Thursday, May 24, 2007

Science is a Symphony

I came into work this morning thinking that it was about time I found an interesting paper to summarise here. My inbox contained table of contents alerts from various journals, so I ignored the strictly work-related ones and went straight for the interesting stuff. Well, I felt like a kid in a candy store this morning. Thank you Genome Biology and Trends in Genetics for an excellent half hour of abstract reading. Several papers have been printed out and are duly awaiting some spare time with a nice cup of tea.

All that can wait though, because one paper really caught my eye this morning. Take a look at the wonderful “Conversion of amino-acid sequence in proteins to classical music: search for auditory patterns” by Rie Takahashi and Jeffrey Miller of UCLA.

Hey, I like searching for patterns in genomic sequences. I love music. And now I love finding MP3s in the Supplemental Information section of online scientific journals.

The first audio clip sounded distinctly weird. Each of the 20 amino acids found in a stretch of the human Thymidylate Synthase A protein was assigned an individual note. The result is a random assortment of evenly spaced notes.

The next clip assigns each amino acid a unique 3-note chord. Amino acids with similar chemical properties were given different versions of the same chord - basically different arrangements of the same notes, in the same way that similar amino acid molecules might have different rearrangements of the same atoms. The derived music whips along at a cracking (albeit monotonous) pace, and even has some quite pleasant moments.

Finally, rhythm was introduced by looking at which specific DNA sequence was used to encode each amino acid. Some amino acids can be encoded by 2 or more different codons (stretches of 3 DNA base pairs), and each codon is used with a different frequency in the human genome. Amino acids encoded by the most common codons were assigned longer note lengths. At this point we’re getting (slightly) closer to something that sounds like real, human music. It might have rhythm, but it ain't got no soul.

The researchers’ website contains some further examples of protein sequences converted to music. I was particularly interested in listening to the c-Jun protein clip, as I spent a lot of time and effort working on this protein during my postgraduate research. Much like my PhD experience, the music was frustrating to sit through with the occasional enjoyable patch. It ended very abruptly, which may represent submitting a thesis and getting on a plane to Canada. Who knows? I’m no expert music critic.

Takahashi and Miller hope that their work will open up the field of genomics to visually impaired researchers and make genomics more attractive to a wider audience, especially young people. This paper could definitely be converted into a fun classroom activity, perhaps comparing the music derived from the same protein in different species. I look forward to hearing clips from the next stage of their work, with different instruments representing DNA sequences with different roles in the genome.

I’m sure that some creationists will jump on this paper and claim that it proves some kind of design in the human genome sequence. This is a fun study, but if there does happen to be an Intelligent Composer out there, may I suggest some more music lessons?

5 comments:

  1. Hi CAD,
    I found you blog through Pharyngula. This is really cool stuff. I'll link to your post later today. Thanks for the links.

    ReplyDelete
  2. Thanks, I'm glad you enjoyed it! Funnily enough I picked up a random New Scientist last night when I got home (there are piles of them all over my house) and they had mentioned the same article.
    I was always more interested in gene promoters than in protein sequences, so I can't wait to hear their new music with a second instrument playing the transcription factor binding sites...

    ReplyDelete
  3. Hi again,
    In the interest of (relative) anonymity, I'd prefer not to give the identity of my goi away on my blog, but if you shoot me an e-mail, I'd be all too happy to tell you all about it in my response. My e-mail can be found on my blog.

    ReplyDelete
  4. If you haven't read "Dirk Gently's Holistic Detective Agency" (Douglas Adams) you might enjoy it. One of the characters develops software to convert business spreadsheets to music.

    I agree that Pennisi is consistently interesting, as is Susan Milius of Science News.

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  5. I love both Dirk Gently novels, and I can't believe I forgot about the musical spreadsheets when I was writing this post! In my defense, most of my books are still in my parents' house in England so I haven't read any of my old favourites for a while.

    I always liked the description of the software in HHGG that initially considered all aspects of a problem and then suggested a course of action. It didn't do very well until version 2 was launched. Version 2 let you describe the course of action you wanted to take, and would then construct arguments to make it sound like a good idea.

    I suspect that someone somewhere has come up with such a programme already. It would explain a lot.

    ReplyDelete

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