It was not until 5,500 years ago the systematic methods for writing numerals were invented
→
It was only then that any sort of computation became possible
The big gap here is that the argument is assuming that the systematic methods of writing numerals was necessary for computation. How do we know this? We know this because of the phrase, "only then." The conclusion is basically saying, "computation became possible → systematic methods of writing numerals were invented." In other words, IF there is computation THEN it absolutely must be the case that systematic methods for writing numerals were invented.
(A) So what if there were some grooves and scratches found on bones/stones that weren't made by people? Listen to how ridiculous this sounds: it is saying that it must be the case that natural processes did not scratch or groove any bone or stone. This is absolutely not necessary for the argument. We are still wanting to bridge the gap between computation and systematic methods!
(B) This, like (A), has no bearing on the argument. So what if there were some kinds of surfaces that were not used for writing numbers?
(C) We don't need to assume anything about when the earliest people. By the way, who ever said that humans were necessary for computation? Maybe apes could compute?
(E) We don't care about why the numerals were invented and we definitely don't need to conclude that the numerals were invented only because the need arose.
(D) This helps us beautifully with the gap. This can be a bit of a tricky answer because you may see "computation of any sort" and think that it is too wide of a scope but the argument itself talks about "computation of any sort" so this answer choice is not too broad for a necessary assumption.