The central objective of this work is to present the discussion around the objective of science teaching in the light of an epistemological approach, in order to verify how this debate reverberates in the teaching of chemistry. Given this discussion, in which different theses are defended, I argue in favor of the thesis that considers that one of the objectives of science education is the formation of a critical citizen with intellectual autonomy. A critical subject is considered to be one who seeks to discuss the reasons involved in a dispute by submitting them to the sieve of reason. Here, critical-reflective action is essential for the formation of a responsible epistemic agent. And, in this sense, responsibility implies autonomy. Thus, autonomy is understood as a virtue or a quality. When I consider that a student (as an epistemic agent) has a virtue, I want to argue that he has a disposition to be motivated in a certain way and to act in a given way in relevant circumstances, and, furthermore, he is successful in achieving the end of his virtuous motive. To illustrate the idea of autonomy, a central theme in the teaching of chemistry was used as an example: the "disagreement" about the concept of molecular structure. For this, a scenario was proposed in which reflection is important and has epistemic value: the ontological status of molecular structure -reducible or non-reducible to quantum theory? Faced with the views of the authors, it was found that some adopt the reductionist perspective which defends the reconstruction of the concept within the quantum structure of atoms in molecules. Others, while recognizing the conceptual discontinuity between quantum mechanics and molecular chemistry, keep alive the hope for reduction. From an explicitly non-reductionist position, authors conceive molecular structure as an emergent phenomenon.In this scenario, reflection was understood as a performance, an activity from which the agent examines the reasons, the evidence, the content involved, the reliability of his own beliefs and, in the face of proposed disagreement, decides what is epistemically reliable to believe or not. This is a theoretical-reflexive research, for its value and normativity, based on the analysis and review of the literature.