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Trying to squeeze sense out of chemical data

Squeezing Journal Space?

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An article by Steven Bachrach in the Journal of Cheminformatics has an excellent disscusion on Open Access journals. He notes that one of the problems with current scientific publishing is the plethora of journals. He also points out the huge amount of publications being generated. He succinctly states it as

We simply publish way too much

No one can keep up with a literature like this. It is time for the scientific community to rethink the role of publication. Should every little idea, every minor work receive the same treatment as the great discovery?

Most articles barely get cited – many never get cited; they are simply maintained within this ever-growing collective of scientific work, with the chaff growing at a rate exceeding the production of the wheat

He then proposes a two pronged approach in which 1) we reduce the number of full service journals, restricting it to just the top ranked journals and 2) the remaining journals  publishing the “remaining 80% of the scientific literature” be replaced with institutional respositories.

I think this is a very sensible approach. But I see one major question that needs to be considered, before this approach might take off. And that is, why do we publish so much? As opposed to, say, putting papers up on web pages.

I think it wouldn’t be far from the mark, to say that a major push for publishing is credit. From an idealistic point of view, one can say that scientific results need to be disseminated. Therefore, by publishing in journals which everyone reads, we achieve this result. But the fact is, publications are academic currency – they help academics get tenure and get money. Ideally, committees and funders would be able to differentiate between the really significant publications and the “chaff” and maybe even penalize the latter. That doesn’t seem to be the case – hence publish whatever you can, whenever you can.

But, if this is the current atmosphere, what are the chances of success for Bachrachs proposal? Clearly his first point would be supported – publications in Tier 1 journals would be a bundle of currency. But that is the case, even now. The problem is that the bulk of scientific output would end up in repositories. Personally, that would be fine by me – easy access to papers and data, ability to interact with authors and so on. But, would anything and everything by an institutions scientists be deposited in such a repository? If so, how does one differentiate between the good and the bad? Maybe good papers would get a lot of comments and feedback? Bachrach already notes that participation in journal supported forums is generally low. Why would participation in  forums maintained by institutional repositories be any greater?

Personally, I’d love to be in a universe where I could simply write up a study and publish it on the web along with code and data and then move on. Unfortunately, in this universe, resources are limited and I must compete. Hence some form of external validation (or at least the appearance thereof)  comes into play. And as a result I have to play the publishing game.

Bachrach mentions that Open Notebook Science as a publishing model is far too radical for near term adoption. I agree with this. But it seems that pushing 80% of the literature into institutional repositories also requires a fundamental (even radical?) rethinking of how academia rewards acheivement.

Update: As noted by Egon, the world is a better place if one links to DOI’s rather than PDF’s. In that spirit I updated the link to the Bachrach paper to point to the DOI.

Written by Rajarshi Guha

March 18th, 2009 at 1:37 am

Posted in Literature

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10 Responses to 'Squeezing Journal Space?'

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  1. There’s a lot of mythology around why scientists publish, and I’m concerned that many advocating Open Access/Institutional Repositories as a solution to the publishing crisis aren’t realistically addressing the unvarnished motivations for publication in the first place:

    http://depth-first.com/articles/2007/05/14/scientific-publication-and-the-seven-deadly-sins

    Maybe the problem isn’t that we publish too much. Could it be instead that that our collective energies and resources are being wasted by a publication system that’s breaking down in our brave new world?:

    http://zusammen.metamolecular.com/2009/02/27/micropublication-in-chemistry

    Rich Apodaca

    18 Mar 09 at 2:19 am

  2. Are people reading all the blog posts as well as papers :)

    I liked Bachrach’s talk at GCC on this topic, but there are even more fundamental reasons for more being published – more people doing science, and better technology.

    My PhD supervisor told me that when he wrote his thesis, you sent revisions back to the women in the typing pool, who then re-typed it.

    Nowadays, every scientist has an electronic secretary…

    gilleain

    18 Mar 09 at 9:41 am

  3. I just think it is good that the conversation about this issue in chemistry is continuing and expanding. Chemists are a heterogeneous bunch with a distribution of motives. As the discussions continue some will find certain tools to become more open appealing and try them out. I think chemical information communication is going to get more fragmented because of this as well – and that is not a bad thing – it just requires a new set of skills to learn and teach.

  4. @Rich, good points. I certainly agree that the “next step” in publishing (out of all the possibilities) will probably be selected only after the motivation for publication is addressed

    @Gilleain, indeed, more people mean more publications. But what drives them to publish in journals? If people could get the same effect by publishing on blogs and web pages, life would be much easier :)

    Rajarshi Guha

    19 Mar 09 at 2:46 pm

  5. It’s not just that there are more chemists and that’s why there are more publications. Individual chemists are publishing more!! I did a study a few years back on the publication rate of professors, associate professors and assistant professors over the past 3 decades – and the rate of publication per professor grew for each level (though slowly for the assistants).

    I agree that the community should really reassess what is to be accomplished by publication. It’s is not just information distribution – we judge tenure and promotion and grant renewals, etc on the basis of publication.

    If blogging and institutional repositories and other next-gen tools can be regarded as acceptable practices for chemists, then much of the journals crisis will simply evaporate – much in line with Rich’s posts.

    Steven Bachrach

    19 Mar 09 at 7:57 pm

  6. My suggestion: instead of publishing journal articles of limited scope, collaborate on large, open projects and publish a big article with a large number of co-authors. Fewer papers of higher impact, possibly published more quickly. There are serious diplomatic issues, naturally – how much does someone have to contribute before becoming an author, rather than just being acknowledged? But we stay with Bachrach’s idea of publishing only important papers in journals.

    Mat Todd

    19 Mar 09 at 9:57 pm

  7. @Steven, wrt individual chemists publishing more – that’s quite an interesting point and makes sense if we are judging accomplishments by publications (or maybe it’s the cause for such judgments?).

    I certainly hope IR’s/blogs etc reach acceptable status – writing journal articles is tedious for most things. If the chemistry community is so fast moving (that we have to publish so much), we should be looking at CS and other engineering fields where tech reports, conference reports are accorded some measure of acceptability

    Rajarshi Guha

    19 Mar 09 at 10:35 pm

  8. Just a crazy thought touched on by Gilleain, but why isn’t this discussion happening over at J. Cheminformatics?

    This might sound off-topic, but bear with me.

    The link to follow would seem to be this one:

    http://www.jcheminf.com/content/1/1/2/postcomment

    But when I click, I’m taken to a login page. Ugh, I’ve got to create an account. No thanks.

    This blog post, on the other hand, imposes no such barrier. And all it takes are one or two comments (and maybe a moderator) to get the ball rolling.

    Couple of ideas:

    1. If I’m going to need to sign in, at least let me use OpenID:

    http://openid.net/

    Readership presumably consists of highly computer-literate folks, so this should be no problem.

    2. Do away with login altogether and use reCatpcha and/or spam protection.

    3. Whatever you do, don’t hold comments for approval before publishing. It’s a powerful de-motivator.

    4. If 1 or 2 are implemented, put a BIG button together with the abstract and the full paper that says “Your Comments.” Don’t hide it.

    5. Some form of trackback to capture discussions happening outside the scope of the article page itself (i.e., reward mechanism).

    I realize this pushes the boundary between ‘serious science’ and the ‘casual web’ and that some are quite uncomfortable with that idea. The problem is that nothing J. Cheminformatics nor anybody else does can stop this from happening. Besides, isn’t science all about democratizing the discussion of ideas?

    Why not lead the way?

    Rich Apodaca

    19 Mar 09 at 11:29 pm

  9. Rich, indeed excellent points! I think the trackback mechanism would be very useful, as some commenters may want to expound more elsewhere (blogs etc). Trackbacks are certainly not difficult!

    Rajarshi Guha

    22 Mar 09 at 5:23 am

  10. Egon Willighagen

    22 Mar 09 at 9:24 am

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