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Improving scientific literacy requires examining both what people believe about scientific issues and why they hold those beliefs. We examined how people justified their agreement with statements regarding evolution, climate change, genetically modified foods, and vaccinations. Participants rated their level of agreement with statements reflecting the scientific consensus on these topics, then responded to open-ended questions asking them to justify their position and to generate challenges to their belief. Responses to individual difference measures allowed us to assess the relationship between participants' positions on these scientific issues and cognitive style, conspiracy ideation, religious service attendance, and political ideology. Qualitative analyses revealed inconsistent and topic-specific patterns of reasoning. Additionally, greater agreement with scientific conclusions was related to a greater predisposition towards analytical thinking and stronger self-reported political liberalism. These findings provide a next step for better understanding why some individuals reject science and for developing more effective means of improving science acceptance.