Aristotle argues that a particular substance is only given to sensation per accidens, and that all that is known to intellect is universal. So what knows the particular substance as such?
St. Thomas usually appeals to some sort of “reflection on the phantasm” to explain this, but it’s unclear how this is supposed to work. How does this retorsive action give a power to see something that neither sense nor intellect as such can see?
To appeal to an instinct here is to change the question. All instinct would mean is that some power or another is naturally moved to see individuals. But what power are we talking about?
Josiah Royce raises this problem in his Lecture on the Conception of Immortality.
[O]ur human type of knowledge never shows us existent individuals as being truly individual. Sense, taken by itself, shows us merely sense qualities, — colors, sounds, odors, tastes. These are general characters.
Abstract thinking defines for us types. A discriminating comparison of many present objects of experience, such as autumn leaves, or human faces, or handwritings, shows us manifold differences, but always along with and subject to the presence of likenesses, so that we never find what common sense assumes to exist, namely, such a difference between any individual and all the rest of the world as lies deeper than every resemblance. And even if by comparisons and discriminations we had found how one being appears to differ from all other now existent beings, we should not yet have seen what it is that distinguishes each individual being from all possible beings. Yet such a difference from all possible beings is presupposed when you talk, for instance, of your own individuality.