Video Game Players Wanted for Science Project
12/8/2011 by: Darleen Hartley
In a Win-Win project, competing video game players are contributing to scientist's DNA research. Teachers, scientists and students teamed up to develop a game that provides clues to the genetic basis of well-known and less familiar diseases. Their work has already shed light on disease histories.
Phylo is an online game wherein players match DNA sequences. The research team loaded the DNA sequence of over 900 diseases into the data base.
A player's "wins" provide the research team with pictures of similarities. These multiple sequence alignments help biologists infer shared evolutionary origins, identify functionally important sites, and illustrate mutation events. The real goal is tracing the source of certain genetic diseases.
Dr. Jérôme Waldispuhl, a professor at the McGill School of Computer Science and MIT research affiliate, created a team consisting of Mathieu Blanchette, a comparative genomics specialist, and students Alex Kawrykow and Gary Roumani. They designed Phylo, a DNA puzzle game that doesn't require any scientific knowledge to play. Another game, Foldit, created at the University of Washington, has helped scientists solve questions about proteins, but requires players to have some science background. Phylo "confirms that difficult computational problems can be embedded in a casual game that can easily be played by people without any scientific training," Waldispuhl said.
In Phylo, players often choose a specific genetic disease to work on. The diseases are ranked in 11 categories: Blood and immune system, Bone and skin, Brain and nervous system, Cancer, Digestive system, Heart and circulatory system, Metabolic disorders, Muscles, Reproduction system, Respiratory system, and Sensory system. Sensory systems have been called into question when diagnosing children suspected of ADHD.
Gamers can choose to work on familiar diseases such as osteoarthritis, dermatitis, schizophrenia, Parkinson's, Alzheimer's, leukemia, and hypertension. They might want to work with a less familiar problem such as lupus erythematosus, synpolydactyly, adrenoleukodystrophy, adenocarcinoma, or aortic aneurysm. Too many choices? Then play with random puzzles just for the fun of it. Your efforts still help the research project.
DNA sequences can identify the evolution of disease
The game sounds simple, actually. You work with four colored squares – green, blue, violet, and orange – that represent A (adrenine), C (cytosine), G (guanine), and T (thymine). By matching the squares you will identify sections of DNA that are similar across species and contribute to traits such as eye color or medical conditions. However, lining them up is the challenge [especially if you are color blind. Ed.]. It's a kind of vertical Rubik's Cube. Phylo's top user has completed over 6000 levels.
People are better recognizing and sorting visual patterns than computers according to Waldispuhl. The genome consists of approximately three billion base pairs. At McGill, those they are working on have already been pre-aligned by computers, but the results contain several flaws. Asking a single computer to use computationally complex heuristics to align the sequences becomes an exponentially large task. Putting the eyes and brains of 17,000 registered users to work – as volunteers – seems to be the economical, and more efficient, answer.
With people getting so much flack about extensively playing video games, Blanchette said about participating in Phylo, "It's guilt-free playing; now you can tell yourself it's not just wasted time."
The scientist has not been wasting his time either. When he's not skiing, he can be found on the lecture circuit. Blanchette presented "Ancestral Mammalian Genome Reconstruction and its Uses toward Annotating the Human Genome" (Video) at the November symposium Computational Biology of Molecular Sequences.
Phylo has gone mobile and should be available for cell phones and tablets. Their website has a tutorial in English and French. They are looking for more players to speed the research along.
Why not give Phylo a try?
Phylo, DNA, McGill School of Computer Science, MIT, Mathieu Blanchette, genome, Alex Kawrykow, Gary Roumani, Foldit, ACGT, disease, osteoarthritis, dermatitis, schizophrenia, Parkinson's, Alzheimer's, leukemia, hypertension, adrenine, cytosine, guanine, thymine, University of Washington
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