Gene duplication

One things that the attackers of science (including ID advocates) frequently do is accuse scientists of constructing 'just-so stories'.

A scientist while investigating a bacterial genome discovered that two genes doing apparently different tasks were almost identical in sequence, only differing by a few base pairs. This was a very interesting discovery, and the scientist decided to investigate a bit further. The first thing he did was to sit down and think about ways in which this related genes could have been produced. He came up with a few explanations, but the one he thought was the most likely was that the original gene had been copied (duplicated) in it's entirety, and then one of the copies had been changed by point mutations until was performing a different task to the original.

(The above explanation is typically labelled a 'just-so story' by ID advocates. We have some evidence. The scientist has constructed a explanation to account for it. There is no other evidence at this point that the explanation is correct. Science typically refers to these kinds of explanations as 'hypotheses', and they are acknowledged to be entirely tentative in nature.)

Having come up with a perfectly reasonable explanation for the origin of these two very similar genes what does the scientists do next? Does he drop the subject having explained it to his satisfaction and then move on to his next project? Actually he doesn't. He decides that this hypothesis needs testing to see if it actually correct. So the scientist has a think about what predictions he can make from his hypothesis, and how he can therefore design some tests for it.