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DBL%20Hendrix%20small.png College chemistry, 1983

Derek Lowe The 2002 Model

Dbl%20new%20portrait%20B%26W.png After 10 years of blogging. . .

Derek Lowe, an Arkansan by birth, got his BA from Hendrix College and his PhD in organic chemistry from Duke before spending time in Germany on a Humboldt Fellowship on his post-doc. He's worked for several major pharmaceutical companies since 1989 on drug discovery projects against schizophrenia, Alzheimer's, diabetes, osteoporosis and other diseases. To contact Derek email him directly: Twitter: Dereklowe

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January 8, 2007

PLoS One

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Posted by Derek

So, what's this "PLoS One" thing I was talking about, anyway? PLoS is, as many will know, the acronym for the Public Library of Science, one of the beacons of the open-access science publishing movement. They had about half a dozen journals (almost entirely in the medical/biological fields) until recently, when they added PLoS One.

No, it's not the one with fewer calories. I'm not sure why the name was chosen, except perhaps as an attention-getting device. (Is there going to be a PLoS Two?) It is a fairly radical publishing move, establishing something that's part preprint server, part refereed journal, and part user-ranked content site. Papers can be submitted in just about any area of science, and will be checked to make sure that they're methodologically sound - that is, that their conclusions can reasonably be drawn from the evidence that they present. And that's it. Once past that point, everything gets in.

So how do you find out what's worth reading? Here's where the user-generated part comes in. You can leave comments on any aspect of any paper, and as long as they're presented reasonably, they're in to stay. The more comments/recommendations a paper gets, the more attention it will continue to draw. And (although they're not enabling this yet), there will be a ranking system, where readers can assign scores to each paper they're read, with visible aggregated ratings: Science meets Slashdot (or Digg, or Reddit, and yeah, I know that readers of each of these sites spend a fair amount of time making fun of each other). The PLoS people are bypassing most of the debate about how to referee papers, setting up what's essentially a garbage filter and letting the readers sort things out after that.

Papers can also be annotated, with comments attached to specific points in the manuscript. This (and the rating system) are the parts I'm most interested in seeing in action. As far as I can tell, they're going to have anonymity, although you'll have to register (confidentially) to use these features. The guidelines for commenting and annotating seem reasonable:

1. Language that is insulting, inflammatory, or obscene will not be tolerated.

2. Unsupported assertions or statements should be avoided. Comments must be evidence-based, not authority-based.

3. When previously published studies are cited, they must be accurately referenced and, where possible, a DOI and link to a publicly accessible version supplied.

4. Unpublished data should be provided with sufficient methodological detail for those data to be assessed. Alternatively, a permanent Web link to such information should be provided.

5. Arguments based on belief are to be avoided. For example the assertion, "I don't believe the results in Figure 2." must be supported.

6. Discussions should be confined to the demonstrable content of papers and should avoid speculation about the motivations or prejudices of authors.

I can see that they've devoted some thought to what might happen. I think that this will be a critical-mass phenomenon - if enough papers get annotated and ranked, it'll become the norm. And if not, these features might wither on the vine, which would be a shame. I've registered with the site as of this morning. Let the experiment begin!

(More useful commentary here at Evolgen, at The Unbearable Lightness. . ., Sciencebase, Bugs n' Gas Gal, ContentBlogger, Digging Digitally, Evangelutionist, and Notes From the Biomass.

Comments (11) + TrackBacks (0) | Category: The Scientific Literature


1. JSinger on January 9, 2007 10:30 AM writes...

As with the Scientific Debate site someone linked on your January 4 post, this is an interesting idea but who has time to participate? I barely get around to using my Slashdot mod points, where it's simply a matter of distinguishing sane from insane, let alone reading, researching and comprehending enough to make professional-grade comments on papers.

On the other hand, where I've found BioMedCentral especially useful is that it reduces the LPU to the point where previously unpublishable things (negative results, mostly) make it into press. It reduces publication bias and contributes many helpful experimental details. This might have similar value.

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2. Deepak on January 9, 2007 12:18 PM writes...

The most interesting aspect of PLoS One is not just the open publishing aspect, but the fact that it is the only journal I can think off that is internet first, and not an online version of a print journal. Without the ability to annotate and comment, and other features that some have requested, it would not be quite as interesting.

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3. milkshake on January 9, 2007 3:14 PM writes...

I wonder if the article submission fee (about $1500) is to discourage graphomaniacs and indian chemists...

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4. Dave on January 9, 2007 3:57 PM writes...

I used to work for a company that used the phrase "Plus 1 customer service". The "Plus 1" I believe came from police training or tactical training where the lead person at the scene needs to always keep in mind and keep lookout for that "one extra thing" that may be important. Maybe PLoS One is in the same vein. Therefore I don't think it will trend to PLoS Two.

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5. KinasePro on January 9, 2007 5:50 PM writes...


Just imagine how well YouTube would have done charging people to submit videos.

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6. Eric J Johnson on January 9, 2007 9:08 PM writes...

> As with the Scientific Debate site someone linked on your January 4 post, this is an interesting idea but who has time to participate?

Who has time to participate in traditional peer review?

Certainly, one will want to read every word of a paper twice over before commenting on it. But for papers right in one's personal subfield, I think one may be able to comment productively without looking up anything further.

I think this is the coolest. It could really be kryptonite to closed-minded mandarinates who suppress novel paradigms - a few of which do exist, I think, at least to an extent.

How many papers do you read where at a certain point or two, you groan about the obviousness and strength of an unmentioned alternative interpretation, or some unrealistic claim. In PloS One you'll be able to do something about that.

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7. Brooks Moses on January 9, 2007 11:57 PM writes...

Eric: I think there's an important point in that last paragraph, there: There's a certain amount of outrage fueling a desire to comment on poor-quality results. I'm notsure if there's a similar sort of thing pushing people to make positive comments (which are, in my experience, often a fair bit harder to make well anyway), which makes me wonder if this is going to end up with mostly negative comments.

Also, something driving peer reviewing that I think is fairly important -- when people do a peer review of an article, it's because someone with a fair amount of status personally asked them to, and their input is going to be taken into account pretty strongly by the authors of the paper. That's not nearly the case on PLoS One, and I'm not sure how much that will affect things -- but I suspect it will quite a lot.

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8. GATC on January 10, 2007 9:30 AM writes...

I seem to remember this open source publishing scheme to be the brainchild of Varmus while he was director of the NIH, or at least he was giving it some pretty heavy endorsements while I was of the few truly visionary ideas of his tenure in Bldg. 1.

I especially like the list of the six guidelines for commenting/annotating, and how it is too bad these criteria are not followed by the atmospheric science community and various assorted libtards in their quest for anthropogenic warming relevance.

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9. Theodore Price on January 10, 2007 12:47 PM writes...

I knew this was coming out (PLOS One) but your post reminded me it was there. I went over to check out what was there and immediately found an article of direct interest to my research (role of TOR1 in LTP). Read the paper and had a couple of questions, although I have to say I found the article to be of a very high quality. Looked at the discussion and found one of my questions had already been posted by someone else and that the main author had already provided a detailed answer. Color me impressed. I will strongly consider submitting my work to this journal. I really like the idea of recieving feedback in this fashion and I think the more people get used to the format the more they will like it.

On the Nature trial, my opinion is that it was doomed to fail. Nature is far too high profile for such a thing. I think if something like The Journal of Neuroscience (JN) would have tried it it would have been a big success. EIther way, based on the recent surveys I have received from JN I think they are strongly considering giving something along the lines of a mix of the Nature trial and PLOS One a shot.

FInally, I am in agreement with the 6 guidelines, like everyone else. Many peer reviews I have recieved failed to follow those guidelines or be anything even close to resembling civil, for that matter.

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10. mas on January 18, 2007 4:30 PM writes...

To clarify some snark...@milkshake:

From PLoS ONE's Journal Information:

"...our expenses—including those of peer review, journal production, and online hosting and archiving—are recovered in part by charging a publication fee to the authors or research sponsors for each article they publish. For PLoS ONE the publication fee is US$1250...We offer a complete or partial fee waiver for authors who do not have funds to cover publication fees."

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11. Erik Svensson on June 30, 2007 4:25 PM writes...


I understand your concern about "who will have time to participate"? I am worried about this too, and I am member of the Editorial Board of PLoS ONE, so this is a big concern of mine. However, the fact that you spend time commenting on this blogg indicates, to me at least, that you are one of the persons who actually COULD have time to comment also on PLoS ONE articles. Most welcome with your comments!

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