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Author Topic:   Evidence against chromosome 2 fusion???
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 1 of 10 (688331)
01-21-2013 7:39 PM


Hi all, (moved this from Message 53 so it would have its own topic)
This is something that was posted over at EvolutionFairyTale but I never got around to discussing it because those guys over there don’t even have a grip on the basic pricipals of science, let alone the ability to comprehend something like this. So now that I am banned from there, I want to see what people who actually know stuff have to say about it.
So this is the video Refuting Ken Miller on chromosome 2 (the refutation starts at 6:24 - references are listed in the video description)
He claims that there is a 95,313BP difference between the predicted site and the purported site of fusion. I am uncertain how he determined where the predicted site was. He makes this quote in the references
quote:
The article mentions the region name, which contains more than 160,000 BP. I copied the entire sequence into a text editor, then searched for part of the sequence that was displayed in the article, for which I found one match as predicted. I then recorded the location that the 798 BP sequence started relative to my starting point, and then recorded the location of the predicted fusion relative to the start of the 798 BP sequence.
The article I think he is referring to is Chromosome 2 fusion.
It appears that what they did was to find a location that had the highest concentration of telomeric repeats and called that the predicted site. The purported site would then be where the fusion is claimed to have occurred. But what confuses that interpretation was that they claimed that the predicted site looks more like a fusion than the purported site. Well if they chose that site because it looks more like a fusion site then of course it looks more like a fusion site. It doesn’t seem to me to be the proper way to predict where the fusion site should be.
Has anyone heard this claim before and know anything about it?
Another major claim they are making is that the telomeric sequences around the fusion site are degenerate beyond what should be expected. The reasoning is that regions surrounding a centromere should be well conserved due to lack of recombination. I suspect that since this is in an intergenetic region that SNPs would be common. If I remember correctly, purine to purine and pyrimidine to pyrimidine substitutions are relatively common and I suspect that if this was taken into account that the presence of telomere repeats would be much higher in this region.
It seems that the major sources for these claims are
http://creation.com/chromosome-2-fusion-2
http://www.nature.com/...al/v434/n7034/full/nature03466.html
http://genome.cshlp.org/content/12/11/1651.full.pdf+html
(other sources in the video description)
So what do you think?
Another part of this discussion may include some help understanding how to use sequence search tools and blastn alignments. I can't figure out how they searched for these sequences. The reference he uses in the video is here
HBD
Edited by herebedragons, : fixed link

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

Replies to this message:
 Message 4 by Genomicus, posted 01-22-2013 11:22 AM herebedragons has replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 5 of 10 (688431)
01-22-2013 1:55 PM
Reply to: Message 4 by Genomicus
01-22-2013 11:22 AM


Thanks Genomicus ...
I fixed the link to the video, but it looks like you have the right one.
Just to clarify a few things. It looks like most of his referenced material comes from this article Chromosome 2 fusion. It is a creationist article, not a peer reviewed paper, but it does contain a methods and materials section and references which is unusual. In it they state:
quote:
The human 2qfus region has been sequenced and annotated for telomeric repeats, a variety of important functional genes, processed pseudogenes, and various open reading frames (ORFs). A fairly thorough and complete 614 kb (614,000 bases) annotated genomic landscape was constructed that encompasses the fusion site and was published by a lab in several related reports shortly after the initial first working draft of the human genome project.
So I think the 600k bp region they refer to is 2qfus.
Fig 2 shows a 798bp sequence that they used to test the idea that this sequence was "some form of a distinct genomic motif." They apparently found this sequence scattered throughout the genome (159 hits with 80% - 100% match).
The other thing about this region is they claim there are few telomere repeats, but most of the sequences vary by only one base pair and from a quick look it appears many of them are purine to purine of pyrimidine to pyrimidine substitutions. I would think that should factor into the search for telomere repeats since that would be common (if I am remembering correctly)
the genomic region that was searched was 114,251,945-114,426,678.
The region appear to be
quote:
a 177 kb region of contiguous sequence directly surrounding the 2qfus site corresponding to BAC clone RP11-395L14 (accession number AL078621)
It seems the maker of the video only actually referenced the Chromosome 2 fusion paper cited above and just added the other references for good measure ... idk??
HBD
Edited by herebedragons, : No reason given.

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

This message is a reply to:
 Message 4 by Genomicus, posted 01-22-2013 11:22 AM Genomicus has not replied

  
herebedragons
Member (Idle past 857 days)
Posts: 1517
From: Michigan
Joined: 11-22-2009


Message 6 of 10 (688518)
01-23-2013 9:55 AM
Reply to: Message 3 by Taq
01-22-2013 10:46 AM


Re: More than one step
I would strongly recommend that you check out this well written blog post by Carl Zimmer:
When I first looked at the link, I didn't realize there was four pages. Some good points refuting at least part of the claims are on the 4th page. It doesn't address all the issues (for instance the predicted vs. the purported site) but its a good start. I still need to look over the links that Zimmer provides in his blog post. But Thanks
HBD

Whoever calls me ignorant shares my own opinion. Sorrowfully and tacitly I recognize my ignorance, when I consider how much I lack of what my mind in its craving for knowledge is sighing for. But until the end of the present exile has come and terminated this our imperfection by which "we know in part," I console myself with the consideration that this belongs to our common nature. - Francesco Petrarca
"Nothing is easier than to persuade people who want to be persuaded and already believe." - another Petrarca gem.

This message is a reply to:
 Message 3 by Taq, posted 01-22-2013 10:46 AM Taq has not replied

Replies to this message:
 Message 7 by Genomicus, posted 01-24-2013 12:13 AM herebedragons has not replied

  
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