Phylo uses video game format to assist in scientific research
// Sarah Deshales

MONTREAL (CUP) – Imagine if all the hours you spent moving coloured blocks on Tetris or cultivating wheat on FarmVille actually led to something productive – terminal disease research, perhaps?

Two McGill University academics are tapping into the growing appetite for casual video games in order to further research into illnesses like cancer, Alzheimer’s, and diabetes.

Jérôme Waldispuhl and Mathieu Blanchette launched Phylo in November 2010 and, since then, 17,000 registered users have played the game. Collectively, those users have produced information, released last December, which researchers can use to improve knowledge about genetic disorders.

Waldispuhl, whose personal gaming preferences involve the empire-building game Civilization, among others, came up with the idea when he would be playing games on his laptop as a break from work every few hours: “I was asking myself, how can I use this energy in these casual games to do something useful?”

“Basically, solving a puzzle [in a game] is solving a problem,” the computer scientist explains. “If you can find the equivalence between the problem you’re solving in your puzzle, and another problem, you can re-use the solution to do something.”

Phylo is a simple, Tetris-like game where players line up blocks in colours of orange, purple, blue, and green on either their computer or mobile or tablet device. Each block is human DNA, and all the genetic information is sourced from the University of California, Santa Cruz Genome Browser.

A line of DNA blocks represents a genetic sequence. Underneath is a sequence from another species, and the goal is to line up blocks that are the same colour. When this happens, players are forming a genetic sequence alignment; in other words, they’re finding similar genetic regions from different species.

“The thing is that the sequence by itself doesn’t tell us a lot. What we need to understand from this genome – this DNA that we are sequencing – is to compare the DNA from a lot of different species in order to reveal a similarity between the different DNAs,” said Waldispuhl. As Phylo’s website explains, alignments help scientists trace the evolution of some genetic diseases. Each sequence in the game is thought to be linked to a genetic disorder.

“The goal of Phylo is to produce the data to make the comparisons of DNA easier,” explained Waldispuhl. Once you complete an alignment, it’s stored and fed back to the “global alignment.”

Meanwhile, you’ll get a message on your screen that goes something like this: “We appreciate your contribution to science: Congratulations! You've completed the final stage, and we just submitted your alignment for this session. You played level 902. The DNA in this puzzle has been linked to: FAMILIAL ARRHYTHMOGENIC RIGHT VENTRICULAR DYSPLASIA.”

Since the game launched, players have produced over 350,000 different alignment solutions over about 500,000 games. With each game taking about one to two minutes to play, Waldispuhl estimates that a beginner can produce a solution in between 10 to 15 minutes.

The idea is that humans can do this sort of work better than computers. While the human genome itself is too large for a human to completely decode, a computer cannot be relied upon, either. Even completed algorithms designed to do this kind of work aren’t guaranteed to find all the alignments.

GalaxyZoo, he adds, is another example of human computing that is harnessing people power to improve science. Its 250,000 users help sort through a million images of galaxies produced by a robotic telescope. By answering visual questions about an image, users have produced endless classifications that help scientists shape understanding of the cosmos.

Most of Phylo’s thousands of players are located in North America, with others in Europe and Brazil. Media coverage has helped spread the word to India and Asia as well.

Waldispuhl said that the game is also diversifying into other languages, with recent launches in Spanish and Hebrew, and Russian and Chinese versions on the horizon.

But the goal is also to keep a game with a serious objective light-hearted: “We’re still trying to make it even more fun,” says Waldispuhl. “Fun and creative.”

// Sarah Deshales, CUP Quebec Bureau Chief
// Illustration by JJ Brewis

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