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This article argues that interdisciplinary collaboration can offer significant intellectual gains to political science in terms of methodological insights, questioning received assumptions and providing new perspectives on subject fields. Collaboration with natural scientists has been less common than collaboration with social scientists, but can be intellectually more rewarding. Interdisciplinary work with biological scientists can be especially valuable given the history of links between the two subjects and the similarity of some of the methodological challenges faced. The authors have been involved in two projects with biological scientists and this has led them critically to explore issues relating to the philosophy of science, in particular the similarities and differences between social and natural science, focusing on three issues: the problem of agency, the experimental research design and the individualistic fallacy. It is argued that interdisciplinary research can be fostered through shared understandings of what constitutes ‘justified beliefs’. Political science can help natural scientists to understand a more sophisticated understanding of the policy process. Such research brings a number of practical challenges and the authors explain how they have sought to overcome them.