Today, I participated in a panel -- along with super-smart colleagues Alex Konings and Kabir Peay -- for the first-year Ph.D. students in the E-IPER program, an interdisciplinary, graduate interdepartmental program (IDP) at Stanford. As is the idiom for any E-IPER event, we spent a lot of time fretting about interdisciplinarity: what it means, how you achieve it, what costs it entails for jobs, etc.
I expressed the slightly heretical opinion that we should not pursue interdisciplinarity for interdisciplinarity's sake. What matters -- both in terms of the science and more instrumental outcomes such as getting published, getting a job, getting tenure -- are questions. Yes, questions. One should ask important questions that people care about. Why are there so many species in the tropics? Where do pandemic diseases come from and how can we best control them? Does democracy and the rule of law provide the best approach to governance? How do people adapt to a changing climate?
Where the interdisciplinary Ph.D. program comes in is it provides students the opportunity to pursue whatever tools and approaches are required to answer the question in the best way possible. You don't need to use a particular approach because that's what people in your field do. Sometimes the best thing to do will be totally interdisciplinary; sometimes it will look a bit more like what someone in a disciplinary program would do. Always lead with the question.
Answering important questions using the best tools available is probably the best route to managing the greatest risk of an interdisciplinary degree. This risk, of course, is the difficulty in getting a job when you don't look like what any given department had in mind when they wrote a job ad. The best way to manage this risk is simply to be excellent. If your work is strong enough, the specific discipline of your Ph.D. doesn't really matter. Now, there are certainly some disciplines that are more xenophobic than others (anthropology and economics come immediately to mind), but if your work is really outstanding, the excuse that you don't have the right degree for a given job gets much more tenuous. Two people who come immediately to mind are my colleague David Lobell and my sometime collaborator and former Stanford post-doc Marcel Salathé.
Is David a geographer? Geologist? Economist? Doesn't really matter because he's generally recognized as being a smart guy doing important work. Similarly with Marcel: population geneticist? Epidemiologist? Computer scientist? Who cares? He has important things to say and gets recognized for it.
Now, alas, we can't all be David and Marcel, but we can strive to ask important scientific questions and let these questions lead us to both the skills and the bodies of knowledge we need. These then form the foundation of our research careers. Interdisciplinarity then is about following the question. It is not an end to itself.