Book I of the Essay is Locke's attempt to refute the rationalist notion of innate ideas. Book II sets out Locke's theory of ideas, including his distinction between passively acquired simple ideas—such as "red", "sweet", "round"—and actively built complex ideas, such as numbers, causes and effects, abstract ideas, ideas of substances, identity, and diversity. Locke also distinguishes between the truly existing primary qualities of bodies, like shape, motion and the arrangement of minute particles, and the secondary qualities that are "powers to produce various sensations in us" such as "red" and "sweet." These secondary qualities, Locke claims, are dependent on the primary qualities. He also offers a theory of personal identity, offering a largely psychological criterion. Book III is concerned with language, and Book IV with knowledge, including intuition, mathematics, moral philosophy, natural philosophy ("science"), faith, and opinion

Book I The main thesis is that there are "No Innate Principles." Locke wrote, "If we will attentively consider new-born children, we shall have little reason to think, that they bring many ideas into the world with them." Rather, "by degrees, afterwards, ideas come into their minds; and...they get no more, nor no other, than what experience, and the observation of things, that come in their way, furnish them with." Book I of the Essay is an attack on nativism or the doctrine of innate ideas; Locke indeed sought to rebut a prevalent view of innate ideas that was, in his words, an "established opinion" firmly held by philosophers of his time. While he allowed that some ideas are in the mind from an early age, he argued that those ideas are furnished by the senses starting in the womb—for instance, differences between colours or tastes. If we have a universal understanding of a concept like sweetness, it is not because this is an innate idea, but because we are all exposed to sweet tastes at an early age. One of Locke's fundamental arguments against innate ideas is the very fact that there is no truth to which all people attest. He took the time to argue against a number of propositions that rationalists offer as universally accepted truth, for instance the principle of identity, pointing out that at the very least children and idiots are often unaware of these propositions. In anticipating a counterargument, namely the use of reason to comprehend already existent innate ideas, Locke states that "by this means, there will be no difference between the maxims of the mathematicians, and theorems they deduce from them; all must be equally allowed innate; they being all discoveries made by the use of reason."

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