Article <1014f30$2kve3$1@dont-email.me>

Deutsch English Français Italiano
<1014f30$2kve3$1@dont-email.me>

View for Bookmarking (what is this?)
Look up another Usenet article
Path: ...!weretis.net!feeder8.news.weretis.net!newsfeed.xs3.de!nntp-feed.chiark.greenend.org.uk!ewrotcd!news.eyrie.org!beagle.ediacara.org!.POSTED.beagle.ediacara.org!not-for-mail
From: RonO <rokimoto557@gmail.com>
Newsgroups: talk.origins
Subject: Re: More stupid denial about DNA sequence analysis
Date: Tue, 27 May 2025 08:35:25 -0500
Organization: A noiseless patient Spider
Lines: 120
Sender: to%beagle.ediacara.org
Approved: moderator@beagle.ediacara.org
Message-ID: <1014f30$2kve3$1@dont-email.me>
References: <1010026$1im3n$1@dont-email.me>
Reply-To: rokimoto557@gmail.com
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8; format=flowed
Content-Transfer-Encoding: 8bit
Injection-Info: beagle.ediacara.org; posting-host="beagle.ediacara.org:3.132.105.89";
	logging-data="13217"; mail-complaints-to="usenet@beagle.ediacara.org"
User-Agent: Mozilla Thunderbird
To: talk-origins@moderators.isc.org
Cancel-Lock: sha1:2HO/ga4ytP8gYWIec3WudsvUd/o=
In-Reply-To: <1010026$1im3n$1@dont-email.me>
Content-Language: en-US
	DKIM_ADSP_CUSTOM_MED,FORGED_GMAIL_RCVD,FREEMAIL_FORGED_REPLYTO,
	FREEMAIL_REPLYTO_END_DIGIT,HEADER_FROM_DIFFERENT_DOMAINS,
	NML_ADSP_CUSTOM_MED,RCVD_IN_DNSWL_BLOCKED,
	RCVD_IN_VALIDITY_CERTIFIED_BLOCKED,RCVD_IN_VALIDITY_RPBL_BLOCKED,
	RCVD_IN_ZEN_BLOCKED_OPENDNS,SPF_HELO_NONE,SPF_PASS,URIBL_BLOCKED,
	URIBL_DBL_BLOCKED_OPENDNS,URIBL_ZEN_BLOCKED_OPENDNS,
	USER_IN_WELCOMELIST,USER_IN_WHITELIST autolearn=ham autolearn_force=no
	version=3.4.6
	smtp.eternal-september.org
Bytes: 9833

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