From: rokimoto557@gmail.com   
      
   On 6/30/2025 1:44 PM, John Harshman wrote:   
   > On 6/30/25 9:01 AM, RonO wrote:   
   >> https://evolutionnews.org/2025/06/on-human-chimp-genetic-differences-   
   >> the-critics-misstate-my-arguments/   
   >>   
   >> He is claiming that his critics are not addressing his claims or   
   >> misstating them.  Luskin is falsely claiming that the 1% difference   
   >> between chimp and human genomic DNA that had been determined for the   
   >> sequence that was compared in order to determine the evolutionary   
   >> relationship between extant life forms is some type of Icon of   
   >> evolution.  It is just what the sequence difference was.  It wasn't   
   >> the 1% number that determined that chimps are the most closely related   
   >> species to humans it was how that 1% difference related to all the   
   >> other species that we had the same sequence for and could compare them.   
   >>   
   >> Coding sequence is still 0.7% different between chimps and humans, and   
   >> the sequence around the genes that we can compare are between 1 and   
   >> 1.8% different.  We can't use a lot of the sequence around the coding   
   >> sequence to compare extant species to each other because it is so   
   >> different between species that we can't compare it accurately.  I took   
   >> around 800 base-pairs of the tyrosinase exon 1 coding sequence and the   
   >> following 900 base-pairs of the first intron.  Chimps and humans were   
   >> 99% similar by BLAST for this sequence.  Green monkey was 95% similar   
   >> for the sequence compared to humans, but the coding sequence was less   
   >> than 3% different and the intron sequence was almost 9% different   
   >> (there were also a couple of indels in the intron).  I tried the same   
   >> sequence for mouse and BLAST would not align the intron sequence.  It   
   >> was just too different.  Even under BLAST for more relaxed conditions   
   >> it would only align bits of the intron in around 60 base-pair pieces   
   >> where there was enough similarity where they might be the same   
   >> sequence (many of these short matches were not the same sequence and   
   >> were on other chromosomes of the genome assembly).  The 826 base-pairs   
   >> of coding sequence was 87% similar, but the intron sequence was not   
   >> matched up. It might be expected to be around 60% similar if you could   
   >> align it, but any alignment likely would not be that accurate.   
   >>   
   >> This just means that the sequence that we determined to be around 1%   
   >> different (coding sequence) is the sequence that would be used to   
   >> determine evolutionary relationships between mammals.  It is the   
   >> sequence that can be used to determine that chimps are the most   
   >> closely related species to humans that exist on this planet today.   
   >> But outside of mammals the accuracy of coding sequence decreases   
   >> because of the degenerate code and multiple substitutions at the third   
   >> position of codons that you can't tell if they have been mutated   
   >> multiple times or not.  You can only use noncoding sequence like   
   >> introns to compare closely related taxa because they change too fast   
   >> to be useful.   
   >   
   > All fine except for that last bit. Introns and other junk sequences are   
   > perfectly useful to considrable phylogenetic depth. They work for the   
   > deepest divergences in birds, for example, and I imagine they work for   
   > pretty deep divergences in mammals too, certainly for all primates.   
      
   That is what I meant when I wrote that "You can only use noncoding   
   sequence like introns to compare closely related taxa because they   
   change too fast to be useful."  I just didn't put in useful to   
   descriminate deeper divergences.   
      
   Ron Okimoto   
   >   
   >> The additional sequence that Luskin is beefing about was sequence that   
   >> we could not obtain in all taxa, and it is still sequence that can't   
   >> be accurately compared between the taxa with complete genome sequences   
   >> because of the repetitive nature of the sequence and the rapid copy   
   >> number variations between species and the rapid evolution of the   
   >> sequence of the heterochromatin repeats.   
   >>   
   >> Luskin is literally beefing about something that never mattered, and   
   >> still does not matter.   
   >>   
   >> The mitochondrial DNA sequence is 8.9% different between chimps and   
   >> humans and still indicates that chimps are the most closely related   
   >> species to humans.  In the 1980's mitochondrial DNA was the first   
   >> sequence used to determine that of the other great apes chimps were   
   >> our closest relative.  It wasn't the 1% genomic coding sequence   
   >> difference. For the tyrosinase sequence that I used in the above   
   >> analysis both gorilla and chimps are 99% similar (16 mismatches with   
   >> Gorilla and 20 mismatches with chimps) by blast alignment.   
   >>   
   >> Ron Okimoto   
   >>   
   >>   
   >   
      
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