Scientific knowledge is the outcome of a collective, for example, of experts, methods, equipment and experimental sites. The configuration of the collective shapes the scientific findings, allowing some interactions to become visible and meaningful at the expense of others. PROTEE is a methodology that aims to increase the reflexivity of research and innovation projects by helping to sensitise practitioners to the demarcations their projects enact, and to think through how these may affect the relevance of the outcomes. We used PROTEE to structure a series of dialogues with a research project that wanted its findings to make a contribution to the heated debate on transgenic trees. Through this process, the project did indeed become more articulated whilst we ourselves became engaged with the project in a very particular way, by becoming loyal to it. The dialogues also made the risks that engagement with public debate entails for scientists very apparent. Like us, the scientific project chose its loyalties, but what PROTEE did was to help to make these explicit.