2016-10-23 02:44:16
Trilobites: Studying the Building Blocks of Life in Stereo Sound

02:44, October 23 203 0

This is your Friday cryptography problem: There are about 100,000 different kinds of proteins in the human body, each made out of different combinations of amino acids. They are the building blocks of life. When something goes wrong in our body’s mini-machinery and botches the shape of some proteins, they can’t do their job.

How do we crack the code to tell one combination from another? Plug some data into a computer, and you’ll get back loads and loads of strings of numbers. Now sift. Find what’s different. It’s pretty difficult.

“It’s like Alan Turing solving the enigma codes. You get a message. You do not understand it. You have to convert it to something you do understand,” said Robert Bywater, a now retired chemical biologist from the Francis Crick Institute in Britain.

To make sifting through this data less taxing, he teamed up with a composer with a penchant for math. Together, they set out to render proteins into a melodic form that would allow researchers to hear differences from one protein, or its family, to another. Their paper, published Thursday in the journal Heliyon, shows that it’s possible to listen to the structure of a protein as a melody, as it turns, twists, flattens and folds like a wild hair. The authors think turning data into music offers another way for scientists and nonscientists alike to engage with, analyze and interpret data.

“It’s used for the concert hall. It’s used for sports. It’s used for worship. Why can’t we use it for our data?” said Jonathan Middleton, the composer at Eastern Washington University and the University of Tampere in Finland who worked with Dr. Bywater.

Proteins have been around for billions of years, but humans still haven’t come up with a good way to visualize them. Right now scientists can shoot a laser at a crystallized protein (which can distort its shape), measure the patterns it spits out and simulate what that protein looks like. These depictions are difficult to sift through and hard to remember.

“There’s no simple equation like e=mc2,” said Dr. Bywater. “You have to do a lot of spade work to predict a protein structure.”

Dr. Bywater had been interested in assigning sounds to proteins since the 1990s. After hearing a song Dr. Middleton had composed called “Redwood Symphony,” which opens with sounds derived from the tree’s DNA, he asked for his help.

Using a process called sonification (which is the same thing used to assign different ringtones to texts, emails or calls on your cellphone) the team took three proteins and turned their folding shapes — a coil, a turn and a strand — into musical melodies. Each shape was represented by a bunch of numbers, and those numbers were converted into a musical code. A combination of musical sounds represented each shape, resulting in a song of simple patterns that changed with the folds of the protein. Later they played those songs to a group of 38 people together with visuals of the proteins, and asked them to identify similarities and differences between them. The two were surprised that people didn’t really need the visuals to detect changes in the proteins.

Dr. Bywater and Dr. Middleton think turning data to sounds may help scientists spot differences in proteins — which are important for understanding their function — more easily. It also provides a new path to engaging students otherwise turned off by science and math.

“You get the impression that you’re hearing something, that it’s got patterns or it’s changing,” said Dr. Middleton. “I think there’s a lot of potential to that.”

Another researcher, who studies patients with “hearing motion” synesthesia, a miswiring of the brain that allows them to hear sounds when they see movement or flashes, agreed.

“I think they have an interesting approach, since people are better at ‘getting’ certain patterns using sound than vision,” Melissa Saenz, a neuroscientist at the University of Lausanne in Switzerland, wrote in an email.

She says, for instance, that we’re often better at detecting morse code, which can be a flash of light or a beep, for example, with sound rather than sight.

Sensing visual data with sound isn’t that crazy. It’s like sensing underground treasure with the beeps of a metal detector or leaving the room when the clicks of a Geiger counter suggest dangerous radiation. It’s just cracking a code with your ears.

It’s far-off in the distance, but Dr. Bywater thinks sonification could one day help scientists identify genetic mutations associated with diseases like Alzheimer’s or Parkinson’s. He envisions a website where scientists could upload a genome, or what’s called the proteome — the amino acids chains that make up a protein — and exchange it for a music file. Rather than visually or mathematically sifting through the seemingly endless patterns in this data, a person could just listen for the wrong note in a song.