What role does scientific claims-making play in the worldwide promotion of biofuels for transport, which continues despite serious concerns about its potentially adverse social and environmental effects? And how do actors with very different and conflicting viewpoints on the benefits and drawbacks of biofuels enrol scientific authority to support their positions? The sociological theory of functional differentiation combined with the concept of advocacy coalition can help in exploring this relationship between scientific claims-making and the policy stance of different actors in public debates about biofuels. In Denmark two distinct scientific perspectives about biofuels map onto the policy debates through articulation by two competing advocacy coalitions. One is a reductionist biorefinery perspective originating in biochemistry and neighbouring disciplines. This perspective works upwards from the molecular level and envisions positive synergies in the use of biomass. The other is a holistic bioscarcity perspective originating in life-cycle analysis and ecology. This perspective works downwards from global resource scope conditions, and envisions negative consequences from an increased reliance on biomass. Understanding how these scientific perspectives and policy stances are coupled sheds light on three contentious policy questions: how Denmark should include biomass in its energy provision, what role Denmark might play in the global development of biofuels and what kind of subsidy schemes should be implemented.