Recently I got a comment to my peer-reviewed publication on PubPeer. I am a new researcher who just started my research career, and I feel I am overreacting and over-worried. But please advise and help.

Long story in short: I published a manuscript in a top-level journal in my field (IF > 20). Recently, I got a comment on the “PubPeer,” and the person left a comment and challenged my research methodology. So I responded to the comment politely and defended myself, and that person said he/she appreciated my response. I personally do believe this is just a pure and objective scientific discussion about my paper. I welcome all the challenges and questions about my publications, and I believe these challenges are the driving force to push science move forward.

However, one of my co-authors called me yesterday. I could feel that he was not really happy that our paper appeared on PubPeer. At the very beginning, I really had no idea why he was pissed off. Then I went over PubPeer carefully, and I finally realized that PubPeer is a website mainly dedicated to exposing research misconduct, such as manipulating data and faking figures. Therefore, I know why many researchers don’t remotely wanna associate with PubPeer in life.

But the bottom line is that my publication is clean and has nothing to do with research misconduct. It went through rigorous peer-reviewed processes and I have full confidence. So I believe this objective discussion about my publication on PubPeer should not affect me in a bad way, right? I am kinda worried and hope I am overreacting.


1 Answer 1


You don't get to choose whether your papers appear on PubPeer, any more than you can choose whether people discuss your paper in their lab meeting, in a journal club, at a coffee shop, or anywhere else. If you could choose whether your paper is discussed, you should certainly choose "yes" if you have any faith at all in your work: work that is discussed is useful; work that no one ever reads isn't really contributing much to knowledge (arguably still better to have published a paper that no one reads so that it at least could be read). You don't want to stop people from reading and discussing your work!

I don't think you have an obligation to respond to every comment on your work, any more than you have an obligation to respond to every comment on social media or this website or when someone asks you a question on the street. However, if someone has put effort into understanding your work and makes a reasonable commentary, it's certainly to the benefit of academic discourse that you respond to the best of your ability.

For a venue like PubPeer, it's important that your responses are well-crafted, as unlike in some one-off conversation, posts there will remain indefinitely. Because of that, you may want to consider working with your coauthors for sensitive issues (for example, if there are allegations of misconduct).

PubPeer is a website mainly dedicated to exposing research misconduct, such as manipulating data and faking figures

I don't think this is the goal of PubPeer, it just happens that these issues are of broad general interest. I'm sure PubPeer and advocates for open academic discussion and post-publication review would appreciate if the site would be used for more than just pointing out fraud.

It sounds like someone posted a reasonable critique/question, you were able to assuage their concerns, and there are no accusations of misconduct. If anyone were to view this interaction and believe that it reflects negatively on you that you are able to defend your work in public, that's their problem, not yours. I understand your coauthor's fears/concerns, but it's wrong for them to put any blame on you for this. They'll have to figure out for themselves how to handle the fact that published work is published so that others can read and react to it. I'd perhaps explain to them a bit how the site works, and clarify that if you did not respond, all that would exist on the site is the comment challenging your work, and that it's possible other readers would assume the lack of response suggests that the challenge cannot be countered by the authors (though I'd also recommend a bit of hesitancy in using this criteria to judge papers yourself, as participation on sites like PubPeer is not yet part of academic norms).

  • Thanks and I think you are right. I just hope all the comments on PubPeer are objective, and hope no kind of personally vicious comments. But yes, it is out of my control, seems anybody can post comments there. Sep 6, 2022 at 18:34
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    @Part-timeEngineer Certainly it will vary, and some disciplines in particular will attract crankery and other unproductive responses. A recent example might be papers published about COVID-19, where commenters are likely to include not only people interested in epidemiology, virology, public health, etc, but also people who think the whole pandemic is some government conspiracy. I believe PubPeer does some limited filtering but I doubt they are exhaustive and I'm not particularly knowledgeable about their processes, but certainly those sorts of comments do not require author response.
    – Bryan Krause
    Sep 6, 2022 at 18:39

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