In recent decades agriculture has undergone rapid technological and structural changes. This development has raised concerns about the sustainability of modern agriculture and motivated an interest in alternative and, perhaps, more sustainable agricultural systems. Agriculture involves both ecological and social systems, and research in agricultural systems therefore faces the dual challenge of understanding complex agro-ecosystem interactions and handling the involvement of human actors, their practices and preferences. A major survey to assess the consequences of phasing out pesticide use in Denmark is presented as an example of a study confronting this dual challenge. The survey included the modelling of a total organic conversion of Danish agriculture, and this work is used to illustrate significant methodological issues in agricultural systems research. The removal of pesticides implies radical changes, and although the models implemented in the survey were based on all the available scientific knowledge, the work revealed insufficient knowledge in many areas. This, in turn, made it clear that the modelling could not be done without an inquiry into the different values involved. In particular, different conceptions of precaution and sustainability played major roles in the work
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