Monday, May 04, 2009

Swine flu is music to the ears

"Swine flu has been sequenced. More out of curiosity than anything else, I wrote code to translate a key gene into a piece of ambient music:

* “Swine Flu Hemagglutinin” (download from
* “Swine Flu Hemagglutinin” (local system heavily taxed as of 2009-04-30, so will be slow: mp3, 6.7 megabytes)

The algorithm I used is a bit complicated, but just in case you’re curious: since the gene is expressed as a surface protein antibodies can sense, it’s considered as a string of amino acids. Each beat corresponds to one amino acid, and the piece is in 3/4 time, so each six measures would correspond to five turns around the alpha structure. (I’m weaseling because I haven’t the foggiest idea how the protein actually gets folded.) Amino acids with side chains that are neither aromatic not aliphatic control the piano and organ: the nine non-hydrophobics the piano, and the four hydrophobics the organ. The three amino acids with aliphatic side chains control the low synthesizer, while the four with aromatics control the percussion" - from
Avian flu H5N1 unsequenced here.
Section of flu virus from Wikipedia. Any copyrighted material on these pages is included as "fair use", for the purpose of study, review or critical analysis only, and will be removed at the request of copyright owner(s). Report errors to - overgrownpath at hotmail dot co dot uk

1 comment:

Pliable said...

Looking again at that post I can see the choice of graphic was subconsciously influenced by the wonderful 1971 book Behind Appearances - a study of the relations between paintings and the natural sciences in this century by C.H. Waddington published by Edinburgh University Press and MIT Press.

The book is out of print, but copies are available from secondhand dealers.

Conrad Hal Waddington FRS FRSE (1905–1975) was a developmental biologist, paleontologist, geneticist, embryologist and philosopher who laid the foundations for systems biology. He had wide interests that included poetry and painting, as well as left-wing political leanings -