Drew Endy vs. Jim Thomas, “Synthetic Biology Debate” (MP3 audio), Longnow Foundation, 2008/11/17

Can biology be componentized in the way that information technologies have been?

“I want to develop tools that make biology easy to engineer,” Drew Endy began. The first purpose is better understanding fundamental biological mechanisms through “learning by building.” The toolkit of Synthetic Biology starts with DNA construction and ascends through DNA parts, to devices, to standardized systems. [….] So far 3,500 standard “BioBrick” parts have been developed for free distribution, and the number is growing geometrically. The number of amateur and student bioengineers also is growing geometicallly.

[….]

Jim Thomas asked Endy how he would defend against commercial interests locking up Synthetic Biology with patents? Endy said the best hope is building an open-source community that grows faster than businesses and out-innovates them.

Thomas began his statement by pointing out that it usually takes a whole generation to understand a new technology, so he urges moving slowly and cautiously, but Synthetic Biology is advancing at breakneck speed, and the window of opportunity to have effective public discussion and control is closing.

He cited the history of synthetic chemicals, which began in mid-19th century. [….]

There’s so much novelty coming so fast from Synthetic Biology, no predictive models or regulatory models can hold them. He recommends these new tools be strictly contained so there is no release of new life forms into the biosphere, and there should be no commercialization of the technology at all.

Endy asked Thomas if it’s okay to make anything in a bioreactor vat? Thomas said, “Yes, beer.”

For different reasons, both debaters wanted to see Synthetic Biology kept from domination by commercial patents. For Thomas, it would lead to unjust monopoly answering only to profit. For Endy, it would paralyze open-ended research.

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One comment on “Drew Endy vs. Jim Thomas, “Synthetic Biology Debate” (MP3 audio), Longnow Foundation, 2008/11/17
  1. Bruce Hubbard says:

    As an ex-biologist who moved into computer science, I am fascinated that synthetic biology is following the same enthusiast pathways as has garage computers and more recently groups such as Make and Instructables and FabLab. It is intriguing to see experimenters moving from soldering bits of wire to bits of DNA. This is an example of how a new technology gives birth to invention. Let me react to some of the issues.

    First, I think that if you are going to get good at a complex subject, it is better to start young. You can see this just by looking at the current morass of jargon and relationships in any of the gene databases (ex. IHOP-net). It’s better than average and still boggles the mind of the uninitiated. I’d make analogy with the evolution of the running passing game in football – you had to grow up with it to be good at it.

    A large part of the discussion was concerned with risk. I think that this door has already closed. How would you regulate it? Ban it – consider how well that has worked with guns, drugs, and alcohol. The very worst elements of society take over the manufacture and distribution. Regulate it – maybe but not likely. Every country (and company) that I know of has decided to break virtually every treaty or agreement when it proved useful to do so. Bioweapons treaties? We may have stopped (?) stockpiling Anthrax, but the Soviet Union certainly didn’t stop stockpiling Anthrax or Smallpox. I wouldn’t expect synthetic biology to fare any better. Make it illegal or restricted and all you will get are secret Presidential decrees to perform secret research. Look at our secret and possibly unconstitutional responses to 9-11. Legal or not, they certainly didn’t win us any ethics awards.

    On the story of GMO crops, there is an upside: Monsanto’s Roundup-ready crops use less herbicide than others and this could be seen as beneficial. On the other hand, Monsanto has hardly been a model corporate citizen of the world as it sues individual farmers when it finds its IP somehow mixed into their crops. I’d be scared of them too. Bt has helped reduce insecticide use as well. But it has also been reported to be killing off Monarch butterflies, one of those unexpected ecological side effects. Even in a century, I doubt that we will be able to foresee all of these effects. But, by then, climate change may have made most ecological issues academic.

    Technological advance has always destroyed old professions, but it has also created new ones. One could have asked all of the women in a 1960’s corporate typing pool in 1960 if they wanted to lose their jobs to mechanical printers and Xerox machines and the answer would have been “No”. Ask someone today of she wants to be in a mass typing pool and the answer would be a fairly resounding “F No”, “Give me a computer”.

    Applied to Africa, although many small farmers are cultivating sweet wormwood for Artemisinin, I gather that the yields are small and that the supply will never provide cost effective doses of the drug to those who need it. (Pacific Yew would never have yielded enough Tamoxifen for widespread use.) This need is not abstract or simply a matter of long term economics; it is one of immediate life and death.

    Following the examples of quinine and chloroquinine, p. falciparum will eventually become resistant to artemisinin too, ending any wormwood-based economy regardless. One should not thoughtlessly destroy a distant economy, but this one seems unsustainable. We need to offer reasonable alternatives if and when we do damage one. But, in the case of Artemisinin, I can imagine years of negotiations with distant governments and dictators while more millions of children die of malaria.

    Finally, there is nothing to keep a small farmer from taking advantage of this technology, as it becomes affordable, and improving his own crops for his own needs. Locally, the farmer’s market used to sell “Jasper’s corn”, one of the sweetest that I ever tasted. It is gone now, but I still think about it and wonder if it was someone’s private hybrid.

    Bioterrorism and virus creators. This is a considerable worry. Consider the Internet for a good example of how a new and beneficial public technology can be corrupted by a small minority of virus and spam creators. (Organized crime is here too.) But, if I was a garage bioterrorist somewhere in Asia, would I go to the considerable effort of assembling the many thousands of nucleotides from a public sequence to create my weapon? Unlikely. I’d dig up some Anthrax or go to the market, get a sick duck with H5N1 and create a plague the old fashioned way: by passaging it through “volunteers”. There is no need for high tech to create havoc.

    So, we have an exciting intellectual discovery (DNA building blocks), an associated fabrication technology, and both are already out there in the public domain. Will Monsanto and others try and control this new technology? I’m sure they will. Will irresponsible people create pests and viruses? I’m sure they will. People also drive drunk and come to work when they have the flu, so what do we do?

    Thinking about the klebsiella which could have altered soil ecology – I am concerned about the many cellulose digesting bacteria strains which will be created in the next decade. I’m positive that more than a few of them will turn out to be pests if they escape. How big of a problem will this likely become?

    At the industrial scale, cell-free extracts may be one solution to this problem. After all, what we need is chemistry, not life. I am less enthusiastic about biosafety via schemes like 4-nucleotide codes: these are evolutionarily excessive and deletion of excess is a common evolutionary strategy. Finally, microorganisms which need to compete in the wild also tend to shed unnecessary genes, including ones which we have added. Even at the level of horizontal gene transfer, a recent report indicates that reduced use of antibiotics in Norway (?) has decreased the frequency of MRSA organisms. MR is evidently not an evolutionarily useful trait in the absence of antibiotics. Making gasoline probably isn’t one either.

    What about open communities of synthetic biologists? One, they may be less massively creative than anticipated. Consider the Internet again. While there are many open software projects, many are essentially hobbies and move slowly. The successful ones such as Linux and GNU have many contributors looking over each other’s shoulders, testing, and watching for errors. So might massive open biological projects. The GPL license helps too, by keeping publicly developed projects in the public domain. Also, the many knowledgeable people out there do constitute a sort of “million eyes” and are constantly on the alert for mischief.

    Finally, the ecological damage that our civilization has done to the Earth is already massive and we show limited inclination to stop. Unless we want to start bicycling more, turning off appliances, and replanting parking lots (apparently not), we are going to need a different fix for our problems, and soon. As unattractive as its worst case downsides may appear, doing nothing to move off a petroleum-based synthetic economy for another 100 years may be worse.

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