When scientific research collides with social values, science's right to self-governance becomes an issue of paramount concern. In this article, I develop an account of scientific autonomy within a framework of public oversight. I argue that scientific autonomy is justified because it promotes the progress of science, which benefits society, but that restrictions on autonomy can also be justified to prevent harm to people, society, or the environment, and to encourage beneficial research. I also distinguish between different ways of limiting (...) scientific autonomy, and I argue that government involvement in scientific decision-making should usually occur through policies that control the process of science, rather than policies that control the content of science. (shrink)