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The next generation standards framework encourages students to engage in authentic scientific practices. To engage students in authentic inquiry tasks, students need to learn not only scientific knowledge and process skills, but also disciplines in the nature of sought explanations, methods adopted for investigations, and reasoning with the evidence in each practice. However, such disciplinary knowledge can substantially differ across practices, and as result some students may conflate one discipline with another and even reject the validity of one discipline based on the other. The present paper discusses how to disentangle “discipline-specific” epistemologies across different practices and propose a conceptual framework to help students overcome such epistemological conflation and conflicts through curriculum and instructional design.