The structure of higher education organizations always reflect the belief of those who develop the institutions. This article discusses some impacts of goverment's intervention regarding university organizations in newly drafted higher education regulation. The author believes that higher education paradigm shift only occurs when a university essentially adopts a bundle of new modes of of thinking in dealing with economic, political, social, and cultural phenomena. The shift should not be intervened by any other parties outside the university including by the government through certain regulation. Such intervention will only harm the heterogenous scientific thinking among Indonesian academic communities.