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Playing Games For The Good Of Humanity, With Phylo

Sequencing genomes for fun.

Featured post Science!

Hopefully you remember FoldIt, the protein manipulating game that instantly solved years-old biological puzzles. It’s probably the most well known example of a crowd-sourced citizen science project that had immediately remarkable success. It’s in this same field that Phylo exists – a game designed to sequence genomes, while the player is enjoying some fairly familiar match-3-style colour matching. I spoke to designer Jerome Waldispuhl, Assistant Professor at the School of Computer Science McGill University, Montreal, to find out how it is that fun can be recycled into progress. This is gaming literally changing the world, perhaps even saving lives.

Multiple sequence alignment. That’s the key phrase to stare at in some confusion here. It means, to the best of my limited understanding, to compare the DNA, RNA or proteins (anything made up of nucleotides – the building blocks of life – basically) from different species, to seek commonality, and from that, infer a common ancestor. This is phylogenetic analysis, and it’s from this that the game, Phylo, gets its name. And it’s all pretty bemusing stuff, depicted as sequences of what look like the scribblings of a lunatic, madly complex collections of capital letters in row after row, with highlighted colours representing the most complicated washing up rota anyone has ever constructed.

Crowd-sourcing/citizen science is certainly not a new phenomenon. In fact, there are examples going back over a hundred years, with projects like Audubo’s annual Christmas bird count. Getting lots of people to do a small amount is a great way to get lot of stuff done in a small amount of time. And observation is one field where computers haven’t so neatly stepped in. It seems that working out the best patterns for aligning genomes is best done if human imagination is involved. But for a research group, that’s an improbable volume of man-hours to get done.

So turning that outward requires incentive. Getting the general public to do your research for you requires a couple of elements – interest and entertainment. And if that can be combined, you may well find an enormous audience willing to help with your multiple sequence alignment genome project. In Phylo you’re asked to move coloured blocks in horizontal rows, to create groups of matching colours while avoiding leaving gaps.

“If the game is not fun nobody will play it and it’ll be useless,” explains Waldispuhl, who has already seen remarkable success with Phylo. “The success of these approaches reside in the entertaining value of the game. It is nicely quoted in a paper of Luis von Ahn, arguably one if not the most important pioneer of this field, on human computation.”

Of course, that’s true of any game. If you want people to play your game, it needs to be good, right? So why especially here? “It is even more important for a game like Phylo which aims to fully abstract the research problem to a tetris-like game,” the scientist told me, stressing that they were focusing on constantly improving this.

That’s the key here. I’ve attended a talk by Waldispuhl, asked him questions after, and exchanged emails, and I still don’t understand how it is that my playing a puzzle game directly correlates to my helping to sequence the nucleotides of various species in a way that could dramatically advance scientific knowledge. And while I have a peculiarly good memory of DNA structure and synthesis from exams I failed sixteen years ago, and indeed a wife who works as a research biologist, I’m fairly sure that actually knowing what it’s all about would require a few years of study, rather than a scan of a Wikipedia article and some well-worded bedtime queries. If I’m to usefully play this game, it’s because I’m going to be enjoying myself, not because of an informed altruism.

But can that get in the way of pragmatic progress? Doesn’t needing to focus on being fun mean you’re distracted from the core purpose, or at least taking the long way around? “I don’t think so,” says the professor. Instead he argues that it requires someone to be more creative, and stresses the need to work with game design experts. “It actually opens a new avenue of research,” Waldispuhl suggests. “What can be solved with fun?”

It strikes me that there could be another issue here. At the start of the article I asked whether you remember FoldIt, and not whether you were still playing it. While I’m sure a few readers are, it seems realistic that what received a lot of play when the press covered it and word spread, will see a significant drop off. Keeping that interest long-term is a lot harder. And while that’s normal for the average puzzle game, it seems to have slightly farther reaching consequences for a project that has such significant consequences.

“That’s a very good point, replies Waldispuhl. “That’s also why I wanted to design a casual puzzle game that could be a ‘classic’.” Which is a big ask. “We’re still working actively on improving the game design. My goal is to have a Tetris-like puzzle that everybody can play (from children to seniors), that is easy to understand and that will never look outdated.” Ambitious, certainly, but then it would seem foolish to go into such a project without those ambitions, especially with the intended goals.

And those goals are being met. The game has already had 600,000 visits, with 450,000 puzzles completed. And perhaps more importantly, 70% of regions analysed have been improved. That’s 521 genes better understood. And the resources were free – the consequences of that are enormous. If you’re looking for a grant, and you can tell your committee that you can get half a million people to work on your project, without having to pay them, you may well get some attention. Waldispuhl describes this as recycling. A casual game that recycles the energy spent by gamers to solve a scientific problem.

There are gaming problems to solve too, and that’s partly found in competitiveness. With high score tables, measuring both immediate points scored playing, and usefulness of the time spent playing, there’s an incentive to have another go, to do better, and therefore to increase the findings of the project. But I wonder whether the largest problem here is the sell. Might it not be tough to ensure I care about genome sequencing in the first place, motivating me to opt for this game, rather than any number of others?

“That’s a risk,” says Waldispuhl. “But I think that very soon genome sequencing will be everywhere.” But it’s harder to convince people that the multiple sequence alignment is important, surely? “Having its genome will be essential for public health and understanding the risks for the individual, thus to prevent them. I think it’s easier for the public to understand the importance of genomes which has a broad impact on our health, than the specific interest of a group a researcher on a particular molecule. That’s a personal point-of-view of course.”

But really, the success or failure of the project really falls on whether people enjoy playing the game. Which strikes me as, well, a remarkable situation. Progress in scientific fields (and when you look at FoldIt’s astonishing results, and the success Phylo has already shown, we’re talking genuine progress) depending upon the appeal of a puzzler. Or as Waldispuhl puts it, “Playing games for the good of humanity.”

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John Walker

Senior Editor

One of the original co-founders of Rock, Paper, Shotgun, I'm now a senior editor and hero of humanity. Old and special.

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