The works of Isaac Newton reveal that his scientific insights usually came about not in a burst of insight but developed gradually from his studies of the previous accomplishments of scientists and mathematicians.

Parallelism idiom being tested here is "Not X...but Y", so let's look at each possible parallel structure:

(A) NOT in a burst of insight BUT developed gradually
(B) NOT in a burst... BUT were developed
(C) NOT come about...BUT developed
(D) NOT come about...BUT had developed
(E) NOT come about...BUT they were

We can see right from the start that (A), (B), and (E) have no chance. (A) has the first part of the idiom use the preposition "in" but drops it in the second part of the idiom, as does (B). (E) tries to put a verb "come" in parallel with a pronoun "they." The GMAT hates inserting pronouns to break up parallelism.

(C) and (D) correctly use verbs, but the tenses are different. (C) is more parallel with "come" and therefore correct. With (D), we would only use the past perfect tense if we were discussing two past tense events, and we had to make it clear that one event completed in the past before another past tense event started. When you have two verbs and one is a simple tense and the other is more complicated, unless you can justify why you NEED the more complex verb, stick to what is simpler and, in this case, most parallel.
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