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Author | Topic: molecular genetic proof against random mutation (1) | ||||||||||||||||||||
Percy Member Posts: 23175 From: New Hampshire Joined: Member Rating: 5.7 |
A link to the paper and to the figure you reference have been added to your original post by the Admin, making it easier to actually comment on the contents of your post.
peter borger writes: That mistakes occur in transmitting the genetic code from one generation to the next has been established beyond any reasonable doubt.
It would only "question the validity of the concepts" if it were a mechanism contradicting NDT, not merely missing from it.
You draw conclusions from this paper in areas unrelated to the issues it addresses. Certainly the authors wouldn't agree with you.
If you're talking about the figure, the authors do not add the polymorphisms together, they merely present them in the same table for comparison. Since the two species share a recent common ancestor, genetic similaries are expected, and the table shows this. If the two species were really as different as apples and algae (I can't use your analogy of apples and pears, since they, too, share a recent common ancestor) then they wouldn't even share this 1G5 gene.
And this is why you shouldn't attempt to draw conclusions outside the specific topic of paper. As the title of the paper clearly states, there were developing a screening technique for identifying fast evolving genes within the Drosophila genome. Their technique evidently requires ignoring base substitutions. You can't draw conclusions about the consistency of the Drosophila genome with mutational theory from this paper.
First, while introns are not expressed in the organisms phenotype, there are still clear limits on permissible mutations. In particular, they have to remain recognizable as introns else they may result in expression, which would be equivilent to a massive multi-nucleotide polymorphism and probably catastrophic to the organism. Second, and orthogonal to the first point, with a data set of two introns your conclusions have practically zero statistical significance. The authors conclusions are inconclusive for the same reasons. Replication of this process by other scientists using other genes must be performed before, over time and only if congruent results are obtained, the author's results can become generally accepted.
First, and as already mentioned, there are still clear limits on permissible mutations within introns. Second, it's not mentioned in the paper because it isn't relevant to their goal of identifying a screen for fast evolving genes.
But don't forget the relatively local differences, such as between populations in Australia, and between populations in the US. Without speculating as to possible reasons, it doesn't seem like either simple migration or Noah's Ark account for it very well.
Uh, nothing else would make sense. Naturally there are fewer genetic differences within a species than between species.
The paper is about identifying fast evolving genes, and 1G5 was chosen because it is precisely that, a fast evolving gene. As they state in the introduction, the fast evolving genes were identified by comparison with Drosophila virilis, which is thought to have diverged with Drosophila melanogaster some 40-60 million years ago. They then compare the IG5 gene of Drosophila melanogaster with Drosophila yakuba, divergence thought to be 10-15 million years ago, in order to test their hypothesis that "under a neutral model of molecular evolution that a gene that shows a high divergence rate between species should also be polymorphic within a species." In other words, the identification of fast evolving genes does not derive from the data in Figure 1. If you're trying to figure out how they identified fast evolving genes from this data you are doomed to failure because this is not the data they used. As far as I could tell, they don't actually present this data in the paper. These misinterpretations suggest that a reassessment of your conclusion that the Drosophila genome is "completely stable" might be appropriate.
Uh, without rate information the percentages mean nothing, and certainly 30% polymorph implies considerable variability for which you need some kind of source. --Percy
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Percy Member Posts: 23175 From: New Hampshire Joined: Member Rating: 5.7 |
peter borger writes: Charmed, I'm sure!
You're referring to the continguous set of nucleotide differences in the intron of 1G5? If so, you made a lot of points, and I addressed a lot of points. Is this one you feel is key? The possibility I mentioned previously was that you don't know what the requirements of the intron are. There may be limitations on where changes can be made in the intron without causing disruption of its very behavior as an intron. There are of course other possibilities. Heads *can* come up ten times in a row. The substitution may have been a single, large replication error. I'm sure there are other possibilities. You can't conclude non-randomness from the data available. This was not a topic the paper even remotely addressed, you're just using it to mine data. It appeared to me that your primary claim was that the 1G5 gene exhibited relative stability between Drosophila melanogaster with Drosophila yakuba, when in reality the paper used that gene because it exhibited fast evolution when Drosophila melanogaster and Drosophila virilis were compared. The data for that comparison isn't present in the paper. --Percy
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Percy Member Posts: 23175 From: New Hampshire Joined: Member Rating: 5.7 |
You believe that the sequence of ten differing nucleotides within the intron of the 1g5 gene in Drosophila melanogaster and Drosophila yakuba could not have arisen randomly. I offered several possible random sources, but that doesn't mean you are wrong, only that you were leaving out some possibilities.
Perhaps some non-random sources *are* responsible. What do you think they could be? --Percy
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Percy Member Posts: 23175 From: New Hampshire Joined: Member Rating: 5.7 |
peter borger writes: Sorry, Peter, didn't mean to seem like I was ignoring your question, but it was *you* who assigned me the viewpoint of neutral selection, not me. Neutral selection isn't a possibility I would have considered. If you want to make "answer my question" demands, then me first, you addressed almost none of the points in my first post. Your opening post claimed proof against random mutation in the form of consecutive nucleotide differences in the intron of the 1G5 gene of two closely related Drosophila species. I've pointed out the statistical insignificance of small data sets, suggested possible sources, at least one of which was non-random, and in my previous post I granted that perhaps the source *was* non-random, and inquired what you thought the possible sources might be. There's something about the paper that I wasn't able to figure out, and maybe you know the answer. Table 3 has a AF005851 link for the MEL-1G5 gene. I expected it to contain the full base sequence for the 1G5 gene, but it doesn't come close to matching the sequence segments from Figure 1. Do you know what the sequence represents? --Percy
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Percy Member Posts: 23175 From: New Hampshire Joined: Member Rating: 5.7 |
What'd I say, what'd I say!! (so I can remember for next time -
--Percy
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