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  Topic: The Origin of "Information" via natural causes, Refuting a key ID claim (refs, webpages)< Next Oldest | Next Newest >  
theyeti



Posts: 97
Joined: May 2002

(Permalink) Posted: May 31 2002,00:21   

Here's the most recent one that I know of off hand:

PNAS, Vol. 99, Issue 7, 4448-4453, April 2, 2002

Origin of sphinx, a young chimeric RNA gene in Drosophila melanogaster

Quote
Non-protein-coding RNA genes play an important role in various biological processes. How new RNA genes originated and whether this process is controlled by similar evolutionary mechanisms for the origin of protein-coding genes remains unclear. A young chimeric RNA gene that we term sphinx (spx) provides the first insight into the early stage of evolution of RNA genes. spx originated as an insertion of a retroposed sequence of the ATP synthase chain F gene at the cytological region 60DB since the divergence of Drosophila melanogaster from its sibling species 2-3 million years ago. This retrosequence, which is located at 102F on the fourth chromosome, recruited a nearby exon and intron, thereby evolving a chimeric gene structure. This molecular process suggests that the mechanism of exon shuffling, which can generate protein-coding genes, also plays a role in the origin of RNA genes. The subsequent evolutionary process of spx has been associated with a high nucleotide substitution rate, possibly driven by a continuous positive Darwinian selection for a novel function, as is shown in its sex- and development-specific alternative splicing. To test whether spx has adapted to different environments, we investigated its population genetic structure in the unique "Evolution Canyon" in Israel, revealing a similar haplotype structure in spx, and thus similar evolutionary forces operating on spx between environments.


This is an RNA gene, and the role that RNAs play in terms of regulation is only now starting to be fully realized.  RNA genes can probably evolve by retrotransposition easier than protein coding genes can, since the characteristic 5' truncation is less likely to have a major effect, and there is no worry about frameshifts.  In the case of small RNAs, there should be no 5' truncation.  (Retrogenes and processed pseudogenes are caused when a reverse transcriptase creates a cDNA from a mature mRNA (or other RNA).  The reverse transcrpitase starts at the poly A tail and works its way 3'.  However, if the mRNA is of decent size, it usually falls off before finishing, resulting in a cDNA that is truncated at the 5' end.  This truncation, along with a degenerate poly A tail and flanking repeats, are smoking gun evidence of a retrogene or processed pseudogene.  There's just no denying it, Johnson.)  Furthermore, many small RNAs can act as anti-sense oligos, binding complemetary mRNA or DNA for regulation.  These are easy to evolve, because they can be derived straight from the complemetary strand of the gene they regulate.

There is a furhter significance to this example in the fact that sphinx was derived from retrotransposition of an ATP synthase gene.  But sphinx is not a protein coding gene as ATP synthase is, so the functionality of the sequence is not derived from the already adapted sequence of ATP synthase.  Rather, this is more like a random sequence becoming functional, and is thus similar to the example of URF13 that Dembski sweats over in NFL (idea: let's apply Dembski's uniform probability to sphinx like he did with URF13 and see if it beats his universal probability bound.  Better yet, let's multiply the probabilities of both).

On top of all of this, we have a (potential) transposition event too.  So the origin of the gene goes something like this:

Quote
Although the role of retroposition is well defined in the origin of this gene, it should be pointed out that this is an unusual retroposition process. An independent DNA transposon, S element, moved together in the process with the ATP synthase chain F gene. A consequence of this process leaves a partial S fragment attached to the ATP synthase element-derived region in spx. There are several hypothetical scenarios for the origin of this complex structure. The first hypothesis is that the retroposed sequence of ATP synthase gene might have been inserted first into the S element located in the current position of the chromosome. Then the chimeric gene structure evolved by using the sequence of degenerated S element as the recipient site for splicing of the newly created intron between the recruited exon and ATP synthase chain F derived exon. The second hypothesis is that the retrosequence might have landed first in the S element, located in another portion of the genome, before the S element carrying the retrosequence jumped into the current position and degenerated in the S element structure. The third hypothesis is that the portion of the S element, which was located upstream of spx, might have been cotranscribed with the ATP synthase chain F gene and retroposed. The observation that the short repeats flank both S element fragment and the ATP synthase derived portion of spx is consistent with the third hypothesis.


theyeti

Edited by theyeti on May 31 2002,00:22

  
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