Feb 1

Quinn Norton

Quinn Norton

Play God for fun and profit (mostly fun)

Note: This is the third of Quinn Norton's five-part series on Drew Endy and synthetic biology. The earlier installments are Everything you needed to know about human-created life forms but were afraid to ask and The dummy's guide to engineering genes.

cell-gears.jpg Three years after Tom Knight invented the first standard for hooking together genetic parts in a living programming language, the BioBricks standard, MIT put the idea to work. They started a contest for students around the world called the International Genetically Engineered Machines (iGEM) competition. Students began to make and put together parts of DNA code into repurposed organisms. Some were bacteria that smelled like bananas, some glowed red or green, one team even created a cell that built itself protein balloons. Every year the teams can build on the parts they and other students have created. Theoretically, this means next year's iGEM winner could be a balloon-building organism that glows green and fills a room with banana scent. Today, the parts database at MIT boasts an impressive 2,500 reusable snippets of public domain DNA -- all for the taking.

Stringing together many parts or devices, creates systems -- those are what can sniff arsenic or take light impression like a film emulsion. They are the complex forms of many connected devices. Being student work, the quality of iGEM systems is all over the place. But once one student group has put something in the archive, anyone can see how it was done and how it was used. They can contribute novel combinations back into the archive, creating systems of DNA that still others can expand on. It's not at a commercial level, but provides a proof of concept for a much more sophisticated archive. In the mean time Endy sees this open source genetic model as a vital key to getting people playing with DNA.

Endy refers to the students in iGem as "freeform teenage genetic poets." He points out that what they do for fun is still a bottom line business decision in the real world of biotech. It's clear that he's not just trying to create an academic or business model for synthetic biology, but a full culture. Genetic artists as well as students, hobbyists, activists, researchers, and businesses are part of Endy's future. Genetics will be social, political, mainstream, and constructive in an entirely new ways.

[Also: Dr. Endy on Biobricks, iGEM, and a new project that takes parts to the next level. (MP3 format, 3.9M)]

The success of iGEM and BioBricks led Endy and others to believe this approach, open and available parts for any and all, could have a big impact on the field of synthetic biology.

This fall, Endy plans to leave MIT for parts west. He will set up at Stanford, and work with UC Berkeley and UC San Francisco to create the big brother to MIT's student created parts library. This 'Bay Area Parts Fab" will be a repository of genetic code engineered by professionals and scientists at a high caliber, documented, and published openly. The Fab, envisioned as a public benefit with university support, will employ 25 genetic engineers full time to produce parts they believe will be generally useful. "A collection of parts will let you work with off the shelf components. You won't need to be a Ph.D researcher with a laboratory in order to get stuff to work," says Endy.

When genetic engineering started there wasn't a lot of call for sharing with the uninitiated, and certainly not with the competition. Traditionally, one of the things that has kept genetic engineering in the hands of monied institutions is the intellectual property. Genes are often patented, that's how pharmaceutical and biotech companies protect their investments. This model is incoherent in a world of openly available synthetic biology. Patents are expensive and cumbersome, and abstraction requires freely building on the work of others.

Endy and others are looking for an alternative to the costly and hampering patent model. The goal is to create something that can be shared with anyone doing research. Issues with this would remain if and how DNA could be used commercially, and if including a given chunk would require reuse to be licensed under a similar open license, like GPL'd software. In short, will synthetic viruses be viral? Ideas like Creative Commons copyright licensing and voluntary blanket licensing are floating in the air, still untried and untested.

Next: Synthetic biology gets mean and scary.

tags: biology  | comments: 4   | Sphere It

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Comments: 4

  Thomas Lord [02.01.08 03:44 PM]

Strange. The experience of commercialization of software freedom in the form of "open source" hasn't slowed down the development of closely held, monopoly controlled software at all. On the contrary, the wide spread cheer-leading to encourage the gratis spread of a little bit of "systems software" has accelerated proprietary software's impact on the world. Just ask Google, for example.

Open source hasn't much slowed down patent fights, either. On the contrary, it created the conditions that gave us things such as Amazon's infamous patents. Open source has a shifted around patent liability a bit. I guess that by analogy, when "green goo" breaks out somewhere, and the sequencing reveals an improper use of "GPL"-ed sequences, well, we'll have a very good idea that someone should be sued for copyright violation. Quite comforting, isn't it?

In the comments of part 1, in response to charges of these labs having too much money for the good of any of us, Drew responded by crying "poor" citing the budgets for his lab and the biobricks foundation. Hearing of 25 full-timers, starting this fall, cranking out open source synthbio parts -- I must cry foul, at least as far as the conversation here on the Radar goes. That aside...

The main effect here will be to accelerate demand for the tools of the trade of an existentially threatening program of profit-oriented "tinkering" with the entire biosphere at the level of the genome, a central control point for all life-making feedback processes.

Curie carried around radium in her pocket and mostly horked just herself. The bio student today, with a little bit of cruft under his fingernail, threatens to hork us all. The threat of that student, though, pales in comparison to the threat of efforts to accelerate the industrialization of opportunities to hork us all.


  kanzure [02.01.08 05:52 PM]

See the recent open source biotech/synthetic biology DIY kit. You don't need to be with Tom Knight or Endy to get things done. (Hi Drew!)

  Thomas Lord [02.01.08 07:54 PM]


If yr point is that the cat is out of the bag (which is at least sightly exaggerated) then fine. So the cat's out of the bag. Worry about the neighbors elsewhere -- I care about what the big guy's are doing closer to home. Our friends don't make things better by making things worse and shirking their best possible callings.


  Thomas Lord [02.02.08 04:26 PM]

GMOs have come up in the discussion but mostly as if they were something separate from synthetic biology.

Review, critique, commentary, etc. especially from greater experts in the techniques being applied are welcome in a related discussion about tearless onions at Technocrat. (Are "welcome" unofficially -- I don't own or have authority over that site.)


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