From: rokimoto557@gmail.com   
      
   On 7/1/2025 11:31 PM, John Harshman wrote:   
   > On 7/1/25 8:07 AM, RonO wrote:   
   >> On 6/30/2025 10:02 PM, John Harshman wrote:   
   >>> On 6/30/25 1:32 PM, RonO wrote:   
   >>>> 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.   
   >>>   
   >>> Perhaps we have different understandings of "closely related". Are   
   >>> all mammals closely related?   
   >>   
   >> No.  I did not mean as deeply as you seem to be claiming.  I noted   
   >> that the human and mouse intron sequence could not be matched up.   
   >> Humans and mice separated before a lot of avian lineages in terms of   
   >> time of separation, but not by much, and you can't use introns for any   
   >> accurate type of phylogenetic analysis for such mammalian lineages.   
   >> Birds seem to be a separate case.  The introns are shorter and more   
   >> conserved in some of the sequence.  I knew that they used intron   
   >> sequences in the phylogenetic analysis to place some avian lineages,   
   >> but it was not for the deepest branch nodes.   
   >   
   > Not true. Even the deepest avian nodes can be resolved using introns.   
   > There are even a few introns that can be aligned between birds and   
   > crocodiles, though they're unusually slow-evolving.   
      
   I did find that out, but you can't match up the introns of mammals.  I   
      
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