Re: More stupid denial about DNA sequence analysis

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/
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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.
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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.
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Telomere to telomere sequences of the ape genomes have been published.
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https://www.nature.com/articles/s41586-025-08816-3
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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.
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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.
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Ron Okimoto
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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 the genome sequencing centers that had been developed and they actually had a relative excess capacity for sequencing even though the human genome had not been completed.
Large contigs of other ape chromosomes started to be assembled, and we were able to compare long stretches of continuous sequence for the first time.  It may be recalled that a 5% sequence difference was claimed between chimps and humans in this initial long contig analysis, and creationists wanted to make a big deal about the difference between 1% and 5%.  It turned out that the 5% number came from including transposon and retroviral insertions that chimps and humans did not share.  There is a 300 base-pair ALU transposon sequence around every 3,000 base-pairs in the human genome (parasitic ALU transposons are classified as junk DNA and comprise around 10% of the human genome) and humans do not share all of those insertions with chimps because, of the ones that the common ancestor had some have been lost in one lineage or the other and others have jumped into new positions after the split between chimps and humans.  It turned out that if you counted all base-pairs of the unshared transposon or retroviral insertions that it would make the two different by 5% of the sequence compared.  In terms of evolutionary considerations it was a stupid way to estimate the difference between the sequences because the transposon events were single events, and it was stupid to count all the nucleotides involved (they counted an ALU insertion as 300 events instead of just one event), but just like the current IDiotic stupidity the creationists just do not get how sequence analysis has to be done.
The current IDiotic stupidity is just a continuation of that initial creationist misunderstanding of what the 5% difference meant.
Ron Okimoto