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.

The Long Now Blog » Blog Archive » Drew Endy & Jim Thomas “Synthetic Biology Debate”

MP3 audio

Advertisements
About

David Ing blogs at coevolving.com , photoblogs at daviding.com , and microblogs at http://ingbrief.wordpress.com . See .

Tagged with: , ,
Posted in Talk Audio Download
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.

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out /  Change )

Google+ photo

You are commenting using your Google+ account. Log Out /  Change )

Twitter picture

You are commenting using your Twitter account. Log Out /  Change )

Facebook photo

You are commenting using your Facebook account. Log Out /  Change )

w

Connecting to %s

Translate
Beyond this media queue
This content is syndicated to Twitter. For professional perspectives, look to Coevolving Innovations; for a photoblog, look to Reflections, Distractions.
  • Open Innovation Learning, Book Launch
    Video and audio recordings of the launch of my book, Open Innovation Learning, may be a more accessible preliminary way into the content, with the open access publication better as a reference.
  • Eight infographics on Systems Methods (UToronto iSchool 2018)
    The UToronto iSchool graduate student groups created 8 infographics reflecting impressions on the systems methods most relevant to their research in winter 2018.
  • Negotiating Order with Generative Pattern Language
    A workshop at PLoP 2017 framed dialogue as "Creating Order of" and "Negotiating Order with" frames of reference, to encourage collective sensemaking
  • Exploring the Context of Pattern Languages
    Pattern language is not for wicked problems, said Max Jacobson, coauthor with Christopher Alexander of the 1977 A Pattern Language: Towns, Building, Construction.  In addition, the conventional definition of an Alexandrian pattern as “a solution to a problem in context” when applied to social change might better use the term “intervention”, rather than “solu […]
  • Multiparadigm Inquiry Generating Service Systems Thinking
    Expanding pattern language to service systems through multiparadigm inquiry sweeps in research by scholars contemporaneous to Christopher Alexander.
  • Christopher Alexander, Horst Rittel, C. West Churchman
    Christopher Alexander (pattern languages), Horst Rittel (wicked problems) and C. West Churchman (the systems approach) were neighbours on campus at U.C. Berkeley in the 1960s and 1970s. What might we synthesize from their joint wisdom?
  • 2018/05 Moments May 2018
    Barely recovered from jet lag from China, bounced back to west coast for some continuing research. Returned home as spring turns into summer.
  • 2018/03 Moments March 2018
    A month in Toronto, as I came out of the Air Cast for my Achilles Tendon injury from December, and started physiotherapy.
  • 2018/04 Moments April 2018
    Relearning to walk, after ankle in cast, across Shanghai, Wuhan and Vancouver, with DY as my sherpa.
  • 2018/02 Moments February 2018
    A second month when the only occasions to leave the house required my spouse to accompany me.
  • 2018/01 Moments January 2018
    Ankle in a cast, a limited mobility month, maximum 10km from home
  • 2017/12 Moments December 2017
    Completed round-the-world trip Helsinki-Hameenlinna-London, then busy holiday season including an Achilles tendon injury from parkour, and our da shou Double 60 celebration.
  • The Systems Approach and its Enemies Helps Us Find the Morality of a Revised Democracy | van Gigch | 2006
    In a book series celebrating C. West Churchman, John P. van Gigch digests (and portends to extend) The Systems Approach and its Enemies. On enemies … 4.1 A MATTER OF DEFINITIONS: ADVERSARIES VERSUS ENEMIES I note the similarity/difference between the words ‘enemy’ and ‘adversary.’ Other authors use the word adversary (ies) to denote all the […]
  • Restoring Legitimacy to the Systems Approach | Clinton J. Andrews | 2000
    A public policy professor, Clinton J. Andrews, looks at how The Systems Approach may encounter problems in skepticism from engineering practice. The systems approach is one general way of going about tackling a problem; some others include the experimental, political, moral, religious, and aesthetic approaches [1,p. 5], [2]. The systems approach to a problem […]
  • The Systems Approach: Its Variety of Aspects | Richard Mattessich | 1982
    An informed view of the Systems Approach from 1982.  (Richard Mattessich was a well-respected professor at UBC when I started in the doctoral program in 1982, but I wouldn’t get to appreciate the Systems Approach as described by C. West Churchman until the ISSS 1998 meeting). In his latest work [The Systems Approach and its […]
  • A logic model for philanthropic effectiveness | Peter Frumkin | 2006
    Program evaluation can be approached from the philanthropic perspective. In searching for ways to give money effectively, donors have many options and confront a wide range of theories about how to achieve impact. It is possible to think about these theories as falling into three main categories: theories of change, theories of leverage, and theories […]
  • Program Logic Models and Theory of Change | Kellogg Foundation | 2004
    From the program evaluation community, with the W.K. Kellogg Foundation … The program logic model is defined as a picture of how your organization does its work – the theory and assumptions underlying the program. A program logic model links outcomes (both short- and long-term) with program activities/processes and the theoretical assumptions/principles of t […]
  • Restoring Manjaro Grub after Ubuntu upgrade
    On a multi-boot Linux computer where Ubuntu has already been installed, adding on Manjaro Linux installs its own version of Grub (that I’ll call Arch-Grub) that is different but compatible with that previously installed (that I’ll call Debian-Grub). Updating Ubuntu to a newer version (or installing an older version) restores Debian-Grub, replacing the workin […]
Contact
I welcome your e-mail. If you don't have my address, here's a contact page.
%d bloggers like this: