Sunday, September 07, 2008

Evolution, labeling, Sarah Palin, Palin-McCain

What do evolution, labeling, "Sarah Palin", and "Palin McCain" have in common? Not much, you would think, but check out what sort of thing comes up when you do a search for these name combinations in amino acid abbreviations.

From Jonathan Eisen:
Anyway, alas, three of the major candidates for the US election have names that do not use traditional amino acid abbreviations so I am stuck with analyzing Sarah Palin. But that is OK because of her professed aversion to evolution and support to Creationism (and since sequence analysis is inherently an evolutionary study).

So - I took here name and went to the NCBI Blast page and did some searches. And what came up? Well, here are some of the top hits from the blastp searches (which I used to compare the pretend peptide "SARAHPALIN" with all the peptides in the non redundant collection at Genbank).
There does not appear to be a perfect match in the NCBI NR protein database. But take a close look at the #1 scoring hit. That is right, it is from and organism called Botryotinia fuckeliana. No comment on the appropriateness of this name, but it does contain a term I will probably use a lot if she gets elected.
Though making trees from really short sequences is not ideal, in this tree, Sarah Palin is shown to be at the root of a branch including a protein from the parasitic nematode Brugia malayi. So if we take an evolutionary interpretation it seems that this causative agent of filariasis (well, a protein from this agent) is descended from SarahPalin. In other words, she seems to be ancestral to this parasite.

So in conclusion - by similarity - SarahPalin is closest to a plant pathogen with an unusual name. And by phylogeny SarahPalin is ancestral to a parasitic nematode. Sounds about right.

Okay, so it's a bunch of geeky humor. However, looking in the comments, J.E. wrote:
I may write a new post on this --- but the best blast hit for "MCCAINPALIN" is ....

>gb|ACE82429.1| polyprotein [Hepatitis C virus subtype 1a]

Score = 26.1 bits (54), Expect = 339
Identities = 8/10 (80%), Positives = 9/10 (90%), Gaps = 1/10 (10%)

_____Query 1 MCCAINPALI 10
____________MC AI+PALI
___Sbjct 877 MC-AIHPALI 885

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