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Author Topic:   Evidence against chromosome 2 fusion???
herebedragons
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Posts: 1322
From: Michigan
Joined: 11-22-2009
Member Rating: 5.8


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 responded

  
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Message 2 of 10 (688333)
01-21-2013 9:35 PM


Thread Copied from Proposed New Topics Forum
Thread copied here from the Evidence against chromosome 2 fusion??? thread in the Proposed New Topics forum.
    
Taq
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(2)
Message 3 of 10 (688400)
01-22-2013 10:46 AM


More than one step
I would strongly recommend that you check out this well written blog post by Carl Zimmer:

http://blogs.discovermagazine.com/...m-facebook-creationists

As it turns out, the fusion in humans was not as simple as some make it out to be, and the homologous chromosomes in chimps continued to evolve since we split from our common ancestor. As you will see from one of the illustrations towards the end, the fusion even in humans resulted in a deletions of one major region which may account for the discrepencancies they are pointing to.


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Genomicus
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(1)
Message 4 of 10 (688408)
01-22-2013 11:22 AM
Reply to: Message 1 by herebedragons
01-21-2013 7:39 PM


I hope to cover this in more depth later on, but for right now I'll limit myself to a few points.

The link to the video is not listed in the OP, but I suspect the video is the following:

I haven't read the ICR articles, but I watched the video and have the following points in mind:

1. In reference 1 in the description box, the genomic region that was searched was 114,251,945-114,426,678. But the Nature paper never mentioned this region, so I have no idea where this number came from. I posted a comment on the video with that inquiry, and hopefully it'll go through the comment pending.

2. The Nature paper linked to above states that the fusion site is located in 2q13–2q14.1 of chromosome 2. I searched for subtelomeric sequences in various areas of this region, using the NCBI Human Map Viewer, with the result that there are quite a few TTAGGG repeats, but few of them are directly in sequence (i.e., very few TTAGGGTTAGGG repeats).

3. The maker of the video states that:

"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."

Not sure what article he's referring to, but if it's the Nature paper then it never mentions a region of ~160,000 bp.

This is just a cursory overview. I'll see what the ICR articles have to say, and then provide my thoughts on that.

Edited by Genomicus, : No reason given.

Edited by Genomicus, : No reason given.


This message is a reply to:
 Message 1 by herebedragons, posted 01-21-2013 7:39 PM herebedragons has responded

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 Message 5 by herebedragons, posted 01-22-2013 1:55 PM Genomicus has not yet responded

  
herebedragons
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Posts: 1322
From: Michigan
Joined: 11-22-2009
Member Rating: 5.8


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 yet responded

  
herebedragons
Member
Posts: 1322
From: Michigan
Joined: 11-22-2009
Member Rating: 5.8


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 yet responded

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

  
Genomicus
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Posts: 815
Joined: 02-15-2012
Member Rating: 4.7


Message 7 of 10 (688627)
01-24-2013 12:13 AM
Reply to: Message 6 by herebedragons
01-23-2013 9:55 AM


Re: More than one step
Another link you might find of interest: here.
This message is a reply to:
 Message 6 by herebedragons, posted 01-23-2013 9:55 AM herebedragons has not yet responded

  
derwood
Member (Idle past 673 days)
Posts: 1455
Joined: 12-27-2001


Message 8 of 10 (689508)
01-31-2013 11:20 AM


I suspect that the youtuber got his information from one of several essays by former geneticist Jeff Tomkins at the ICR (one example can be seen here). He makes the same basic clams. He sometimes refers to an upcoming actual research paper, but as far as I know, it is still forthcoming.

I have not delved into this issue much, but I am not that impressed with Tomkins' previous genetics-related essays at ICR. Despite having been in the genetics department at Clemson for a time, many of his essays that I have read contain errors - and really basic errors, things that someone with a degree in Genetics should not be making. I would be careful when looking into Tomkins' stuff, for his 'credentials' do not impart the expertise that they should.


    
Taq
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Posts: 6409
Joined: 03-06-2009
Member Rating: 4.4


(3)
Message 9 of 10 (689524)
01-31-2013 5:04 PM


Argument from Incredulity
The ICR argument seems to boil down to one fallacy,

"1.The reputed fusion site is located in a peri-centric region with suppressed recombination and should exhibit a reasonable degree of tandem telomere motif conservation. Instead, the region is highly degenerate—a notable feature reported by a previous investigation."
http://creation.com/chromosome-2-fusion-2

They are incredulous that the region could have accumulated that many mutations since the fusion. It is an argument from incredulity. Once this fallacy is thrown out many of the ICR arguments go away.


Replies to this message:
 Message 10 by kofh2u, posted 02-13-2013 11:43 PM Taq has not yet responded

  
kofh2u
Member (Idle past 1228 days)
Posts: 1162
From: phila., PA
Joined: 04-05-2004


Message 10 of 10 (690523)
02-13-2013 11:43 PM
Reply to: Message 9 by Taq
01-31-2013 5:04 PM


Re: Argument from Incredulity
They are incredulous that the region could have accumulated that many mutations since the fusion. It is an argument from incredulity. Once this fallacy is thrown out many of the ICR arguments go away.

They will soon drop their arguments against this fusion and claim to understand the mutation as that Act-of-God that created the first man from the thin air and dust of the DNA chemistry.

They will see this evolution evidence as theistic in nature, because Gen 5:2 subtly announced that the first man and woman were called "Adams," as species:

Gen 5:2 Male and female created he THEM; and blessed THEM, and called THEIR name Adam, (a species), in the day when THEY were created.

This is the transition of theology into the theistic use of Science in support of scripture.
In the short run, the aging elders of the churches will wiggle as much as they can around this fusion, which produces that much demanded Macro-evolution example they have used to resist the ToE.

The next generation will replace these elders with a story written in the stone of Science as Genesis, verse by verse, finds academic support,... forever.


This message is a reply to:
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