The problem is when the paper is from one side in a heated controversy. In my field of work, generously circumscribed as ranging from systematics across biogeography to evolutionary biology, the following come to mind:
- Mainstream biogeographers versus panbiogeographers
- Phylogenetic systematists versus 'evolutionary' systematists
- Adaptationists versus neutralists
- Parsimony purists versus Bayesian phylogenetics purists, with those preferring likelihood analysis thrown into the mix
Anyway, assume you are an entirely neutral journal editor and you need to get reviewers' reports for a paper from one of those sides, let us say from a panbiogeographer doing a panbiogeographic analysis. Who do you send it to?
If you send it to a mainstream biogeographer, you already know that they are going to recommend rejection because they consider the entire methodology and its assumptions to be unscientific. The same if the roles are reversed; a colleague had a paper rejected because he found evidence for long distance dispersal and ran into a reviewer (and an editor) who don't believe that it is possible. Send it to somebody who isn't on either side? Well, they are likely not qualified to review in the first place, otherwise they would already have picked a side.
So how does such a conflict ever get resolved? Keep the two parties carefully separated and hope that one of them dies out? That is also a form of post-publication review I guess.
My perspective is currently that of having been asked to review a paper from a representative of a school of thought that looks to me kind of like this:
What to do? I informed the editor that I should be considered biased, but he wanted my opinion anyway. Having an editor who listens to both sides, takes their respective views with a grain of salt, and then makes up their own mind is probably the best one can hope for. But pre-publication peer review is still a very imperfect tool in such a situation.