In human hearing, subtle differences in how the two ears hear a given sound help the listener determine the qualities of that sound.
in how the two ears hear a given sound help the listener determine
in the two ears hearing a given sound help the listener in determining
in how a sound is heard by the two ears helps the listener determine
between how the two ears hear a given sound helps the listener in determining
between how a sound is heard by the two ears help the listener in determining
"Difference in" is usually used to refer to a change in one thing, instead of noting the dissimilarity between two things.
"In" is also used when you are referring to the difference between two things by pointing out the difference itself (i.e. the ONE thing that's different).
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