This article reflects on current debate over transformations of scientific research and universities. Four well-known mutation theories (Mode-2 knowledge production, triple helix of university-industry-government relations, academic capitalism and enterprise university), and their recent critiques, are reviewed. It is suggested that a better understanding of the changes can be achieved by drawing analytic insight from research that speaks about scientific practices. Advantages that may be so attained are illustrated through a case study of a plant-biotechnology research group that pursued to straddle the fuzzy university-business boundary. On such grounds, three arguments that pertain to the mutation theories are put forward: (1) the need to appreciate the dynamics between theoretical, experimental and applied dimensions of research work; (2) the fact that external research funding intermingles with the complex social ecology of disciplines at the departmental level of universities; (3) the difficulties academics encounter as they try to fuse their university activities with private commercial development.