Well, if there were any, you didn't address them. First, I made no mention of It makes no judgements about how close two species' sequences "should" be to each other.".
Second, my example showed that a 110 base sequence comparison resulted in a match of only 19 bases. The resulting expectation was high(or not surprising) even though the 19 identities were 100%.
Finally it was not AndrewC that chose the sequences mentioned in the "junk" DNA study. That was done by comparison of the mouse and man genomes. They were alike between mouse and man. They were "conserved" between mouse and man. And they were not genes between mouse and man.
They also give a figure of 98% similarity between us and chimps. Now, this is unclear exactly what they're saying - "share 90% of our genes"? Do they mean 27,000 human genes are identical to mouse genes, or do they mean that an average of 1 in every 10 letters throughout the coding part of the genome are different? Sheesh, science writers!
Well, here's a news article. It says
"About 99 percent of genes in humans have counterparts in the mouse," said Eric Lander, Director of the Whitehead Institute Center for Genomic Research in Cambridge, Massachusetts. "Eighty percent have identical, one-to-one counterparts."Also:
Of course, there are also important differences. The mouse genome is about 14 percent smaller than the human version. ... But about 40 percent of the two genomes are directly aligned.OK, with 80% of human genes being exactly equal to their mouse counterparts, and 19% of the rest of our genes having recognizable "counterparts" in the mouse, I think we can safely assume that the AMNH's figure of 90% must mean overall sequence similarity. At any rate, the overall sequence similarity figure must be somewhere higher than 80% if 80% of our genes are identical to the mouse versions.
Now, we go back to the gene desert knockout experiment. There they clearly said that the homology with the human sequence was only 70%. So yes, it did diverge more than the coding regions did. IOW, the junk DNA that they knocked out were not more highly conserved than the coding regions.
Nope, sorry Andrew, but it's junk. Or else the Designer is a packrat. :-)