Variation and when to ignore it
Recognising that two objects or concepts are ‘the same but different’ ought to present a major philosophical problem; the phrase itself seems self-contradictory. However, in practice we categorise elements of our world in just this way on an everyday basis. A two-year-old can grasp the fact that his right shoe and left shoe are very similar, but actually belong on different feet; and as adults, we have no difficulty in recognising that lemons and limes are different but both citrus fruits, or that misery and happiness are different but both emotions. This sort of hierarchical classification is exactly what is at issue when we turn to the notion of the phoneme.
Humans excel at ignoring perceptible differences which are not relevant for particular purposes. To illustrate this, take a piece of paper and write your normal signature six times. There will certainly be minor differences between them, but you will still easily recognise all those six signatures as yours, with the minor modifications only detectable by uncharacteristically close scrutiny. Perhaps more to the point, someone else, checking your signature against the one on your credit card, will also disregard those minor variants, and recognise the general pattern as identifying you. There are exceptions, of course: some alterations are obvious, and usually environmentally controlled, so if someone jolts your elbow, or the paper slips, you apologise and sign again. On the whole, however, the human mind seems to abstract away from irrelevant, automatic variation, and to focus on higher-level patterns; though we are typically unaware of that abstraction, and of the complex processes underlying it. This relatively high tolerance level is why mechanical systems constructed to recognise hand-written or spoken language are still elementary and highly complex, and why they require so much training from each potential user.
Conditioned variation in written language
Since we are more used to thinking explicitly about written language than about our speech, one way of approaching this issue of abstraction is through our conscious knowledge of the rules of writing. When children learn to write, they have to master the conventions governing the use of capital and lower-case letters.