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Scientists' Newest Tool To Fight Agricultural Toxin: A Video Game

Feb 28, 2018

It wasn’t long after the invention of the internet that scientists discovered the potential for using computing power as a citizen science tool. One of the earliest examples was a computer program developed in the 1990s that allowed users to search for life on other planets. Now a new collaboration takes aim at something a little closer to home: An intersection between citizen science, health, and agriculture, with implications right here in the San Joaquin Valley.

It’s 1 p.m. on a Friday, and Patrick Camarador is getting ready to livestream a video game. The UC Davis senior puts down his textbooks, puts on his headset and clicks on music.

Some days, he plays games like Legend of Zelda or Splatoon, but for today’s game he puts on safety glasses and a lab coat. It’s a kind of inside joke with his streaming audience. “My name is Sockrates, also known as Patrick, and welcome back to Sock’s Lab,” he begins.

"Foldit Friday," which sometimes involves a lab coat and safety glasses, is a weekly feature of UC Davis senior Patrick Camarador's livestream page.
Credit Twitch screenshot

The game is called Foldit. And it transforms hundreds of thousands of gamers like Camarador into citizen scientists. Rather than collecting treasure or destroying evil villans, the goal is to tweak the structures of proteins to solve real-world biological problems.

Players get a molecular model of a protein and are instructed to fold, twist and rotate it into new configurations. They’re awarded points for efficiency. The game offers hundreds of molecular challenges. “Foldit is what I would describe as a protein folding sandbox puzzle game,” Camarador says.

One of the newest puzzles involves aflatoxin, a family of carcinogens that contaminate crops around the globe and lead to serious health problems. In Foldit’s Aflatoxin Challenge, players try to fold a protein into a shape that’ll break down the aflatoxin molecule into something harmless.

Camarador didn’t know much about aflatoxin beforehand, but he’s learned about it by playing—and the mission speaks to him. “This could have very real effects on the food supply, the economy, food supplies overseas,” he says. “And there’s just a lot of context behind it that makes it too important to ignore.”

Aflatoxin is the most potent natural carcinogen known. It’s caused by a fungus that can grow in crops like pistachios, peanuts and cotton. A single outbreak in corn in Kenya killed 125 people in 2004, while long-term exposure is responsible for tens of thousands of liver cancer diagnoses each year.

Themis Michailides has been studying aflatoxin and other diseases afflicting agriculture for nearly 30 years.
Credit Kerry Klein / Valley Public Radio

That’s why Themis Michailides is grinding up pistachios to test for aflatoxin. He’s studied plant diseases for almost 30 years with the University of California Research Extension in Parlier. “My emphasis is how we can manage it, how can we reduce it so that these crops are free from aflatoxin,” he says.

Michailides says a lot has been done to control aflatoxin. Rigorous regulations prevent the compound from being a major health problem in the U.S. and Europe. But prevention is expensive, and still not 100% effective, despite a new biopesticide Michailides helped bring to the Valley. And the problem is far worse abroad. That’s why more solutions are needed—and why researchers are excited about an unorthodox strategy like Foldit.

If experts like Michailides are struggling to find a solution, crowdsourcing it may seem like a surprising move. But it makes sense to Justin Siegel. He’s a biochemist at UC Davis and one of the minds behind the Aflatoxin Challenge.

In his office at the Kearney Agricultural Research and Extension Center in Parlier, Michailides has dozens of notebooks organized by crops and their diseases.
Credit Kerry Klein / Valley Public Radio

Proteins are giant molecules made mostly of carbon, hydrogen, oxygen and nitrogen, and when their structures change so do their functions. Siegel says the protein players use in the game is so big, there are far more possible structures than any individual could find. “The number of potential confirmations is bigger than the number of stars in the universe,” he says. “It’s a ridiculous number. So it’s really a very, very difficult problem.”

Foldit has a history of crowdsourcing difficult problems. In 2012, players redesigned a protein to speed up chemical reactions, and players have been listed as authors on a handful of scientific papers.

Since October, Siegel says players have already submitted nearly half a million possible solutions to the Aflatoxin Challenge. Siegel plans to test a few thousand of those in his lab to find one that destroys aflatoxin. The ultimate goal is to then create some way of delivering it to the fields. “You can imagine a spray that goes over the crop,” he says, “or you could imagine other mechanisms to help maybe wash away and get rid of aflatoxin and take highly concentrated bits of aflatoxin and use these catalysts to destroy it.”

Bob Klein of the California Pistachio Research Board explains that visibly flawed and stained pistachios, like these that were sorted out from a local pistachio crop, are more likely to contain aflatoxin than healthy-looking ones.
Credit Kerry Klein / Valley Public Radio

So could the Foldit strategy work? Barbara Stinson says maybe. She’s a senior partner with the Meridian Institute and a project manager with the Partnership for Aflatoxin Control in Africa. She’a excited about Foldit, but warns that local variations in climate, regulation, and the need to train farmers could make a huge difference in the effectiveness of the final product. “No matter what continent you’re using it for, those considerations need to be taken early and understand that it’s going to be different in different regions of the world,” she says.

Bob Klein agrees. He’s manager of the California Pistachio Research Board, and he estimates California’s pistachio industry alone spends millions on aflatoxin testing and lost product. Foldit’s basic premise sounds promising, he says, but “how to get the enzyme to the place where the aflatoxin is in the contaminated nut or contaminated product becomes the big challenge.”

The final product will be important, but it’s only thanks to players like Patrick Camarador, putting on lab coats and playing a game between classes, that researchers may even get that far.

Music by Popskyy.