Hi, I've been watching this forum for quite sometime and I think i like to contribute my thoughts too....
I think answer C is correct.
My 2cents for this question is:
1. "with great certainty" is much more precise than "beyond a shadow of the doubt". It also sounds more formal and less flowery for this kind of topic.
2. Just for making things more clear (although it may look silly), let's try to reconstruct the sentence in present tense:
<The scientist knew for a long time beyond a shadow of a doubt> that
she discovered the double helix
In this sentence, the statement exist only because she had thought about discovering the double helix before she actually discovered the double helix, so the thought must exist before the actual the discovery, and the thought must still be true even in the 0.001 sec before she discovered the helix, which warrants a perfect tense.
so in present tense:
the scientist has known for a long time, ... that she discovers/will discover the double helix.
and in past tense it is true that:
the scientist had known for a long time,... that she discovered the double helix.
(she would have thought about until she actually discovered it and since it is in past tense we need to use: simple past and past in the past (past perfect).[/quote]