In the Discourse on Method, Descartes writes that in order to constitute a real man, a rational soul cannot derive from matter. Nevertheless, it must be “closely joined and united with the body” (AT VI 59, CSM I 141). The expression “real man” echoes the Treatise on Man (AT XI 202, CSM I 108), and is also found later in the Sixth Meditation (AT VII 90, CSM II 62). In this meditation, Descartes writes that “the mind is not immediately affected by all parts of the body, but only by the brain, or perhaps just by one small part of the brain, namely the part which is said to contain the common sense” (AT VII 86, 90; CSM II 59, 62). The Discourse had mentioned the “common sense” (AT VI 55, CSM I 139), as had the Dioptrics, where its “seat” is located in a “small gland … in the middle of the concavities” in the brain (AT VI 129). In the Passions of the Soul, Descartes writes that this gland is the part of the body where the soul “ exercises its functions more particularly than in all the others.” Descartes is referring to the pineal gland or conarium, which he calls “the principal seat of the soul” (AT XI 351–52, CSM I 340).

This gland, already mentioned by the physician Galen and, owing its name to its pinecone shape (De usu partium, book VIII, ch. XIV), is denominated by the letter “H” in the Treatise on Man (AT XI, 176, CSM I 106) (see Figure 27). This letter identifies the pineal gland in a Vesalian-style anatomical plate dealing with the internal structure of the brain in Caspar Bauhin's treatise Theatrum anatomicum, a book that was of use to Descartes when he was writing the Treatise on Man and “was dissecting the heads of various animals” to “explain what imagination, memory, etc. consist of” (AT I 263, CSMK 40). Descartes clearly distinguishes this gland from the pituitary gland or hypophysis, located at the base of the brain (AT III 263, CSMK 162; AT XI 270, 582). He also rejects the “processus vermiformis” (or vermis) of the cerebellum to be a suitable organ devoted to the union (AT III 124).