Phylo: Turning Biology Puzzles Into Interactive Games
Gaming to Understand Disease
Sponsored
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Barry Starr","firstName":"Dr. Barry","lastName":"Starr","slug":"dr-barry-starr","email":"bstarr@thetech.org","display_author_email":false,"staff_mastheads":[],"title":null,"bio":"Dr. Barry Starr (\u003ca href=\"https://twitter.com/geneticsboy\">@geneticsboy\u003c/a>) is a Geneticist-in-Residence at The Tech Museum of Innovation in San Jose, CA and runs their Stanford at The Tech program. The program is part of an ongoing collaboration between the \u003ca href=\"http://genetics.stanford.edu/\">Stanford Department of Genetics\u003c/a> and \u003ca href=\"http://www.thetech.org/\">The Tech Museum of Innovation\u003c/a>. Together these two partners created the \u003ca href=\"http://www.thetech.org/exhibits/permanent/index.php?sGalKey=gtwt&galKey=lt\">Genetics: Technology with a Twist\u003c/a> exhibition.\r\n\r\nYou can also see \u003ca href=\"https://ww2.kqed.org/science/author/dr-barry-starr/\">additional posts by Barry at KQED Science\u003c/a>, and read his \u003ca href=\"http://science.kqed.org/quest/author/dr-barry-starr/\">previous contributions\u003c/a> to \u003ca href=\"http://science.kqed.org/quest/\">QUEST\u003c/a>, a project dedicated to exploring the Science of Sustainability.","avatar":"https://secure.gravatar.com/avatar/4a5680e4c642ea0f0f3041af16018969?s=600&d=blank&r=g","twitter":"geneticsboy","facebook":null,"instagram":null,"linkedin":null,"sites":[{"site":"science","roles":["author"]},{"site":"quest","roles":["subscriber"]}],"headData":{"title":"Dr. Barry Starr | KQED","description":null,"ogImgSrc":"https://secure.gravatar.com/avatar/4a5680e4c642ea0f0f3041af16018969?s=600&d=blank&r=g","twImgSrc":"https://secure.gravatar.com/avatar/4a5680e4c642ea0f0f3041af16018969?s=600&d=blank&r=g"},"isLoading":false,"link":"/author/dr-barry-starr"},"kamal":{"type":"authors","id":"10345","meta":{"index":"authors_1591205172","id":"10345","found":true},"name":"Kamal Menghrajani","firstName":"Kamal","lastName":"Menghrajani","slug":"kamal","email":"kamal@kqed.org","display_author_email":false,"staff_mastheads":[],"title":null,"bio":"Kamal Menghrajani reports and blogs on issues related to health and science. 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FM","link":"/"}},"quest_32568":{"type":"posts","id":"quest_32568","meta":{"index":"posts_1591205157","site":"quest","id":"32568","score":null,"sort":[1331326480000]},"guestAuthors":[],"slug":"phylo-turning-biology-puzzles-into-interactive-games","title":"Phylo: Turning Biology Puzzles Into Interactive Games","publishDate":1331326480,"format":"standard","headTitle":"QUEST | KQED Science","labelTerm":{"site":"quest"},"content":"\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/03/6960873861_c54bffdb62_z-e1331325559827.jpg\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/03/6960873861_c54bffdb62_z-e1331325559827.jpg\" alt=\"\" title=\"6960873861_c54bffdb62_z\" width=\"640\" height=\"360\" class=\"alignnone size-full wp-image-32748\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/03/6960873861_c54bffdb62_z-e1331325559827.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/03/6960873861_c54bffdb62_z-e1331325559827-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003ca href=\"http://www.flickr.com/photos/officialgdc/6960873861/in/photostream\">Photo courtesy of Official GDC\u003c/a>\u003c/p>\n\u003cp>People often think of medicine as hard work, but an emerging group of tech-savvy entrepreneurs is looking to re-shape people’s perspectives and turn health, and health research, into a form of play.\u003c/p>\n\u003cp>At the \u003ca href=\"http://www.gdconf.com/\">Game Developers’ Conference\u003c/a> here in San Francisco this week, computer scientist Jérôme Waldispühl showed off a project that he and colleagues at McGill University just published in \u003ca href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031362\">PLoS ONE\u003c/a>. (KQED QUEST blogger \u003ca href=\"http://ww2.kqed.org/quest/author/dr-barry-starr/\">Dr. Barry Starr\u003c/a> wrote about this \u003ca href=\"http://ww2.kqed.org/quest/2011/12/12/gaming-to-understand-disease/\">game\u003c/a> in December.)\u003c/p>\n\u003cp>It’s called Phylo, and it turns the puzzles of biology into a game anyone can play.\u003c/p>\n\u003cp>Phylo takes a fresh approach to sorting through the data produced by the \u003ca href=\"http://www.genome.gov/10001772\">Human Genome Project\u003c/a>, some three billion bits that spell out the instructions for how to make and maintain a human being.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Researchers are continuously looking through this genetic code to search for genes that may make us susceptible to a particular disease. Finding that needle in the haystack takes time, as scientists must look at each piece of data to evaluate its potential to wreak biological havoc. They also need context to understand the significance of each gene’s sequence.\u003cstrong>\u003c/strong>\u003c/p>\n\u003cp>“By themselves, sequences tell us nothing,” Waldispühl said. To make sense of this data, researchers are interested in comparing human DNA to that of other animals, like monkeys or mice. This gives us a window into evolution – if the exact same sequence ended up in horses and humans, then it is probably important, and a change, or mutation, would be bad news.\u003c/p>\n\u003cp>Waldispühl turned these inter-species comparisons into a game by color-coding the DNA and laying out human and animal sequences on top of each other, the way many scientists do to make sense of it.\u003c/p>\n\u003cp>“In the puzzle, you’re trying to make columns of the same color, [and] you’re finding evolutionarily conserved regions.”\u003c/p>\n\u003cp>The result is a game that looks something like a mash-up of \u003ca href=\"http://www.tetrisfriends.com/games/Marathon/game.php\">Tetris\u003c/a> and a \u003ca href=\"http://www.rubiks.com/\">Rubik’s cube\u003c/a>. To play, you try to arrange the rows to get the same color going down across different species, and you can introduce gaps if necessary. The computer’s score is the ‘Par’, and your goal is to beat it.\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/03/phylo.png\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/03/phylo-300x150.png\" alt=\"\" title=\"phylo\" width=\"300\" height=\"150\" class=\"alignleft size-thumbnail wp-image-32587\">\u003c/a>\u003c/p>\n\u003cp>Competing with the computer may sound daunting at first. After all, this process seems like something computers should be really good at. But for this kind of pattern recognition, humans turn out to be much smarter than computers at figuring out which mutations can be thrown away, and which may be a red flag for disease.\u003c/p>\n\u003cp>For all the nuances of the science behind the game, it should ultimately still be fun to play. I asked Jon Bernstein, a doctor and researcher at \u003ca href=\"http://med.stanford.edu/\">Stanford\u003c/a>, to try it out. “I thought it was very interesting – it was visually appealing, the interface was nice, and fun to play around with.”\u003c/p>\n\u003cp>The game is focused on genetics, Dr. Bernstein’s area of expertise, but that didn’t mean it was easy. “Many of the levels were pretty challenging.”\u003c/p>\n\u003cp>The game is timely, as DNA sequencing is becoming more and more useful in terms of diagnosing and treating all sorts of illnesses\u003c/p>\n\u003cp>“There are many, many situations in which genetic information is helpful in understanding the cause of human disease,” said Bernstein. “There are many cases in which it impacts how you take care of people and the counseling you can provide them.”\u003c/p>\n\u003cp>But as Bernstein told me, some forms of sequencing are still very expensive, on the order of $10,000. “And most of the cost is really the interpretation, not running the test itself.”\u003c/p>\n\u003cp>Games like Phylo are an effort to help scientists interpret these data. By making these problems fun, easy to play with, and accessible to anyone in the world, game designers like Waldispühl are essentially crowd-sourcing solutions to complex problems in health.\u003c/p>\n\u003cp>And there are plenty of gamers who would be willing to help out. Waldispühl told me that McGill put out a press release on the game and got a much larger response than they expected.\u003c/p>\n\u003cp>“A couple of hours after we launched the game, the server was saturated and we put all of the department in an emergency state because everything was blocked,” he said.\u003c/p>\n\u003cp>“We had basically a puzzle downloaded every half-second. It was just crazy.”\u003c/p>\n\u003cp>Finding innovative ways to quickly make sense of genetic data is becoming more important as sequencing becomes faster and more widely used. However, there are many questions that come up between sequencing a person’s DNA and pinpointing the cause of their disease, and Phylo may be answering the wrong one.\u003c/p>\n\u003cp>“This particular game is about aligning DNA sequences. In clinical medicine, a lot of questions are asked and answered at the level of protein,” Stanford’s Bernstein said.\u003c/p>\n\u003cp>DNA is the blueprint for protein, and bad proteins can cause disease. Looking at information from the protein perspective would be much more useful to doctors, and games like \u003ca href=\"http://fold.it/portal/\">Foldit\u003c/a> are already looking at some aspects of that problem.\u003c/p>\n\u003cp>Foldit is a science-focused game that was first released to the public in 2008, and it has had considerable success since then. It allows players to virtually interact with proteins and solve puzzles about their shape. Foldit was able to harness the power of the game-playing masses to determine the shape of the AIDS virus in rhesus monkeys, a problem that had eluded researchers for 15 years. They even \u003ca href=\"http://www.nature.com/nsmb/journal/v18/n10/full/nsmb.2119.html\">published their findings\u003c/a> in a sub-journal of Nature.\u003c/p>\n\u003cp>Phylo may not be as useful as Foldit in its current incarnation, but it does have potential. Since its launch in November 2010, Phylo has contributed to 450,000 solutions through the work of 20,000 registered players and thousands more who play anonymously. Its interface could easily be adopted to compare proteins instead of DNA sequences, but the challenge would be in making it enjoyable for anyone to play.\u003c/p>\n\u003cp>[ad floatright]\u003c/p>\n\u003cp>“We really wanted to make a casual game – that people can play it without thinking they are solving a problem,” Waldispühl said. “People want to have fun. And we can reuse the energy they spend gaming to do something useful.”\u003c/p>\n\n","blocks":[],"excerpt":"People often think of medicine as hard work, but an emerging group of tech-savvy entrepreneurs is looking to re-shape people’s perspectives and turn health, and health research, into a form of play.","status":"publish","parent":0,"modified":1443830590,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":29,"wordCount":1092},"headData":{"title":"Phylo: Turning Biology Puzzles Into Interactive Games | KQED","description":"People often think of medicine as hard work, but an emerging group of tech-savvy entrepreneurs is looking to re-shape people’s perspectives and turn health, and health research, into a form of play.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":"","schema":{"@context":"http://schema.org","@type":"Article","headline":"Phylo: Turning Biology Puzzles Into Interactive Games","datePublished":"2012-03-09T20:54:40.000Z","dateModified":"2015-10-03T00:03:10.000Z","image":"https://cdn.kqed.org/wp-content/uploads/2020/02/KQED-OG-Image@1x.png"}},"disqusIdentifier":"32568 http://science.kqed.org/quest/?p=32568","disqusUrl":"https://ww2.kqed.org/quest/2012/03/09/phylo-turning-biology-puzzles-into-interactive-games/","disqusTitle":"Phylo: Turning Biology Puzzles Into Interactive Games","path":"/quest/32568/phylo-turning-biology-puzzles-into-interactive-games","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/03/6960873861_c54bffdb62_z-e1331325559827.jpg\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/03/6960873861_c54bffdb62_z-e1331325559827.jpg\" alt=\"\" title=\"6960873861_c54bffdb62_z\" width=\"640\" height=\"360\" class=\"alignnone size-full wp-image-32748\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2012/03/6960873861_c54bffdb62_z-e1331325559827.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2012/03/6960873861_c54bffdb62_z-e1331325559827-400x225.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003c/a>\u003ca href=\"http://www.flickr.com/photos/officialgdc/6960873861/in/photostream\">Photo courtesy of Official GDC\u003c/a>\u003c/p>\n\u003cp>People often think of medicine as hard work, but an emerging group of tech-savvy entrepreneurs is looking to re-shape people’s perspectives and turn health, and health research, into a form of play.\u003c/p>\n\u003cp>At the \u003ca href=\"http://www.gdconf.com/\">Game Developers’ Conference\u003c/a> here in San Francisco this week, computer scientist Jérôme Waldispühl showed off a project that he and colleagues at McGill University just published in \u003ca href=\"http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031362\">PLoS ONE\u003c/a>. (KQED QUEST blogger \u003ca href=\"http://ww2.kqed.org/quest/author/dr-barry-starr/\">Dr. Barry Starr\u003c/a> wrote about this \u003ca href=\"http://ww2.kqed.org/quest/2011/12/12/gaming-to-understand-disease/\">game\u003c/a> in December.)\u003c/p>\n\u003cp>It’s called Phylo, and it turns the puzzles of biology into a game anyone can play.\u003c/p>\n\u003cp>Phylo takes a fresh approach to sorting through the data produced by the \u003ca href=\"http://www.genome.gov/10001772\">Human Genome Project\u003c/a>, some three billion bits that spell out the instructions for how to make and maintain a human being.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Researchers are continuously looking through this genetic code to search for genes that may make us susceptible to a particular disease. Finding that needle in the haystack takes time, as scientists must look at each piece of data to evaluate its potential to wreak biological havoc. They also need context to understand the significance of each gene’s sequence.\u003cstrong>\u003c/strong>\u003c/p>\n\u003cp>“By themselves, sequences tell us nothing,” Waldispühl said. To make sense of this data, researchers are interested in comparing human DNA to that of other animals, like monkeys or mice. This gives us a window into evolution – if the exact same sequence ended up in horses and humans, then it is probably important, and a change, or mutation, would be bad news.\u003c/p>\n\u003cp>Waldispühl turned these inter-species comparisons into a game by color-coding the DNA and laying out human and animal sequences on top of each other, the way many scientists do to make sense of it.\u003c/p>\n\u003cp>“In the puzzle, you’re trying to make columns of the same color, [and] you’re finding evolutionarily conserved regions.”\u003c/p>\n\u003cp>The result is a game that looks something like a mash-up of \u003ca href=\"http://www.tetrisfriends.com/games/Marathon/game.php\">Tetris\u003c/a> and a \u003ca href=\"http://www.rubiks.com/\">Rubik’s cube\u003c/a>. To play, you try to arrange the rows to get the same color going down across different species, and you can introduce gaps if necessary. The computer’s score is the ‘Par’, and your goal is to beat it.\u003c/p>\n\u003cp>\u003ca href=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/03/phylo.png\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2012/03/phylo-300x150.png\" alt=\"\" title=\"phylo\" width=\"300\" height=\"150\" class=\"alignleft size-thumbnail wp-image-32587\">\u003c/a>\u003c/p>\n\u003cp>Competing with the computer may sound daunting at first. After all, this process seems like something computers should be really good at. But for this kind of pattern recognition, humans turn out to be much smarter than computers at figuring out which mutations can be thrown away, and which may be a red flag for disease.\u003c/p>\n\u003cp>For all the nuances of the science behind the game, it should ultimately still be fun to play. I asked Jon Bernstein, a doctor and researcher at \u003ca href=\"http://med.stanford.edu/\">Stanford\u003c/a>, to try it out. “I thought it was very interesting – it was visually appealing, the interface was nice, and fun to play around with.”\u003c/p>\n\u003cp>The game is focused on genetics, Dr. Bernstein’s area of expertise, but that didn’t mean it was easy. “Many of the levels were pretty challenging.”\u003c/p>\n\u003cp>The game is timely, as DNA sequencing is becoming more and more useful in terms of diagnosing and treating all sorts of illnesses\u003c/p>\n\u003cp>“There are many, many situations in which genetic information is helpful in understanding the cause of human disease,” said Bernstein. “There are many cases in which it impacts how you take care of people and the counseling you can provide them.”\u003c/p>\n\u003cp>But as Bernstein told me, some forms of sequencing are still very expensive, on the order of $10,000. “And most of the cost is really the interpretation, not running the test itself.”\u003c/p>\n\u003cp>Games like Phylo are an effort to help scientists interpret these data. By making these problems fun, easy to play with, and accessible to anyone in the world, game designers like Waldispühl are essentially crowd-sourcing solutions to complex problems in health.\u003c/p>\n\u003cp>And there are plenty of gamers who would be willing to help out. Waldispühl told me that McGill put out a press release on the game and got a much larger response than they expected.\u003c/p>\n\u003cp>“A couple of hours after we launched the game, the server was saturated and we put all of the department in an emergency state because everything was blocked,” he said.\u003c/p>\n\u003cp>“We had basically a puzzle downloaded every half-second. It was just crazy.”\u003c/p>\n\u003cp>Finding innovative ways to quickly make sense of genetic data is becoming more important as sequencing becomes faster and more widely used. However, there are many questions that come up between sequencing a person’s DNA and pinpointing the cause of their disease, and Phylo may be answering the wrong one.\u003c/p>\n\u003cp>“This particular game is about aligning DNA sequences. In clinical medicine, a lot of questions are asked and answered at the level of protein,” Stanford’s Bernstein said.\u003c/p>\n\u003cp>DNA is the blueprint for protein, and bad proteins can cause disease. Looking at information from the protein perspective would be much more useful to doctors, and games like \u003ca href=\"http://fold.it/portal/\">Foldit\u003c/a> are already looking at some aspects of that problem.\u003c/p>\n\u003cp>Foldit is a science-focused game that was first released to the public in 2008, and it has had considerable success since then. It allows players to virtually interact with proteins and solve puzzles about their shape. Foldit was able to harness the power of the game-playing masses to determine the shape of the AIDS virus in rhesus monkeys, a problem that had eluded researchers for 15 years. They even \u003ca href=\"http://www.nature.com/nsmb/journal/v18/n10/full/nsmb.2119.html\">published their findings\u003c/a> in a sub-journal of Nature.\u003c/p>\n\u003cp>Phylo may not be as useful as Foldit in its current incarnation, but it does have potential. Since its launch in November 2010, Phylo has contributed to 450,000 solutions through the work of 20,000 registered players and thousands more who play anonymously. Its interface could easily be adopted to compare proteins instead of DNA sequences, but the challenge would be in making it enjoyable for anyone to play.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"floatright"},"numeric":["floatright"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>“We really wanted to make a casual game – that people can play it without thinking they are solving a problem,” Waldispühl said. “People want to have fun. And we can reuse the energy they spend gaming to do something useful.”\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/32568/phylo-turning-biology-puzzles-into-interactive-games","authors":["10345"],"categories":["quest_8","quest_12"],"tags":["quest_848","quest_1166","quest_10782","quest_13201","quest_10539","quest_13"],"featImg":"quest_32587","label":"quest"},"quest_28279":{"type":"posts","id":"quest_28279","meta":{"index":"posts_1591205157","site":"quest","id":"28279","score":null,"sort":[1323708504000]},"guestAuthors":[],"slug":"gaming-to-understand-disease","title":"Gaming to Understand Disease","publishDate":1323708504,"format":"standard","headTitle":"QUEST | KQED Science","labelTerm":{"site":"quest"},"content":"\u003cfigure id=\"attachment_28280\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/12/Phylo1.jpg\" alt=\"\" title=\"Phylo1\" width=\"640\" height=\"371\" class=\"size-full wp-image-28280\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/12/Phylo1.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2011/12/Phylo1-400x232.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003cfigcaption class=\"wp-caption-text\">Line up the blocks and help cure a disease!\u003c/figcaption>\u003c/figure>\n\u003cp>Yesterday I discovered an online game called \u003ca href=\"http://phylo.cs.mcgill.ca/\">Phylo\u003c/a>. No, it isn’t about Greek pastry dough. It has more to do with phylogenetics.\u003c/p>\n\u003cp>Phylogenetics is the study of how living things are related to each other. It takes advantage of the fact that DNA changes slowly over time. So the more distantly related two things are, the less DNA they will share.\u003c/p>\n\u003cp>You can also learn which bits of DNA are important for life (or good health) by seeing which ones stay pretty constant between various animals. Since these don’t change, they are probably being used for something. And if they get changed in people who have a disease, then they may be involved in that disease.\u003c/p>\n\u003cp>This is what Phylo is based on. In the game, you are trying to line up the DNA sequences of various animals to figure out which DNA is important and which isn’t. This is a lot harder than it sounds.\u003c/p>\n\u003cp>While DNA changes slowly, we’re dealing with some pretty long spans of time since two animals shared a common ancestor (i.e. had the same DNA). This means that the DNA can start to look pretty different.\u003c/p>\n\u003cp>[ad fullwidth]\u003c/p>\n\u003cp>Phylo gives you sets of DNA sequences that haven’t been lined up yet and has you try to line them up manually. Apparently people are still better at this than computers!\u003c/p>\n\u003cp>Lining these sequences up helps scientists discover which DNA bases are important. It can also give us some basic knowledge about the evolutionary relationship of various animals.\u003c/p>\n\u003cp>Since DNA sequence might be a little intimidating, Phylo uses colored blocks instead. Each different colored block represents one of the four DNA bases.\u003c/p>\n\u003cp>In the game, you have a certain amount of time to align the sequences as best you can. You want the fewest mismatches with the fewest gaps.\u003c/p>\n\u003cp>The game is pretty hard but it is engaging. And you’re doing your bit for science which is always a good thing.\u003c/p>\n\u003cp>What would make it even better is more explanation about what I am doing and why it is important. This could make the game fun and educational. (I’d also like to see the DNA sequences I aligned but that’s probably just me.)\u003c/p>\n\u003cp>So give it a whirl and do your bit to help humanity. And have a little fun in the process.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003ca href=\"http://realdoctorstu.com/2011/02/15/earn-a-nobel-prize-in-your-lunch-break-the-best-citizen-science-games-reviewed/\">Nice list of top 5 citizen scientist games (Phylo is number 1).\u003c/a>\u003c/p>\n\n","blocks":[],"excerpt":"By playing Phylo, you help scientists better understand human disease and you get to have fun. Doing good by having fun is a win-win for scientists and the public.","status":"publish","parent":0,"modified":1325108433,"stats":{"hasAudio":false,"hasVideo":false,"hasChartOrMap":false,"iframeSrcs":[],"hasGoogleForm":false,"hasGallery":false,"hasHearkenModule":false,"hasPolis":false,"paragraphCount":15,"wordCount":425},"headData":{"title":"Gaming to Understand Disease | KQED","description":"By playing Phylo, you help scientists better understand human disease and you get to have fun. Doing good by having fun is a win-win for scientists and the public.","ogTitle":"","ogDescription":"","ogImgId":"","twTitle":"","twDescription":"","twImgId":"","schema":{"@context":"http://schema.org","@type":"Article","headline":"Gaming to Understand Disease","datePublished":"2011-12-12T16:48:24.000Z","dateModified":"2011-12-28T21:40:33.000Z","image":"https://cdn.kqed.org/wp-content/uploads/2020/02/KQED-OG-Image@1x.png"}},"disqusIdentifier":"28279 http://science.kqed.org/quest/?p=28279","disqusUrl":"https://ww2.kqed.org/quest/2011/12/12/gaming-to-understand-disease/","disqusTitle":"Gaming to Understand Disease","path":"/quest/28279/gaming-to-understand-disease","audioTrackLength":null,"parsedContent":[{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003cfigure id=\"attachment_28280\" class=\"wp-caption aligncenter\" style=\"max-width: 640px\">\u003cimg src=\"http://ww2.kqed.org/quest/wp-content/uploads/sites/39/2011/12/Phylo1.jpg\" alt=\"\" title=\"Phylo1\" width=\"640\" height=\"371\" class=\"size-full wp-image-28280\" srcset=\"https://ww2.kqed.org/app/uploads/sites/39/2011/12/Phylo1.jpg 640w, https://ww2.kqed.org/app/uploads/sites/39/2011/12/Phylo1-400x232.jpg 400w\" sizes=\"(max-width: 640px) 100vw, 640px\">\u003cfigcaption class=\"wp-caption-text\">Line up the blocks and help cure a disease!\u003c/figcaption>\u003c/figure>\n\u003cp>Yesterday I discovered an online game called \u003ca href=\"http://phylo.cs.mcgill.ca/\">Phylo\u003c/a>. No, it isn’t about Greek pastry dough. It has more to do with phylogenetics.\u003c/p>\n\u003cp>Phylogenetics is the study of how living things are related to each other. It takes advantage of the fact that DNA changes slowly over time. So the more distantly related two things are, the less DNA they will share.\u003c/p>\n\u003cp>You can also learn which bits of DNA are important for life (or good health) by seeing which ones stay pretty constant between various animals. Since these don’t change, they are probably being used for something. And if they get changed in people who have a disease, then they may be involved in that disease.\u003c/p>\n\u003cp>This is what Phylo is based on. In the game, you are trying to line up the DNA sequences of various animals to figure out which DNA is important and which isn’t. This is a lot harder than it sounds.\u003c/p>\n\u003cp>While DNA changes slowly, we’re dealing with some pretty long spans of time since two animals shared a common ancestor (i.e. had the same DNA). This means that the DNA can start to look pretty different.\u003c/p>\n\u003cp>\u003c/p>\u003c/div>","attributes":{"named":{},"numeric":[]}},{"type":"component","content":"","name":"ad","attributes":{"named":{"label":"fullwidth"},"numeric":["fullwidth"]}},{"type":"contentString","content":"\u003cdiv class=\"post-body\">\u003cp>\u003c/p>\n\u003cp>Phylo gives you sets of DNA sequences that haven’t been lined up yet and has you try to line them up manually. Apparently people are still better at this than computers!\u003c/p>\n\u003cp>Lining these sequences up helps scientists discover which DNA bases are important. It can also give us some basic knowledge about the evolutionary relationship of various animals.\u003c/p>\n\u003cp>Since DNA sequence might be a little intimidating, Phylo uses colored blocks instead. Each different colored block represents one of the four DNA bases.\u003c/p>\n\u003cp>In the game, you have a certain amount of time to align the sequences as best you can. You want the fewest mismatches with the fewest gaps.\u003c/p>\n\u003cp>The game is pretty hard but it is engaging. And you’re doing your bit for science which is always a good thing.\u003c/p>\n\u003cp>What would make it even better is more explanation about what I am doing and why it is important. This could make the game fun and educational. (I’d also like to see the DNA sequences I aligned but that’s probably just me.)\u003c/p>\n\u003cp>So give it a whirl and do your bit to help humanity. And have a little fun in the process.\u003c/p>\n\u003cp>\u003c/p>\n\u003cp>\u003ca href=\"http://realdoctorstu.com/2011/02/15/earn-a-nobel-prize-in-your-lunch-break-the-best-citizen-science-games-reviewed/\">Nice list of top 5 citizen scientist games (Phylo is number 1).\u003c/a>\u003c/p>\n\n\u003c/div>\u003c/p>","attributes":{"named":{},"numeric":[]}}],"link":"/quest/28279/gaming-to-understand-disease","authors":["6177"],"categories":["quest_4"],"tags":["quest_10541","quest_1032","quest_10542","quest_1197","quest_10539","quest_10540","quest_13202","quest_3319"],"featImg":"quest_28280","label":"quest"}},"programsReducer":{"possible":{"id":"possible","title":"Possible","info":"Possible is hosted by entrepreneur Reid Hoffman and writer Aria Finger. Together in Possible, Hoffman and Finger lead enlightening discussions about building a brighter collective future. The show features interviews with visionary guests like Trevor Noah, Sam Altman and Janette Sadik-Khan. Possible paints an optimistic portrait of the world we can create through science, policy, business, art and our shared humanity. It asks: What if everything goes right for once? How can we get there? Each episode also includes a short fiction story generated by advanced AI GPT-4, serving as a thought-provoking springboard to speculate how humanity could leverage technology for good.","airtime":"SUN 2pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Possible-Podcast-Tile-360x360-1.jpg","officialWebsiteLink":"https://www.possible.fm/","meta":{"site":"news","source":"Possible"},"link":"/radio/program/possible","subscribe":{"apple":"https://podcasts.apple.com/us/podcast/possible/id1677184070","spotify":"https://open.spotify.com/show/730YpdUSNlMyPQwNnyjp4k"}},"1a":{"id":"1a","title":"1A","info":"1A is home to the national conversation. 1A brings on great guests and frames the best debate in ways that make you think, share and engage.","airtime":"MON-THU 11pm-12am","imageSrc":"https://ww2.kqed.org/radio/wp-content/uploads/sites/50/2018/04/1a.jpg","officialWebsiteLink":"https://the1a.org/","meta":{"site":"news","source":"npr"},"link":"/radio/program/1a","subscribe":{"npr":"https://rpb3r.app.goo.gl/RBrW","apple":"https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?s=143441&mt=2&id=1188724250&at=11l79Y&ct=nprdirectory","tuneIn":"https://tunein.com/radio/1A-p947376/","rss":"https://feeds.npr.org/510316/podcast.xml"}},"all-things-considered":{"id":"all-things-considered","title":"All Things Considered","info":"Every weekday, \u003cem>All Things Considered\u003c/em> hosts Robert Siegel, Audie Cornish, Ari Shapiro, and Kelly McEvers present the program's trademark mix of news, interviews, commentaries, reviews, and offbeat features. Michel Martin hosts on the weekends.","airtime":"MON-FRI 1pm-2pm, 4:30pm-6:30pm\u003cbr />SAT-SUN 5pm-6pm","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/All-Things-Considered-Podcast-Tile-360x360-1.jpg","officialWebsiteLink":"https://www.npr.org/programs/all-things-considered/","meta":{"site":"news","source":"npr"},"link":"/radio/program/all-things-considered"},"american-suburb-podcast":{"id":"american-suburb-podcast","title":"American Suburb: The Podcast","tagline":"The flip side of gentrification, told through one town","info":"Gentrification is changing cities across America, forcing people from neighborhoods they have long called home. Call them the displaced. Now those priced out of the Bay Area are looking for a better life in an unlikely place. American Suburb follows this migration to one California town along the Delta, 45 miles from San Francisco. But is this once sleepy suburb ready for them?","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/American-Suburb-Podcast-Tile-703x703-1.jpg","officialWebsiteLink":"/news/series/american-suburb-podcast","meta":{"site":"news","source":"kqed","order":"13"},"link":"/news/series/american-suburb-podcast/","subscribe":{"npr":"https://rpb3r.app.goo.gl/RBrW","apple":"https://itunes.apple.com/WebObjects/MZStore.woa/wa/viewPodcast?mt=2&id=1287748328","tuneIn":"https://tunein.com/radio/American-Suburb-p1086805/","rss":"https://ww2.kqed.org/news/series/american-suburb-podcast/feed/podcast","google":"https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy5tZWdhcGhvbmUuZm0vS1FJTkMzMDExODgxNjA5"}},"baycurious":{"id":"baycurious","title":"Bay Curious","tagline":"Exploring the Bay Area, one question at a time","info":"KQED’s new podcast, Bay Curious, gets to the bottom of the mysteries — both profound and peculiar — that give the Bay Area its unique identity. And we’ll do it with your help! You ask the questions. You decide what Bay Curious investigates. 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You can also visit the MindShift website for episodes and supplemental blog posts or tweet us \u003ca href=\"https://twitter.com/MindShiftKQED\">@MindShiftKQED\u003c/a> or visit us at \u003ca href=\"/mindshift\">MindShift.KQED.org\u003c/a>","imageSrc":"https://cdn.kqed.org/wp-content/uploads/2024/04/Mindshift-Podcast-Tile-703x703-1.jpg","imageAlt":"KQED MindShift: How We Will Learn","officialWebsiteLink":"/mindshift/","meta":{"site":"news","source":"kqed","order":"2"},"link":"/podcasts/mindshift","subscribe":{"apple":"https://podcasts.apple.com/us/podcast/mindshift-podcast/id1078765985","google":"https://podcasts.google.com/feed/aHR0cHM6Ly9mZWVkcy5tZWdhcGhvbmUuZm0vS1FJTkM1NzY0NjAwNDI5","npr":"https://www.npr.org/podcasts/464615685/mind-shift-podcast","stitcher":"https://www.stitcher.com/podcast/kqed/stories-teachers-share","spotify":"https://open.spotify.com/show/0MxSpNYZKNprFLCl7eEtyx"}},"morning-edition":{"id":"morning-edition","title":"Morning Edition","info":"\u003cem>Morning Edition\u003c/em> takes listeners around the country and the world with multi-faceted stories and commentaries every weekday. 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On Our Watch brings listeners into the rooms where officers are questioned and witnesses are interrogated to find out who this system is really protecting. 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