Ideally, one would be engaged in a collaboration wherein structure can be linked to function and published together. For most of us, that indeed would require a collaboration, since resources for most of us (at least in the US at present) are scant. Few crystallographers have the ability and resources to follow-up on the structure with mutagenesis or other data by themselves. For me, mammalian cell culture and transfection experiments are not feasible. Of course, in some cases, a structure can “explain” existing biological/biochemical data. These are the “primo” projects in which the structure by itself is valuable enough to merit publication in a top-tier journal. This is great when you can find it. However, those cases are becoming increasingly rare. One undercurrent in this discussion is this: a structure by itself is not enough to make it to the top tier journals in most cases. So what are we to do? My belief is that we have to share the credit and accept the fact that sometimes we will be secondary authors on major publications where the biology really counts. I guess I would rather be part of a team effort like that, in which I am not the first or last author, when the work is of high value, than publish my structure in a specialty journal. In a really competitive field, the choice can be difficult without collaborators. Yet, over time, even secondary authorship on high-profile projects, can accumulate justified scientific praise. At least I hope so.  With diminishing resources, what choice do we really have?

Dave


On 3/28/13 5:06 PM, "Scott Pegan" <[log in to unmask]> wrote:

Hey everyone,

Both Mark and Fred make some good points.  I totally agree with Nat (beat me to the send button).  Although in an ideal world with all the advancements in crowd sourcing and electronic media, one might think that posting data on a bulletin board might be considered marking one's turf and protect the scientist place in that pathway towards discoveries.  Regrettably, the current reality doesn't' support this case.  As structural biologists, we are still in the mode of first to publish gets the bulk of the glory and potentially future funding on the topic.

For instance, when I was in graduate school, the lab I was in had KcsA crystals at the same time as a couple of competing groups.  Several groups including the one I belong to had initial diffraction data.  One group was able to solve KcsA, the first K channel trans-membrane protein structure, first.  That group was led by Roderick Mackinnon, now a Noble Laureate partly because of this work.  Now imagine if one of Mackinnon's student would have put up the web their initial diffraction data and another group would have used it to assist in their interpretation of their own data and either solved the structure before Mackinnon, or at least published it prior.  Even if they acknowledged Mackinnion for the assistance of his data (as they should), Mackinnion and the other scientists in his lab would likely not have received the broad acclaim that they received and justly deserved.  Also, ask Rosalind Franklin how data sharing worked out for her.

Times haven't changed that much since ~10 years ago.  Actually, as many have mentioned, things have potentially gotten worse.  Worse in the respect that the scientific impact of structure is increasingly largely tide to the biochemical/biological studies that accompany the structure.  In other words, the discoveries based on the insights the structure provides.  Understandably, this increasing emphasis on follow up experiments to get into high impact journals in many cases increases the time between solving the structure and publishing it.  During this gap, the group who solved the structure first is vulnerable to being scoped.  Once scoped unless the interpretation of the structure and the conclusion of the follow up experiments are largely and justifiably divergent from the initial publications, there is usually a significant difficulty getting the article published in a top tier journal. Many might argue that they deposited it first, but I haven't seen anyone win that argument either.  Because follow up articles will cite the publication describing the structure, not the PDB entry.

Naturally, many could and should argue that this isn't they way it should be. We could rapidly move science ahead in many cases if research groups were entirely transparent and made available their discovers as soon as they could meet the veracity of peer-review.   However, this is not the current reality or model we operate in.  So, until this changes, one might be cautious about tipping your competition off whether they be another structural biology group looking to publish their already solved structure, or biology group that could use insights gathered by your structure information for a publication that might limit your own ability to publish. Fortunately, for Tom his structure sounds like it is only important to a pretty specific scientific question that many folks might not be working on exactly.

Scott




On Thu, Mar 28, 2013 at 12:28 PM,  <[log in to unmask]> wrote:
No. :-)

When you are a reviewer for structural papers in journals (I do this work sometimes), and when you see an article that has (in this example) Tom's structure in it, but he and/or his mentor is not an author, then you call the editor and tell them "you may have a problem". I realize that the case may not be closed with that statement because the manuscript could indeed be totally legitimate and genuine, but it would be a signal in my mind to watch for. A "friend" could not just run with the data and publish. A competing group could take advantage and get ahead in their project inexpensively (provided that the posted data are what you think they are). But that is sort of the point of publishing result (I must remember to leave my idealism at home tomorrow).

Our old approach is to keep a lid on all your data until the paper is published. Although it is hard to imagine, there could be a mechanism by which you make all your data public, immediately when you get it and this public record shows who "owns" it.

The advantage (in my mind) of such a system would be that you would also make public the data that does not make sense to you (it does not fit your scientific model) and this could (and has) lead to great discoveries.  The disadvantage to the method is that you will sometimes post experiments that are just completely wrong (you did not measure what you said you measured) and this might make you look "dumb" (not really, this happens all the time; a favorite saying is 'we all make mistakes, we just make sure they don't leave the room'). And furthermore, you would finally have a "journal of unpublishable data", where all the experiments that we should not have done for one reason or another reside and can act as a warning what not to do in the future.

It is possible that I am socialist. In the US that is not a good thing, but I don't worry about it.

Furthermore, teaching/learning is a concern. More and more places no longer have the resources or the patience to teach or learn crystallography. I once heard a friend say something along these lines: people who did not learn crystallography are now teaching the next generation. As proof for that, he explained that experiments are done at synchrotrons that clearly show that not the beamline is broken, but the operator does not understand the concepts and therefore the data collected are not useful. In my world I see crystallography as a tool, and no  longer as a goal all by itself (it was a goal when I was a graduate student). I am frequently concerned that protein crystallography will go the way of "small molecule crystallography": a few places provide this service and as an experimentalist you don't much worry about how they do it. Of course, until it becomes super-easy to produce high-quality protein and crystals, this won't happen.

Mark

With apologies to Tom, I don't have a stop-button, Raji is right about that.




-----Original Message-----
From: vellieux <[log in to unmask]>
To: CCP4BB <[log in to unmask]>
Sent: Thu, Mar 28, 2013 1:54 am
Subject: Re: [ccp4bb] delete subject


Hello,

 I stayed away from this thread until now - the major reason being that I was fitting snugly under my quilt.

 However I feel compelled to react now: placing your data in a public repository (thereby "proving" that you did the work) also means that a "colleague", "friend" or whatever can and will publish your work for you. Once your work has been published you cannot publish it again, you did the work and the "colleague", "friend" or whatever has in fact appropriated your work.

 In the world of dreams I was living in until a few moments ago (it was night time), this is perhaps the way we should act. In the real world we live in, even your "colleague" upstairs will publish your work if he / she has a chance to do it because by doing so he / she will improve his / her career while ensuring that yours doesn't take off.

 Fred.

 On 28/03/13 01:34, [log in to unmask] wrote:


Earlier today, I thought this and did not write it. It is a slightly different theme on your suggestion:

 I hear  there are now (but have not seen examples of)  "journals" (web sites) where you do exactly what Tom did: you put your data there, which "proves" that you did the work (first) and you do not worry about the fact that you are making it public before formal publication, because making data public is the reason why you got the data in the first place. And nobody can claim to have done the work, because everybody knows that someone else was first - the web site is "proof". The results are not peer-reviewed of course (even though, in the case of CCP4, things are inherently peer-reviewed to some extent, that is what he asked us to do).  And I hear that there are now journals that will accept references to such web sites.

 Freely sharing unpublished data on a public forum might well be the future, even if in our corner of science this is not yet commonplace.

 The pivotal point to Tom is that he can learn from the suggestions that have been made. I hope he will. I actually hope that he will follow up on the suggestions (privately maybe).  Unlike some, I do not feel that it was bad to find a big file in my inbox, this is what "move to" is for. I think my reaction was "ouch, he did not want to do what he just did and it cannot be undone". But maybe this is not true. There is definitely value in sharing preliminary data, especially for junior people. To have such a function as part of CCP4 might be a very good suggestion, but I agree with you that perhaps it should not land in its full glory in everyone's mailbox.

 Mark










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Macromolecular Crystallography Laboratory
Center for Cancer Research
National Cancer Institute
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