We think that although it is off to a rocky start by being overly exclusive, PubMed Commons is a great initiative and a big step in the right direction towards effective post-publication peer review. We shall of course be following the experiment with interest.
The obvious difference with PubPeer is the lack of any anonymity. PubPeer offers three levels of anonymity: registered academics can post signed or anonymous comments, and we also host moderated comments from unregistered contributors, who could be anyone, anywhere.
Our own experience suggests that strong anonymity is the key to encouraging useful comments, as do the failed experiments with journal-run commenting systems. We suspect that PubMed will eventually come to the same conclusion. Thus, a majority of comments on PubPeer are from unregistered contributors, whereas only a tiny minority are signed; registered academics commenting anonymously make up the balance.
Examination of the typical contents of PubPeer comments can easily explain why users choose anonymity. It turns out that the strongest motivation to comment arises when people see a problem with a paper, often a serious one indicative of incompetence, deceit or misconduct. But such critical comments are those most likely to attract reprisals. Most of the comments we receive would not have been made in the absence of the anonymity we provide.
Anonymity does allow low quality and bad faith comments to be made with impunity, but we have found this concerns only a small minority of comments and we feel that it is a necessary price to pay to encourage frank and worthwhile discussion.
Finally, if PubMed does start offering strong anonymity, that is likely to disrupt our plans (and save us money!) but for the moment we are continuing to develop PubPeer to facilitate all formats of scientific discussion.
*Note that PubPeer is open to all sciences, not just biomedical sciences.