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.  


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:


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

Apr 27 2009

Sunday Streets San Francisco

This year’s first Sunday Streets San Francisco took place on 2009 April 26.

Apr 22 2009

2009 Cherry Blossom Festival Grand Parade

The 2009 Cherry Blossom Festival Grand Parade took place on 2009 April 19.

Apr 20 2009

Cherry Blossom Festival 2009, street fair

All of these are from 2009 April 18. 

Apr 15 2009

Tea Party Protest

A “Tea Party” protest took place on 2009 April 15.

Tea Party Protest

25 Photos

Apr 5 2009

Cesar E. Chavez Holiday Parade & Festival

This year’s Cesar E. Chavez Holiday Parade & Festival was on 2009 April 4.

Apr 4 2009

Wishing you a hateful Hate Week 2009!

In honor of Hate Week—during which, as Orwell notes, new slogans are introduced—I would like to offer the following. It may not be destined to become a classic, but it does honor the work the current “loyal opposition” is doing on the national scene:

Obstruction is Construction.

Your attention, please: a newsflash has this moment arrived from Airstrip One.  Here is the newsflash:

Surveilance is Privacy.