On the recent embargo breach involving GWAS data and a PNAS publication (which was recently retracted). - Hilary

Good to see people taking the ethical side of this seriously. I'm less convinced about the value of specific rules and more by the idea that this should just be seen as bad behaviour but very glad to see people coming down on it like a ton of bricks. That's what will make people feel safe - not rules, not regulations, and not compulsions either, but very strong and public responses to breaches. - Cameron Neylon

@Cameron +1 . But ideally some kind of consequences/punishment surely would be order as well, e.g. the authors responsible would not be kindly received next time they ask for ethical approval to access controlled-access data from NIH (or other) repositories. Some sort of blacklisting for 'repeat offenders'? - 'Mummi' Thorisson

Not greatly in favour of blacklisting per se. I would say that it was a disciplinary offence though that ought to consider dismissal from post. Which really amounts to the same thing. - Cameron Neylon

Please correct me if I'm wrong, but I thought the consequences ("punishment") was that their paper was retracted. - Hilary

The paper was published Aug 31, retracted Sep 9, when all the authors had to do was to ask PNAS to publish it no earlier than Sep 23 to comply with the GENEVA data embargo policy. The closeness of all the dates suggests to me that it was more a serious messup than a malicious breach of policy. http://www.pnas.org/content... - Iddo Friedberg

Hilary, I would say that the retraction is just the reversal of the act rather than punishment. Paper shouldn't have been published, therefore it was "unpublished". If (and there should definitely be a proper investigation) someone thought they could get away with playing outside the rules there should be punishment above and beyond simple reversal in my view. This is "conduct unbecoming..." etc. But as Iddo says, not clear from the dates whether it might just have been a screwup. - Cameron Neylon

Cameron: a retraction is a very bad thing to have on your record. It is for all intents and purposes synonymous with"fraud". - Iddo Friedberg from Android

Without *knowing* the intent was malicious, forcing a retraction seems a bit harsh. If data is online it should be intended for use by the public. IMO this is just another argument for mandatory DOI's and better dataset citations. On the other hand, calling out a group for not having the courtesy or awareness to contact the originating lab is a good thing. Like Cameron said, the social norms are probably the best way to play this. - Paul J. Davis

Also, don't physicists have a pretty good system for the whole idea of citing datasets? NCBI's ability to provide transparency in terms of what data came from where and when is pretty atrocious, so its a bit weird to consider for biology. But I thought I read that the LHC data was pretty much available for citation. - Paul J. Davis

Iddo - I disagree on two counts with that. There are plenty of retractions out there that are honest mistakes or re-assessments. Embarrassing yes, emblematic of sloppy work yes, synonomous with fraud, nah. But more importantly if we take that kind of attitude then people will be too scared to correct things in the future - when we will (hopefully) have much more fine grained approaches available. Like Paul has said, retraction seems a bit harsh but it is absolutely necessary in this case to enable the original group to have their six months - even if it was just the result of a mistake. So let us imagine that this is the _journals_ fault for instance. A retraction (or at least a delay on the publication date) should still be in place - even if its not the authors fault. Therefore if we treat it as punishment, they are being potentially punished for something that isn't they're fault. Obviously in practice we have a mixture of both going on here which is probably not helpful and muddies the waters somewhat. - Cameron Neylon

Paul - I think citing datasets at NCBI isn't so hard. I'm not sure that's really the problem in this case (if it is then it's a definite mark against the authors). The problem is the culture in biology that collecting the data isn't worth anything so having a highly cited dataset isn't useful on your CV - no matter how good or useful it is. Only the paper matters. I have to say I haven't actually had the time to look over this case in detail though. - Cameron Neylon

This also raises issues of roles of journals, institution employing authors (often several, in different countries/legal systems, as papers now almost all multi-author), and funders in "policing" sci ethics. Lots of talk everywhere about this. Journals can publish policies and retract/correct (ensuring linking in A&I dbase searches etc) - but how can sci community deal with wider issues beyond the paper? (quite apart from the technical problems with enforcing eg "blacklisting") - Maxine

Neil - in response to your Q above - v hard in practice to be perfect but from journal's perspective: (1) consult with relevant community and state policies for standards all agree and (2) the peer-review process (advice from reviewers on repeatability). Also, of course, journals can in general encourage authors to disclose more rather than less. - Maxine

+1 Neil and Maxine. There is too much of an expection for "the journals" to sort this out. Publishers have an important role to play but we need to clean our own house. Or someone will do it for us. Probably the public. And probably by saying that they're not so interested in funding science any more. - Cameron Neylon

Thanks, Cameron. I agree, journals can and should help but as part of a wider process that scientists themselves (as a profession) decide is "best practice". Neil - have had this "code" discussion with eds here before - one view is that the documentation better/more meaningful to scientists (who aren't programmers in the main) - also many programmes are not open-source. Probably other points which I don't immediately recall. Nature Biotech is running community consult at the moment on this, I think. - Maxine