P.C. Shannon

I was reading this article yesterday in Wired (the part about “Regeneration”), and earlier in the week, I read about using nanotechnology in a similar fashion. In terms of fields of study, I am interested in tissue engineering as well as bioinformatics. One possible way to combine the two would be, for instance, if there was a motif that represented growth factors, you could search all the ORFs for similar motifs. I don’t know much of anything about growth factors, but this approach should work reasonably well for, say, 7TM receptors. It’s sort of “reverse proteomics.” Another technique might be to use proteomics to identify the genes for growth factors present in, for example, a developing liver. Or even if you had just one growth factor identified, you could search for similar promoter regions.

There are a couple of catches to these genomic searches. With a search for promoters, you’d have to be so many base pairs upstream from the start codon, and you’d have to incorporate a certain amount of “fuzziness” to the search. The motif search would be harder. You’d have to know which residues were important, what other amino acids could substitute, and then look for all the possible base combinations in an ORF. To some degree, it would help to know what the active site looked like, how the important residues related both three-dimensionally and in sequence, and so on. But this is something people are currently putting a lot of effort into, so you couldn’t expect a computer to do it very well at the present moment.

I was listening to “The Flashback Lunch” on 101X today as I went to get some food and heard a song which I though was called “Dead Come Home.” Apparently it’s actually “Nemesis” by Shriekback, but the chorus is still the same:

Priests and cannibals, prehistoric animals
Everybody happy as the dead come home
Big Black Nemesis, parthenogenesis
No one move a muscle as the dead come home

Parthenogenesis is a means of asexual reproduction that occurs in higher animals, such as snakes, under certain conditions. It amuses me greatly to hear this in a song. It is perhaps the longest word in a rhyming couplet in a pop song ever!

For some reason, I’m also reminded of War Games. When Matthew Broderick’s science teacher asks him, “Who first proposed the theory of asexual reproduction?” he responds, “Your wife?”