The farmers' protests against field trials of genetically engineered Bt-cotton in India highlighted the controversies surrounding genetic engineering technology in agriculture. Molecular biological, organismal, ecological and societal issues surrounding the Bt-cotton controversy are examined in order to identify the level of organization at which known and potential problems arise and, thereby, to suggest the level at which such problems are best addressed. The analysis suggests that information available to the public was incomplete, irrelevant, or obfuscated such that the technological and societal issues were neither well characterized, nor well separated; scientists have an important role in making available undistorted information to the public, thus enabling informed, democratic decision making.