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Contemporary naturalism is supposed to be the exact opposite of dualism, regarding current studies in cognitive science, in particular between philosophy and neuroscience. Indeed, one of the key principles of naturalism and materialism is the rejection of any kind of dualism, in favour of a monistic view of the world and man. However, examining Descartes' dualism and mechanism in relation to the body, it is highlighted that conceptual signs of his philosophical doctrine are still rooted in the alleged anti-cartesian naturalism. Interestingly enough, common sense, contemporary medicine and scientific paradigm reveal dualistic structures between subject and body, mental and physical diseases, brain and body, which implicitly refer to the cartesian mind-body relation, though with less ontological commitment. The "ghost in the machine" has become the "brain in the machine", therefore, this means that some conceptual features of dualism lie unaltered at the basis of contemporary science and philosophy. Finally, they will be specified some possible alternatives to the mechanist idea of the body as a machine, through the recent 4E cognition movement and the phenomenological distinction between objective-cartesian corpse and temporal-lived body.