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The politization of academia is a major concern in contemporary America. We sought to address the prevalence and of political conflict in scientific training – including the extent to which conservative students perceive discrimination and whether this shapes their academic plans. We survey 337 graduate students from 12 randomly sampled programs in physics, chemistry, biology, and psychology. We asked about their political identity and beliefs, their academic experiences and career plans, and their experiences with conflict over political and social views. We find that conservative students are more likely to report conflict in the abstract, while liberal students are more likely to report concrete instances of giving and taking offense. We explain this apparent contradiction with differing levels of political engagement as well as with the commonality of covert forms of conflict management. We discuss the effects of such conflict on academic career trajectories. Conservatives already in graduate education do not appear to be dissuaded from academic careers by their perceptions of political deviance, but do indicate that it was a factor in their decisions to pursue graduate education in the first place.