Though the Meditator can reach conclusions about his own body and also conclude that there are other bodies which are the source of his many sensory perceptions, there are certain claims about material things he is not justified in making. For instance, he cannot claim that the heat, color, and taste that he perceives resides in that object in the same way as it is present to his senses. Nature, as the combination of mind and body, teaches us to seek out pleasure and avoid pain, among other things, but it does not teach us to draw any conclusions about material objects based solely on sensory perception. Correct judgment in such matters depends on the intellect alone and not the senses. It would be unreasonable to infer from the sensation of heat or pain in approaching a flame that the heat or the pain reside in the flame itself. The fact of the matter is that the senses are meant only to inform us as to what is beneficial and what is harmful, and in that respect they are perfectly clear and distinct. Our mistake comes in expecting them also to inform us of the true nature or essence of the things we are perceiving, when they can only give us very obscure information in this regard.
But we often make mistakes even with regard to what is harmful to us. For instance, a sick person may crave food or water even if food or water will only make him sicker. To begin answering this objection, the Meditator notes that while body is divisible, mind is indivisible. While we can break extended things into smaller parts, the mind can in no such way be divided up. There are different faculties of the mind: the imagination, the senses, the will, the intellect, etc., but these are not different parts of the mind. When the mind imagines, it is the whole mind that imagines, and not some part of it. Since the mind is totally indivisible and bodies can be easily divided, it is clear that the mind and body are two very distinct things. Further, there is only a small part of the body that can affect the mind. In Descartes' day, it was thought that the pineal gland was the seat of the "common" sense, which sends all sensory perceptions to the mind. Thus, the Meditator concludes, only the pineal gland can send messages from the body to the mind. A sensation in another part of the body must then be transmitted through the body to the pineal gland. Further, these transmissions must take place by means of nervous signals that have a limited range of expression. All these facts combine to suggest that sometimes the body is incapable of sending the right message to the mind.
The Meditator concludes that, on the whole, he can be quite certain of things that he had cast into doubt in the First Meditation. The senses are normally quite adequate in helping us get around in the world, and when in doubt, we can double-check our sensory perceptions with our intellect or our memory. The Meditator also notes that our memory can dispel the doubt presented in the Dream Argument. Any waking experience can be connected through memory to all other waking experiences, whereas in dreams, things happen in a disconnected and somewhat random manner. Since God is not a deceiver, the Meditator is safe from erroneous judgment as long as he applies her mind carefully.
Descartes draws an important distinction between properties such as heat, color, and taste on the one hand, and size, shape, and texture on the other hand: the latter are primary qualities while the former are secondary qualities. The Meditator can be certain with regard to the primary qualities of a body since he can clearly and distinctly perceive them. They are all geometric qualities and relate to the extension of a body in space, which connects with its essence. On the other hand, the Meditator can often be misled regarding secondary qualities because they are non-geometric and can only be perceived obscurely and confusedly.
Here it might be useful to draw a distinction between sensory and intellectual perception. Sensory perception is perception using the imagination, while intellectual perception uses the understanding. In discussing a thousand-sided figure in the Sixth Meditation, Part 1, we concluded that the imagination can only give us a confused and obscure visual representation of geometrical figures whereas the intellect could clearly and distinctly perceive the figure no matter how many sides it has. Similarly, the intellect can grasp the primary qualities of body as they all relate to extension. However, there is no clear way that we can divorce secondary qualities from the imagination. I cannot easily think of the color red without thinking of the visual appearance of red.
There are two major conflicting interpretations of how Descartes views the ontology of secondary qualities. One is called sensationalism, and suggests that secondary qualities exist exclusively in the mind and not in any way in bodies. Secondary qualities do not represent anything in the corporeal world, according to this interpretation, though they may be caused by things in the world. Sensationalism seems then to imply that when one perceives red, the mind is, in some sense, red. This claim sounds very odd and it is not entirely clear how we are to make sense of it.