Contrary to popular belief, neuroscience poses no threat to human freedom, as there is no fundamental conflict between the manifest image of man and the naturalism of neurobiology and other neuroscientific disciplines. It cannot be denied that neuroscience does not leave our self-understanding untouched but it is difficult to ascertain how deep this influence reaches. While naturalistic approaches in general presuppose the ontological unity of reality and the formal unity of the sciences, scientific eliminativism takes the language of natural science as the ultimate semantics for describing what there is. This approach excludes the most important aspects of the mind: the epistemic, emotive and moral states of self-conscious persons. In contrast, varieties of integrative naturalism such as the one defended here do not give primacy to a particular scientific position, but rather distinguish between the space of reasons and the realm of causes and grant both a non-eliminable methodological status. Moreover, integrative naturalism takes account of the fact that the remarkable quality of self-consciousness consists in the fact that reference arises through an act of self-reference that in itself is referentially differentiated. In order to gain an understanding of the identity of a person over time in its entirety, one has to refer to psychological and physical constituents of her continuity in space and time. Thus, while neuroscience can identify aspects of the manifest mind, only an integrative naturalism can meet the requirements for explaining the phenomenon of self-conscious being in the world.