“Now ifinnegan wishes us to understand that non-coding DNA can have important functions, but that idea is not fully accepted”
Yes it is. Questions exist as to the degree of “functionality” and what is considered functional, hence my quotes.
“The key point then is: if non-coding regions have no or little functions, then **any** differences there are totally irrelevant and should not be used in percent comparisons.”
No. Apples must be compared to apples so if it is a whole genome comparison all base pairs in each entire genome are compared, if it is a coding sequence then coding sequences are compared.
It’s not hard to understand. Neither is “better”.
Bob434 is calling comparisons of just the coding regions "deceitful" because they give us figures like 98% similarity between chimps & humans.
ExDemMom points out that non-coding regions are much more subject to enduring mutations, since such mutations have no known effects on survival or reproduction.
Hence non-coding mutations are not weeded out by Natural Selection and thus accumulate generation to generation.
So, if you wish to compare 100% genome to genome and arrive at a figure of 85% similarity, I have no real problem with it, so long as you properly identify what you did.
But in terms of actual working parts -- protein coding DNA -- the old number of 98% (plus or minus) similarity remains as valid as ever.
And the reason is Natural Selection.