Monday, February 02, 2009

Please - bash my latest paper - for the benefit of humanity

My lab has a new paper that just came out on the sequencing and analysis of the genome of a pretty cool (or hot actually) bacterium, Thermomicrobium roseum, which was isolated from a Toadstool Spring, an alkaline siliceous hotspring in Yellowstone National Park. This paper is from a grant we had when I was at TIGR as part of the "Assembling the Tree of Life" program at NSF. Our grant was focused on generating genome sequences from phyla of bacteria for which no genomes were available.

At the time this species was a representative of a phylum that had no genomes. After we started sequencing, the phylum was dissolved, but never mind that for now. We report what I think are some very interesting things in the paper. Among them:
  • We report the first example of a plasmid that encodes all the genes needed for chemotaxis including all the genes for making a flagellum. Given that they are on a plasmid this suggests that motility could be easily transfered between species.
  • We report experimental work and genome analysis that helps understand the novel membrane and cell wall structure in this species.
  • This is the first thermophile known to oxidize carbon monoxide
But I am not writing per se about the things I like about our paper. I am instead asking people out there to find things wrong with our paper. Why am I doing this? Because this paper is part of a broader experiment in publishing in that it is in PLoS One. And one of the main benefits of PLoS One is the features that allows commenting on publications. I personally believe such features are part of the future of scientific publication. But it is currently unclear just how effectively such commenting features are used (note Euan Addie is doing a survey about comments on PLoS One papers here).

So I am offering up my paper as a case study. If you comment and ask questions or make critiques, I will try to respond. And if you think something in our paper is wrong or weird, please say so. If you think something in our paper is supported by other work we do not cite, please say this too. If you have anything useful to say, please make comments.

How do you do this?
  • Go to the paper at the PLoS One Web Site.
  • In the upper right click on "Login" if you have an account or "Create account" if you do not.
  • Return to the paper once you are logged in
  • Find some part of the text you want to comment on
  • Highlight that text and click over on the right "Add a note" or "Make a comment"
  • Fire away.


  1. I guess the paper is perfect ;-)

    I was excited when I saw there were two notes on the PLoS One site -- but they were from you!

    But seriously, I wonder if this is a very good test case. I mean, T. roseum has very little prior work done on it, so people may not have much to say. It might be more interesting with an organism were people can say "I've worked on bacterium X for 40 years and it can't use glucose as a carbon source. Your annotation is screwed up."

  2. Fine fine. You are right. I should have talked more about how the flagellar stuff supports intelligent design.

    What I need is a more controversial PLoS One paper. How about APIS?

  3. I think a lot of people find it intimidating to comment negatively on papers or award them low star ratings. If the people in question are in the same field as you then it may be that they end up reviewing your paper (or grant application). I think this is more intimidating when the person leaving the comment has a more junior position relative to the author of the paper.

    Whilst I'd like to think that most scientists would be above the idea of retribution, I still think that a negative comment risks reciprocal criticism later on (even if it is on a subconscious level).

    Has PLoS ever surveyed people to see what deters them from rating or leaving comments?



  4. I'm excited how easy it was to make a comment (even a lame one) about your paper. When I tried to add some notes to my PLoS ONE paper (in March of 2007) I couldn't get the system to work. It seems like they now have the bugs worked out.

  5. Thanks Eileen. I wrote a response ...

    Keith - not sure if PLoS has done such a survey. I think negative comments are not needed nor wanted per se. I was just trying to attract attention. Better for everyone are critical and additive comments.

  6. Jonathan, I've been pondering about this for a while so I'll post it here with the risk of starting a long discussion. I won't disagree that comments from the readers can add to the value of a paper. But how much do they really add? Is the ability to add comments, at least partly, reducing the need for stringent review? For example, I often use customer reviews in amazon, but 90% of the time I do not find them useful/informative. The "traditional" publication model attempts to guarantee that the work published is relevant to the Journal's audience, is significant, and has been vetted by experts in the field. Can the readers' comments shift some of this burden from the editorial board and reviewers to the general public? I am personally not convinced that this is true.

    Note: I'm not defending the traditional model and the PlosOne experiment is a good try at finding an alternative solution. But is it successful and how will we know?

  7. Mihai

    I too believe PLOS One is an experiment. I do not know if all aspects of what they are doing will work but I think many will.

    One thing I definitely like is their review policy which asks reviewers to review for technical merit but not for novelty or importance. This will accelerate the publication of sound papers by allowing reviewers to focus a bit more than normal.

    As for the commenting functions, I think they have enormous potential, but not as an Amazon like system with ranking and reviews but instead as a way for the scientific community to interact with the authors and each other. So no I do not think the commenting should replace peer review per se. But I can imagine that it might supplement it quite well.

    As for determining if it is successful - that is beyond me but I think something that Euan Addie who I linked to is looking at.

  8. Here's a thought why people may not be commenting much online on papers published in PlosOne. If I leave a comment on a manuscript or annotate it at PlosOne I do not really get credit for doing so. I do hate the idea, but credit in form of citations is ultimately what gives us a job, promotions, grants etc.

    So instead of improving someone else's work by annotating it online I may sit down with my lab mates and talk about a specific paper until I may have enough points together to write a response, publish it and get cited for it.

    I think that more direct communication with authors of controversial papers may speed up science, but unless we find a way to give credit to those who leave important comments at places like the PlosOne website I think that the vast majority of scientists may hold back on experiments like PlosONe.

    Don't get me wrong, I love the idea of open access and direct exchange, but the lack of gain for the individuals who leave comments on the PlosOne site may lead to hesitation.

  9. Yes, Bastodian, giving credit for ideas is useful and important. But lets think this through in a little more detail. Does posting something on PLoS One prevent you from doing what you said - working up something and writing it up as a paper? I think not. Might you get scooped if your idea is absurdly brilliant and then others run with it based on your comments from PLoS One? Well, yes, that is possible. But in reality this type of thing would be very very very rare. Consider an analogous situation, where you are at a conference and you make comments about someone's poster or talk. Those initial comments can extract some very useful and interesting information. But in and of themselves they do not make a paper. This is what I think PLoS One commenting and related activities can help with. They enhance a paper just like questions enhance a poster or talk. But they do not prevent anyone from taking an idea and doing some work to turn it into scientific discovery.


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