27 May 2009


Others have said it before me, but I think PLoS ONE and online journals like it represent the future of scientific publishing. Quick turnaround, open access, unlimited space (not just for text, but also images, data files, etc.)—I just don't see how the older forms of journal can possibly persist for long.

Perhaps the most useful feature, though, is sadly underutilized. Imagine this—you're reading a paper and you come across an error, or a questionable inference, or an unclear point. With printed journals, you have the following options:
  1. Write to the editor and/or primary author and hope they have a moment to respond.
  2. Complain to whomever will listen.
  3. Write a frustrated note in the margin and move on.
  4. Fume silently.
But with PLoS ONE, you can accomplish #1–3 all at once. (And #4, if you want.) Simply log in, highlight the text you want to comment on (or click on "Leave a general comment"), and you can leave a publicly-visible note that anyone, authors and editors included, can respond to.

People have been slow to take advantage of this wonderful system, but it's starting to take off, I think. As many are aware, there's been a big media hubbub about a new fossil primate (Darwinius masillae) that may or may not be a stem-haplorhine (i.e., part of the group that gave rise to tarsiers and monkeys, including apes, including humans). I've seen a lot of discussion of it in various venues, and some of that is finally starting to spill over into the paper's comments section. (You may note a couple of comments left by myself.)

One notable outcome of the discussion on Darwinius is the rectification of an incompatibility between PLoS ONE's publication methods and the current requirements of the ICZN. This meant that the new scientific names published in the journal (e.g., "Darwinius", "Darwinius masillae") were nomenclaturally unavailable. Happily, this was quickly resolved, and the remedy was also carried out for the names introduced in some earlier papers.

Other discussions, on such topics as the scoring of characters as "Derived" or "Primitive", are still ongoing.

PLoS ONE also allows readers to rate the articles and leave reviews. (As of this writing, there is one review by Andy Farke, and I think he makes some excellent points.)

Science open to everyone! Go ahead—get involved.


  1. I was talking to a prominent dinosaur worker about this just yesterday and he isn't such a big fan. Apparently some papers are accepted without review and there is a lot of power with the handling editor (i.e. letting their mates publish and holding up the manuscripts of workers they aren't such a fan of).

  2. Perhaps, but surely this is offset by the fact that ANYONE CAN WRITE NOTES ON THE PAPER ITSELF? I.e., if a paper is shoddy, mark it up!

  3. True. But these still count towards your CV (and possibly shouldn't if they are shoddy pieces of work that only got through because you're mates with the handling editor). Plus I really don't want to have to trawl through a "flame war" addendum to each and every paper I read. Geesh! Can you imagine...

  4. So far the comments I've seen have been pretty civil (and sometimes even include references). I think the fact that you're writing on the canonical form of the article itself prompts some (much-needed) emotional restraint.

    It's a bit like questions after a presentation, except anyone in the audience can answer as well. (Okay, sometimes those don't stay civil, but usually....)

    Also, if PLoS ONE "holds up" a manuscript, I'll bet the turnaround is still shorter than average for most high-impact journals.

  5. And, what, shoddy pieces have never been published in paper journals?

  6. "a lot of power with the handling editor (i.e. letting their mates publish and holding up the manuscripts of workers they aren't such a fan of)."

    what does this have to do with the online format?

  7. It just happens that PLoS one has his. Not necessarily related to online publishing. I also submit this for your consideration.

  8. You know this is great, but how useful is it when ratings that are nothing but high marks with no commentary are accepted and considered in the ranking.

    It's a good idea (maybe), but I am skeptical of how well it's actually working in practice.

    For example with the paper you linked, how do we really know that it's Callum Ross and Andy Farke who are posting the comments reviewing the paper? I mean, I realize that's a problem with any system, but is there some kind of verification for whether or not a person is who they say they are?


  9. For that matter, what's to prevent me from submitting a paper to JVP claiming I'm Andy Farke? Or writing an angry letter to National Geographic claiming I'm Callum Ross? How is this a problem for online publication only?

    I am pretty sure it is Andy Farke since he also mentioned rating the article in his blog. Apart from that, you have to register an account to post comments, so PLoS ONE has user's email addresses on hand. Not that email is never hacked, but how paranoid are we willing to get here?

  10. Yes, it is the Andy Farke and the Callum Ross who commented on that article. Although the point about faking comments is well-taken, this could just as easily happen on a mailing list, blog, social networking site, or even within a journal. And, given that the comments are tied to a specific email, this could be traced to a certain degree.

    At any rate, I also share Nick's hesitation on the present usefulness of the rating system. Some ratings are more useful than others - I would submit that the ratings submitted by Callum and I are infinitely more useful than the "Darwinius RULEZ!!11!" ratings of four stars and no explanation. Perhaps we'll eventually be headed towards an Amazon-style ratings system, where users are allowed to "rate the ratings" for helpfulness. But at present, I would think that the larger problem is that relatively few people are taking advantage of the comments and ratings system. I mean, to use Darwinius yet again as an example, were Callum and I really the only people who thought the article was worth rating? Judging by blogosphere and mailing list chatter, this is not the case. It will primarily take a culture change.

    And finally, papers are not accepted without review--at the minimum, the academic editor (who works with the paper in addition to the equivalent of the handling editor) reviews the work. Many (if not most) editors also choose to get additional referees. Based on my experiences with some rather respected journals as of late, a big name and long history doesn't mean that accepted papers get a decent review (ask me about the single six line review for a 50 page manuscript sometime - the paper was good, but it wasn't that good!). And, the issue of academic editors meddling with the process (either wilfully or through sheer laziness) happens in pretty much every journal I know of (but this doesn't make it right, of course!). Authors should, whenever possible, be pro-active and squeaky wheels to the relevant powers-that-be whenever this happens (again, I've had to do this once or twice myself).

    At any rate, my two cents. Good comments all, though.

    [as full disclosure, I am an academic editor at PLoS ONE, but this post does not imply endorsement of the PLoS ONE journal or staff - these are my own comments]