May
8
2009
Apr
28
2009
“Swine Flu Hemagglutinin”: amino acid sequence as ambient music
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” (MP3)
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.
ש
Update 2009-04-30: For folks coming in from the cnn.com article Making music out of swine flu and wondering about the line, “Zielinski saw it as a form of highly organized information that a human did not design.”: Yes, that phrasing raises the question of who or what I think DID design it. (God? Aliens?) In reality, self-organizing systems evince great complexity without need for a conscious designer. Swine flu was not designed at all– it evolved.
Strictly speaking, this is a version of swine flu hemagglutinin, FJ966952. The actual amino acid sequence:
MKAILVVMLYTFATANADTLCIGYHANNSTDTVDTVLEKNVTVTHSVNLLEDKHNGKLCK LRGVAPLHLGKCNIAGWILGNPECESLSTASSWSYIVETSSSDNGTCYPGDFIDYEELRE QLSSVSSFERFEIFPKTSSWPNHDSNKGVTAACPHAGAKSFYKNLIWLVKKGNSYPKLSK SYINDKGKEVLVLWGIHHPSTSADQQSLYQNADAYVFVGSSRYSKKFKPEIAIRPKVRDQ EGRMNYYWTLVEPGDKITFEATGNLVVPRYAFAMERNAGSGIIISDTPVHDCNTTCQTPK GAINTSLPFQNIHPITIGKCPKYVKSTKLRLATGLRNVPSIQSRGLFGAIAGFIEGGWTG MVDGWYGYHHQNEQGSGYAADLKSTQNAIDEITNKVNSVIEKMNTQFTAVGKEFNHLEKR IENLNKKVDDGFLDIWTYNAELLVLLENERTLDYHDSNVKNLYEKVRSQLKNNAKEIGNG CFEFYHKCDNTCMESVKNGTYDYPKYSEEAKLNREEIDGVKLESTRIYQILAIYSTVASS LVLVVSLGAISFWMCSNGSLQCRICI
Maggie Koerth-Baker’s excellent article from 2009 April 28, “Swine Flu Q&A”, is available here:
Maggie Koerth-Baker, “Swine Flu Q&A”, at boingboing.net