Solving Puzzles for Science

Postdoctoral researcher Firas Khatib and Baker Lab mate James Moody float from computer to computer, recruiting everyone who will listen to join the quest to cure cancer and many other infamous diseases — by playing video games!

 

Fold.it :: Life Sciences Research Weekend 2010 :: Photo by Mohini Patel Glanz

Researchers Firas Khatib and James Moody demonstrate Fold.it.

Can the brainpower of people volunteering around the world solve a computational problem so huge that all the computers in the world couldn’t solve it? In 2010, every field of science seems to have a “Big Data” problem but the data about proteins are as Khatib describes, “really, really big.”

Predicting the structures of disease related proteins is both one of the most promising and the most daunting problems in biology. Uses for designed proteins include fighting HIV, malaria, cancer, and Alzheimer’s.

Incredibly and wonderfully, there is something we can all do to help. Fold.it is the relatively new part of the answer, and its origins are an intriguing story in the saga of humans v. machines, brains v. computers.

Fold.it :: Life Sciences Research Weekend 2010 :: Photo by Mohini Patel Glanz

The Rosetta@home screensaver project began just over five years ago, in 2005. You can still download and run the program on your own computer, contributing your extra computing resources to a project which has now been helped by almost 1 million volunteered computers.

Many obsess over their statistics, whether contributing on their own or competing in teams. I, NWABR blog author Brian Glanz contribute via the International High IQ Society BOINC platform team, which last I looked was in about 820th place in the world, just ahead of University College London and we had recently pulled ahead of my old team, slashdot. I had originally joined SETI@home, precursor to BOINC on which Rosetta@home et al. now run, in 1999 and my team in 2002.

Why obsess so, over the stats? Even in the early days of SETI@home, contributing became a competition which has helped fuel advances in distributed computing and other fields. Of course this also benefits the science depending on these computing resources, which are far beyond those commonly available in one’s own lab. What Geeks will do to out-geek each other, in the name of science, has been wonderful to watch in these ten years 🙂

Once upon a time, Khatib describes, people running the Rosetta@home screen saver noticed that the program was making mistakes. They wanted to interact, to correct the computer — and got in touch with project leaders in David Baker‘s lab in the University of Washington Department of Biochemistry.

Fold.it was the result — an interactive Rosetta-based program developed by the Baker Lab and the University of Washington’s Computer Science and Engineering. “I didn’t even know that!” mused Jeff Flatten of UW CSE, who was helping people try Fold.it as Firas Khatib told the story of its origins.

Fold.it :: Life Sciences Research Weekend 2010 :: Photo by Mohini Patel Glanz

People have 3D problem solving skills which are, in many cases superior to those of computers. People can guide the computers, and with the game they can manipulate models of protein structures to speed up the processing over all.

Fold.it :: Life Sciences Research Weekend 2010 :: Photo by Mohini Patel Glanz

Dawn Tessandore, teacher of AP Biology at Highline High School came to the table at Life Sciences Research Weekend and asked “Do you have something online I can take my class to?”

Firas Khatib enthusiastically responded “Of course!” and handed Tessandore a print-out with the URL — Fold.it.

 

Fold.it :: Life Sciences Research Weekend 2010 :: Photo by Mohini Patel Glanz

Jeff Flatten, James Moody, and Firas Khatib are amused as blog author Brian Glanz breaks a LOT of bonds -- to make the photo more interesting! of course 🙂

You, too can contribute to science by playing Fold.it on your computer. It is free to download and fun to play.

Fold.it competitions are especially popular in schools! The above photo, Fold.it, and this story are also featured in biology text books published by Scholastic Inc.

About the University of Washington Department of Biochemistry

Modern biochemical research is based on the premise that life can ultimately be explained as a coordinated series of chemical reactions. The field grew steadily through the first half of the 20th century, then explosively after the discovery of the genetic material that is DNA.

Today, biochemistry includes the structure and function of the protein, RNA, and membrane components that carry out life processes (structural biology and biophysics). It also includes regulation of the genes that encode these components (molecular and systems biology), functional integration of these components within cells and tissues (cell and developmental biology), and coordination of the myriad components responsible for complex behaviors in unicellular and multicellular organisms (neurobiology, immunology, physiology, and microbiology).

Just as importantly, progress in basic science has inevitably led to progress in understanding the causes, diagnosis, and treatment of human diseases as diverse as cancer, obesity, muscular dystrophy, and malaria. The Department of Biochemistry at the University of Washington has contributed to many phases of this research.

About UW Computer Science and Engineering

University of Washington Computer Science & Engineering includes roughly fifty faculty members, fifty staff members, three hundred graduate majors (165 in the Doctoral program and 135 in the Professional Masters Program), and five hundred undergraduate majors (160 graduates per year) in Computer Science and Computer Engineering programs. Ranked among the top ten programs in the nation, we are active in most of the principal areas of the field, and are engaged in a broad range of interdisciplinary initiatives. We are located in the spectacular Paul G. Allen Center for Computer Science & Engineering at the center of the UW campus in Seattle, Washington – a national and international technology center in software, biotech, the health sciences, and other fields.

By Brian Glanz for NWABR. Please reuse and remix! We share with a Creative Commons Attribution License.

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