding paper submissions, I think it would be a good idea to include e.g. the Molprobity Ramachandran plot the summary attached to the cover letter when submitting - additional to the table 1 of course. Bill Scott once mentioned that he provides a Pymol scene file with PDB coordinates electron density map to reviewers, if one could ensure that the coordinates can not be extracted from this file, I would be willing to do the same, but it's to easy to extract the coordinates and save them for 'other purposes'. My 2.5 cents, Jürgen On Dec 13, 2009, at 1:35 PM, Nicholas M Glykos wrote: Those Greeks again ... Finally, validation tools are not there to pass judgement. They are tools to be used by depositors, referees, and users alike, to help them make a better informed interpretation of crystallographic *models*. Servers like EDS and PDB_REDO must be seen in that light, Validation tools are programs written by crystallographers and structural biologists. As it happens, most crystallographers that write programs, have the neurotic belief that they can treat others' people data better than those other people. And, I share that neurosis ;-)) -- Dr Nicholas M. Glykos, Department of Molecular Biology and Genetics, Democritus University of Thrace, University Campus, Dragana, 68100 Alexandroupolis, Greece, Tel/Fax (office) +302551030620, Ext.77620, Tel (lab) +302551030615, http://utopia.duth.gr/~glykos/ - Jürgen Bosch Johns Hopkins Bloomberg School of Public Health Department of Biochemistry Molecular Biology Johns Hopkins Malaria Research Institute 615 North Wolfe Street, W8708 Baltimore, MD 21205 Phone: +1-410-614-4742 Lab: +1-410-614-4894 Fax: +1-410-955-3655 http://web.mac.com/bosch_lab/
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...
On Dec 13, 2009, at 11:00 AM, Jürgen Bosch wrote: If you can't confirm your structure by solid biochemical or biophysical methods what conclusions should you draw ? Don't you wish it worked the other way in that every time someone had a biochemical, physiological, or genetic result, they would be required to get a structure before they published in a good journal. That would even the playing field a bit.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
In fact, if you want the truth, what I now do is to download the sf.cif file, use ccp4i to regenerate the MTZ (with the same Free R-factor flags that the authors have used for structure refinement). Then feed that into Phenix for a few rounds of positional and temperature factor refinement with TLS (very few, I am not really re-refining the structure) and look at the resulting e.d. maps. If the structure is old then I get improved model statistics and (I assume) improved electron density maps. Fred. Message du 12/12/09 00:33 De : Eric Bennett A : CCP4BB@JISCMAIL.AC.UK Copie à : Objet : Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures Fred V wrote: I personally like to visualise the electron density as well, however, I do think that a non-crystallographer will go through the trouble of downloading the structure factors, installing ccp4/coot etc. Fred. They shouldn't have to go through some of that trouble. Maps should be deposited. Even if you have good crystallography knowledge can you exactly reproduce the map the authors were looking at? Software algorithms change over the years... the software version the authors used might not even be compilable on modern systems... some authors may not fully specify all software settings required to get the same map (perhaps they used NCS but you have to re-determine the NCS yourself)... etc. -- Eric Bennett, er...@pobox.com
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....þ
Dear Fred, People have already done this for all PDB entries: - http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats - http://www.cmbi.ru.nl/pdb_redo : maps and re-refinement. And yes, the stats and maps do improve most of the time, unfortunately also for structures that are not old (but to a lesser extent). Something else: Many people have shown that their 'new' validation tool would have detected the fraud. Good for them, many 'old' validation tools also show that there is something wrong with the KM structures/homology models. The point is that we have never actively looked for such fraud. Another thing (and this annoys the bioinformatician in me) is that many validation tools do not provide validation reports of the entire PDB ready for someone else (who like these things) to data mine. If we spend so much time discussing which experimental data should be made available, then surely validators should give the right example. Fortunately there are some good exceptions/exmaples (EDS, PROCHECK, and WHAT_CHECK) and the PDB is doing its best to make more validation information available. Cheers, Robbie In fact, if you want the truth, what I now do is to download the sf.cif file, use ccp4i to regenerate the MTZ (with the same Free R-factor flags that the authors have used for structure refinement). Then feed that into Phenix for a few rounds of positional and temperature factor refinement with TLS (very few, I am not really re-refining the structure) and look at the resulting e.d. maps. If the structure is old then I get improved model statistics and (I assume) improved electron density maps. Fred.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Yes, totally agree that the good thing about it all is that the problems have been identified and the wrong data will hopefully be eliminated. Shame it took almost 10 years since the first fabricated structure was published and more then 2 since questions were first risen about this work... Paula 2009/12/11 Dale Tronrud det...@uoxray.uoregon.edu Paula Salgado wrote: Actually, I don't think that should be any consolation at all... As scientists, from whatever field, we should be appalled by this kind of mischief from anyone that calls themselves scientists. Not only it has effects on further research, delaying science sometimes by years, but it just gives an appalling image of science and scientists. And of course, is unethical and wrong... Today is a sad moment for crystallography and science. There are reasons for optimism. The self-correcting nature of the scientific method worked in this case. Kudos to the University of Alabama at Birmingham for facing this problem and following through with their investigation of earlier allegations. Dale Tronrud = Dr Paula Salgado Division of Molecular Biosciences Department of Life Sciences Faculty of Natural Sciences Biochemistry Building, 5th Floor Imperial College London South Kensington Campus SW7 2AZ London Tel: 02075945464 2009/12/10 Boaz Shaanan bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il If that's of any consolation for us crystallographers, this situations arise in other fields too. Here is another example. See this link: http://www.biotechniques.com/news/Glycosylation-methods-paper-retracted/biotechniques-182060.html Boaz - Original Message - From: Roger Rowlett rrowl...@colgate.edu mailto: rrowl...@colgate.edu Date: Thursday, December 10, 2009 21:07 Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK This kind of unfortunate situation only reinforces the notion that there must be some sort of laboratory oversight/communication/mentoring/documentation procedures in place. In my research lab (populated by a postdoc and a bunch of undergraduates) raw images and data processing log files are visible to everyone on the central XRD server, there is a lot of intra-laboratory communication about every structure that is processed, and lots of required documentation that must go onto our electronic laboratory notebook/wiki. While a determined individual could still find a way to perpetrate fraud, it is a lot more difficult when there are a lot of eyes looking at every structure, and raw data and documentation is widely visible within the lab. This is not a bad thing for co-authorship purposes, also. Nathaniel Echols wrote: On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: I assume this is the denouement of the Ajees et al debacle a while back? Does this mean all authors on all of those papers were complicit? Otherwise, how would one author alone perpetrate this kind of thing? He pretends to go to the synchrotron, comes back with the hkl file, and goes from there? What about the crystals? Grows some lysozyme crystals, labels as protein x, proceeds to go to the synchrotron and then...? This whole thing is really hard to imagine--is there an initiation procedure in that lab, when the noble lie is revealed to all would-be authors? I'm curious about this too, but it is actually very likely that some (perhaps the majority) of the co-authors were unaware of the fraud, especially those whose name is only present on a single paper. I didn't look closely, but I recognized one name of someone who certainly doesn't need to fake anything at this point in his career; I would be shocked if he had any clue what was going on. Likewise, if there were co-authors from entirely different fields, I'm sure they wouldn't know what a Wilson plot is supposed to look like. Many excellent scientists have been burned like this before; wouldn't you assume that your collaborators are acting in good faith? There are two other things to keep in mind: 1. The standard for co-authorship is often very low. This is a problem by itself, and it's one reason why Nature (and a few others) now list author contributions by name. 2. Rumor has it that in some labs, the PI may take the data and solve the structure personally, cutting out the postdoc or grad student who did most of the benchwork. (I've seen one or two author contribution sections that indicated
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....?
Dear Fred, People have already done this for all PDB entries: - http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats - http://www.cmbi.ru.nl/pdb_redo : maps and re-refinement. And yes, the stats and maps do improve most of the time, unfortunately also for structures that are not old (but to a lesser extent). Except it doesn't work for _all_ PDB entries, even when SF are available. On your site, for example, the Current entries link on the home page seems to be broken and entry 3G6A (which was released 8 months ago) is not available for some unspecified reason. For some cases (like twinned structures) EDS won't have a map. Rather than relying on availability of a third party server to enable viewing the map, it would be a much cleaner solution if authors just deposited their own maps in the PDB. --
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
I agree with Randy Read though - it's a mistake to get too carried away with the foul-play aspect of this. There were clearly very serious problems with those structures anyway. What it shows is that you can desposit just about anything in the PDB, which is quite worrying when you consider how much more accessible crystallography has become to non-specialists. If it is to continue to be a valuable resource, then everyone needs to know that structures in the PDB meet some basic quality criteria. Yes, totally agree that the good thing about it all is that the problems have been identified and the wrong data will hopefully be eliminated. Shame it took almost 10 years since the first fabricated structure was published and more then 2 since questions were first risen about this work... Paula 2009/12/11 Dale Tronrud det...@uoxray.uoregon.edu Paula Salgado wrote: Actually, I don't think that should be any consolation at all... As scientists, from whatever field, we should be appalled by this kind of mischief from anyone that calls themselves scientists. Not only it has effects on further research, delaying science sometimes by years, but it just gives an appalling image of science and scientists. And of course, is unethical and wrong... Today is a sad moment for crystallography and science. There are reasons for optimism. The self-correcting nature of the scientific method worked in this case. Kudos to the University of Alabama at Birmingham for facing this problem and following through with their investigation of earlier allegations. Dale Tronrud = Dr Paula Salgado Division of Molecular Biosciences Department of Life Sciences Faculty of Natural Sciences Biochemistry Building, 5th Floor Imperial College London South Kensington Campus SW7 2AZ London Tel: 02075945464 2009/12/10 Boaz Shaanan bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il If that's of any consolation for us crystallographers, this situations arise in other fields too. Here is another example. See this link: http://www.biotechniques.com/news/Glycosylation-methods-paper-retracted/biotechniques-182060.html Boaz - Original Message - From: Roger Rowlett rrowl...@colgate.edu mailto: rrowl...@colgate.edu Date: Thursday, December 10, 2009 21:07 Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK This kind of unfortunate situation only reinforces the notion that there must be some sort of laboratory oversight/communication/mentoring/documentation procedures in place. In my research lab (populated by a postdoc and a bunch of undergraduates) raw images and data processing log files are visible to everyone on the central XRD server, there is a lot of intra-laboratory communication about every structure that is processed, and lots of required documentation that must go onto our electronic laboratory notebook/wiki. While a determined individual could still find a way to perpetrate fraud, it is a lot more difficult when there are a lot of eyes looking at every structure, and raw data and documentation is widely visible within the lab. This is not a bad thing for co-authorship purposes, also. Nathaniel Echols wrote: On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: I assume this is the denouement of the Ajees et al debacle a while back? Does this mean all authors on all of those papers were complicit? Otherwise, how would one author alone perpetrate this kind of thing? He pretends to go to the synchrotron, comes back with the hkl file, and goes from there? What about the crystals? Grows some lysozyme crystals, labels as protein x, proceeds to go to the synchrotron and then...? This whole thing is really hard to imagine--is there an initiation procedure in that lab, when the noble lie is revealed to all would-be authors? I'm curious about this too, but it is actually very likely that some (perhaps the majority) of the co-authors were unaware of the fraud, especially those whose name is only present on a single paper. I didn't look closely, but I recognized one name of someone who certainly doesn't need to fake anything at this point in his career; I would be shocked if he had any clue what was going on. Likewise, if there were co-authors from entirely different fields, I'm sure they wouldn't know what a Wilson plot is supposed to look like. Many excellent scientists have been burned like this before; wouldn't you assume that your collaborators are acting in good
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures...
Dear Eric Bennett, 3g6a was processed by PDB_REDO (without the original R-free set which sadly wasn't deposited) on Monday, 20 July 2009 at 21:35 CEST with PDB_REDO version 2.6: http://www.cmbi.ru.nl/pdb_redo/g6/3g6a/index.html That was roughly two months after the last revision (the entry is replaced each time the timestamp of either the PDB or SF file changes). Okay, it is not done instantly but we keep up with the PDB reasonably well. If you cannot find the PDB_REDO entry directly, you can always try the link on the PDBe entry page. You are quite right saying that EDS and PDB_REDO do not work for all structures. They do however work for 98% of all structures (at least PDB_REDO does). Of the 2% percent that is missing, 1% is caused by things we understand and are annotated in WHY_NOT (www.cmbi.ru.nl/WHY_NOT), the other 1% is caused by cases where we cannot reproduce R(-free) to within 10 percentage points. We are currently investigating those and the PDB has been a great help in that. Oh, and PDB_REDO does take twinning into account (at least to the extent Refmac does). You were also right about the list of all entries. We recently moved to a newer version of WHY_NOT which broke the link. My bad, I have fixed it. On topic: I think the deposition of maps is a waste of space. Maps may describe what the depositors paranoidwant you to think they/paranoid have looked at. But that does not mean they looked at the right thing. Who knows what they did to the maps in terms of (unwarrented) density modefication to make them look cleaner? The advantage of the EDS is that it is impartial and uniform. The maps are generated in a clear and well-described way. Cheers, Robbie Date: Sat, 12 Dec 2009 10:33:04 -0500 From: er...@pobox.com Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures=?UNKNOWN?Q?=FE?= To: CCP4BB@JISCMAIL.AC.UK Dear Fred, People have already done this for all PDB entries: - http://eds.bmc.uu.se/eds/ : maps and many crystallographic stats - http://www.cmbi.ru.nl/pdb_redo : maps and re-refinement. And yes, the stats and maps do improve most of the time, unfortunately also for structures that are not old (but to a lesser extent). Except it doesn't work for _all_ PDB entries, even when SF are available. On your site, for example, the Current entries link on the home page seems to be broken and entry 3G6A (which was released 8 months ago) is not available for some unspecified reason. For some cases (like twinned structures) EDS won't have a map. Rather than relying on availability of a third party server to enable viewing the map, it would be a much cleaner solution if authors just deposited their own maps in the PDB. --
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Would the exact analysis of how each of these things were wrong and fabricated be somewhere available Would be fair (apart from the known case of C3b) to have the whole analysis available instead of just this kind of news feed. I suspect its not obvious by five minute check in all cases. Perhaps there needs to be ways within PDB in form of automated tools that would raise those red flags in suspicious cases (e.g. some data analysis --such as the contribution by solvent etc now that data beyond 8Å is by default used in refinement) - as it appears peer review/editing by journals isn't/cant always be(?) stringent enough. In any case, some type of automated analysis of the whole data base might be a good idea, as there can be other cases (with another couple of thousand papers citing them..). tommi On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote: 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.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
11-Dec-2009 11:30 Rehovot Dear All, I Agree fully with Tommi, and feel, in parallel, we in the MX community must think of better tools for referees to review papers and insist that these be followed. For example we should insist on getting BOTH the coords and structure factors for papers submitted, so it would be possible to do test on the structures which appear to have 'question marks'. Without this data, it is very difficult to do a serious job in refereeing. Also, any manuscript, submitted to any journal, where BOTH the structure factors and coords are not submitted to the PDB should be rejected immediately without further review. This should be the policy of the reviewer, independent of any particular policy of the journals. It might be worthwhile for the MX community to also consider writing a strong letter to the journals in which published the papers for which the structures have now been retracted, to state just how serious this matter is and that the journals should also take much more responsibility of finding better ways to have these papers and structures reviewed. Joel - Prof. Joel L. Sussman Director, Israel Structural Proteomics Center Dept. of Structural Biology Weizmann Institute of Science Rehovot 76100 ISRAEL Tel: +972 8-934 4531 Fax: +972 8-934 6312 joel.suss...@weizmann.ac.il www.weizmann.ac.il/~joel; www.weizmann.ac.il/ISPC - On 11 Dec 2009, at 11:19, Tommi Kajander wrote: Would the exact analysis of how each of these things were wrong and fabricated be somewhere available Would be fair (apart from the known case of C3b) to have the whole analysis available instead of just this kind of news feed. I suspect its not obvious by five minute check in all cases. Perhaps there needs to be ways within PDB in form of automated tools that would raise those red flags in suspicious cases (e.g. some data analysis --such as the contribution by solvent etc now that data beyond 8Å is by default used in refinement) - as it appears peer review/editing by journals isn't/cant always be(?) stringent enough. In any case, some type of automated analysis of the whole data base might be a good idea, as there can be other cases (with another couple of thousand papers citing them..). tommi On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote: 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.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Fraud is an arms race between the technology to perpetrate it and the technology to detect it. In the end it is up to individual scientists to act nobly and institutions to act vigilantly. Speaking of the latter, where is the fallout from the Hellinga debacle? Is everyone associated with it still gainfully employed at the world's finest institutions? I thought so. James On Dec 11, 2009, at 1:30 AM, Prof. Joel L. Sussman wrote: 11-Dec-2009 11:30 Rehovot Dear All, I Agree fully with Tommi, and feel, in parallel, we in the MX community must think of better tools for referees to review papers and insist that these be followed. For example we should insist on getting BOTH the coords and structure factors for papers submitted, so it would be possible to do test on the structures which appear to have 'question marks'. Without this data, it is very difficult to do a serious job in refereeing. Also, any manuscript, submitted to any journal, where BOTH the structure factors and coords are not submitted to the PDB should be rejected immediately without further review. This should be the policy of the reviewer, independent of any particular policy of the journals. It might be worthwhile for the MX community to also consider writing a strong letter to the journals in which published the papers for which the structures have now been retracted, to state just how serious this matter is and that the journals should also take much more responsibility of finding better ways to have these papers and structures reviewed. Joel - Prof. Joel L. Sussman Director, Israel Structural Proteomics Center Dept. of Structural Biology Weizmann Institute of Science Rehovot 76100 ISRAEL Tel: +972 8-934 4531 Fax: +972 8-934 6312 joel.suss...@weizmann.ac.il www.weizmann.ac.il/~joel; www.weizmann.ac.il/ISPC - On 11 Dec 2009, at 11:19, Tommi Kajander wrote: Would the exact analysis of how each of these things were wrong and fabricated be somewhere available Would be fair (apart from the known case of C3b) to have the whole analysis available instead of just this kind of news feed. I suspect its not obvious by five minute check in all cases. Perhaps there needs to be ways within PDB in form of automated tools that would raise those red flags in suspicious cases (e.g. some data analysis --such as the contribution by solvent etc now that data beyond 8Å is by default used in refinement) - as it appears peer review/ editing by journals isn't/cant always be(?) stringent enough. In any case, some type of automated analysis of the whole data base might be a good idea, as there can be other cases (with another couple of thousand papers citing them..). tommi On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote: 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.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
I uploaded an archive( pdf of emails plus text log files) of all the conversations that took place around Eleanor Dodsons Original thread on 08/17/07 discussing the 2HR0 structure along with the attached log files to an archive available at http://harijaycrystdata.s3.amazonaws.com/ccp4bb_archive_thread_withlogfiles_08_17_07_2HR0.zip I tried to get the threads with attached logs to a single link using other email thread viewers , but in the end put it into the above file using gmail . Since I missed most of the original discussion, re-reading it was very enlightening. Hope this helps Hari Jayaram On Fri, Dec 11, 2009 at 4:19 AM, Tommi Kajander tommi.kajan...@helsinki.fiwrote: Would the exact analysis of how each of these things were wrong and fabricated be somewhere available Would be fair (apart from the known case of C3b) to have the whole analysis available instead of just this kind of news feed. I suspect its not obvious by five minute check in all cases. Perhaps there needs to be ways within PDB in form of automated tools that would raise those red flags in suspicious cases (e.g. some data analysis --such as the contribution by solvent etc now that data beyond 8Å is by default used in refinement) - as it appears peer review/editing by journals isn't/cant always be(?) stringent enough. In any case, some type of automated analysis of the whole data base might be a good idea, as there can be other cases (with another couple of thousand papers citing them..). tommi On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote: 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.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
The PDB is already taking action on this question by setting up validation task forces for X-ray and NMR structures. I'm chairing the X-ray task force, which is finally nearing completion of its report after working on it since April 2008. One of our recommendations (of most relevance to this discussion) is that, when a structure is deposited, a validation report should be generated in the form of a PDF file, including an intuitive representation of overall quality that should be understandable even by non-crystallographers. Editors and referees would know that this report was available and could (should) request it; eventually journals could require it, in the same way that they now require PDB codes. Probably the best way forward is for professional bodies such as the IUCr to consider this as policy, which they could recommend to the journals. Credit where credit is due: George Sheldrick originally proposed such a mechanism, as part of the previous discussion on using our validation tools. Although improved validation tools (especially ones using the newly- required diffraction data) will make it harder to commit convincing fraud, someone determined to do it will find a way to satisfy whatever tools exist at the time; it will only be tools developed later that will catch them. But fraud is very rare, and my personal opinion is that it would be counter-productive to be so suspicious of our colleagues that we spend our time running forensic checks on every result. Far more damage is done by well-intentioned incompetence, and that's the main purpose of validation. Regards, Randy Read On 11 Dec 2009, at 09:30, Prof. Joel L. Sussman wrote: 11-Dec-2009 11:30 Rehovot Dear All, I Agree fully with Tommi, and feel, in parallel, we in the MX community must think of better tools for referees to review papers and insist that these be followed. For example we should insist on getting BOTH the coords and structure factors for papers submitted, so it would be possible to do test on the structures which appear to have 'question marks'. Without this data, it is very difficult to do a serious job in refereeing. Also, any manuscript, submitted to any journal, where BOTH the structure factors and coords are not submitted to the PDB should be rejected immediately without further review. This should be the policy of the reviewer, independent of any particular policy of the journals. It might be worthwhile for the MX community to also consider writing a strong letter to the journals in which published the papers for which the structures have now been retracted, to state just how serious this matter is and that the journals should also take much more responsibility of finding better ways to have these papers and structures reviewed. Joel - Prof. Joel L. Sussman Director, Israel Structural Proteomics Center Dept. of Structural Biology Weizmann Institute of Science Rehovot 76100 ISRAEL Tel: +972 8-934 4531 Fax: +972 8-934 6312 joel.suss...@weizmann.ac.il www.weizmann.ac.il/~joel; www.weizmann.ac.il/ISPC - On 11 Dec 2009, at 11:19, Tommi Kajander wrote: Would the exact analysis of how each of these things were wrong and fabricated be somewhere available Would be fair (apart from the known case of C3b) to have the whole analysis available instead of just this kind of news feed. I suspect its not obvious by five minute check in all cases. Perhaps there needs to be ways within PDB in form of automated tools that would raise those red flags in suspicious cases (e.g. some data analysis --such as the contribution by solvent etc now that data beyond 8Å is by default used in refinement) - as it appears peer review/ editing by journals isn't/cant always be(?) stringent enough. In any case, some type of automated analysis of the whole data base might be a good idea, as there can be other cases (with another couple of thousand papers citing them..). tommi On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote: 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. -- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: + 44 1223 336500 Wellcome Trust/MRC Building Fax: + 44 1223 336827 Hills RoadE-mail: rj...@cam.ac.uk Cambridge CB2 0XY, U.K. www- structmed.cimr.cam.ac.uk
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Hey Tommi, I am under the impression that Zbyszek Otwinowski has looked in depth at all of the structures that have now been retracted and has prepared a long manuscript detailing the evidence for fabrication and falsification. As far as I know, this manuscript hasn't been published yet (shame!), but it's bound to come out soon. Keep you patience just a little longer. Andreas On Fri, Dec 11, 2009 at 9:19 AM, Tommi Kajander tommi.kajan...@helsinki.fi wrote: Would the exact analysis of how each of these things were wrong and fabricated be somewhere available Would be fair (apart from the known case of C3b) to have the whole analysis available instead of just this kind of news feed. I suspect its not obvious by five minute check in all cases. Perhaps there needs to be ways within PDB in form of automated tools that would raise those red flags in suspicious cases (e.g. some data analysis --such as the contribution by solvent etc now that data beyond 8Å is by default used in refinement) - as it appears peer review/editing by journals isn't/cant always be(?) stringent enough. In any case, some type of automated analysis of the whole data base might be a good idea, as there can be other cases (with another couple of thousand papers citing them..). tommi On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote: 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.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
I think also the editors are sometimes to blame. I once refereed a paper and pointed out that the resolution was overstated (I/s(I) = 1.05 in the last resolution shell, as well as a couple of comments that clearly suggested that the density wasn't very good). The editor ignored my comments. Silvia Silvia Onesti Sincrotrone Trieste S.C.p.A. SS 14 - km 163,5 - AREA Science Park, 34149 Basovizza, Trieste ITALY Email: silvia.one...@elettra.trieste.it Tel. +39 040 3758451 Mob +39 366 6878001 http://www.elettra.trieste.it/PEOPLE/index.php?n=SilviaOnesti.HomePage http://www.sissa.it/sbp/web_2008/research_structuralbio.html On Fri, 11 Dec 2009 10:48:41 +0100 Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Hi Fred, It could also be that the high impact factor of these journals, and their 'tabloid' character ensures that they are read by more people than other journals. So any bad data or fraud that gets published in Nature, Cell or Science is more likely to get noticed and talked about, than something that appears in smaller impact journals. And even some very big names aren't spared, which is a good thing. This one, for example http://www.nature.com/nature/journal/v452/n7183/full/nature06819.html Ganesh On Fri, 11 Dec 2009 10:48:41 +0100, Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred. -- What is true for E. coli is also true for an elephant - Jacques Monod.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
It could also be that the high impact factor of these journals, and their 'tabloid' character ensures that they are read by more people than other journals. So any bad data or fraud that gets published in Nature, Cell or Science is more likely to get noticed and talked about, than something that appears in smaller impact journals. And even some very big names aren't spared, which is a good thing. This one, for example http://www.nature.com/nature/journal/v452/n7183/full/nature06819.html The first author of this paper (the one who provided all figures and data that are inconsistent with the original data) has never admitted anything, continues to publish and hold tenure-track position. Ganesh On Fri, 11 Dec 2009 10:48:41 +0100, Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred. -- What is true for E. coli is also true for an elephant - Jacques Monod.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Paula Salgado wrote: Actually, I don't think that should be any consolation at all... As scientists, from whatever field, we should be appalled by this kind of mischief from anyone that calls themselves scientists. Not only it has effects on further research, delaying science sometimes by years, but it just gives an appalling image of science and scientists. And of course, is unethical and wrong... Today is a sad moment for crystallography and science. There are reasons for optimism. The self-correcting nature of the scientific method worked in this case. Kudos to the University of Alabama at Birmingham for facing this problem and following through with their investigation of earlier allegations. Dale Tronrud = Dr Paula Salgado Division of Molecular Biosciences Department of Life Sciences Faculty of Natural Sciences Biochemistry Building, 5th Floor Imperial College London South Kensington Campus SW7 2AZ London Tel: 02075945464 2009/12/10 Boaz Shaanan bshaa...@bgu.ac.il mailto:bshaa...@bgu.ac.il If that's of any consolation for us crystallographers, this situations arise in other fields too. Here is another example. See this link: http://www.biotechniques.com/news/Glycosylation-methods-paper-retracted/biotechniques-182060.html Boaz - Original Message - From: Roger Rowlett rrowl...@colgate.edu mailto:rrowl...@colgate.edu Date: Thursday, December 10, 2009 21:07 Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures To: CCP4BB@JISCMAIL.AC.UK mailto:CCP4BB@JISCMAIL.AC.UK This kind of unfortunate situation only reinforces the notion that there must be some sort of laboratory oversight/communication/mentoring/documentation procedures in place. In my research lab (populated by a postdoc and a bunch of undergraduates) raw images and data processing log files are visible to everyone on the central XRD server, there is a lot of intra-laboratory communication about every structure that is processed, and lots of required documentation that must go onto our electronic laboratory notebook/wiki. While a determined individual could still find a way to perpetrate fraud, it is a lot more difficult when there are a lot of eyes looking at every structure, and raw data and documentation is widely visible within the lab. This is not a bad thing for co-authorship purposes, also. Nathaniel Echols wrote: On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: I assume this is the denouement of the Ajees et al debacle a while back? Does this mean all authors on all of those papers were complicit? Otherwise, how would one author alone perpetrate this kind of thing? He pretends to go to the synchrotron, comes back with the hkl file, and goes from there? What about the crystals? Grows some lysozyme crystals, labels as protein x, proceeds to go to the synchrotron and then...? This whole thing is really hard to imagine--is there an initiation procedure in that lab, when the noble lie is revealed to all would-be authors? I'm curious about this too, but it is actually very likely that some (perhaps the majority) of the co-authors were unaware of the fraud, especially those whose name is only present on a single paper. I didn't look closely, but I recognized one name of someone who certainly doesn't need to fake anything at this point in his career; I would be shocked if he had any clue what was going on. Likewise, if there were co-authors from entirely different fields, I'm sure they wouldn't know what a Wilson plot is supposed to look like. Many excellent scientists have been burned like this before; wouldn't you assume that your collaborators are acting in good faith? There are two other things to keep in mind: 1. The standard for co-authorship is often very low. This is a problem by itself, and it's one reason why Nature (and a few others) now list author contributions by name. 2. Rumor has it that in some labs, the PI may take the data and solve the structure personally, cutting out the postdoc or grad student who did most of the benchwork. (I've seen one or two author contribution sections that indicated this had occurred.) After all, spinning dials and looking at electron density is the fun part of crystallography. Who is going to second-guess the professor when a recommendation letter (and future career) is at stake? -Nat -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Yes, as much as I like to pick on the tabloids and their somewhat iffy quality control, it looks like this guy got away with faking structures for 10 years UNTIL he published in Nature. Even Acta Cryst has egg on its face. So the bottom line is that sunlight is indeed the best disinfectant, and Nature is one of the best-lit journals? Phoebe Original message Date: Fri, 11 Dec 2009 13:36:38 +0100 From: Ganesh Natrajan natra...@embl.fr Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures To: CCP4BB@JISCMAIL.AC.UK Hi Fred, It could also be that the high impact factor of these journals, and their 'tabloid' character ensures that they are read by more people than other journals. So any bad data or fraud that gets published in Nature, Cell or Science is more likely to get noticed and talked about, than something that appears in smaller impact journals. And even some very big names aren't spared, which is a good thing. This one, for example http://www.nature.com/nature/journal/v452/n7183/full/nature06819.html Ganesh On Fri, 11 Dec 2009 10:48:41 +0100, Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred. -- What is true for E. coli is also true for an elephant - Jacques Monod. Phoebe A. Rice Assoc. Prof., Dept. of Biochemistry Molecular Biology The University of Chicago phone 773 834 1723 http://bmb.bsd.uchicago.edu/Faculty_and_Research/01_Faculty/01_Faculty_Alphabetically.php?faculty_id=123 RNA is really nifty DNA is over fifty We have put them both in one book Please do take a really good look http://www.rsc.org/shop/books/2008/9780854042722.asp
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
I have to say to the credit of Nature and competent authors that in every case I have requested structure factors and coordinates for review they have arranged to provide these. AFAIK this is their editorial policy, but it requires that at least one of the reviewers knows what to do with the SF as and coordinates. That, however, does not (yet??) seem to be policy, i.e. to pair a technical crystallography review with one that evaluates biological and other relevance. BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Prof. Joel L. Sussman Sent: Friday, December 11, 2009 1:31 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures 11-Dec-2009 11:30 Rehovot Dear All, I Agree fully with Tommi, and feel, in parallel, we in the MX community must think of better tools for referees to review papers and insist that these be followed. For example we should insist on getting BOTH the coords and structure factors for papers submitted, so it would be possible to do test on the structures which appear to have 'question marks'. Without this data, it is very difficult to do a serious job in refereeing. Also, any manuscript, submitted to any journal, where BOTH the structure factors and coords are not submitted to the PDB should be rejected immediately without further review. This should be the policy of the reviewer, independent of any particular policy of the journals. It might be worthwhile for the MX community to also consider writing a strong letter to the journals in which published the papers for which the structures have now been retracted, to state just how serious this matter is and that the journals should also take much more responsibility of finding better ways to have these papers and structures reviewed. Joel - Prof. Joel L. Sussman Director, Israel Structural Proteomics Center Dept. of Structural Biology Weizmann Institute of Science Rehovot 76100 ISRAEL Tel: +972 8-934 4531 Fax: +972 8-934 6312 joel.suss...@weizmann.ac.il www.weizmann.ac.il/~joel; www.weizmann.ac.il/ISPC - On 11 Dec 2009, at 11:19, Tommi Kajander wrote: Would the exact analysis of how each of these things were wrong and fabricated be somewhere available Would be fair (apart from the known case of C3b) to have the whole analysis available instead of just this kind of news feed. I suspect its not obvious by five minute check in all cases. Perhaps there needs to be ways within PDB in form of automated tools that would raise those red flags in suspicious cases (e.g. some data analysis --such as the contribution by solvent etc now that data beyond 8Å is by default used in refinement) - as it appears peer review/editing by journals isn't/cant always be(?) stringent enough. In any case, some type of automated analysis of the whole data base might be a good idea, as there can be other cases (with another couple of thousand papers citing them..). tommi On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote: 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.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
You are absolutely right, more information describing to what extents these structures were falsified will be valuable to the community. Actually, it will be more useful if the investigators can publish their report as an article in Acta D (as a case study for tracking falsified structures). I have a suggestion (actually a request) to the expertise in the field to write a kind of review article about sources of error in crystallography and how to hunt these errors. It will be even better if it is written considering the non-crystallographers (scientists who use the structural information - like the co-authors on structural papers). This will help to educate the non-crystallographers how to look at the structures critically. Ibrahim -- Ibrahim M. Moustafa, Ph.D. Biochemistry and Molecular Biology Dept. 201 Althouse Lab., University Park, Pennsylvania State University PA 16802 Tel. (814) 863-8703 Fax (814) 865-7927 On 12/11/09 4:19 AM, Tommi Kajander tommi.kajan...@helsinki.fi wrote: Would the exact analysis of how each of these things were wrong and fabricated be somewhere available Would be fair (apart from the known case of C3b) to have the whole analysis available instead of just this kind of news feed. I suspect its not obvious by five minute check in all cases. Perhaps there needs to be ways within PDB in form of automated tools that would raise those red flags in suspicious cases (e.g. some data analysis --such as the contribution by solvent etc now that data beyond 8Å is by default used in refinement) - as it appears peer review/editing by journals isn't/cant always be(?) stringent enough. In any case, some type of automated analysis of the whole data base might be a good idea, as there can be other cases (with another couple of thousand papers citing them..). tommi On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote: 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.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Ibrahim Moustafa wrote: This will help to educate the non-crystallographers how to look at the structures critically. The first thing that a non-crystallographer should be aware of is the existence of the temperature factors. It is a pity that the displays of biological macromolecules on the data bases do not show these. These temperature factors clearly indicate which areas of the molecule are more/less ordered and more/less reliable (there is a correlation between the 2, when one gets to regions of high isotropic temperature values, I'm not talking of differences between an isotropic B value of say 15 and one of say 17). I personally like to visualise the electron density as well, however, I do think that a non-crystallographer will go through the trouble of downloading the structure factors, installing ccp4/coot etc. Fred.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Most of these structures can be easily identified as very suspicious in a few seconds using POLYGON tool (Acta Cryst. D65, 297-300 (2009)); see pictures here (courtesy of Sacha Urzhumtsev): http://cci.lbl.gov/~afonine/fakes/Murthy-polygon-1.pdf Pavel. P.S. POLYGON tool is available as part of validation tools in PHENIX. On 12/10/09 6:16 AM, Ibrahim Moustafa wrote: Hi all, I want to share the following e-mail received from pdb-l. It is sad to see something like that! regards, Ibrahim -- Forwarded Message From: Michael Sadowski mockeldri...@yahoo.com Date: Thu, 10 Dec 2009 04:22:28 -0800 (PST) To: pd...@rcsb.org Subject: pdb-l: Retraction of 12 Structures Dear All, Better check your data! Apologies to those who have seen this. S. - The University of Alabama at Birmingham has issued a statement indicating that a former UAB researcher may have fabricated or falsified data about protein structures that are contained in the Protein Data Bank. The university did not include a name of the researcher, but the Birmingham News this week reported that the scientist is H.M. Krishna Murthy and an independent review by BioInform of the PDB shows that Murthy is associated with all of the proteins that UAB said were falsified. The newspaper said that a probe of Murthy's research has been underway since 2007. 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. - http://www.genomeweb.com/informatics/university-alabama-says-researcher-fabr icated-protein-structures-now-protein-dat?utm_source=feedburnerutm_medium=f eedutm_campaign=Feed%3A+genomeweb%2Fbioinform+%28BioInform%29 http://main.uab.edu/Sites/reporter/articles/71570/ http://blog.al.com/birmingham-news-stories/2009/12/ex-uab_researchers_work_m ay_be.html TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . -- End of Forwarded Message
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Not to derail the thread, but there is nothing, imho, wrong with I/s=1 cutoff (you expect I/s=2, I assume?). R-factors will get higher, but there are good reasons to believe that model will actually be better. This has been discussed many times before and there is probably no resolution, so why not just let people choose whatever resolution cutoff they want (as long as the I/s is clearly stated)? Disclaimer: I always use I/s=1 cutoff (assuming that completeness is good, of course). Compared to I/s=2 it doesn't really overstate resolution all that much (e.g. 2.1 vs 2.2). On Fri, 2009-12-11 at 13:18 +0100, Silvia Onesti wrote: I think also the editors are sometimes to blame. I once refereed a paper and pointed out that the resolution was overstated (I/s(I) = 1.05 in the last resolution shell, as well as a couple of comments that clearly suggested that the density wasn't very good). The editor ignored my comments. Silvia Silvia Onesti Sincrotrone Trieste S.C.p.A. SS 14 - km 163,5 - AREA Science Park, 34149 Basovizza, Trieste ITALY Email: silvia.one...@elettra.trieste.it Tel. +39 040 3758451 Mob +39 366 6878001 http://www.elettra.trieste.it/PEOPLE/index.php?n=SilviaOnesti.HomePage http://www.sissa.it/sbp/web_2008/research_structuralbio.html On Fri, 11 Dec 2009 10:48:41 +0100 Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
I think that when a model's resolution is clearly stated in a paper, many readers still assume the pre-maximum likelihood definition (i.e. high I/sigma, low Rsym in the high resolution shell). I've never seen a paper where the I/sigma was given in the abstract after stating a resolution. This can potentially mislead the average reader's perception of the actual resolution (if it exists). It is my opinion that authors should not proclaim a resolution for their structure if they aren't employing the same stringency that has classically guided the limits of resolution. Just leave that sentence out and let the statistics table do the talking. -Chris -- Christopher Bahl Department of Biochemistry Dartmouth Medical School 7200 Vail Building, Rm 408 Hanover, NH 03755-3844 USA phone: (603) 650-1164 fax: (603) 650-1128 e-mail: christopher.b...@dartmouth.edu Ed Pozharski wrote: Not to derail the thread, but there is nothing, imho, wrong with I/s=1 cutoff (you expect I/s=2, I assume?). R-factors will get higher, but there are good reasons to believe that model will actually be better. This has been discussed many times before and there is probably no resolution, so why not just let people choose whatever resolution cutoff they want (as long as the I/s is clearly stated)? Disclaimer: I always use I/s=1 cutoff (assuming that completeness is good, of course). Compared to I/s=2 it doesn't really overstate resolution all that much (e.g. 2.1 vs 2.2). On Fri, 2009-12-11 at 13:18 +0100, Silvia Onesti wrote: I think also the editors are sometimes to blame. I once refereed a paper and pointed out that the resolution was overstated (I/s(I) = 1.05 in the last resolution shell, as well as a couple of comments that clearly suggested that the density wasn't very good). The editor ignored my comments. Silvia Silvia Onesti Sincrotrone Trieste S.C.p.A. SS 14 - km 163,5 - AREA Science Park, 34149 Basovizza, Trieste ITALY Email: silvia.one...@elettra.trieste.it Tel. +39 040 3758451 Mob +39 366 6878001 http://www.elettra.trieste.it/PEOPLE/index.php?n=SilviaOnesti.HomePage http://www.sissa.it/sbp/web_2008/research_structuralbio.html On Fri, 11 Dec 2009 10:48:41 +0100 Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
I would like to point out that this outright fabrication remains an isolated incident. There are over 50,000 crystal structures in the PDB, which means that this is only ~0.02% of the total. This is all quite bad, but let's not overstate the problem. Maybe such report is not a great idea after all - don't you think it will help the next troublemaker to fabricate structures better? :) I wonder if there are any structures from the author in question that were not fabricated. After all, some serious mistakes were made in 2hr0 (how can you not know about bulk solvent and B-factor variation?). There is 1BGX which was not on retraction list (I guess since it was done at Temple University, not UAB), but it looks weird too: the B-factors of main chain and side chain atoms are not much different from each other and this 2.3A-diffracting crystal has very few crystal contacts (it's the Taq DNA polymerase in complex with inhibitory Fab and the whole heavy chain makes no crystal contacts at all which is probably unique). On Fri, 2009-12-11 at 15:30 -0500, Ibrahim Moustafa wrote: You are absolutely right, more information describing to what extents these structures were falsified will be valuable to the community. Actually, it will be more useful if the investigators can publish their report as an article in Acta D (as a case study for tracking falsified structures). I have a suggestion (actually a request) to the expertise in the field to write a kind of review article about sources of error in crystallography and how to hunt these errors. It will be even better if it is written considering the non-crystallographers (scientists who use the structural information - like the co-authors on structural papers). This will help to educate the non-crystallographers how to look at the structures critically. Ibrahim -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
I have to agree with Ed Pozharski here. It has been shown that it can be valid to use I/sigma levels as low as ~1 for refinement (Ling, Read, et al, Biochemistry 1998; Delabarre, Brunger, Acta Cryst D, 2006). I am bothered more when I see I/sigma cutoffs of 4, where Rsym is 30% in the high resolution bin. It makes me think the authors might be hiding something, or stuck with the ancient notions of a not-to-be-exceeded, sacred Rsym value. Just because the reader might not read the statistics table does not mean legitimate data should be discarded during refinement. At the end, it is what inferences you make from your model that determine your claim of resolution limit (2.5 or 2.6 A!) to be much relevant. And I do agree with not making too much of the resolution limit, and presenting your statistics plainly and clearly in a table (probably not buried in supplementary table 3). Engin P.S. Oh well, the thread is hijacked now. Original Message Subject:Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures Date: Fri, 11 Dec 2009 16:58:07 -0500 From: Christopher Bahl ccp4.b...@gmail.com Reply-To: Christopher Bahl ccp4.b...@gmail.com To: CCP4BB@JISCMAIL.AC.UK I think that when a model's resolution is clearly stated in a paper, many readers still assume the pre-maximum likelihood definition (i.e. high I/sigma, low Rsym in the high resolution shell). I've never seen a paper where the I/sigma was given in the abstract after stating a resolution. This can potentially mislead the average reader's perception of the actual resolution (if it exists). It is my opinion that authors should not proclaim a resolution for their structure if they aren't employing the same stringency that has classically guided the limits of resolution. Just leave that sentence out and let the statistics table do the talking. -Chris -- Christopher Bahl Department of Biochemistry Dartmouth Medical School 7200 Vail Building, Rm 408 Hanover, NH 03755-3844 USA phone: (603) 650-1164 fax: (603) 650-1128 e-mail: christopher.b...@dartmouth.edu Ed Pozharski wrote: Not to derail the thread, but there is nothing, imho, wrong with I/s=1 cutoff (you expect I/s=2, I assume?). R-factors will get higher, but there are good reasons to believe that model will actually be better. This has been discussed many times before and there is probably no resolution, so why not just let people choose whatever resolution cutoff they want (as long as the I/s is clearly stated)? Disclaimer: I always use I/s=1 cutoff (assuming that completeness is good, of course). Compared to I/s=2 it doesn't really overstate resolution all that much (e.g. 2.1 vs 2.2). On Fri, 2009-12-11 at 13:18 +0100, Silvia Onesti wrote: I think also the editors are sometimes to blame. I once refereed a paper and pointed out that the resolution was overstated (I/s(I) = 1.05 in the last resolution shell, as well as a couple of comments that clearly suggested that the density wasn't very good). The editor ignored my comments. Silvia Silvia Onesti Sincrotrone Trieste S.C.p.A. SS 14 - km 163,5 - AREA Science Park, 34149 Basovizza, Trieste ITALY Email: silvia.one...@elettra.trieste.it Tel. +39 040 3758451 Mob +39 366 6878001 http://www.elettra.trieste.it/PEOPLE/index.php?n=SilviaOnesti.HomePage http://www.sissa.it/sbp/web_2008/research_structuralbio.html On Fri, 11 Dec 2009 10:48:41 +0100 Vellieux Fredericfrederic.velli...@ibs.fr wrote: Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred.
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Fred V wrote: I personally like to visualise the electron density as well, however, I do think that a non-crystallographer will go through the trouble of downloading the structure factors, installing ccp4/coot etc. Fred. They shouldn't have to go through some of that trouble. Maps should be deposited. Even if you have good crystallography knowledge can you exactly reproduce the map the authors were looking at? Software algorithms change over the years... the software version the authors used might not even be compilable on modern systems... some authors may not fully specify all software settings required to get the same map (perhaps they used NCS but you have to re-determine the NCS yourself)... etc. -- Eric Bennett, er...@pobox.com
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
There is nothing wrong per se with the cutoff level selected, but it is the inconsistency of that level with Rmerge and the Rvalues for the highest shell. BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ed Pozharski Sent: Friday, December 11, 2009 12:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures Not to derail the thread, but there is nothing, imho, wrong with I/s=1 cutoff (you expect I/s=2, I assume?). R-factors will get higher, but there are good reasons to believe that model will actually be better. This has been discussed many times before and there is probably no resolution, so why not just let people choose whatever resolution cutoff they want (as long as the I/s is clearly stated)? Disclaimer: I always use I/s=1 cutoff (assuming that completeness is good, of course). Compared to I/s=2 it doesn't really overstate resolution all that much (e.g. 2.1 vs 2.2). On Fri, 2009-12-11 at 13:18 +0100, Silvia Onesti wrote: I think also the editors are sometimes to blame. I once refereed a paper and pointed out that the resolution was overstated (I/s(I) = 1.05 in the last resolution shell, as well as a couple of comments that clearly suggested that the density wasn't very good). The editor ignored my comments. Silvia Silvia Onesti Sincrotrone Trieste S.C.p.A. SS 14 - km 163,5 - AREA Science Park, 34149 Basovizza, Trieste ITALY Email: silvia.one...@elettra.trieste.it Tel. +39 040 3758451 Mob +39 366 6878001 http://www.elettra.trieste.it/PEOPLE/index.php?n=SilviaOnesti.HomePage http://www.sissa.it/sbp/web_2008/research_structuralbio.html On Fri, 11 Dec 2009 10:48:41 +0100 Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
I'm not arguing to exclude high resolution reflections. I just think that authors shouldn't claim to have a 1.3 angstrom structure if they have 0.5 I/sigma and 90% Rsym in the high resolution shell. -Chris -- Christopher Bahl Department of Biochemistry Dartmouth Medical School 7200 Vail Building, Rm 408 Hanover, NH 03755-3844 USA phone: (603) 650-1164 fax: (603) 650-1128 e-mail: christopher.b...@dartmouth.edu Engin Ozkan wrote: I have to agree with Ed Pozharski here. It has been shown that it can be valid to use I/sigma levels as low as ~1 for refinement (Ling, Read, et al, Biochemistry 1998; Delabarre, Brunger, Acta Cryst D, 2006). I am bothered more when I see I/sigma cutoffs of 4, where Rsym is 30% in the high resolution bin. It makes me think the authors might be hiding something, or stuck with the ancient notions of a not-to-be-exceeded, sacred Rsym value. Just because the reader might not read the statistics table does not mean legitimate data should be discarded during refinement. At the end, it is what inferences you make from your model that determine your claim of resolution limit (2.5 or 2.6 A!) to be much relevant. And I do agree with not making too much of the resolution limit, and presenting your statistics plainly and clearly in a table (probably not buried in supplementary table 3). Engin P.S. Oh well, the thread is hijacked now. Original Message Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures Date: Fri, 11 Dec 2009 16:58:07 -0500 From: Christopher Bahl ccp4.b...@gmail.com Reply-To: Christopher Bahl ccp4.b...@gmail.com To: CCP4BB@JISCMAIL.AC.UK I think that when a model's resolution is clearly stated in a paper, many readers still assume the pre-maximum likelihood definition (i.e. high I/sigma, low Rsym in the high resolution shell). I've never seen a paper where the I/sigma was given in the abstract after stating a resolution. This can potentially mislead the average reader's perception of the actual resolution (if it exists). It is my opinion that authors should not proclaim a resolution for their structure if they aren't employing the same stringency that has classically guided the limits of resolution. Just leave that sentence out and let the statistics table do the talking. -Chris
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
On Fri, 11 Dec 2009 15:30:53 -0500, Ibrahim Moustafa i.moust...@psu.edu wrote: You are absolutely right, more information describing to what extents these structures were falsified will be valuable to the community. Actually, it will be more useful if the investigators can publish their report as an article in Acta D (as a case study for tracking falsified structures). Early this morning I put together a post that attempts to describe how one structure (1BEF) was falsified. I do not have any direct proof. I would be interested if others think the hypothesis is reasonable or better yet have a better idea. http://bit.ly/4vjLbE Thanks. Sean I have a suggestion (actually a request) to the expertise in the field to write a kind of review article about sources of error in crystallography and how to hunt these errors. It will be even better if it is written considering the non-crystallographers (scientists who use the structural information - like the co-authors on structural papers). This will help to educate the non-crystallographers how to look at the structures critically. Ibrahim
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
Bernhard, I understand that you are referring to the 2hr0, right? There the Rmerge was unexpectedly low given the I/sigma. What I meant, of course, is that I/sigma=1 is legitimate choice in general. Ed. On Fri, 2009-12-11 at 15:33 -0800, Bernhard Rupp wrote: There is nothing wrong per se with the cutoff level selected, but it is the inconsistency of that level with Rmerge and the Rvalues for the highest shell. BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ed Pozharski Sent: Friday, December 11, 2009 12:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures Not to derail the thread, but there is nothing, imho, wrong with I/s=1 cutoff (you expect I/s=2, I assume?). R-factors will get higher, but there are good reasons to believe that model will actually be better. This has been discussed many times before and there is probably no resolution, so why not just let people choose whatever resolution cutoff they want (as long as the I/s is clearly stated)? Disclaimer: I always use I/s=1 cutoff (assuming that completeness is good, of course). Compared to I/s=2 it doesn't really overstate resolution all that much (e.g. 2.1 vs 2.2). On Fri, 2009-12-11 at 13:18 +0100, Silvia Onesti wrote: I think also the editors are sometimes to blame. I once refereed a paper and pointed out that the resolution was overstated (I/s(I) = 1.05 in the last resolution shell, as well as a couple of comments that clearly suggested that the density wasn't very good). The editor ignored my comments. Silvia Silvia Onesti Sincrotrone Trieste S.C.p.A. SS 14 - km 163,5 - AREA Science Park, 34149 Basovizza, Trieste ITALY Email: silvia.one...@elettra.trieste.it Tel. +39 040 3758451 Mob +39 366 6878001 http://www.elettra.trieste.it/PEOPLE/index.php?n=SilviaOnesti.HomePage http://www.sissa.it/sbp/web_2008/research_structuralbio.html On Fri, 11 Dec 2009 10:48:41 +0100 Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
What I meant, of course, is that I/sigma=1 is legitimate choice in general. For refinement, yes, as long as the program weights them properly, and your Rmerge is about 0.8/I/Sig(I) in that shell. High resolution cutoff in refinement should not be necessary as long as the program applies proper bulk solvent correction. Different for phasing, where much higher high-res cutoffs are needed to suppress dominating high delta**2 values resulting from noise difference, or in MR to suppress reflections giving rise to certain Patterson distances of less relevance (to short or too long). I say this just to impress on the beginners that cutoffs and outlier downscaling are quite different depending on the use of the data! BR -Original Message- From: Ed Pozharski [mailto:epozh...@umaryland.edu] Sent: Friday, December 11, 2009 3:45 PM To: b...@ruppweb.org Cc: CCP4BB@JISCMAIL.AC.UK Subject: RE: [ccp4bb] FW: pdb-l: Retraction of 12 Structures Bernhard, I understand that you are referring to the 2hr0, right? There the Rmerge was unexpectedly low given the I/sigma. What I meant, of course, is that I/sigma=1 is legitimate choice in general. Ed. On Fri, 2009-12-11 at 15:33 -0800, Bernhard Rupp wrote: There is nothing wrong per se with the cutoff level selected, but it is the inconsistency of that level with Rmerge and the Rvalues for the highest shell. BR -Original Message- From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Ed Pozharski Sent: Friday, December 11, 2009 12:58 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures Not to derail the thread, but there is nothing, imho, wrong with I/s=1 cutoff (you expect I/s=2, I assume?). R-factors will get higher, but there are good reasons to believe that model will actually be better. This has been discussed many times before and there is probably no resolution, so why not just let people choose whatever resolution cutoff they want (as long as the I/s is clearly stated)? Disclaimer: I always use I/s=1 cutoff (assuming that completeness is good, of course). Compared to I/s=2 it doesn't really overstate resolution all that much (e.g. 2.1 vs 2.2). On Fri, 2009-12-11 at 13:18 +0100, Silvia Onesti wrote: I think also the editors are sometimes to blame. I once refereed a paper and pointed out that the resolution was overstated (I/s(I) = 1.05 in the last resolution shell, as well as a couple of comments that clearly suggested that the density wasn't very good). The editor ignored my comments. Silvia Silvia Onesti Sincrotrone Trieste S.C.p.A. SS 14 - km 163,5 - AREA Science Park, 34149 Basovizza, Trieste ITALY Email: silvia.one...@elettra.trieste.it Tel. +39 040 3758451 Mob +39 366 6878001 http://www.elettra.trieste.it/PEOPLE/index.php?n=SilviaOnesti.HomePage http://www.sissa.it/sbp/web_2008/research_structuralbio.html On Fri, 11 Dec 2009 10:48:41 +0100 Vellieux Frederic frederic.velli...@ibs.fr wrote: Hi all, Like everyone else, I was appalled. My two cents worth: Nature and Science are not scientific journals in the strict sense of the term. They are more like magazines (I won't go all the way to say tabloids), and as such will do anything to publish what seems to be hot. And will reject very good scientific papers. So it's not a surprise that retractions affect magazines such as Science and Nature. Fred. -- Edwin Pozharski, PhD, Assistant Professor University of Maryland, Baltimore -- When the Way is forgotten duty and justice appear; Then knowledge and wisdom are born along with hypocrisy. When harmonious relationships dissolve then respect and devotion arise; When a nation falls to chaos then loyalty and patriotism are born. -- / Lao Tse /
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures....
*** This message has been scanned by the InterScan for CSC SSM by IICT security policy and found to be free of known security risks. *** Bernhard, I would be worried about sending the structure factors and the coordinates along with the manuscript. However, once the scientific merits of the paper are judged and it can be acceptable for the journal, the coordinates and the data have to be reviewed and then only the paper has to be completely accepted. Important, these data either should be directly from the PDB database or the identical set from the authors. This, not only will give confidence to the genuine scientist but will also keep a check on the perpetrators and more responsibility on the reviewers/publishers. Anthony - Dr. Anthony Addlagatta Scientist E1 Indian Institute of Chemical Technology [IICT] Tarnaka, Hyderabad AP-500 607, INDIA Tel:91-40-27191812 -- Original Message --- From: Bernhard Rupp b...@ruppweb.org To: CCP4BB@JISCMAIL.AC.UK Sent: Fri, 11 Dec 2009 11:47:24 -0800 Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures *** This message has been scanned by the InterScan for CSC SSM at IICT and found to be free of known security risks. *** I have to say to the credit of Nature and competent authors that in every case I have requested structure factors and coordinates for review they have arranged to provide these. AFAIK this is their editorial policy, but it requires that at least one of the reviewers knows what to do with the SF as and coordinates. That, however, does not (yet??) seem to be policy, i.e. to pair a technical crystallography review with one that evaluates biological and other relevance. BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Prof. Joel L. Sussman Sent: Friday, December 11, 2009 1:31 AM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures 11-Dec-2009 11:30 Rehovot Dear All, I Agree fully with Tommi, and feel, in parallel, we in the MX community must think of better tools for referees to review papers and insist that these be followed. For example we should insist on getting BOTH the coords and structure factors for papers submitted, so it would be possible to do test on the structures which appear to have 'question marks'. Without this data, it is very difficult to do a serious job in refereeing. Also, any manuscript, submitted to any journal, where BOTH the structure factors and coords are not submitted to the PDB should be rejected immediately without further review. This should be the policy of the reviewer, independent of any particular policy of the journals. It might be worthwhile for the MX community to also consider writing a strong letter to the journals in which published the papers for which the structures have now been retracted, to state just how serious this matter is and that the journals should also take much more responsibility of finding better ways to have these papers and structures reviewed. Joel - Prof. Joel L. Sussman Director, Israel Structural Proteomics Center Dept. of Structural Biology Weizmann Institute of Science Rehovot 76100 ISRAEL Tel: +972 8-934 4531 Fax: +972 8-934 6312 joel.suss...@weizmann.ac.il www.weizmann.ac.il/~joel; www.weizmann.ac.il/ISPC - On 11 Dec 2009, at 11:19, Tommi Kajander wrote: Would the exact analysis of how each of these things were wrong and fabricated be somewhere available Would be fair (apart from the known case of C3b) to have the whole analysis available instead of just this kind of news feed. I suspect its not obvious by five minute check in all cases. Perhaps there needs to be ways within PDB in form of automated tools that would raise those red flags in suspicious cases (e.g. some data analysis --such as the contribution by solvent etc now that data beyond 8Å is by default used in refinement) - as it appears peer review/editing by journals isn't/cant always be(?) stringent enough. In any case, some type of automated analysis of the whole data base might be a good idea, as there can be other cases (with another couple of thousand papers citing them..). tommi On Dec 10, 2009, at 4:16 PM, Ibrahim Moustafa wrote: 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
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
I assume this is the denouement of the Ajees et al debacle a while back? Does this mean all authors on all of those papers were complicit? Otherwise, how would one author alone perpetrate this kind of thing? He pretends to go to the synchrotron, comes back with the hkl file, and goes from there? What about the crystals? Grows some lysozyme crystals, labels as protein x, proceeds to go to the synchrotron and then...? This whole thing is really hard to imagine--is there an initiation procedure in that lab, when the noble lie is revealed to all would-be authors? Jacob Keller *** Jacob Pearson Keller Northwestern University Medical Scientist Training Program Dallos Laboratory F. Searle 1-240 2240 Campus Drive Evanston IL 60208 lab: 847.491.2438 cel: 773.608.9185 email: j-kell...@northwestern.edu *** - Original Message - From: Ibrahim Moustafa i.moust...@psu.edu To: CCP4BB@JISCMAIL.AC.UK Sent: Thursday, December 10, 2009 8:16 AM Subject: [ccp4bb] FW: pdb-l: Retraction of 12 Structures Hi all, I want to share the following e-mail received from pdb-l. It is sad to see something like that! regards, Ibrahim -- Forwarded Message From: Michael Sadowski mockeldri...@yahoo.com Date: Thu, 10 Dec 2009 04:22:28 -0800 (PST) To: pd...@rcsb.org Subject: pdb-l: Retraction of 12 Structures Dear All, Better check your data! Apologies to those who have seen this. S. - The University of Alabama at Birmingham has issued a statement indicating that a former UAB researcher may have fabricated or falsified data about protein structures that are contained in the Protein Data Bank. The university did not include a name of the researcher, but the Birmingham News this week reported that the scientist is H.M. Krishna Murthy and an independent review by BioInform of the PDB shows that Murthy is associated with all of the proteins that UAB said were falsified. The newspaper said that a probe of Murthy's research has been underway since 2007. 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. - http://www.genomeweb.com/informatics/university-alabama-says-researcher-fabr icated-protein-structures-now-protein-dat?utm_source=feedburnerutm_medium=f eedutm_campaign=Feed%3A+genomeweb%2Fbioinform+%28BioInform%29 http://main.uab.edu/Sites/reporter/articles/71570/ http://blog.al.com/birmingham-news-stories/2009/12/ex-uab_researchers_work_m ay_be.html TO UNSUBSCRIBE OR CHANGE YOUR SUBSCRIPTION OPTIONS, please see https://lists.sdsc.edu/mailman/listinfo.cgi/pdb-l . -- End of Forwarded Message
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
He pretends to go to the synchrotron, comes back Thats what I do all the time. Instead, I go to lane splitters / jupiter for pizza and beer. P
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: I assume this is the denouement of the Ajees et al debacle a while back? Does this mean all authors on all of those papers were complicit? Otherwise, how would one author alone perpetrate this kind of thing? He pretends to go to the synchrotron, comes back with the hkl file, and goes from there? What about the crystals? Grows some lysozyme crystals, labels as protein x, proceeds to go to the synchrotron and then...? This whole thing is really hard to imagine--is there an initiation procedure in that lab, when the noble lie is revealed to all would-be authors? I'm curious about this too, but it is actually very likely that some (perhaps the majority) of the co-authors were unaware of the fraud, especially those whose name is only present on a single paper. I didn't look closely, but I recognized one name of someone who certainly doesn't need to fake anything at this point in his career; I would be shocked if he had any clue what was going on. Likewise, if there were co-authors from entirely different fields, I'm sure they wouldn't know what a Wilson plot is supposed to look like. Many excellent scientists have been burned like this before; wouldn't you assume that your collaborators are acting in good faith? There are two other things to keep in mind: 1. The standard for co-authorship is often very low. This is a problem by itself, and it's one reason why Nature (and a few others) now list author contributions by name. 2. Rumor has it that in some labs, the PI may take the data and solve the structure personally, cutting out the postdoc or grad student who did most of the benchwork. (I've seen one or two author contribution sections that indicated this had occurred.) After all, spinning dials and looking at electron density is the fun part of crystallography. Who is going to second-guess the professor when a recommendation letter (and future career) is at stake? -Nat
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
This kind of unfortunate situation only reinforces the notion that there must be some sort of laboratory oversight/communication/mentoring/documentation procedures in place. In my research lab (populated by a postdoc and a bunch of undergraduates) raw images and data processing log files are visible to everyone on the central XRD server, there is a lot of intra-laboratory communication about every structure that is processed, and lots of required documentation that must go onto our electronic laboratory notebook/wiki. While a determined individual could still find a way to perpetrate fraud, it is a lot more difficult when there are a lot of eyes looking at every structure, and raw data and documentation is widely visible within the lab. This is not a bad thing for co-authorship purposes, also. Nathaniel Echols wrote: On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: I assume this is the denouement of the Ajees et al debacle a while back? Does this mean all authors on all of those papers were complicit? Otherwise, how would one author alone perpetrate this kind of thing? He pretends to go to the synchrotron, comes back with the hkl file, and goes from there? What about the crystals? Grows some lysozyme crystals, labels as protein x, proceeds to go "to the synchrotron" and then...? This whole thing is really hard to imagine--is there an "initiation" procedure in that lab, when the "noble lie" is revealed to all would-be authors? I'm curious about this too, but it is actually very likely that some (perhaps the majority) of the co-authors were unaware of the fraud, especially those whose name is only present on a single paper. I didn't look closely, but I recognized one name of someone who certainly doesn't need to fake anything at this point in his career; I would be shocked if he had any clue what was going on. Likewise, if there were co-authors from entirely different fields, I'm sure they wouldn't know what a Wilson plot is supposed to look like. Many excellent scientists have been burned like this before; wouldn't you assume that your collaborators are acting in good faith? There are two other things to keep in mind: 1. The standard for co-authorship is often very low. This is a problem by itself, and it's one reason why Nature (and a few others) now list author contributions by name. 2. Rumor has it that in some labs, the PI may take the data and solve the structure personally, cutting out the postdoc or grad student who did most of the benchwork. (I've seen one or two author contribution sections that indicated this had occurred.) After all, spinning dials and looking at electron density is the "fun" part of crystallography. Who is going to second-guess the professor when a recommendation letter (and future career) is at stake? -Nat -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
If that's of any consolation for us crystallographers, this situations arise in other fields too. Here is another example. See this link: http://www.biotechniques.com/news/Glycosylation-methods-paper-retracted/biotechniques-182060.html Boaz - Original Message - From: Roger Rowlett rrowl...@colgate.edu Date: Thursday, December 10, 2009 21:07 Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures To: CCP4BB@JISCMAIL.AC.UK This kind of unfortunate situation only reinforces the notion that there must be some sort of laboratory oversight/communication/mentoring/documentation procedures in place. In my research lab (populated by a postdoc and a bunch of undergraduates) raw images and data processing log files are visible to everyone on the central XRD server, there is a lot of intra-laboratory communication about every structure that is processed, and lots of required documentation that must go onto our electronic laboratory notebook/wiki. While a determined individual could still find a way to perpetrate fraud, it is a lot more difficult when there are a lot of eyes looking at every structure, and raw data and documentation is widely visible within the lab. This is not a bad thing for co-authorship purposes, also. Nathaniel Echols wrote: On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: I assume this is the denouement of the Ajees et al debacle a while back? Does this mean all authors on all of those papers were complicit? Otherwise, how would one author alone perpetrate this kind of thing? He pretends to go to the synchrotron, comes back with the hkl file, and goes from there? What about the crystals? Grows some lysozyme crystals, labels as protein x, proceeds to go to the synchrotron and then...? This whole thing is really hard to imagine--is there an initiation procedure in that lab, when the noble lie is revealed to all would-be authors? I'm curious about this too, but it is actually very likely that some (perhaps the majority) of the co-authors were unaware of the fraud, especially those whose name is only present on a single paper. I didn't look closely, but I recognized one name of someone who certainly doesn't need to fake anything at this point in his career; I would be shocked if he had any clue what was going on. Likewise, if there were co-authors from entirely different fields, I'm sure they wouldn't know what a Wilson plot is supposed to look like. Many excellent scientists have been burned like this before; wouldn't you assume that your collaborators are acting in good faith? There are two other things to keep in mind: 1. The standard for co-authorship is often very low. This is a problem by itself, and it's one reason why Nature (and a few others) now list author contributions by name. 2. Rumor has it that in some labs, the PI may take the data and solve the structure personally, cutting out the postdoc or grad student who did most of the benchwork. (I've seen one or two author contribution sections that indicated this had occurred.) After all, spinning dials and looking at electron density is the fun part of crystallography. Who is going to second-guess the professor when a recommendation letter (and future career) is at stake? -Nat -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Thanks for bringing this article to our attention. I went ahead and created a table of the PDBs in question including links to the structures, journals and citations. My hope is that it will save others time trying to track down this information. http://bit.ly/5KqaRF Hope it helps. Sean
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
Actually, I don't think that should be any consolation at all... As scientists, from whatever field, we should be appalled by this kind of mischief from anyone that calls themselves scientists. Not only it has effects on further research, delaying science sometimes by years, but it just gives an appalling image of science and scientists. And of course, is unethical and wrong... Today is a sad moment for crystallography and science. = Dr Paula Salgado Division of Molecular Biosciences Department of Life Sciences Faculty of Natural Sciences Biochemistry Building, 5th Floor Imperial College London South Kensington Campus SW7 2AZ London Tel: 02075945464 2009/12/10 Boaz Shaanan bshaa...@bgu.ac.il If that's of any consolation for us crystallographers, this situations arise in other fields too. Here is another example. See this link: http://www.biotechniques.com/news/Glycosylation-methods-paper-retracted/biotechniques-182060.html Boaz - Original Message - From: Roger Rowlett rrowl...@colgate.edu Date: Thursday, December 10, 2009 21:07 Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures To: CCP4BB@JISCMAIL.AC.UK This kind of unfortunate situation only reinforces the notion that there must be some sort of laboratory oversight/communication/mentoring/documentation procedures in place. In my research lab (populated by a postdoc and a bunch of undergraduates) raw images and data processing log files are visible to everyone on the central XRD server, there is a lot of intra-laboratory communication about every structure that is processed, and lots of required documentation that must go onto our electronic laboratory notebook/wiki. While a determined individual could still find a way to perpetrate fraud, it is a lot more difficult when there are a lot of eyes looking at every structure, and raw data and documentation is widely visible within the lab. This is not a bad thing for co-authorship purposes, also. Nathaniel Echols wrote: On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: I assume this is the denouement of the Ajees et al debacle a while back? Does this mean all authors on all of those papers were complicit? Otherwise, how would one author alone perpetrate this kind of thing? He pretends to go to the synchrotron, comes back with the hkl file, and goes from there? What about the crystals? Grows some lysozyme crystals, labels as protein x, proceeds to go to the synchrotron and then...? This whole thing is really hard to imagine--is there an initiation procedure in that lab, when the noble lie is revealed to all would-be authors? I'm curious about this too, but it is actually very likely that some (perhaps the majority) of the co-authors were unaware of the fraud, especially those whose name is only present on a single paper. I didn't look closely, but I recognized one name of someone who certainly doesn't need to fake anything at this point in his career; I would be shocked if he had any clue what was going on. Likewise, if there were co-authors from entirely different fields, I'm sure they wouldn't know what a Wilson plot is supposed to look like. Many excellent scientists have been burned like this before; wouldn't you assume that your collaborators are acting in good faith? There are two other things to keep in mind: 1. The standard for co-authorship is often very low. This is a problem by itself, and it's one reason why Nature (and a few others) now list author contributions by name. 2. Rumor has it that in some labs, the PI may take the data and solve the structure personally, cutting out the postdoc or grad student who did most of the benchwork. (I've seen one or two author contribution sections that indicated this had occurred.) After all, spinning dials and looking at electron density is the fun part of crystallography. Who is going to second-guess the professor when a recommendation letter (and future career) is at stake? -Nat -- -- Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315)-228-7935 email: rrowl...@colgate.edu Boaz Shaanan, Ph.D. Dept. of Life Sciences Ben-Gurion University of the Negev Beer-Sheva 84105 Israel Phone: 972-8-647-2220 ; Fax: 646-1710 Skype: boaz.shaanan
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
I wish to point out (as I unsuccessfully did to Nature) that by just READING the infamous Table 1 (data collection and refinement stats, hidden in the supplemental material) any review worth its name should immediately have raised multiple red flags. Check for yourself. Also the B-factor distribution is worth a look (Fig 13-20 in my paper weight). Also, the report by Zbysek Otwinowsky is most gripping forensic yarn. http://bones.swmed.edu/people.html BR From: CCP4 bulletin board [mailto:ccp...@jiscmail.ac.uk] On Behalf Of Paula Salgado Sent: Thursday, December 10, 2009 2:06 PM To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures Actually, I don't think that should be any consolation at all... As scientists, from whatever field, we should be appalled by this kind of mischief from anyone that calls themselves scientists. Not only it has effects on further research, delaying science sometimes by years, but it just gives an appalling image of science and scientists. And of course, is unethical and wrong... Today is a sad moment for crystallography and science. = Dr Paula Salgado Division of Molecular Biosciences Department of Life Sciences Faculty of Natural Sciences Biochemistry Building, 5th Floor Imperial College London South Kensington Campus SW7 2AZ London Tel: 02075945464 2009/12/10 Boaz Shaanan bshaa...@bgu.ac.il If that's of any consolation for us crystallographers, this situations arise in other fields too. Here is another example. See this link: http://www.biotechniques.com/news/Glycosylation-methods-paper-retracted/biotechniques-182060.html Boaz - Original Message - From: Roger Rowlett rrowl...@colgate.edu Date: Thursday, December 10, 2009 21:07 Subject: Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures To: CCP4BB@JISCMAIL.AC.UK This kind of unfortunate situation only reinforces the notion that there must be some sort of laboratory oversight/communication/mentoring/documentation procedures in place. In my research lab (populated by a postdoc and a bunch of undergraduates) raw images and data processing log files are visible to everyone on the central XRD server, there is a lot of intra-laboratory communication about every structure that is processed, and lots of required documentation that must go onto our electronic laboratory notebook/wiki. While a determined individual could still find a way to perpetrate fraud, it is a lot more difficult when there are a lot of eyes looking at every structure, and raw data and documentation is widely visible within the lab. This is not a bad thing for co-authorship purposes, also. Nathaniel Echols wrote: On Thu, Dec 10, 2009 at 5:59 PM, Jacob Keller j-kell...@md.northwestern.edu wrote: I assume this is the denouement of the Ajees et al debacle a while back? Does this mean all authors on all of those papers were complicit? Otherwise, how would one author alone perpetrate this kind of thing? He pretends to go to the synchrotron, comes back with the hkl file, and goes from there? What about the crystals? Grows some lysozyme crystals, labels as protein x, proceeds to go to the synchrotron and then...? This whole thing is really hard to imagine--is there an initiation procedure in that lab, when the noble lie is revealed to all would-be authors? I'm curious about this too, but it is actually very likely that some (perhaps the majority) of the co-authors were unaware of the fraud, especially those whose name is only present on a single paper. I didn't look closely, but I recognized one name of someone who certainly doesn't need to fake anything at this point in his career; I would be shocked if he had any clue what was going on. Likewise, if there were co-authors from entirely different fields, I'm sure they wouldn't know what a Wilson plot is supposed to look like. Many excellent scientists have been burned like this before; wouldn't you assume that your collaborators are acting in good faith? There are two other things to keep in mind: 1. The standard for co-authorship is often very low. This is a problem by itself, and it's one reason why Nature (and a few others) now list author contributions by name. 2. Rumor has it that in some labs, the PI may take the data and solve the structure personally, cutting out the postdoc or grad student who did most of the benchwork. (I've seen one or two author contribution sections that indicated this had occurred.) After all, spinning dials and looking at electron density is the fun part of crystallography. Who is going to second-guess the professor when a recommendation letter (and future career) is at stake? -Nat -- _ Roger S. Rowlett Professor Department of Chemistry Colgate University 13 Oak Drive Hamilton, NY 13346 tel: (315)-228-7245 ofc: (315)-228-7395 fax: (315
Re: [ccp4bb] FW: pdb-l: Retraction of 12 Structures
For previous debate on this issue see (in CCP4 archives) https://www.jiscmail.ac.uk/cgi-bin/webadmin?S2=CCP4BBq=s=The+importanc e+of+USING+our+validation+toolsf=a=b= I think Eleanor started it https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0708L=CCP4BBP=R75676 And of course it is deja vu once again as Jacob Keller pointed out https://www.jiscmail.ac.uk/cgi-bin/webadmin?A2=ind0708L=CCP4BBP=R86792 Quarter of a century gap between the two incidents though Colin -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. If you are not the intended addressee or an authorised recipient of the addressee please notify us of receipt by returning the e-mail and do not use, copy, retain, distribute or disclose the information in or attached to the e-mail. Any opinions expressed within this e-mail are those of the individual and not necessarily of Diamond Light Source Ltd. Diamond Light Source Ltd. cannot guarantee that this e-mail or any attachments are free from viruses and we cannot accept liability for any damage which you may sustain as a result of software viruses which may be transmitted in or with the message. Diamond Light Source Limited (company no. 4375679). Registered in England and Wales with its registered office at Diamond House, Harwell Science and Innovation Campus, Didcot, Oxfordshire, OX11 0DE, United Kingdom
