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President Obama’s Educate to Innovate initiative seeks to increase students’ engagement in the STEM fields. Such efforts must be informed by and grounded in an understanding of how students, particularly those who have been historically marginalized from such fields, become productively engaged in STEM activity, and in what instructional contexts. This paper examines a project-based classroom marked by student autonomy as one possible approach to engaging students. Previous analyses suggest that the ability to draw on one’s out-of-school experiences supported engagement, while group members’ assumptions about authority privileged some group members while marginalizing others. This paper extends prior analyses by focusing on the role of student autonomy on the interplay between patterns of student engagement and positions of authority.