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In peer instruction, instructors pose challenging questions to students, students answer questions individually, students discuss their answers with a peer in the class, and finally students answer questions again. A large body of evidence shows that peer instruction benefits student learning. To determine the mechanism for these benefits, we collected semester-long data from six classes, involving a total of 208 undergraduate students. Students were more accurate and confident after discussion than before. Initially-correct students were more likely to keep their answers than initially-incorrect students, and this tendency was partially but not completely attributable to differences in confidence. We discuss the benefits of peer instruction in terms of differences in the coherence of explanations, social learning, and contextual factors.