[10:00] Troy McLuhan: Okay so I’ll give a little intro then Max will give her talk “The Music of Proteins”.
[10:00] Troy McLuhan: This talk is a series of talks associated with the “Science Center” group in Second Life
[10:01] Troy McLuhan: and also with the SciLands
[10:01] Troy McLuhan: which is a new region in SL, a collection of sims
[10:01] Troy McLuhan: with a focus on science and technology.
Note: A “sim” is a volume of simulated land, water and air in Second Life. A sim is 256 meters wide, 256 meters long, and hundreds of meters tall.
/>[10:03] Max Chatnoir: Thank you so much, Troy.
[10:03] Max Chatnoir: I want to say something about the music feed.
[10:04] Max Chatnoir: I’ve turned ambient music off, so you won’t see the music player on your SL screen.
[10:04] Max Chatnoir: All of the music files are MP3 files that are linked from another site.
[10:04] Max Chatnoir: So if you click on the appropriate object, which I’ll identify for you,
[10:04] Max Chatnoir: that should open the MP3 file on whatever your usual music player is.
[10:05] Max Chatnoir: If you want to try it out now, just click on the scale below the screen to check it.
[10:05] Max Chatnoir: I’m very happy to see all of you here.
[10:06] Max Chatnoir: This presentation is stored on the “speak easy” player, but feel free to stop me for questions at any time.
[10:06] Max Chatnoir: Welcome to Genome Island and to this Science Center Presentation on Musical Representation of Protein Structure.
[10:06] Max Chatnoir: This is an area I’ve been interested in for quite a few years, because of similarities between protein compositions and musical compositions.
[10:06] Max Chatnoir: Many people have noticed this relationship.
[10:07] Max Chatnoir: The first to comment on it was Douglas Hofstadter , who noted in 1980 that both proteins and music achieve meaning at their higher structural levels,
[10:07] Max Chatnoir: that both music and protein were more than just a linear string of individual subunits.
[10:07] Max Chatnoir: Both proteins and music have themes
[10:07] Max Chatnoir: The first person to publish music based on protein structure was Susumo Ohno in 1986.
[10:07] Max Chatnoir: He actually published a score based on phosphoglycerate kinase in the journal Immunogenetics.
[10:08] Max Chatnoir: Probably a dozen or so other people have done serious work in this area since then, and at least another dozen or so have done a few protein or DNA based pieces.
[10:08] Max Chatnoir: There is an annotated history at http://whozoo.org/mac/Music/Sources.htm
[10:08] Max Chatnoir: I got interested in this relationship about 1989 and went in search of software that could convert database text to musical notes.
[10:09] Max Chatnoir: I found several programs written by John Dunn (http://algoart.com), and bought the simplest of them, Melodia.
[10:09] Max Chatnoir: I could just about figure that one out!
[10:09] Max Chatnoir: Since then I’ve used many of his music conversion programs, the most recent of which is MusicWonk.
[10:09] Max Chatnoir: In 1997, we put out a CD called “Life Music”.
[10:09] Max Chatnoir: Why would anybody want to turn protein structures into music?
[10:10] Max Chatnoir: Well, first, it’s just fun to hear what a protein might sound like.
[10:10] Max Chatnoir: Second, I think it gives people who don’t spend a lot of time thinking about proteins an appreciation of the patterns and complexities of their structure.
[10:10] Max Chatnoir: Proteins have a primary structure that consists of a string of amino acids.

[10:10] Max Chatnoir: (Human Beta Globin Primary Structure)
[10:11] Max Chatnoir: In the genetics data bases, each amino acid is represented by a letter from the English alphabet.
[10:11] Max Chatnoir: If you just read one of these, it looks like gibberish, because the patterns that you want to look for are familiar words.
[10:11] Max Chatnoir: when you read text
[10:11] Max Chatnoir: For example, you can see “PEEKS” and “FAT” and “PEN” in this sequence.
[10:11] Max Chatnoir: But if you convert it to sounds, you can start to hear patterns.
[10:12] Max Chatnoir: I’ll play you an example in a minute.
[10:12] Max Chatnoir: that comes from this sequence
[10:12] Max Chatnoir: Because we communicate by speech, our ears are very sensitive to sound patterns, and we can hear patterns we might not be able to see in text.
[10:12] Max Chatnoir: Proteins also have higher levels of structure:
[10:12] Max Chatnoir: Secondary structure: repetitious kinds of folding patterns like alpha helix.
[10:13] Max Chatnoir: the alpha helix is in pink on this slide

[10:13] Max Chatnoir: (Beta Globin sequence showing regions of alpha helix).
[10:13] Max Chatnoir: Tertiary structure: compact 3D folding pattern
[10:13] Max Chatnoir: You can see the sections of alpha helix in this larger structure.

[10:13] Max Chatnoir: (Tertiary structure of the globin fold)
[10:13] Max Chatnoir: I try to represent all of these in the music.
[10:14] Max Chatnoir: Primary structure—amino acid sequence—is represented by the specific pitches assigned to each amino acid.
[10:14] Max Chatnoir: Pitches are assigned by amino acid solubility.

[10:14] Max Chatnoir: (Protein Scale)
[10:14] Max Chatnoir: More hydrophobic—less water soluble—amino acids have lower pitches.
[10:14] Max Chatnoir: More hydrophilic—more water soluble—amino acids have higher pitches.
[10:14] Troy McLuhan: Are there other ways to assign pitches?
[10:15] Max Chatnoir: You could assign pitches any way you like.
[10:15] Max Chatnoir: I like the hydrophobicity scale because it makes biological sense.
[10:15] Max Chatnoir: Solubility of an amino acid is related to where it is located in a folder protein.
Someone commented, saying, “This is well above me.”
[10:16] Max Chatnoir: Oh, please ask any questions you like.
[10:16] Troy McLuhan: Maybe we need to go to the basics: What is an amino acid?
[10:16] Max Chatnoir: Amino acids are the subunits that compose proteins.
[10:16] Max Chatnoir: They would be analogous to letters in a long word.
[10:16] Max Chatnoir: There are 20 different amino acids.
[10:17] Max Chatnoir: and they have different properties.
[10:17] Max Chatnoir: different sizes, different charges, different solubilities.
[10:17] bluefog001 Ling: I would like to ask a question but I don’t know if it’s [on] the subject
[10:17] Max Chatnoir: Go right ahead.
[10:17] Troy McLuhan: So each letter here (I, V, L, F, etc.) stands for a different amino acid?
[10:18] Max Chatnoir: Yes, that’s exactly right.
[10:18] Max Chatnoir: and each letter is different.
[10:18] Arnout Gunawan: isovaline, valine, leucine..
[10:18] bluefog001 Ling: Well I ask my question: is schizophrnia genetic?
[10:19] Max Chatnoir: You’re right; that is a little off topic, but I’d be happy to discuss it later with you.
[10:19] bluefog001 Ling: ok Max sorry
[10:19] Arnout Gunawan: http://en.wikipedia.org/wiki/Amino_acid [has] info on amino acids and their properties.
[10:19] Max Chatnoir: Thanks, Arnout!
[10:19] Max Chatnoir: Well, you can hear what this protein scale sounds like by clicking on the picture below the screen.
[10:19] Max Chatnoir: Below the screen is a playable scale. Just click on it to hear the scale.
[10:20] Max Chatnoir: I’ll give you time to be sure you can hear it.

[10:20] Max Chatnoir: You’ll hear the amino acids and also the DNA codons that represent each of the amino acids when you play the scale.
[10:21] Max Chatnoir: Protein structure is encoded in the sequences of genes—in DNA
[10:21] Arnout Gunawan: ohh ok that’s nice
[10:21] Max Chatnoir: Some amino acids have several different DNA codons that represent them.
Aside: This is because there are 64 codons but only 20 amino acids. Codons are like three-letter words spelled using four different letters (the four DNA bases). With four choices for the first letter, four choices for the second letter, and four choices for the third letter, there are 4×4x4 = 64 possible words (codons).
[10:21] Arnout Gunawan: all the codons??
[10:21] Max Chatnoir: up to six!
[10:21] Arnout Gunawan: ok
[10:21] Max Chatnoir: The last three codons you’ll hear only the DNA because these are “stop” codons that don’t correspond to any amino acid.
[10:21] Max Chatnoir: Did that answer your question, Arnout?
[10:22] Arnout Gunawan: yes
[10:22] Max Chatnoir: The range of codons/amino acid is 1-6.
[10:22] Max Chatnoir: Most amino acids have either 2 or 4 codons.
[10:22] Max Chatnoir: and THAT’s another interesting story!
[10:22] Xzavia Yifu: if you are creating music based on dna does that mean that each person literally has their own unique ‘song’?
[10:23] Max Chatnoir: Yes, because every person has a unique DNA pattern.
[10:23] Troy McLuhan: Cool
[10:23] Max Chatnoir: But not VERY different!
[10:23] Max Chatnoir: Humans are quite uniform as a species.
[10:23] Arnout Gunawan: about 99.999% similar
[10:23] Max Chatnoir: We’re about 99.98% similar.
[10:23] Xzavia Yifu: so would family members song be similar something akin say to different movements within a symphony?
[10:24] Max Chatnoir: Not even that different.
[10:24] Max Chatnoir: If you want different movements, you might think about the genes active in different tissues.
[10:24] Max Chatnoir: Liver, skin, blood, etc.
[10:24] Arnout Gunawan: based on the 99.98% you would have 2 notes on any 10000 different
[10:25] Max Chatnoir: Actually, I think the number is more like 99.95%
[10:25] Max Chatnoir: it’s about 1/2000.
[10:25] Xzavia Yifu: has any of this music been done utilising the dna of other species?
[10:25] Arnout Gunawan: no one would hear the difference
[10:25] Max Chatnoir: This morning, you’ll hear some spider silk!
[10:26] Max Chatnoir: To represent the overall folding pattern, or tertiary structure, of a protein, I sometimes split the scale into two voices.
[10:26] Xzavia Yifu: it would be interesting to hear a different kind of whale song
[10:26] Max Chatnoir: More hydrophobic amino acids tend to be folded into the interior of a protein, with more hydrophilic ones on the outside.
[10:26] Max Chatnoir: I think I actually have done a piece using whale DNA.
[10:26] Max Chatnoir: So using different instrumental voices for the hydrophobic and hydrophilic amino acids, I get a sort of interior/exterior duet.
[10:26] Max Chatnoir: You can hear one of these duets in this piece based on mammalian beta globins.
[10:27] Max Chatnoir: This one includes several species.
[10:27] Max Chatnoir: Just click on the white box to hear the piece.
[10:27] Max Chatnoir: (Globin Improv)
[10:27] Max Chatnoir: It takes about 4 minutes to play through, so I’ll give you time to listen to it.
[10:27] Arnout Gunawan: Starts as 1 string?
[10:27] Max Chatnoir: The flute voice is the more hydrophilic amino acids, and the harp voice is the more hydrophobic ones.
[10:28] Arnout Gunawan: ohh ok.
[10:28] Max Chatnoir: Insoluble inside, soluble outside, in general.
[10:28] Max Chatnoir: There are four species represented in succession in this piece: tree shrew, human, tiger and elephant.
[10:28] Max Chatnoir: These represent four major mammalian lineages.
[10:29] Max Chatnoir: It ends with a duet between tree shrew and human and in places where two of the species diverge, you’ll hear a little chord.
[10:30] Max Chatnoir: As you can hear, all four species are fairly similar.
[10:30] Max Chatnoir: Because the protein has to function.
[10:30] Max Chatnoir: So only a certain amount of variability can be tolerated.
[10:31] Max Chatnoir: Just let me know when the piece stops playing for you.
[10:32] Arnout Gunawan: ended
[10:32] Delia Lake: ended
[10:32] Max Chatnoir: OK, we’ll go on to the next example.
[10:32] Max Chatnoir: Finally, different regions of secondary structure can be assigned different instruments.
[10:32] Max Chatnoir: This is the structure of a protein called calmodulin.
[10:33] Max Chatnoir: it mediates physiological activities triggered by calcium ions.

[10:33] Max Chatnoir: (Picture of Calmodulin)
[10:33] Max Chatnoir: In the slide you can see where the regions of alpha helix, one type of secondary structure, are in the protein.
[10:33] Max Chatnoir: those are the little “springs”
[10:33] Max Chatnoir: Another kind of secondary structure is “turns,” where the protein bends and then runs back in another direction.
[10:33] Max Chatnoir: Click on the black box to play this piece.
[10:34] Max Chatnoir: (Calmodulin)
[10:34] Max Chatnoir: It takes about 3 minutes to play through.
[10:35] Kaikou Splash taps his foot
[10:35] Max Chatnoir: The helices are set in one voice and the turns are set in another.
[10:35] Max Chatnoir: You can hear this particularly well in the second part of the piece.
[10:36] Max Chatnoir: I was really surprised when I first played this piece through to hear how tuneful it was.
[10:36] Max Chatnoir: This is because the protein has four calcium binding domains.
[10:36] Barley Oh: yes, me too. It [would] be very nice on a harpsichord
[10:36] Max Chatnoir: You can see the calcium ions as little dark balls in the picture.
[10:37] Max Chatnoir: there are two on each end of the protein.
[10:37] Kaikou Splash: it has some v interesting rythmns
[10:37] oMa Hand smiles at this wonder of life

[10:37] Max Chatnoir: Each of the calcium domains has a similar sequence, and you can hear that repetition in the music. (Calmodulin Sequence)
[10:37] oMa Hand: sweet Thank You Max!
[10:37] Max Chatnoir: The calcium binding domains are in blue in this sequence.
[10:37] Max Chatnoir: You can see the protein itself is like a little poem!
[10:38] Max Chatnoir: It’s one of my favorites!
[10:38] Max Chatnoir: I’m going to play just one more piece, which has a very highly repetitive pattern.
[10:38] Max Chatnoir: This is spidroin, the protein of spider dragline silk.
[10:38] Max Chatnoir: Just click on the greenish box to hear this piece.
[10:39] Max Chatnoir: (Spidroin)
[10:39] Max Chatnoir: It takes about 3 1/2 minutes to play through.

[10:39] Max Chatnoir: You’ll hear two alternating themes, one of which is almost invariant, and the other of which varies more.
[10:39] Max Chatnoir: The two themes are marked on the sequence in the slide.
[10:40] Max Chatnoir: It’s a sort of spinning song!
[10:40] Kaikou Splash: lol
[10:40] Arnout Gunawan: a spiral within a spiral
[10:40] Max Chatnoir: Yes, I also like this protein.
[10:41] Barley Oh: spiders suspended on webs will spin when hit with certain music
[10:41] Max Chatnoir: It hasn’t been fully sequenced yet.
[10:41] Max Chatnoir: Really!
[10:41] Max Chatnoir: I wonder what they would do with this?
[10:41] Kaikou Splash: get down and boogie
[10:41] Arnout Gunawan: lol
[10:41] Max Chatnoir: Dancing spiders!
[10:41] Barley Oh: LOL
[10:41] Max Chatnoir: (Spidroin Sequence)
[10:42] Xzavia Yifu: lol
[10:42] Max Chatnoir: I’m going to stop now and take questions.
[10:42] Barley Oh: also, daddy longlegs gather beneath trees and have group dances
[10:42] Max Chatnoir: I’ve also brought this board down, which has more examples of protein based music, if you’d like to hear some more.

[10:42] Kaikou Splash sniggers
[10:42] Arnout Gunawan: well first I feel you deserve an applause
[10:42] Arnout Gunawan: .’`’. APPLAUSE APPLAUSE .’`’.
[10:43] Kaikou Splash: Thank you Max! :D
[10:43] Max Chatnoir: well, as soon as I FIND it!
[10:43] Claudia Linden: awesome
[10:43] Barley Oh: /clapclapclap
[10:43] Barley Oh: TY Max
[10:43] Max Chatnoir: (Board with Music Samples)
[10:43] Arnout Gunawan: one question: do you “search” for the best type of instruments or can you use a basic set of note/amino acid sequenses on all proteins?
[10:43] Troy McLuhan liked the spider silk one best
[10:44] Elizabeth Gloucester: Yes, Brava indeed!!! Wonderful and really interesting, Max.
[10:44] Xzavia Yifu: i agree with you troy
[10:44] Delia Lake: Max, this is wonderful!! ty so much
[10:44] Max Chatnoir: Thanks very much for coming.
[10:44] Max Chatnoir: You’ll find refreshments in the Abbey!
[10:44] Barley Oh: :)) a real pleasure
[10:44] Max Chatnoir: And feel free to try some of the other pieces.
[10:44] Xzavia Yifu: thanks so much max, this has been a nice boost to my day
[10:45] Arnout Gunawan: you missed my question Max?
[10:45] Max Chatnoir: And also to ask any questions you might have.
[10:45] Max Chatnoir: Oh, I think I did. Please reask.
[10:46] Arnout Gunawan: I asked if you search for the best instruments by protein
[10:46] Max Chatnoir: Ah, I see it now.
[10:46] Max Chatnoir: Usually I just play a protein through and listen to the pattern.
[10:46] Max Chatnoir: ..and then I set the voices to try to bring out elements of that pattern.
[10:47] Max Chatnoir: without obscuring the sequence.
[10:47] Arnout Gunawan: ok, that answers my question
[10:47] Max Chatnoir: I really like the sequence to be able to speak for itself.
[10:47] Kaikou Splash: so the choice of instrument is fairly arbitrary?
[10:47] Max Chatnoir: Because that’s the root of the proteins function and the way it folds.
[10:47] Max Chatnoir: Yes, pretty much.
[10:48] Arnout Gunawan: do you give cys-cys bridges special sounds?
[10:48] Max Chatnoir: I’m glad you asked that.
[10:48] Kaikou Splash: cool, so are there any additional parameters you could use to assign timing to each aa in the sequence?
[10:48] Max Chatnoir: Yes, in some proteins, especially if they have a lot of disulfide bonds,
[10:48] Max Chatnoir: I will assign a particular voice to that.
[10:48] Max Chatnoir: usually percussion.
[10:49] Arnout Gunawan: same for any glycosylations?? or is that for the future??
[10:49] Max Chatnoir: Yes, if there is any particular feature of a protein I want to emphasize, then I’ll give that feature a special voice.

[10:50] Max Chatnoir: So it could be a particular binding site, say ATP binding, or a structural feature.
[10:50] Max Chatnoir: But I haven’t done glycosylations specifically.
[10:50] Arnout Gunawan: ok. clear
[10:51] Max Chatnoir: I’d really like to be able to place the sounds in space corresponding to the folding pattern.
[10:51] Max Chatnoir: So you’d follow the sequence through the protein.
[10:51] Arnout Gunawan: well, I really enjoyed this presentation and your way to present the nice features of natures wonders
[10:51] Max Chatnoir: Thanks you so much!
[10:51] Max Chatnoir: And I appreciate all of you for coming to hear this.
[10:52] Kaikou Splash: could a voice be used with pitch for one axis and another parameter (like frequency) for the other axis?
[10:52] Barley Oh: TY Max
[10:52] Troy McLuhan: Thanks Max
[10:52] Max Chatnoir: Well, that’s an interesting suggestion.
[10:52] Max Chatnoir: Maybe use the pan for one axis and pitch for the other.
[10:53] Max Chatnoir: That would give a 2D map at least.
[10:53] Troy McLuhan: What about using the protein sequence as an input for one of those programs that “can make anything sound like Mozart” (or Beethoven or whoever)?
[10:53] Kaikou Splash: mm yeah, the space you move through to travel the path of the protein string only needs to be defined
Someone commented that they missed most of the talk and asked if it would be archived somewhere.
[10:54] Max Chatnoir: I have a lot of the presentation on the “easy speak” and I have the chat log.
[10:54] Troy McLuhan: I’ll be posting everything in my blog, including photos and links to the music, at Nature Network
[10:54] Max Chatnoir: Thanks, Troy!
[10:54] Barley Oh: BetaGlobin is quite suspenseful!
[10:55] Max Chatnoir: Also I have a kind of “Protein Primer” on the web site where the music is.
Someone asked for Troy’s blog address.
[10:55] Troy McLuhan: It will actually be my first blog post, so there is no link yet
[10:55] Kaikou Splash thinks Aequorin would sound at home in a Japanese Garden
[10:55] Troy McLuhan: The spider silk reminded me of African music
[10:56] Xzavia Yifu: troy, would it be possible to ask someone from the science center to send a group notice with your blog link when it’s ready?
[10:56] Max Chatnoir: It’s the repetition.
[10:56] Kaikou Splash: it all seems to have an identifiable theme though.. surprising really
[10:56] Barley Oh: Max, you are fortunate to bridge science and art in such a way
[10:56] Max Chatnoir: Yes, that would be nice, troy.
[10:56] Troy McLuhan: Yes sure, I’ll send my blog link out in a Science Center group notice
[10:57] Xzavia Yifu: thank you troy
[10:57] Barley Oh: ty Troy. I look forward to your blog
[10:57] Kaikou Splash: so, is there another aspect of every single amino acid (or it’s combination with another) that you could use to assign different timings to each pitch Max?
[10:58] Max Chatnoir: Well, there are size differences, and charge differences.
[10:58] Max Chatnoir: So any of those can be used.
[10:58] Kaikou Splash: thats fascinating
[10:58] Troy McLuhan: Maybe number of Carbon, Hydrogen, Oxygen, etc. atoms?
[10:58] Max Chatnoir: Also somebody recently has used the number of codons associated with an amino acid for rhythms.
[10:59] Max Chatnoir: I get rhythm myself from repeated amino acids.
[10:59] Max Chatnoir: If the amino acid repeats, then the note is prolonged.
[10:59] Xzavia Yifu: so you could get acid jazz? hehe
[10:59] Max Chatnoir: Definitely!
[11:00] Kaikou Splash: yeah, I noticed that the repitition actually allowed you to hear different timings from the arrangement
[11:00] Troy McLuhan is still humming the spider silk tune
[11:00] Max Chatnoir: :-)
[11:00] Kaikou Splash: it made me think of classical music..
[11:00] Kaikou Splash: in it’s complexity
[11:00] Barley Oh: maybe you already answered this: when the same amino has several different codons, what tends to be the difference in pitch or tone?
[11:00] Max Chatnoir: The same sequence can be set in very different ways.
[11:01] Xzavia Yifu: Sonic hedgehog is a bit haunting, sounds like soundtrack music for a dramatic movie.
[11:01] Max Chatnoir: Yes, I like that one!
[11:01] Arnout Gunawan: prion as well
[11:01] Max Chatnoir: The transmembrane proteins all have interesting patterns.
[11:02] Max Chatnoir: Well, this has been fun. The music board is parked on the top floor of the tower.
[11:02] Max Chatnoir: Where the piano is!
[11:03] Delia Lake: the tower?
[11:03] Troy McLuhan: Atop the mountain?
[11:03] Kaikou Splash: ace thanks again Max :)) I thoroughly enjoyed this :)
[11:03] Max Chatnoir: Yes, up on the hill.
[11:03] Xzavia Yifu: thank you max this has been superb
[11:03] Kaikou Splash: Ah…Do..mo..
[11:03] Kaikou Splash: Bye bye!
[11:03] Troy McLuhan: Bye!
[11:04] Max Chatnoir: Bye, Troy. I’ll look forward to your first blog!
[11:04] Delia Lake: thank you very much for the presentation and for your work, Max
[11:04] Max Chatnoir: on Nature Network, that is.
[11:04] Delia Lake: it is beautiful and fascinating
[11:04] Max Chatnoir: You’re very welcome.
[11:06] Troy McLuhan: Oh – feel free to join the Science Center group to be informed of future events like this
[11:06] Delia Lake: wouldn’t it be neat to have the fox music played in sl by touching a sl fox
[11:06] Max Chatnoir: Thanks for suggesting this, Troy.
[11:06] Troy McLuhan: To join, go to the bottom of your screen – Search – Groups – Science Center – Search – Join
[11:07] Max Chatnoir: Yes, Delia.
[11:08] Troy McLuhan: Wow we talked until the sun went down (at least in my view)

The Second Life News Network (SLNN) also wrote an article about this event.
Sarah Everts of Chemical & Engineering News was also at the talk and describes the experience in an article she wrote for that publication.
More links:
Dr. Clark’s website about the music of proteins
Dr. Clark’s class information pages
Note: Some people’s comments were removed because I didn’t get their permission to publish them. The order of statements was changed in some cases to improve flow.
If you’d like to be informed of future events like this in Second Life, then join the “Second Life” group on Nature Network or join the “Science Center” group in Second Life.
Copyright© 2007 by T. Troy McConaghy.
This work is licensed under a Creative Commons Attribution-Share Alike 3.0 License
Oh man! I missed this. I put a little reminder in my calendar but it just flew past me. I would have loved to see this “live” in SL.
Oh well, maybe next time.
Great post, nonetheless.