Synthetic Biology: The conclusion of the very beginning

Note: This ends 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, The dummy's guide to engineering genes, Play God for fun and profit (mostly fun), and Managing the unmanagable future.

"Biology is a technology for manufacturing," says Drew Endy. Engineered genes could remake mass-production and materials. Cells are proven nanotechnology with a history of creating large-scale output. Look around the room, anything manufactured or grown could very well be produced more efficiently in a cell. From impact resistant plastics to water proof fabrics or moisturizing cosmetics -- it could very well make the most financial sense to design an organism that cooks up what you want in almost any existing manufacturing industry.

All of this is still a ways away. A genetic engineering job today requires a Ph.D in a subject like molecular biology. Often postdoc work is on the job description, experience working directly with genetic sequences, and amazingly comprehensive knowledge of a number of organisms ... and, of course, the ability to be a team player. Genetic engineering is a boutique field. High status, highly trained specialists create changes out of the ATGC's each time they are needed to serve specific business goals. "Imagine if you had to build a mechanical device, or a computer, and your work started with the refinining of ores to produce raw materials, and then next the processing of these materials into custom components, that you eventually assembled to produce a perhaps working system. That's what genetic engineering is like today," explains Endy.

Also: Dr. Endy wraps up on the impact of synthetic biology. (mp3, 5.1m)

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Managing the unimaginable future

Note: This is the fourth 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, The dummy's guide to engineering genes, and Play God for fun and profit (mostly fun).

Extraordinary opportunities for yet-unknowable creativity nearly always comes with the threat of catastrophic destruction. In biology, the downside comes up quickly. This is because un-engineered Nature has always been so good at catastrophic destruction on its own.

What happens when the bad guys start making microbes? Thoughts of malicious biology haunt the background of all the miraculous proposals. Indeed, with a little imagination, bioengineered threats could emerge from anywhere. From industrial espionage in the farming sector to massive production of illegal drugs, it's easy to see that a world of synthetic biology will offer challenges well beyond what we can imagine now. Much of our current worry is focused on lethal pathogens, like smallpox or the 1918 flu. The later created a stir in 2005 when a group of researchers published the genome, and then recreated the virus on their own. A bit of nearly all genetic engineers' minds seems to be chewing on the biosecurity problem. Some of the ideas being discussed are controlling access the production of genes, auditing manufactured genes for known pathogenic sequences, and creating comprehensive biosensing in the environment. All of these proposals have well understood flaws.

There is no comprehensive answer to the threats, and it's not likely there will be. While the best minds in bioengineering are thinking a lot about these dangers, it seems likely that management of human created malicious creatures could be its own full time industry, joining our existing war with natural disease. We know we have to go forward. The cat is out of the bag -- even if the good guys complete gave up genetic research, there's no way to stop the bad guys going forward.

Also: Dr. Endy on biotech security. (mp3, 3.2m)

Next: What's next for the microbe hackers.

Wheat Rust is courtesy stellarr on Flickr.

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.

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)]

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The dummy's guide to engineering genes

Note: Yesterday we began Quinn Norton's five-part series on Drew Endy and synthetic biology with "Everything you needed to know about human-created life forms but were afraid to ask."

Photo courtesy of Mike & Amanda Knowles, via flickr.

Dr. Drew Endy's approach to the next generation of bio technology depends on engineers, programmers, hackers, social theorists, lawyers and so forth, to inform biology. He believes we can make genetic engineering, like computers, part of every facet of our lives, changing the way humans do their business.

He seeks to put synthetic biology into the hands of the interested, not merely the professional. The potential is to widen the range of goals, to extend this emerging tool to many disciplines.

The key, says Endy, is what computer scientists call abstraction.

Fundamental to what created modern software was that idea that no one should have to type in that monotonous stuff twice. Once something was there, it should just be reused, not re-created. More important, once it was done the programmer didn't have to know how it worked to do it again. The common wisdom became that no one should have to know how a computer worked to make it do entirely new things.

Also: Dr Endy explains Abstraction (mp3, 4.9mg) and Standards (mp3, 3.1mg) for synthetic biology.

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Everything you needed to know about human-created life forms but were afraid to ask

One of the great pleasures of being involved with O'Reilly Media is learning from the many fascinating people who get involved with the company on one level or another. They're Friends of O'Reilly, or Foos. We have occasional get-togethers with Foos, our own Nat Torkington has taken the concept to New Zealand, and we have one -- on the social graph (see coverage in the next Release 2.0) -- coming up this very weekend. While the Foo events are quite off-the-record, the work Foos do is very much public. So we'd like to share with you some of what we're learning. Over the next few days, we're going to use this blog to introduce you to one Foo in particular, synthetic biology pioneer Drew Endy. This multi-part profile of Drew and his work is, appropriately, written by another Foo, Quinn Norton, who will be talking about body hacking at ETech in March.--Jimmy Guterman

Dr. Drew Endy tends to fidget. He motions frantically when he's trying to get something across. "It's hard because we've never made it simple," he explains with exasperation. Endy, a professor at MIT until the end of the school year (he's headed to Stanford), engineers new life forms. He's spent his life doing the hard work of bending the complexity of DNA to his will.

And he's determined to make it simple for you.

Drew Endy is a leading star in a field that's emerging to be the biggest thing since Walter Brooke suggested to Dustin Hoffman he should think about plastics. He's a synthetic biologist, a group of scientists and engineers that take microbes with familiar names like E. coli and yeast and make them do previously unimagined things.

Also: Dr. Endy explains what synthetic biology is. (mp3, 5.7mg)

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