[An excerpt] – If do-it-yourself biotech has a global hub, Cambridge, Massachusetts, could be it. Not only is it the birthplace of the movement’s major mouthpiece, DIYbio.org, but it is also the originating site of IGEM, an annual competition for well-trained students trying to build synthetic organisms and biological machines. Some retrofit microorganisms with BioBricks, Lego-like snippets of DNA that perform well-defined genetic functions, producing everything from antibiotics to biofuels. Others genetically alter microbes to communicate with computers or even function as crude computers themselves. Thousands of competitors from around the world have taken part in IGEM since its inception by four MIT scientists in 2004, converging on Cambridge each fall for the IGEM Jamboree.

The city is also home to some of the most elite do-it-yourselfers and their celebrated biohacker spaces—independent labs tucked away in closets and lofts. These citizen scientists explicitly identify with the computer hackers of a generation ago. Like those young electronics wizards working out of garages who ushered in the personal computing boom, today’s young DIYbio enthusiasts are driving an underground tech revolution, this time in the science of life.

One of them is Kay Aull, who built a sophisticated biology workstation in her bedroom closet after graduating from MIT. Smart, bespectacled, curious, Aull is a member of its first class to receive bachelor’s degrees in biological engineering, in 2008. She has been tinkering with genes since childhood, when, like an elfin Mendel, she spent long hours crossbreeding plants in her parents’ garden. Today she has one of the tiniest full-fledged synthetic biology laboratories in the world, making her one of DIYbio’s brightest stars.

As soon as Aull decided to build her lab, she knew she would have to follow government safety protocols for a Biosafety Level 1 facility secure enough to handle well-known agents not implicated in human disease. For Aull that meant “being able to close the door of my closet and have screens on the windows. When fruit flies are used in labs,” she says “screens are very important.” But Aull had no plans to work with flies. Her first project involved genetically engineering E. coli into a new life-form.

Lacking space in her bedroom for a lab bench, she bought a vertical shelving unit and built her workstation straight up. Like Rienhoff, she needed a DNA thermocycler to do PCR. She managed to find one on eBay for $59. Her thermocycler is an antique model from the 1990s, but the machine’s age was not an issue. “You can do useful things with cast-off equipment,” Aull says. Encouraged, she went online for more, finding a $20 thermometer and $50 worth of terrarium parts she could assemble into an incubator to heat samples. Each of those units could have cost her thousands of dollars, had she purchased them new and at cost. Inventive in engineering, Aull built a centrifuge that was totally “home brew.” She rigged it from a plastic food container and a power drill. She went online to buy E. coli, DNA, plasmids (self-
replicating particles used to transport genes into foreign organisms), biochemical compounds, and restriction enzymes (proteins that serve as infinitesimal scissors to clip DNA in specific regions). Her total bill, including hardware store purchases, came to $500.

Her closet now humming with technological activity, Aull was ready to hack into the genome of ordinary intestinal bacteria. Her goal was to genetically modify them into a rudimentary logic system resembling the basic logic underlying computer processes. She titled her project “A Binary Counting System” and tweaked E. coli to respond to and then pass on molecular signals that toggle on and off, something like the computer’s alternating binary system of zeros and ones. Computers do this electronically as they process data. But cells also have electrical properties, and by genetically modifying the behavior of E. coli it is possible, Aull says, to reprogram the bacteria to function as units in a counting system; the difference is that the microbes turn on and off via an organic toggle switch composed of plasmids.

Her system included pulse-generating proteins that could send and receive signals. Aull swapped in a gene that colored the E. coli blue, allowing her to see her counting system in action. When she activated the toggle mechanism, she saw tiny pulses of blue, their pattern mimicking a computer’s logic when it carries a digital “one.”

For Aull, this achievement was just the start. Microbes that can be altered to perform simple processes of logic, she says, should also be capable of advanced operations now common to computers. This is a regular theme among DIYbio enthusiasts. Garage and closet techies point out that DNA functions like pieces of digital code, which makes it ideal for custom-designed organic machines. Last year a team of students in Hong Kong —as much data, the students reported, 
as can be stored in 450 state-of-the-art, two-terabyte computer hard drives.

Aull entered her binary counting bacteria into a freewheeling synthetic biology contest hosted by the sci-fi site io9.com, but she did not win first prize. That honor went to Vijaykumar Meli, a graduate student in India. He managed to hack bacteria so they would perform a vital service for young rice plants, helping them utilize nitrogen and grow more efficiently with less fertilizer. Aull did not go without accolades, though. She took second place, and her project was praised by her biohacking colleagues in Cambridge.

For her second DIYbio project, Aull tackled something only slightly less complex: developing a genetic test for the hereditary disorder hemochromatosis. Her father had been recently diagnosed and her paternal grandfather probably also had the condition, which results in the absorption of too much iron, leading to a damaging buildup of the metal in the liver. Hemochromatosis can also affect the joints, heart, pancreas, thyroid, and adrenal glands. It is one of the most common genetic conditions in the United States, and if left untreated, it can cause arthritis, liver cirrhosis, congestive heart failure, and some forms of cancer.

Commercial DNA tests for hemochromatosis have long been available, but Aull’s diagnostic had two specific aims. First, it was personal. She wanted to find out for herself whether she, too, carried the DNA flaw. Symptoms usually do not appear in women until the age of 50, and Aull was just 22. Second, her test would demonstrate that a noteworthy diagnostic could be developed in a makeshift biolab. “It’s not where you’re working, but what you’re working on that’s important,” Aull says, while admitting that she would have preferred a larger station—but “my room is only so big.”

To start, she used a cotton swab to get a sample of cells from her cheek, boiled them in a test tube in her kitchen to free the DNA, then added primers, nucleic acids that mark the part of the sequence. Next Aull put her DNA in the thermocycler for amplification. Finally she ran her genetic material through a gel-electrophoresis machine, a Lucite box containing a semi-porous gel. DNA fragments are placed in the gel and exposed to an electrical field. The DNA migrates in response to the field, with smaller fragments moving most quickly. Her end product looked like a bar code. The distribution of those lines of DNA suggested to Aull that she had the mutation linked to hemochromatosis. Follow-up screening by a professional laboratory confirmed that she is a carrier who can pass on the mutation but is not likely to develop the disease.

Beginners considering home-based biology projects probably would not want to start with complex experiments in synthetic DNA, Aull cautions. “If you start talking about the deep-future benefits, you also bring about the deep-future fears and the Michael Crichton scenarios. I wanted to set a benchmark: I am a professional. I wanted to show what you can do in your closet for $500. It took a month and a half of weekends and whatever supplies I could get my hands on as a private citizen.” After completing her two major closet-based experiments, Aull started working out of a couple of hacker spaces, one in Cambridge and another in nearby Somerville, where she would have more room to spread out.

Source: Dawn of the BioHackers (October 2011 issue)