Christopher Bohar's Debate Challenge

Apologies if I am asking a question you have already
answered (point me to the answer if approriate please),
but how do you determine that a gene is redundant, rather
than of unknown function?And what is the nature of the linking process/system/or whatever
between genes and expressed traits?

quote:

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Originally posted by peter borger:
Dear Peter,

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By knocking the gene out. No effect on the organism's reproductivity and you know. Hundreds of these genes have been found already. They are in the genome without selection and thus they falsify NDT.

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best wishes,
Peter

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I have read this reply before, I don't think it fully answers
what I asked, but I think I see what YOU mean by redundant.If a gene (or whatever is the most approriate terminology)
does not have an effect on survival or sexual selection,
why is it's existence in the genome a refutation of NDT?Do we first have to rule out the possibility that it was of
benefit at some time in the past, and is a 'hang-over'?What about if the gene exists on the same chromosome as a
'selected for' expressed trait? e.g. 'furry eyebrow gene' only
ever showed up on the same chromosome as 'really fast runner'
and these critters got chased a lot.