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At the very moment that humanity is facing a broadening ecological crisis, and that both policy makers and civil society are calling for a transition towards more sustainable societies, modern science seems incapable of providing operational solutions for managing this transition. In this context, both Noble prize laureates and high-level science officials have stressed the need of an in depth transformation of the modes of organization of scientific research for governing the transition to sustainable societies. However, existing analyses of on-going initiatives show that most of the barriers to a major, consolidated effort in sustainability science will not be removed without far-reaching institutional change. To address this challenge, this paper proposes an incremental institutional change approach, based on a gradual institutionalization process of existing initiatives. The analysis in this paper shows that strategic research for sustainability and reform of research funding mechanisms will only be effective if they are supported at the same time by reforms of career and training paths at higher education institutions. To promote this vision, the paper proposes a set of capacity building measures that can be undertaken at the level of research funding, higher education institutions and networking.