The Third Meditation, subtitled "The existence of God," opens with the Meditator reviewing what he has ascertained to date. He is still doubtful of the existence of bodily things, but is certain that he exists and that he is a thinking thing that doubts, understands, wills, imagines, and senses, among other things.

He is certain that he is a thinking thing and he clearly and distinctly perceives this fact. He could not be certain unless all clear and distinct perceptions can be certain. Therefore, he concludes, whatever he perceives clearly and distinctly must be true.

Before, he thought he was certain of all sorts of things that he has now cast into doubt. These things are all apprehended by the senses, and he must acknowledge now that he did not perceive the things themselves, but only the ideas, or thoughts, of those things, which appeared before his mind. He does not even now deny that he perceives ideas of material objects, but concedes that he was mistaken in inferring from these ideas that his perception could inform him about the things themselves. He also seems quite certain of arithmetic and geometry, though he cannot be absolutely certain since God might be deceiving him. To assure himself that he is not deceived, he must inquire into the nature of God.

Before he can do so, however, the Meditator resolves first to classify his thoughts into different kinds. First, there are simply ideas, which he says "are as it were the images of things...for example, when I think of a man, or a chimera, or the sky, or an angel, or God." Second, there are volitions, emotions, and judgments, where there is an idea, which is the object of a thought, and also a further thing, such as an affirmation or a fear, which is directed toward the object of that thought.

The Meditator reasons that he cannot be mistaken with regard to ideas on their own, nor with regard to volitions or emotions: he can only make mistakes with respect to judgments. The most common error in judgment is to judge that the ideas in one's mind conform to, or resemble, things outside the mind. Considering ideas in the mind only as modes of thought and not referring them to anything outside the mind should render him immune from doubt.

It seems there are three sources for ideas: they can be innate; they can be adventitious, coming from outside of us, as with our sensory perceptions; or they can be invented by us, such as our ideas of mermaids or unicorns. The Meditator concedes that he cannot yet be certain which ideas come from where, or even if perhaps all of our ideas are innate, adventitious (not inherent but added extrinsically), or invented. For the moment, he is concerned with adventitious ideas, and why he thinks they come from outside. His will has no effect on adventitious ideas: he cannot prevent himself from feeling hot when it is hot simply through the will, for instance. He has thus come to assume that whatever outside source transmits these adventitious ideas transmits its own likeness rather than something else.

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