20 Jan 2009

Biohacking: The Open Wetware Future

Much of the infotech revolution erupted from garages (Hewlett Packard, Apple, Google), and the same thing is beginning to happen with biotech. Biohacking is in its infancy, but the tools and knowledge to make novel organisms is becoming cheaper and more widely available all the time. Open wetware is the wave of the biotech future. For example, the Associated Press reports:

In her San Francisco dining room lab, for example, 31-year-old computer programmer Meredith L. Patterson is trying to develop genetically altered yogurt bacteria that will glow green to signal the presence of melamine, the chemical that turned Chinese-made baby formula and pet food deadly...

Patterson, the computer programmer, wants to insert the gene for fluorescence into yogurt bacteria, applying techniques developed in the 1970s.

She learned about genetic engineering by reading scientific papers and getting tips from online forums. She ordered jellyfish DNA for a green fluorescent protein from a biological supply company for less than $100. And she built her own lab equipment, including a gel electrophoresis chamber, or DNA analyzer, which she constructed for less than $25, versus more than $200 for a low-end off-the-shelf model.

Patterson is just at the beginning of our biotech future as recently limned by physicist Freeman Dyson:

The domestication of biotechnology in everyday life may also be helpful in solving practical economic and environmental problems. Once a new generation of children has grown up, as familiar with biotech games as our grandchildren are now with computer games, biotechnology will no longer seem weird and alien. In the era of Open Source biology, the magic of genes will be available to anyone with the skill and imagination to use it. The way will be open for biotechnology to move into the mainstream of economic development, to help us solve some of our urgent social problems and ameliorate the human condition all over the earth. Open Source biology could be a powerful tool, giving us access to cheap and abundant solar energy...

Domesticated biotechnology, once it gets into the hands of housewives and children, will give us an explosion of diversity of new living creatures, rather than the monoculture crops that the big corporations prefer. New lineages will proliferate to replace those that monoculture farming and deforestation have destroyed. Designing genomes will be a personal thing, a new art form as creative as painting or sculpture.

Few of the new creations will be masterpieces, but a great many will bring joy to their creators and variety to our fauna and flora. The final step in the domestication of biotechnology will be biotech games, designed like computer games for children down to kindergarten age but played with real eggs and seeds rather than with images on a screen. Playing such games, kids will acquire an intimate feeling for the organisms that they are growing. The winner could be the kid whose seed grows the prickliest cactus, or the kid whose egg hatches the cutest dinosaur.

Seed has an interesting interview with DIYBio co-founder Mackenzie Cowell. The nascent DIYBio aims

...to help make biology a worthwhile pursuit for citizen scientists, amateur biologists, and DIY biological engineers who value openness and safety. This will require mechanisms for amateurs to increase their knowledge and skills, access to a community of experts, the development of a code of ethics, responsible oversight, and leadership on issues that are unique to doing biology outside of traditional professional settings.

Among other things, DIYBio wants to build a public wetlab where citizen scientists have access to the tools needed to advance their projects at minimal cost.

But what about safety? After all, some garage infotech hackers unleashed destructive computer viruses into the internet. Shouldn't we fear that garage biohackers will release actual viruses into the biosphere? Indeed, this will happen, but what's the best way to protect ourselves from malicious biotech viruses and other organisms? More regulation and government restrictions on access to biotech equipment and materials? In his Seed interview, Cowell gets it pretty much right:

All the hazardous sequences are available publicly from GenBank, etc.: Ebola, H5N1, the 1918 plague; they're all there. DIYbio won't change that. We're looking to mostly focus on doing wet lab work in a very public, transparent group setting. So that if anyone — a neighbor, a governmental agent, a journalist — wants to know what is going on, it's evident what we are working on. Forming that community is the first defense so that the 99.9999 percent of the group who are positive will stop the .0001 percent of the group that's negative. Today, at the ground floor, I think it's best if we blaze a path forward in a very public and open way. A small minority may have unleashed computer viruses over the years, but it's the computer hacking community at large who created many of the solutions that safeguard us from them.

Back in 2004, I argued that the best bio-defense is a robust bio-offense:

Biodefense depends not on abandoning technology or appeasing our potential adversaries, but on nurturing a robust biotechnology. Remember, we are talking about "dual use" technologies—for both offense and defense...

...let us assume the worst: that fiendishly clever evildoers could devise some sort of superplague that would kill off some huge fraction of humanity. A plague as deadly as Ebola, more communicable than the common cold, and with a latency period of several weeks to allow it to spread through unwitting populations.

What would it take to counter such a pathogen? A dynamic and extensive diagnostic and biomedical manufacturing system that could deploy multiple levels of defense, including vaccines, new antibiotics, and other novel targeted therapies. To do that, we need to move ahead with innovative biotech.

Fortunately we are well on our way to developing such a biotechnological infrastructure. The future will see a system in which first responders, perhaps using biolabs on a chip, will be able to decode the genomes of pathogens in hours. Once decoded, biotechnologists could quickly identify essential metabolic circuits and then design therapeutic molecules to disrupt them, thus preventing the spread of the bioterror agent. For example, consider neuraminidase inhibitors like Tamiflu, and Relenza which halt flu infections if taken shortly after exposure or onset of symptoms. Similarly, researchers have discovered highly effective compounds like adefovir that block anthrax's deadly edema factor toxin.

Perhaps in the future, labs could design, test, and manufacture vast quantities of antibodies to protect people from bioattacks from newly bioengineered pathogens. Novel vaccines will also be part of any anti-bioterror defense effort.

Because of all of the above, it is vital that bad policies not be permitted to stifle biotechnological research and development. Unfortunately, it will not be possible to stop future bioterrorists from dreaming up and deploying new bioengineered pathogens. But a robust biotechnology should be able to confine the effects of such attacks to no more than the number of people who are killed by car bombs today. Future bioterrorist attacks will be nightmares for those affected, but they ought not be sufficient to destabilize civilization.


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