Controversy abounds in the governance of genetically modified organisms (GMOs) for use in agriculture, partly due to ideological differences. Technological optimism and the "shallow" and the "deep" ecology movements are three influential ideologies that are seen to differ both on value commitments and factual beliefs with respect to GMOs. Factual matters are clarified but not resolved by science, since the scientific community faces uncertainty and apparent contradiction between different research perspectives, notably molecular biology, ecology and the social sciences. Scientific advice plays a key role in the governance of GMOs and ought to be construed so as not to exclude legitimate arguments from ideological perspectives present in the process of governance. This paper analyses the role and use of risk assessments and argues that they be replaced by forms of advice that consider a broader spectrum of scientific evidence and insights, e.g. impact assessments and evaluations of inherent sources of uncertainty and ignorance. A few practical measures to that effect are discussed.