In this paper, we examine two methods of public participation, namely consensus conference (conférence de citoyens) and public hearing (débat public). While both methods are used in order to involve the public in decision making about science and technology policy, they differ in a number of aspects. Consensus conference seeks the active participation of a selected group of citizens who are expected to elaborate cooperatively a text of recommendations. Public hearing seeks to inform the public and to collect as many reactions by it as possible. In our analysis, we consider the characteristics of these two methods described in the social and political sciences literature as institutional constraints that can play a role in the production of argumentative discourse. We focus our study on the discourse produced in two concrete instances of the application of these participatory methods on the deliberation over the development of nanotechnology in France. More specifically, we study the expression of counter discourse and seek to describe how the participants in the two deliberation processes end up managing the institutional constraints in order to have their criticisms expressed. In this way, we propose a bottom-up approach to the theorization of the role that institutional context plays in the practice of argumentation, and discuss the descriptive adequacy of existing definitions of the deliberative genre within argumentation studies.