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Fwd: Wired: Genome at Home: Biohackers Build Their Own Labs

---------- Forwarded message ----------
From: Bryan Bishop <kanzure@gmail.com>
Date: Fri, Aug 19, 2011 at 5:54 PM
Subject: Wired: Genome at Home: Biohackers Build Their Own Labs
To: diybio <diybio@googlegroups.com>, Bryan Bishop <kanzure@gmail.com>

http://www.wired.com/magazine/2011/08/mf_diylab/

A tiny spare bedroom is not an ideal space for a high tech biofabrication facility. To get to the one Josh Perfetto is putting together, visitors must walk all the way to the back of his mostly unfurnished house in Saratoga, California—through the kitchen, past some empty rooms, across a den with a lone couch—then climb a poorly lit staircase and round a corner. The room itself is about 120 square feet and has one big window with a view of an adjacent roof. There's an 8-foot-wide gap in the middle; the rest of the room is for science. "I thought about moving the lab to the empty living room downstairs," Perfetto says. "I really need more space. But that's right by the front door. I don't want to freak people out."

He laughs a little awkwardly, and it's easy to see why he's worried. With its Pyrex containers on metal racks and other clinical-looking equipment, the bedroom looks perfect for cooking crystal meth. A mass of wires spills out of a wooden box; on top sits a metal plate punched full of holes. A table holds several laptops, test tubes, a box of purple surgical gloves, a rack with pipettes in various sizes, rubber tubes connected to vials, an orange plastic box with a blue light in the bottom, and a centrifuge that looks like an oversize rice cooker. The wooden box is actually a homemade device for doing polymerase chain reactions (PCR), a process that turns small samples of DNA into quantities large enough to analyze. And the orange plastic thing runs gel electrophoresis, a way to sort DNA strands by size. Perfetto, an engineer, built a few of the gadgets himself.

"I've been sleeping in here," says Mackenzie Cowell, Perfetto's business partner. "And who knows what kinds of chemicals have soaked into this rug!" He flew out to California from Boston a week earlier and has been working with Perfetto on a DIY genomics kit to sell through their new business, CoFactor. The problem is, right now extracting and amplifying DNA at home still takes too many steps. The guys are worried that people won't enjoy the process if it's too complicated.

And the home audience is their target market. Cowell is the cofounder of DIYbio, a worldwide network of "biohackers" dedicated to creating pop-up labs and doing biology outside the traditional environments of universities and industry. But when he ran into Perfetto at the 2010 Bay Area Maker Faire, the two men agreed that community labs just aren't as exciting as they sound. Not yet anyway. Looking at your blood under a microscope is the opposite of innovation—it's arts and crafts. "People would jump up and say, 'I want to do this. What do I do?' And no one had any good ideas. Or the ideas were too complicated to be translated into a starter project," Cowell says. Before the burgeoning world of garage labs could really take off, it needed to be easier for people to get their own home projects started. And the barrier to entry wasn't education or even space. It was a lack of affordable tools. CoFactor aims to supply them.

Science is all about coming up with smart ways to answer hard questions. But sometimes getting those answers requires expensive machines. Physicists looking to understand the universe don't just set up a pendulum anymore—today they build multibillion-dollar underground particle accelerators. PCR machines, critical to genetics-powered biology, start at around $6,000. And these machines, with their intricately tuned bits and pieces, aren't friendly to the kind of void-your-warranty hacking at the heart of the maker movement (not to mention creative experimental design). In short, no amateur is going to drop tens of thousands of dollars to get a lab running, and many scientists don't understand the inner workings of their expensive, grant-funded gadgetry well enough to whimsically crack the machines open and see how they can be modified. But thanks to the DIY revolution and Arduino, the open source circuit board, big thinkers like Cowell and engineers like Perfetto (whose OpenPCR device sells for just $599) are reverse engineering the big-budget tools. And then they're sharing their methods with the world.

Ask people inside the biohacker movement where they think it will have the biggest impact and they talk about education—being able to do genetics in classrooms. They (regularly) bring up Sushigate, the 2008 case of New York City high school students who used DNA testing to discover that sushi restaurants and supermarkets were mislabeling their fish. The results may be cool, but for now the machines are where the real action is. Behind the scenes, engineers and science enthusiasts are teaming up to mod tools and technologies and then sell their inventions—or simply share tips on how to build them—to anyone interested. Homemade PCR devices are drawing the most attention, since anyone who wants to work with DNA has to put it through a PCR machine first.

That's what has drawn a few hundred people to the online community surrounding Perfetto's OpenPCR project. Polymerase chain reaction is really just a process of heating and cooling genetic material. Weill Cornell Medical College researcher Russell Durrett, cofounder of New York City's community lab GenSpace, built one using a lightbulb, an Arduino board, an old computer fan, and some PVC pipe. Biotech advocate Rob Carlson also has a version, called the LavaAmp, that he says could be easily mass-manufactured just like any consumer product. "It doesn't have to be a big company," Carlson says. "The manufacturing is set up so that if anybody wanted to make 100,000, they could do that, and the quality of the resulting molecules would be just fine."

But PCR machines are only the beginning. Keegan Cooke, a former microbial fuel cell researcher, has been selling a home-built battery called a MudWatt kit. The MudWatt creates energy by capturing electrons released when mud-borne bacteria eat metal oxides. The kit comes with an anode, a cathode, and an LED light. Users fill the box with about two cups of muck—any sort has the right microbes, though stinkier stuff seems to work better—and some leftovers from the fridge (to feed the critters). The microbes generate electricity as they eat, and the electrodes capture it to power the light. This microbial fuel cell tech isn't good enough to be scaled up to wide use yet, but the open source model for distribution means that people can start making advances in their backyards. Cooke has already updated and modified his kit based on user feedback. "One sixth grader found that the mud in his nearby river generated almost double the power. He also recommended that we try a different material for our electrodes, and we found that it also produced double the power. It's nice, this process of people giving us feedback and evolving the technology," Cooke says.

Another example: Cathal Garvey's DremelFuge. The centrifuge—a device for rapidly spinning substances to separate lighter components from heavy ones—is essential in many fields of science, but a professional-grade version can cost thousands of dollars. Garvey, a biologist in Cork, Ireland, designed one that can be made by 3-D printers—either with an at-home printer called a MakerBot or by the 3-D print-on-demand company Shapeways (for $57). The DremelFuge is a small round disk with slots that hold standard microcentrifuge tubes. It's designed to fit snugly onto a rotary tool, which can spin the tubes at 33,000 rpm, producing up to 51,000 g's. (A standard professional centrifuge produces only about 24,000 g's.) Garvey gave his DremelFuge a Creative Commons Attribution ShareAlike license, meaning it can be used or remixed by anyone.

BUILD YOUR OWN LAB

Conventional laboratory equipment is powerful but expensive. The biohacking movement is remaking those tools on the cheap.—E.B.

DIY GEAR		PRO GEAR
OpenPCR Maker: CoFactor  Features: A polymerase chain reaction device. Replicates DNA by heating and cooling so it can be analyzed. Able to perform 16 reactions at once. Comes with temperature sensors, a control board, and control software. Price: $599		StepOne System Maker: Applied Biosystems  Features: Able to run 48 reactions at a time. Touchscreen interface and real- time monitoring. Price: $6,000-17,000
GeneLaser Maker: CoFactor  Features: All the chemicals you need to amplify DNA on a PCR device. Users then send the genetic material to a lab for analysis.  Price: $99 for four reactions		DNA Test Kit Maker: 23andMe  Features: A test tube that you spit into (copiously) and send back to the company, which does all the processing and analysis.  Price: $200-400
MudWatt Microbial Fuel Cell Maker: KeegoTech Features: Fill the plastic box with a handful of mud and food leftovers, and two graphite electrodes capture the electrons released by hungry bacteria. Instant battery!  Price: $45		No laboratory equivalent Custom microbial fuel-cell systems can cost several hundred thousand dollars to assemble.
SpikerBox Maker: Backyard Brains Features: Electrodes and a chip set let you listen to—and with an iPhone, visualize—the neurons firing in, say, a cockroach leg.  Price: $90		Preamplifier Maker: Stanford Research Systems Features: Two inputs and similar noise measurement, but no audio output. Weighs 15 pounds.  Price: $2,400

Perhaps the biggest tool-making success so far, however, comes from the world of neuroscience. It's a hand-sized box made of translucent neon-orange plastic with some electronics inside and a wire sticking out. For just $90, the device—called a SpikerBox—does something remarkable: It records and makes audible the sound of neurons firing. Connect two electrodes to the leg of a live cockroach (included); every time the bug twitches, its neurons emit an electrical spike that translates into a loud click. It sounds simple, but the ability to reveal a spike for such a small amount of money is a bit of a revolution in the study of neurobiology.

The SpikerBox grew out of the frustration of its inventors—engineers Tim Marzullo and Greg Gage—with the high cost of their lab equipment. As students at the University of Michigan's Neural Engineering Laboratory, they came to feel that their work wasn't having enough impact given the money being spent. "In that lab you do silly things like design electrodes that cost thousands and thousands of dollars," Gage says. "And then they would sit on a shelf afterward, because they were someone's PhD project."

Eventually, Marzullo says, they realized that "if the objective is to show spikes, you don't need a million dollars and a clean room." They started on what Gage calls a self-imposed engineering challenge: Make electrodes for $100. They told each other that if they pulled it off, it'd be "funny." Then they wrote an abstract and brought prototypes of their hack to the Society for Neuroscience conference in 2008. At their poster presentation, the prototype SpikerBox didn't work—yet it still caused a stir. "We were flooded with neuroscientists and educators who said they'd been waiting for this for years," Marzullo says. (Shortly thereafter they built a box that worked.)

In 2009, Marzullo and Gage started a company, Backyard Brains, to sell the box. They've shipped over 550 kits and demo'd the device for more than 6,000 people (including passengers on a Delta Air Lines flight, where they stuck a sign to the bathroom door reading free neuroscience lessons at seat 33a and b). Though they're keen to earn a living from their company, they're fine with the relatively small amount of money they're making now—as long as someone out there is learning about neuroscience. (A recent $250,000 grant from the National Institutes of Health also helps.) Which is why they're strong believers in keeping the device and its intellectual property open source. It can be purchased in various stages of assembly, and detailed instructions for building the SpikerBox are available for free download on their website, along with software for interpreting the intensity and duration of the spikes.

SpikerBoxes are even making their way into real science labs. W. David Stahlman, a professor of psychology at UCLA, recently purchased one to use in his research on hermit crab behavior. Traditionally, he says, psychologists don't focus on neuroscience. But while studying attention, learning, and distraction in the hermit crabs, he grew interested in how those behaviors are exhibited in the crabs' brains. A SpikerBox means that doing this kind of experimentation is no longer cost-prohibitive for a young professor. Even better, there's no warranty to void. "When you're working with equipment that's much more expensive, you're more hesitant to open it up and tinker with it," Stahlman says. And as a nifty bonus, he can capture the data right to an iPhone or iPad.

The companies that sell professional-grade PCR machines to laboratories are predictably unimpressed by all this fuss. Jeff Rosner, head of research and development for the PCR division at Life Technologies and a former engineer at Hewlett-Packard, says he's intrigued by the OpenPCR movement, but he hardly sees the gadgets it's producing as competition. "What they're doing is really sort of PCR 101," he says. "The thermal-cycling machine is only a small piece of what's important about PCR and what's required to do it. You need so many other things, including access to chemistry that's way harder to hack than the machinery itself." (Most chemical reagents are proprietary, and every manufacturer has a unique process for making the chemicals work. Perfetto and Cowell have been mixing and matching chemicals and protocols to simplify the process for their home kits.)

Still, it's difficult for Rosner to conceal his excitement over the fact that hackers are getting interested in his technology—and he admits that he actually has a machine shop in his own backyard. "There are some real barriers for them," Rosner says. "The reality is that costs have declined from hundreds of thousands of dollars to tens of thousands, but they have to get down lower before they'll be accessible to hackers." Then, after a pause, he adds, "I hope that happens."

But Perfetto and Cowell don't see any reason to wait. Cowell is churning with ideas for new projects. He organized two weekend prototype-building hackathons last spring called FutureLabCamp—and, of course, he also participated. "I want to build an LED spectrophotometer with an Arduino," Cowell says. "People have done it before, but I want to make it better. I want to build a tiny incubator for test tubes. They're easy to build, but they're all big. There are no tiny ones. Then there's a biology idea, a genetic idea—I can't remember now. Maybe it was building a transluminator gel box for electrophoresis." Sounds like that upstairs bedroom is about to get even more crowded.

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- Bryan
http://heybryan.org/
1 512 203 0507

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