We also can’t say that it’s definitely not a fusion site. These kinds of statements are meaninglessly vacuous. No, we don’t have absolute certainty, but is that really the requirement for us to be very confident in what is ultimately a provisional conclusion?
It is tiresome that we have to spell out these basic things. Suffice it to say that there is only evidence for it being a site where two telomeres fused, and a lot of it, and no evidence against it. Hence the only rational option is to accept provisionally that it is a site of a chromosomal fusion, and to be highly confident in that conclusion.
No, even if there really was a functional gene spanning the locus(which there isn’t), it would not be evidence against it being the site of some ancestral chromosomal telomere-telomere fusion. That would merely imply that subsequently to the fusion, some functional gene emerged across that locus. A functional gene spanning a telomere-telomere fusion site isn’t evidence against a telomere-telomere fusion site looking exactly like a telomere-telomere fusion site.
Well except if ‘definitely’ means with absolute certainty, which is what Bill meant by the word. If that’s not what he meant by it, then his pathological need to even state it makes zero logical sense.