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From: RonO <rokimoto557@gmail.com>
Newsgroups: talk.origins
Subject: Re: More stupid denial about DNA sequence analysis
Date: Tue, 27 May 2025 11:23:37 -0500
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On 5/27/2025 8:35 AM, RonO wrote:
> On 5/25/2025 3:54 PM, RonO wrote:
>> https://evolutionnews.org/2025/05/fact-check-new-complete-chimp- 
>> genome- shows-14-9-percent-difference-from-human-genome/
>>
>> The ID perps just have to lie about how we have had to do sequence 
>> analysis to get useful information about the evolutionary 
>> relationships.   As stupid as it may be they refuse to understand that 
>> we have had to compare sequences that we could be sure were 
>> homologous.  We have always had to rely on more than just sequence 
>> similarity.  When we only had a few sequences to compare there was a 
>> big snit about the difference between sequence similarity and 
>> homology.  What has always been used for sequence analysis are the 
>> sequences that we had a good idea were homologous between species.  We 
>> have always understood that due to insertions and deletions that not 
>> all of the similar sequence had to be homologous, and that factor was 
>> always a concern for trying to align sequences for analysis.  This 
>> means that we have always not been able to deal with insertions and 
>> deletions very well, and have left the large ones out of the 
>> analysis.  We also could not compare the parts of the genome that we 
>> could not sequence accurately because they were highly repetitive or 
>> high GC and were under represented in the databases.
>>
>> Simply put in order to determine the relationship between species you 
>> need to compare sequences that all of the species have.  This means 
>> that if one species has an insertion in the sequence, the insertion 
>> cannot be used in the analysis because all the other species do not 
>> have the insertion.  Highly repetitive sequence could not be in the 
>> analysis because it could not be sequenced accurately, and was 
>> determined to have a high creation and loss rate using the old density 
>> gradient DNA analysis of satellite DNA.  This just meant that we never 
>> tried to seriously use heterochromatin in any evolutionary analysis.  
>> You just have to look at the old data on heterochromatin to know that 
>> we knew that chimps had a lot more heterochromatin on the ends of 
>> their chromosomes than humans (I recall the estimates where that 
>> chimps had more than double the amount as humans).  This is a major 
>> part of the 13% difference that the ID perps are stupidly jumping for 
>> joy over.  Humans just do not have as much heterochromatin on the ends 
>> of their chromosomes as chimps, and what they have has been known to 
>> have a high variation rate before we could easily sequence the DNA.  
>> These large regions of short tandem repeats have a very high mutation 
>> rate.  Most of the larger regions likely change in copy number every 
>> replication cycle.
>>
>> Telomere to telomere sequences of the ape genomes have been published.
>>
>> https://www.nature.com/articles/s41586-025-08816-3
>>
>> The article is open access.  They used the same technology that 
>> allowed the sequencing of nearly all of the human genome to sequence.  
>> They were able to sequence through most of the large regions 
>> containing tandem repeats, but not all, and they couldn't get through 
>> all the repetitive sequence around some of the centromeres.  So what 
>> they found was a lot of basically junk DNA that is a different 
>> sequence between chimps and humans.
>>
>> All of this just doesn't matter.  The sequence analysis that places 
>> chimps as our closest relatives still stands because we used sequence 
>> that chimps and the other apes have that we could compare, like coding 
>> sequences and the noncoding regions around known genes that we could 
>> determine were the same sequences relative to their positions around 
>> known genes.  We do not have to use the sequence that we cannot 
>> reliably determine is the homologous sequence in all taxa in any 
>> particular analysis, so we still will not use the highly repetitive 
>> sequences and indels.  We cannot use sequence that chimps may have, 
>> but humans do not have and vice versa.  Chimps just have a lot more 
>> heterochromatin on the ends of their chromosomes than humans have, and 
>> the additional sequence is useless for the way sequence analysis has 
>> to be done.
>>
>> Ron Okimoto
>>
> https://evolutionnews.org/2025/05/breaking-new-study-shatters-the-1- 
> percent-human-chimp-difference-myth/
> 
> More obfuscation and stupid denial up at the ID perp's creationist news 
> site.
> 
> The plain and simple fact is that the 0.7% difference observered between 
> chimp and human coding sequences is probably never going to 
> significantly change unless we start counting duplications and 
> deletions.  The 0.7% difference has been calculated using thousands of 
> genes that both chimps and humans share.  Confusing what is claimed is 
> just stupid at this time.  We have known for a very long time that the 
> noncoding sequence had more differences in it, and we still were not 
> counting insertions and deletions (about 1 to a little over 2% depending 
> on what type of noncoding sequence was being compared).
> 
> These numbers are not going to change unless we start counting the 
> duplications and deletions.  For transposon examples where the chimp or 
> human genome have an AlU insertion that the other does not it is stupid 
> to count it as over 300 differences (the length of the transposon) when 
> it is a single mutation event.  The same goes for gene duplications and 
> gene loss.
> 
> The bottom line is that nothing is going to change about how we nest 
> within the other great apes in our genome sequence.  We obviously have 
> the basic ape genome template, and it can easily be differentiated from 
> the monkey genome template, but it can easily be demonstrated that the 
> combined simian and ape genome template is different from but related to 
> the prosimian genome template.
> 
> That is just what is expected from descent with modification (descent 
> from a common ancestor).
> 
> Starting to count the insertions and deletions and extra heterochromatin 
> isn't going to change the genetic relationship between species.  Since 
> heterochromatin is known to change very rapidly in sequence and copy 
> number it is likely never going to be used for evolutionary analysis 
> except for within species or between closely related species.  Just like 
> the 3rd codon position of coding sequence, so much evolution occurs at 
> those sites that they quickly (on a geologic time scale) lose 
> phylogenetic information when we can't tell how many substitutions have 
> occurred in that lineage at that position.  It has been a sort of rule 
> of thumb since I started working with DNA sequence in the 1980's that 
> once the sequence difference reaches around 10% that the number of 
> double hits at third positions becomes significant and can interfere 
> with your sequence analysis.
> 
> Coding sequence is still only 0.7% different between chimps and humans, 
> but heterochromatin differences is probably over 50% at this time if you 
> deal with copy number and sequence differences within the short tandem 
> repeats.
> 
> Ron Okimoto
> 
The ID perp's current stupidity jogged my memory and it is possible that 
other TO regulars might recall.  Around the turn of the century (less 
than 25 years ago) scientific creationist denial was still the major 
topic on TO.  The ID perps had started their ID scam unit in 1995, but 
it still had not taken over from the abject failure that scientific 
creationism turned out to be.  The Supreme court decision that 
determined that scientific creationism wasn't anything worth calling 
science was from 1987, but the Biblical creationists could not give up 
on the obfuscation and gap denial.  Of Pandas and People was just the 
usual creationist obfuscation and denial without the Bible verses and 
Biblical mythology, and ended up to be what the ID perps were trying to 
sell as still being teachable science in the public schools.

The ID perps had started barking about the Santorum "amendement" in 
2000, but the ID scam was still second fiddle to the usual scientific 
creationist stupidity on TO.  Most of the creationists posting on TO did 
not know what the ID scam was.  The human genome project was heading to 
an amazing conclusion in 2003.  It would come in billions of dollars 
under budget and years ahead of schedule.  Several years before the 
first draft of the human genome was published it was known that the 
project was going to come in dramatically below budget and ahead of 
schedule, so they expanded the sequencing to other genomes.  They had 
been overly successful in developing automated sequencers and equipping 
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