The following is a letter I submitted to Nature in response to a recent editorial. They decided not to publish it... so... blog fodder it is!
I was pleased to read the recommendation that “scientists, institutions and funding agencies must increase transparency wherever possible” (Nature 465, 7; 2010). To that end, I suggest journals such as Nature consider ways to increase the transparency of the peer review process. The practice of anonymous peer review is at odds with the increasing adoption of transparency and accountability by government, private industry, and elsewhere.
Currently, the identity of reviewers typically remains anonymous to the author(s) of the paper during the editorial process. Even after the peer review process is over and the final article of record has been published, reviewers remain anonymous to the readers. This level of anonymity makes it easy for authors or readers to claim that a shadowy cabal of insiders can effectively block publication of science that is technically sound but controversial. Such accusations were raised by some stem cell researchers earlier this year (http://blogs.nature.com/news/thegreatbeyond/2010/02/bad_reviewers_block_good_resea.html). Cases like it show how a lack of accountability in peer review can be used to cast doubt upon scientific evidence, particularly for controversial subjects like climate change.