Tuesday, December 11, 2007

Endogenous Retroviruses and a Telic Meme

A new blog- Telic Meme- has some blog entries that will be the focus of commentary at Intelligently Sequenced. Two of the blog entries examine the issues of endogenous retroviruses, common descent and more. The first of the two can be accessed here. From the link (in blue):

About 8% of the human genome mass consists of sequences of retroviral origin and it is thought that in the evolutionary past, exogenous retroviruses formed proviruses in the genomes of germ cells of ancestral primate species. Some of the proviruses are thought to have been fixed (through germ-line integration) in the population and were inherited as stable genomic components named ERVs.

New ERVs may arise within genomes by at least four different mechanisms:
1) Horizontal transmission: Infection and integration via an exogenous source virus
2) Replication using LINE machinery
3) Duplication of chromosomal loci during chromosome rearrangement events
4) Retrotransposition from a pre-existing endogenous retrovirus (Experimental proof?)

Genomic similarities attributed to endogenous retroviruses have been used to argue for common descent. Generally those advancing such arguments include random insertion as an operating assumption. In addition it is usually the case that common descent arguments, based on endogenous retroviruses, are also intended to be arguments against intelligent design. More from the Telic Meme link:

There are different strategies to determine evolutionary ages of ERV families and ERV proviral loci.

A) BLAST the hell out of them. When extensive genomic sequence data information is available, BLAST software can be used to determine whether a specific ERV sequence (FASTA format) is present in various species of interest. This NCBI site is probably the best.

Along these lines let it be noted that the Human Endogenous Retrovirus Database can be accessed at this link.

Discussions of this nature tend to include much technical nomenclature but it is my intent to make our blog entries comprehensible to as large a group as possible. Therefore there will be explanatory blog entries in the coming days seeking to define terms that will appear. Analytical blog entries will link to these explanations to enhance clarity.



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