Journals such as AMTD and ACPD contain an open discussion where anybody can comment on papers under review. The peer-reviewers are still anonymous, but other people commenting are not. If I'm reading a paper and have questions about it, what are the pros and cons on posting them as public comments versus writing an e-mail to the author directly? On the one hand my comments may improve the paper; on the other hand, if I write something stupid or step on somebody's toe, that may harm my future career.
What do others think?
(Edit: I might add that in the case I have in mind, I am already in contact with the author)
Answer
As I pointed out recently in http://nuit-blanche.blogspot.com/2012/07/problem-with-pre-publication-peer.html , the problem with the current peer review system is not the rejection and all the horror stories that go with it, it is the secrecy that goes with the process. Make anonymous the reviews but hold the reviewers accountable is the surest way reviews can be both effective and provide some "currency" as +David Ketcheson points out.
In short If I were you, I would send the author some questions, then (after her/his approval) make the whole discussion available on the interwebs (after you have edited the parts that are sensitive or the ones that make you look really clueless). I do this often on Nuit Blanche with good results. Make sure you run the whole thing you are going to publish through the person you talked to as you are not a journalist. If you ask questions, you surely are not the first or the last one and remember what you publish must enlight both the people of your community and your future self.
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