Two new dispatches from the Shiny Digital Future

April 17, 2012

Item 1: With his new piece at the Guardian,  “Persistent myths about open access scientific publishing”, Mike continues to be a thorn in the side of exploitative commercial publishers, who just can’t seem to keep their facts straight. This time Mike unravels some choice bits of nonsense that keep getting circulated about open access publishing: that OA publishing must necessarily cost as much as barrier-based publishing, that the peer review process is expensive for publishers, and that authors who can’t pay OA publication fees will be left out in the cold. It’s cleanly and compellingly argued–go read for yourself.

Item 2: The Yates et al. prosauropod pneumaticity paper is officially published in the latest issue of Acta Palaeontologica Polonica, and I have updated the citation and links accordingly. This may not seem like big news, in that the accepted manuscript has been available online for 13 months, and the final published version does not differ materially from that version other than being pretty. But it’s an opportunity to talk about something that we haven’t really addressed here before, which is the potential for prompt publication to accelerate research.

A bit of background: standard practice at APP is to post accepted manuscripts as soon as they’re, well, accepted, unless the authors ask otherwise (for example, because the paper contains taxonomic acts and the first public version needs to be the version of record). Not everyone likes this policy–I know Darren objects, and I’m sure there are others. The chief complaint is that it muddies the waters around when the paper is published. Is a paper published when a manuscript is posted to a preprint server like arXiv, or when the accepted manuscript is made freely available by a journal, or when the official, formatted version is published online, or when it arrives in printed hardcopy?

Now, this is an interesting question to ponder, but I think it’s only interesting from the standpoint of rules (e.g., codes governing nomenclature) and how we’re going to decide what counts. From the standpoint of moving science forward, the paper is published as soon as it is available for other researchers to use openly–i.e., not just to use in private in their own research, but also to cite. And since that’s the axis I care most about, I prefer to see accepted manuscripts made widely available as soon as possible, and I support APP’s policy. In the case of Yates et al. (2012), having the accepted manuscript online for the past year meant that it was available for Butler et al. (2012) to use, and cite, in their broad reassessment of pneumaticity in Triassic archosaurs. If our manuscript has not been published, that might not have been the case; Adam gave a talk on our project at the 2009 SVP in Bristol, but Butler et al. might have been loathe to cite an abstract, and some journals explicitly forbid it.

So I say bring it on. Let’s really accelerate research, by letting people see the content as early as possible. Making other researchers wait just so they can see a prettier version of the same information seems to me to be a triumph of style over science.

References

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9 Responses to “Two new dispatches from the Shiny Digital Future”

  1. David Hone Says:

    Oh there’s lots of reasons not to like the publciation of accepted manuscript Matt (*ahem* http://archosaurmusings.wordpress.com/2011/04/08/problems-with-advanced-publication/). Post proofing I don’t have a problem, but those uncorrected proofs can (potentially) be a real pain.

  2. Matt Wedel Says:

    They can be, but let me play devil’s advocate. In your post you identify several problems. Here are my responses:

    1. “It’s annoying, I want the final version.” I’ll happily settle for the accepted ms, if it means I can start using that information months earlier.
    2. “It also makes doing media work hard.” Yeah, but as a working scientist my top priority is getting more science done, and I don’t want to hold that up for months just so it will be more convenient to talk to reporters. Media work is on my list of priorities, but it’s nowhere near the top.
    3. “There are taxonomic issues.” Certainly–which is why I was careful in the post to point out that I’m only in favor of this when there are no taxonomic issues.
    4. “Proofs are not really, real. They can be subject to change and these can be profound.” In theory, yes, but then all the examples you cite are trivial. In practice, I think the actual frequency of major change between acceptance and publication is very low, and not nearly important enough to hold up the vast majority of manuscripts for which there will be few or no changes.
    5. “People will read them and cite them. But they will be reading and even citing things you might not officially have said.” Two things here. First, if you don’t intend to stand by a claim, what is it doing in the accepted manuscript to begin with? Second, the fix here is easy: everyone gets comfortable with the idea that posted = published, and adjusts their expectations–as authors and as readers–accordingly.

    I don’t expect you to agree–in fact, I hope you don’t, it will make for a more interesting conversation. Rebut, good sir!

  3. David Hone Says:

    OK I’ll try ;)

    1. Right but it depends on what you take being right (see 4, 5).
    2. No, it’s not a priority, the opposite in fact. But it can be an inconvenience when things don’t run according to plan and if you have been asked / expected to do outreach based on something and it all goes to pot becuase things like this are released in this manner it is frustrating. At best it’s inconvenient, though I accept not a major issue for the science.
    3. Fair enough on your part, but they *are* being released when there are taxonomic issues so it’s still an issue for now.
    4. Yes I suspect they are very low too. But they do / can happen. And so as noted, it’s not a good thing to be working on an assumption that something is at fault.
    5. i) You might not have intended to say it. It might be a typo, badly phrased, something you forgot to take out. Mistakes do happen.
    ii) I don’t think that works. When the corrected proof goes up the uncorrected one goes down. It’s possible that you do write a paper correcting an error that then never appears as between the uncorrected and corrected proofs it goes. And there’s no longer any formal record of that existing. You can adjust your expectations accordingly, but you still need to go and back check etc.

    All of this though still comes down to a point I made you didn’t mention here (since it’s not a complaint, but an observation), in general these uncorrected proofs are generally only up for a few days or weeks. Yeah sure, you really do want to get your hands on those papers before they hit the shelves on paper, and getting things like Yates et al. a good year ahead of time is great. BUT, having to wait just an extra week to make sure you have the exact, proper final version? Does it really make a difference? You can’t have got that far in your analysis, it’s unlikely to cost that guy any citations let alone lots that his paper didn’t appear for another 10 days etc.

    All of it can be avoided by just letting the author correct the proofs then sticking that up. Fast science good, but really, an extra week or two? Not an issue.


  4. APP has a backlog of what – 50 papers? 60? I counted them a while ago and concluded that anything accepted this year would likely get a 2014 stamp. OUCH!

    Yes, I want them early – I just wish APP would not post the accepted MS, but the type-set one!

  5. Matt Wedel Says:

    All right, I can see where you’re coming from. My own thoughts on this are intensely colored by having been on the receiving end of some loooong wait times between acceptance and publication. Right now it’s APP plowing through the backlog. A decade ago it was JVP; my 2003 pneumaticity paper was in press there for about a year before it came out. In those cases, having the accepted manuscript up a year early is plenty of time for it to have a positive impact. But you’re right, if the difference is just a few weeks, it may not be worth the hassle.

    I was talking this over with Brian Kraatz today and we were speculating about what authors would do if a journal–let’s say, hypothetically, APP–offered them a choice of electronic-only publication in a matter of days or paper+electronic in a matter of months (from acceptance in both cases). We both think the vast majority of authors would opt for electronic only. What I hadn’t thought about until just now is that if that’s what most authors chose, then there wouldn’t be a long line of people waiting to get into paper, so the wait time to paper+electronic would come down. It would probably stabilize at a lag time longer than electronic only, because evey time it got close to catching up, the wait for paper would get to be trivial and people would switch over because, hey, why not.

    If I was emperor of the world, I’d add another choice for authors: wait a few days or weeks for a nicely formatted electronic-only publication, or just post the accepted manuscript, with no further formatting, immediately, and that’s all you get.* I don’t know how many people would take the latter option; I suspect it would depend on the length of the wait for the formatted version. But it would be interesting to find out. Then we might see a sort of three-tiered publication hierarchy. At one end of the spectrum–the top in terms of prestige and prettyness–would be the nicely formatted paper+electronic offerings, which would probably only be chosen by people committing acts of taxonomy and maybe monographing really nice specimens. In the middle, arriving a little sooner and costing a little less (to whomever is footing the bill), the nicely formatted electronic-only papers. At the other end, moving fastest and costing the least, would be unformatted or self-formatted papers published online as soon as the manuscripts were accepted.

    I’d like to have those choices.

    * Unless you format it yourself, using LaTeX or some desktop publishing software or just getting fancy with Word or OpenOffice. Physicists can do this–are expected to do this, in fact–why can’t we?

    Well, holy crap, I’ve gone and written another post’s worth of nonsense. Please tear it apart, and I’ll come back and we’ll look at the entrails and try to divine the future.

  6. David Hone Says:

    I see where you’re coming from Matt (I think! ;) ). Again though, for me it’s just these ‘accepted but unproofed’ manuscripts I don’t like for all the above reasons. I’m glad things get out fast and don’t sit in press for months or years, but there are problems (potentially at least major ones) with uncorrected proofs. With the Zhuchengtyrannus paper I got probably a dozen e-mails asking for data that was apparently missing because their formatting had cut a column off a table and a load more asking about an apparent taxonomic revision I’d made (I hadn’t, it was a badly written sentence).
    Not the end of the world for sure, but having to send out multiple e-mails to people to provide that data coz they asked, and to send out copies of the preproofed copy when it came out and then again all the requests when the proofed one came out was a real pain. I lost a lot of working time unnecessarily and some people who didn’t contact me probably thought these were actual errors, when, what, a delay of some 2 weeks would have meant none of it would happen. With a paper that had taken nearly a year to get published and has only just got into print, I really don’t see that I would lose anything by that short delay and would have gained a bit.

  7. Mike Taylor Says:

    Very interesting stuff from Dave and Matt, there. I think there are enough pros and cons here that these comments ought to be edited together into a new post, where more people will see them (and hopefully contribute their perspectives).

    I am totally on the fence regarding this. Or, rather, one moment I strongly agree with one side, then the next with the other.

    I really don’t like Matt’s proposed hierarchy, which amounts to doling out scientific prestige not on the quality of the science but on (A) ability to pay, and (B) willingness to retard progress.

    I’m happy for articles to published “online first” in their formatted version — I think everyone is? — so long as it’s recognised that when it goes up on the web, that’s it, it’s published. No “the real date is 2011 because that’s when the paper copy was issued” nonsense, please. That is a completely artificial problem imposed by tradition rather than reality (and exacerbated by the ICZN’s 20th-Century rules.) And of course it’s a total non-issue in the case of e-only journals like PLoS ONE and PE.

    But posting “accepted manuscripts” feels wrong. I’m not sure whether I can justify that feeling.

    In the end, I think Matt is right on target when he says that “as a working scientist my top priority is getting more science done, and I don’t want to hold that up for months just so it will be more convenient to talk to reporters. Media work is on my list of priorities, but it’s nowhere near the top.” Like so many of the complex how-science-is-done issues we’re all wrestling with at the moment, this comes down to a problem of conflicting goals. How nice it would be if in all cases — where manuscripts should be submitted, when and in what form they should be made available, and so on — we could just pick the option that best serves science.

  8. David Hone Says:

    Well there is that Mike for sure. And as you probably recall we had a long e-mail exchange about dates of things (i.e. is soemthing that is online now, but published on paper next year a 2012 or 2013 paper). At the heart I don’t care which, I just don’t want the confusion and with no clear ruling by anyone and no consensus form the academics or journals, we seem to be in the position where both are used. That’s the core issue – one paper effectievly running around with two different dates attached to it in the literature.

  9. Matt Wedel Says:

    I really don’t like Matt’s proposed hierarchy, which amounts to doling out scientific prestige not on the quality of the science but on (A) ability to pay, and (B) willingness to retard progress.

    All, well, does it?

    First item: I don’t mean in ability to pay. I pointed out that I was presenting the options in order of descending cost to someone, but not necessarily to the author. It could run just like APP does now, where no-one pays unless they go over the length limit (which would obviously only apply to the paper track in my scheme).

    More importantly, you seem to be equating prestige with prettiness of publication. Is that really what it means? And aren’t we trying to actively dissuade people from prestige-based publication (e.g., in the weeklies)?

    I think that unless we can come up with a way to dole out prestige based on the quality of the work–which would pretty much have to be after the fact–we should abandon the idea of prestige as a legitimate thing to be either desired by authors or–and this is particularly corrosive–bestowed by publishers. And if the prestige is post-hoc and quality-based, how would it be different from the kind of scientific reputation that papers and their authors acquire over time already?

    Half the sentences in this comment end in question marks because I am legitimately curious. These aren’t rhetorical questions, so, please, everyone say what you think.


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