A cancerous melody

A linkurl:project;http://bcl.med.harvard.edu/proteomics/proj/csf/menu.php at Harvard Medical School aims to bring music to medicine in a way that goes beyond setting the mood in the waiting room. Gene transcription and translation are anything but simple. But by combining modern statistics with the sounds of a sweet melody, bioinformatician linkurl:Gil Alterovitz;http://www.mit.edu/%7Egil/ may make interpreting these complex phenomena and diagnosing the diseases that result from abnormalities in

Sep 25, 2009
Jef Akst
A linkurl:project;http://bcl.med.harvard.edu/proteomics/proj/csf/menu.php at Harvard Medical School aims to bring music to medicine in a way that goes beyond setting the mood in the waiting room. Gene transcription and translation are anything but simple. But by combining modern statistics with the sounds of a sweet melody, bioinformatician linkurl:Gil Alterovitz;http://www.mit.edu/%7Egil/ may make interpreting these complex phenomena and diagnosing the diseases that result from abnormalities in gene expression much more manageable tasks.
Human embryonic stem cells
Image: Gil Alterovitz
"I think it's brilliant that Gil is using a completely different channel for communicating complex genomic information," Latin and ballroom DJ Taro Muso writes in an email to The Scientist. "I've always wondered why doctors don't seem to use their ears beyond listening for natural bodily sounds." "It's deceptively simple," says bioinformatician linkurl:Yves Lussier;http://home.uchicago.edu/%7Elussier/about-lussier.htm of the University of Chicago. "It was conceptually challenging to come up with it, but once we know of it, it's obvious we should have tried that in addition to visualization techniques we have been using." By boiling down gene expression data to just a few components -- variables that condense one or more parameters of data -- and assigning each of those components a different note and musical instrument, Alterovitz and his colleagues are literally making genetics musical. The team carefully chooses the notes such that normal gene expression patterns sound pleasantly in tune, while abnormal data yield discordant sounds. "When you hear inharmonious music it kind of catches your attention," Alterovitz says, "and that would be a sign of a pathological problem." "Even amateur musicians can tell the difference between various chords," Muso agrees, "so there is a definite potential for motivated biologists to use harmony as a screening method." Alterovitz got the idea ten years ago while doing his PhD at the Massachusetts Institute of Technology. When he donned his scrubs and joined surgeons in the operating room as part of his graduate research project, he was distracted by the numerous monitors measuring nearly two dozen biological signals. Sometimes an alarm would go off, he recalls, but most of the time it wasn't really relevant, and they were simply turned off and ignored. "Wouldn't it be useful if we somehow integrated [all] those variables so that we could present something that was not just a binary alarm but holistic information about the whole system?" Alterovitz remembers thinking. With this goal in mind, Alterovitz set out to make a computer program to do just that. He and his colleagues worked with preexisting gene expression data from a linkurl:colon cancer study,;http://cancerres.aacrjournals.org/cgi/content/full/65/22/10255 and reduced more than 3,000 genes to just four components. "There's a lot of redundancy," Alterovitz explains. "Genes moving together or opposite each other in a predictable way" can be lumped into just one variable without losing much, if any, detail about the system. Assigning notes that form harmonious chords to the data, Alterovitz and his colleagues created a pleasant-sounding 'norm.' When things go awry, such as in the case of p53-null mutant colon cancer cells under inflammatory stress conditions, gene expression varies slightly, and inharmonious chord progressions result. Listening to the results -- a symphony of electronic harpsichords, recorders, flutes, and oboes -- tells the story. "One application I could see in the oncology world is to look for the abnormal cells in fluid," says infectious disease specialist Micah Jacobs, who runs a private practice in Pittsburgh. "Instead of relying on simple visualization of the cells, you could listen and you could hear the abnormal cell in some way." Alterovitz notes that this type of analysis may have applications outside of medicine. He says that the US Navy contacted him about using his method to monitor sonar signals, which can come from many different directions simultaneously. The communications company Verizon also got in touch with Alterovitz looking to keep track of their complicated networks. Even pilots, who must observe the numerous signals beeping and flashing in the cockpit, could benefit from this technology, Alterovitz says. "The implementation obviously has some work to go," says Jacobs, "but it's something that is worth continuing to look into to see how this could be applied in the real world."
**__Related stories:__***linkurl:Medical music;http://www.the-scientist.com/news/display/55826/
[17th July 2009]*linkurl:Music in the genes;http://www.the-scientist.com/blog/display/23227/
[14th March 2006]*linkurl: Gene expression is noisy;http://www.the-scientist.com/article/display/22206/
[28th May 2004]