Problems with peer review are par for the course in academia. Not every reviewer will be evaluating work that is entirely within their area of expertise. Cranky misunderstandings about methodological issues are to be expected, but can be dealt with respectfully and even painlessly.
The issue that we ran into with this round of review did take me aback, however. After months of waiting, our paper was rejected by Molecular Biology and Evolution based on the feedback of a single reviewer. What’s more, this reviewer objected to MOSAIC because he or she did not believe it was possible to integrate ortholog detection methods without degrading the quality of the end product. This is of course something we considered and addressed thorougly in the manuscript. At first when I read this critique, I thought I had perhaps concealed some of the key points of the manuscript within impenetrably drab blocks of text. Looking back, however, I found sections with titles such as:
- The addition of new sequences does not sacrifice average levels of sequence identity
- Integrating methods leads to higher levels of phylogenetic and functional concordance
These claims were supported by well-constructed figures and argumentation. Ultimately, I have trouble coming to any conclusion other than that 1.) the editor didn’t put in enough effort to find more than one reviewer, and 2.) that reviewer didn’t take the time to skim the figures or section titles.
After talking to colleagues, I found out that our experience is in no way singular, which is both comforting and unsettling at the same time. I’m interested in how we can be more faithful to the basic structures that help science function properly. At the same time, I have to start thinking about how I can maximize my contribution given the current circumstance. How much freedom can academia really offer if years of work can be stymied by a single individual who did not even read your manuscript? I think that’s an important question, but for the moment I’ll table it in favor of eating a good meal and going outside :)
Update: After much deliberation, we decided to challenge MBE’s decision. The paper is currently under review once again…