Genome liberation

The information that details who we are is too important to be privately owned.


Annalee Newitz
February 27, 2002 1:30AM (UTC)

At Jim Kent's Human Genome Browser Gateway, anyone curious about the fundamental building blocks of the human body can point and click their way through gigabytes of publicly available genetic data.

The vast data set is only about 90 percent complete, in contrast to the proprietary sequencing of the human genome already assembled by the biotech company Celera, but what is there is open to all -- provided they have the biological chops to make sense of it. Users can click on pictures of chromosomes, drilling down into the data until they reach individual genes or areas of as-yet-unanalyzed sequences of nucleotides.

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The data has been made available for reasons that stretch beyond mere scientific curiosity. When Celera's former CEO Craig Venter pushed his company to finish mapping the human genome before the government-funded, public Human Genome Project (HGP), the move was widely considered an attempt to demonstrate that science is done more efficiently by the private sector. But Celera ended up filing hundreds of patents on discoveries it made while sequencing the genome, and access to the database itself is exorbitantly expensive.

For the scientists working on the Human Genome Project, the data defining who we are is too important to be left to Celera -- or any other company. David Haussler, a team leader at the University of California at Santa Cruz who helped Kent and others put the genome online, expresses the credo of a data liberator succinctly: "Information about the human genome is better in public hands than secretly locked up somewhere."

But it's not just the research data itself that is at the center of the tug of war between corporations and scientists. When working with data as complex and vast as the human genome, the software tools necessary to manipulate that data are as important as the genetic code itself. A whole new science of "bioinformatics" -- a flowering of software and hardware explicitly designed to analyze genomic information at blisteringly fast speeds -- has arisen, operating at the intersection of computers and biology.

Life science researchers -- even those who work in academic settings -- are finding that corporations are just as eager to patent the tools as they are the data, and in many cases, universities are bending over backward to let the private sector have its way. As a result, a growing number of bioinformatics researchers are beginning to look to the free-software and open-source software movements for inspiration in their quest for bio freedom.

In the world of free and open-source software, the underlying code to a software program is made publicly available for anyone to share, copy or modify. For bioinformatics researchers, the idea of being able to share software code and benefit from each other's research exerts a strong appeal that is synergistically linked with their belief that information about human genetic code should also be freely available.

Free software has historically been a realm inhabited by geeks who sometimes have difficulty making their concerns comprehensible to the general public. In contrast, the worries of life sciences workers come at a time when public awareness over the new possibilities of biotech is surging. When kittens and sheep are being cloned, how long can it be before we have the ability to clone humans?

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In addition to scientists, a number of artists and cultural critics -- some of whom are now proudly branding themselves as "biopunks" -- are also sounding warnings about the importance of giving the public a voice in how their bodies' genomic information gets used. The Sausalito offices of Genetic Savings and Clone, the company that announced in February the arrival of "Cc" (Carbon Copy), the cloned kitty, even share space with the brand new BioArts Gallery, a space dedicated to biopunk art.

Not every bioinformatics researcher necessarily considers herself to be pursuing the same cause as self-described biopunks, but together, they may represent a movement in the making, one dedicated to the proposition that the information that defines humanity is too precious to be private.

Two years ago, outspoken U.C. San Diego bioinformatics professor Richard Belew told Science, "In an emerging field like computational biology -- where it seems likely that we will have the worst of both software and biomedical intellectual property issues -- the stakes are enormous. Genomic projects are already generating huge wealth; active academic researchers ... will have great influence on how these assets are ultimately distributed."

For scientists who work with genomes and proteins, possibly the most radical position they can take is that their research is for the public good, and therefore their data should be available in the public domain. The problem is, few members of the general public are well-trained enough to appreciate the value of a software program that, for example, aligns your cDNA sequence to a gene or set of genes. Nor would many care to use their computers to predict the secondary structure of a protein.

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Thus, for many scientists, putting data in the public domain means sharing it with other scientists. Doing this might mean placing your newly discovered protein structures in a public database. Or, if you want to publish your findings, it could mean working with Michael Eisen on the Public Library of Science, a free, peer-reviewed scientific publishing project the U.C. Berkeley professor initiated to combat the problem of having to buy hundreds of prohibitively expensive science journals in order to "share" knowledge with his peers. Like many in the life sciences, Eisen dislikes the commercialization -- and, for all practical purposes, privatization -- that occurs when scientists place their valuable findings in journals that other scientists can't access because their universities or labs haven't got a subscription.

It's this same problem that led European Bioinformatics Institute team leader Ewan Birney to announce emphatically at a recent conference, "I have vowed never to publish in the journal Science." Birney -- whose work is globally renowned -- is one of the founders of the Open Bioinformatics Foundation, a nonprofit that advocates open-source software development in genomics and serves as the umbrella organization for several popular projects.

Open-source development -- in which software code is by definition made publicly available to all -- has become a thorny issue for many scientists whose contracts stipulate that all their intellectual property belongs to the university or company that employs them.

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Chris Dagdigian, a life sciences technology consultant in Boston who builds genome data-crunching clusters of computers running Linux-based operating systems, explains that for many researchers, developing open-source tools is crucial because otherwise each piece of software has to "reinvent the wheel" and may cost the developer several days of valuable work when she could be gathering new data. While it's common to hear that private companies don't want their employees to "give away" software by working on open-source projects, what most people don't realize is that the problem is even more pressing in academia.

The Bayh-Dole Act, passed in 1980, allows universities to claim ownership of patents on academic discoveries made using federal funds. What this means is that the university, as well as the government, stands to profit from what researchers discover. As a result, universities have set up technology transfer departments whose sole purpose is to determine which discoveries the university is going to patent and market to industry. In other words, universities have become minicompanies, wanting to keep all their scientists' research proprietary in case it might turn out to be lucrative.

Licensing issues for software development have long been a focus of conflict between programmers and software companies. But the immense financial bonanzas that many believe will accrue to biotech companies -- which by necessity are heavily involved not just in software development but also in research that could affect human health -- is making such license issues all the more pressing.

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Cynthia Gibas, a bioinformatics professor at Virginia Tech, is very concerned about the way her university and others are using the Bayh-Dole Act to keep her colleagues from contributing to open-source software projects. Although her department allows her to work on open source, she says, "I'm interested in this because we don't have a uniform policy about this across the university. The university doesn't train us in intellectual property issues. Many researchers have to deal with labs where they believe that anything that goes out the door is a potential loss of profitability."

With so many people going into bioinformatics, she notes, it's going to be difficult for them to develop decent software if they're not allowed to participate in already-existing open-source projects. Gibas may be "a commie pinko from way back," as she puts it, but she's also a pragmatist. "I think universities should be allowed to get some butter from these patents because they're so underfunded anyway. But I'm worried when the attitude becomes 'let's grab everything.'"

One solution that Gibas and many other academics favor right now is creating an open-source contract, which would allow academics (and possibly people in industry, too) to make a formal agreement with their employers that allows them to contribute to open-source projects. A group called Openinformatics.org is trying to organize academics around this issue, proposing a number of different kinds of open-source contracts.

Perhaps the only academic to negotiate a blanket open-source contract with his university so far is computational biologist Steven Brenner at U.C. Berkeley, who says that it took several months and hundreds of dollars in legal fees to come to an agreement with the U.C. technology transfer office.

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"I just wanted them to sign a document saying I could modify the copyright [license] on my work and contribute to open source," he says. Eventually, after a great deal of explaining, the tech transfer office came around. Now Brenner is free to contribute to a project called "bioperl" -- which he helped found -- as much as he likes.

Open-source contracts may be the most elegant solution for scientists who want to share their work. "I know many people at U.C. Berkeley produce open-source semi-illicitly," Brenner says. "And I've been contacted by many people who want the [open-source contract] arrangement."

A more radical response to privatization of the genome and bioinformatics software would be to open up the entire scientific process. This is exactly what Jeff Bizzaro, founder of Bioinformatics.org, proposes to do. His site, which has attracted thousands of members from across the globe, hosts several open-source bioinformatics projects. But the site isn't just about software. It's also about making the process of scientific discovery public and collaborative. Bizzaro encourages scientists to post their findings on the site so that, for example, two scientists could conduct complementary experiments halfway across the globe from each other.

Bizzaro and his cohorts at Bioinformatics.org believe that the scientific process has become too competitive and proprietary; ultimately we should share data in the same way a political progressive would suggest we share wealth: democratically, openly and with ethical integrity.

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But what about the people who care passionately about opening up the scientific process, but who have little access to labs and lack formal scientific educations? For them there is always the way of the biopunk.

The term "biopunk" -- an offshoot of "cyberpunk" -- originally described a genre of science fiction dealing with biotechnological themes. But as computer and Internet culture took off, the term came also to be associated with the "information-wants-to-be-free" hacker ethos.

Biopunk shares with cyberpunk a spirit of social critique in the sciences, and a commitment to limiting corporate control of data. Like cyberpunk, it's also a movement that encompasses the work of engineers, scientists, artists and cultural critics. But the biopunk revolution has yet to be codified or legitimized -- it's as ill-defined as the genome itself. While cyberpunk is the familiar stuff of Wired cover stories and desktop computers, biopunk lurks at the corners of bioinformatics conferences and in the late-night lab work of anti-authoritarian university researchers who contribute to open-source software projects on the sly. Cyberpunk finds expression in big-budget Hollywood pictures like "The Matrix"; biopunk animates the bizarre art of people like San Francisco biopunk artist Dale Hoyt, whose cult video "Transgenic Hairshirt" has been passed from hand to hand in the San Francisco art underground.

Biopunk also differs from cyberpunk in that it is associated with the life sciences and medicine, two areas of inquiry that have a long history of ethical debate over the relationship between research and the public good. Biopunks can therefore call on a venerable tradition of philosophical thought when they raise objections to how scientists are gathering and using genomic data. Moreover, biopunks often protest misuses of the human body and its reproductive functions, which makes biopunk a considerably more feminist and queer movement than straight-guy cyberpunk ever was.

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But what do biopunks want? It depends on who you ask. Dale Hoyt says it's all about protesting both "bio-Luddites and apologists for the biotech industry." He adds that it's also about questioning current science. "I think the human genome project is a capitalist fable, a fable in which the government works with private industry. The genome race was ridiculous. Celera came up with this shotgun version of the genome, and I think the results are bogus. I think it was just to get more stock options for Celera and more grants for the NIH." His sentiment, while extreme, is not unfounded: Many scientists have protested the slapdash methods that Celera used to assemble its map of the human genome so quickly. Genomics expert Barry Commoner carefully debunked Celera's dubious achievement in a widely read article in the February issue of Harper's.

Hoyt is the founder of the Coalition of Artists and Life Forms (CALF), a think tank that he says operates "with the utopic idea that artists could contribute to the dialogue about biotech and research about biotech." Hoyt, whose video "Transgenic Hairshirt" is about his relationship with his "ludicrously bred" hairless cat, was excited about the cloned kitty announcement, remarking that "this is as important a step as was the VCR or the first PC since it takes a major technology and brings it into the home in a domesticated version."

Although Hoyt and his biopunk colleagues in CALF remain committed to art that eschews commercialism, it's clear that, as Hoyt worries, "Biopunk could become a capitalist tool." In the meantime, however, he has high hopes for the ways that genomic information, if liberated, could be used. "I want superanimals who turn on their masters and give the world back to the chipmunks who were here first," he laughs, then adds, "This is with our extinction in mind, of course. I'm all for human extinction."

While trickster nihilism works fine as art, it's hardly suitable for scientific inquiry. Perhaps that's why data liberationists who do science and engineering tend to espouse rather more modest goals than the elimination or modification of our troublesome species.

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At a January conference on bioinformatics organized by the computer book publisher O'Reilly & Associates, I chaired a panel called "Open Data Open Source" where data liberationist scientists and code hounds had a chance to debate the value of free software and learn more about their biopunk counterparts in the arts community. Slightly perplexed by stories of biopunk artists who want to wrest control of genomic data from corporations and participate in everything from genetic engineering experiments to protein discovery, Ewan Birney wondered, "Well, we couldn't have people doing genome gazing in the same way amateurs engage in star gazing, could we?"

Several geeks in the audience were quite taken by his comment about genome gazing. Chris Dagdigian immediately brainstormed an idea for a Web site for amateur genomics enthusiasts called Genome Gazer that would broadcast genetic information in a manner analogous to video or audio streaming.

"Basically, you could make a Web site that just streams human genetic code at you," he says. "You can get your hands on all sorts of genomes now -- they're just giant text files of alphabet characters. You could pick your favorite chromosome, download it from the government and get one of those stock ticker programs to stream the genome instead of business information."

Ann Loraine, a staff scientist who studies the human genome at biotech company Affymetrix in Emeryville, Calif., loves the concept. "In 20 years, every high school kid will be surfing the human genome online," she enthuses. "Now that the genome's sequenced, and you can get computing power for not much money, you too can investigate genes and this could help you learn how to do it."

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Bring the genome to the people -- that's the biopunk way.


Annalee Newitz

Annalee Newitz is a writer. Get the gory details at Techsploitation.

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