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Author Topic:   Pseudogene Shared Mistakes
NosyNed
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Posts: 8968
From: Canada
Joined: 04-04-2003


Message 1 of 9 (328736)
07-04-2006 11:49 AM


In the thread about "Nested Biological Hierarchies"
( Message 87

WK gives a partial comment on an AIG article.

quote:

Aside from this, the GLO gene apparently can make jumps in between the evolutionary tree.

http://www.answersingenesis.org/tj/v18/i3/mistakes.asp

The evidence for this seems a bit limp. Certainly there are sites shared between the human and guinea pig sequences which aren't in rat but all that means is that the rat is different. Without more sequences showing that the Rat sequence represents the ancestral sequence I'm not sure how you can argue that this provides any evidence for the GLO pseudogene 'jumping'.


I have been reading over the article. It claims to show that reseach casts doubt on the idea of pseudogenese being support for common ancestry.

I don't thinik the above answers AIG on this and I don't have enough genetics to be able to begin to discuss it. I would appreciate seeing what the geneticists have to say.

I think this belongs in Biological Evolution


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AdminJar
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Message 2 of 9 (328737)
07-04-2006 11:52 AM


Thread moved here from the Proposed New Topics forum.

  
jar
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From: Texas!!
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Message 3 of 9 (328802)
07-04-2006 3:31 PM


Bump
for input from someone who knows genetics


Aslan is not a Tame Lion

  
Wounded King
Member (Idle past 3330 days)
Posts: 4149
From: Edinburgh, Scotland
Joined: 04-09-2003


Message 4 of 9 (328835)
07-04-2006 6:33 PM
Reply to: Message 1 by NosyNed
07-04-2006 11:49 AM


What is it you want?
You want someone to rebut that whole page? There are at least 5 distinct arguments put forward with a variety of different approaches. We usually try and dissuade anti-evolutionists from just asking us to rebut an entire page from AIG, why should people on the evo side do it?

Is there a specific argument that you thought was particularly compelling?

I specifically addressed the GLO section because NJ specifically cited GLO as an example of a 'jumping' pseudogene. I'm happy to specifically address other points but I'm not sure that addressing the entire page is worthwhile.

TTFN,

WK


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pink sasquatch
Member (Idle past 5258 days)
Posts: 1567
Joined: 06-10-2004


Message 5 of 9 (328839)
07-04-2006 7:01 PM
Reply to: Message 1 by NosyNed
07-04-2006 11:49 AM


no "jumping", but really need the primary article...
Nemesis writes:

Aside from this, the GLO gene apparently can make jumps in between the evolutionary tree.

No claims of genes "jumping" were made by the Answers in Genesis article, let alone the original paper.

Nosy writes:

I have been reading over the article. It claims to show that reseach casts doubt on the idea of pseudogenese being support for common ancestry.

Unfortunately, I haven't been able to get a copy of the original paper (which the AIG article chooses to cite with three different footnote numbers rather than one), which would be extremely helpful in analyzing AIG's analysis.

The original paper (PMID: 14703305) is from a Japanese journal I have never heard of before: The Journal of Nutrional Science and Vitaminology. While I'm not saying this discounts the research in any way, it is important to note that it is not in a genetics journal.

Working a bit from the somewhat confusing abstract - the functional rat gene has twelve exons, and the non-functional human pseudogene retains five of these exons. They compared differences in guinea pig and human sequence for these five exons using rat as the baseline sequence.

From the AIG article recounting the paper, it seems that about one-sixth of the nucleotides differed from rat; of these, about half differed at the same position in the same way. They then quote the original article:

This extremely small probability indicates the presence of many mutational hot spots in the sequences.

For some reason AIG "jumps" to the conclusion that this destroys pseudogene-based comparisons as a means of examining common ancestry. There are some issues:

- No one in the scientific community is attempting to build tree-of-life level phylogenies with a single portion of a single gene.

- Mutational hot-spots are an area of active investigation by evolutionary biologists, who exclude some types of hot-spots from phylogenetic analysis.

- They selectively examined exonic sequence that may be under some level of selection even in psuedogene form (which is perhaps why both guinea pig and human genes mutated to having four stop codons - to prevent unnecessary or aberrant transcripts).

- Examination of the entire remnant of the gene in question may have revealed an entirely different pattern of inferred relationships than that using the exonic sequence alone.

- They only used three species. It would be interesting to repeat the research including more than one functional gene, as well other pseudogenes (fruit bat and chimp).

- AIG is assuming that rats and guinea pigs are more genetically similar to each other than humans, simply because they are both in the order rodentia. Without data this is just a layman's assumption.

- The research hasn't been replicated. Maybe some of the "guinea pig" sequencing reactions were contaminated with human DNA.

These are just some potential problems off the top of my head. The primary reference cited by AIG, if reproducible and expanded upon, might serve as an interesting foundation to study how mutations accumulate in a non-random manner as genes "degrade".

However, such a simple analysis of one specific portion of one pseudogene in only three species in no way falsifies the method of using genetic sequence to establish common ancestry.


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Coragyps
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Posts: 5553
From: Snyder, Texas, USA
Joined: 11-12-2002


Message 6 of 9 (328842)
07-04-2006 7:31 PM


Helpful, or perhaps not, is this reference from the same Nishikimi that "Woodmoorappe" cites. Given how often Woody cites himself, my bet is that he's strictly blowing smoke.

  
judge
Member (Idle past 5679 days)
Posts: 216
From: australia
Joined: 11-11-2002


Message 7 of 9 (338312)
08-06-2006 9:21 PM
Reply to: Message 5 by pink sasquatch
07-04-2006 7:01 PM


Re: no "jumping", but really need the primary article...
quote:
- They selectively examined exonic sequence that may be under some level of selection even in psuedogene form (which is perhaps why both guinea pig and human genes mutated to having four stop codons - to prevent unnecessary or aberrant transcripts).

Would this really explain why the mutation happened, or just why it might have been retained?

In this case would we still not be left with the big question of why the exact same mutations happened, on many occaisions.

quote:
The research hasn't been replicated. Maybe some of the "guinea pig" sequencing reactions were contaminated with human DNA.

I have not read the AIG article, but am familiar with the results of the paper. The problem here is that the guinea pig mutations do not exactly match the human mutations.
I think 11 out of 21 sites matched and most but not all of these sites were the same changes IIRC.

If the sequencing reactions were contamninated with human DNa would we no see an exact match.


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randman 
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Posts: 6367
Joined: 05-26-2005


Message 8 of 9 (338322)
08-06-2006 11:57 PM
Reply to: Message 5 by pink sasquatch
07-04-2006 7:01 PM


huh?
I don't know if I have time to really delve into this thread, but this comment caught my eye.

- AIG is assuming that rats and guinea pigs are more genetically similar to each other than humans, simply because they are both in the order rodentia. Without data this is just a layman's assumption.

Um, isn't that a reasonable assumption if we assume orders denote genetic similarity? Are we to think that something can evolve itself into an order from another existing order, and if that is the case, then why do evos assume common descent in the first place?


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crashfrog
Member (Idle past 702 days)
Posts: 19762
From: Silver Spring, MD
Joined: 03-20-2003


Message 9 of 9 (338327)
08-07-2006 1:16 AM
Reply to: Message 8 by randman
08-06-2006 11:57 PM


Re: huh?
Um, isn't that a reasonable assumption if we assume orders denote genetic similarity?

It depends on your model of taxonomy. If you group based on inferred phylogenies, then yes, "order" refers to one or another degree of genetic similarity.

If you group based on morphology, though, then order doesn't necessarily mean that. It'll tend to, because phenotype stems from genotype, but it won't be guaranteed. Of course, morphology in all but a few cases is all we have to go on for fossils.


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