Attention - all interested in synthetic biology - DARPA is interested, big time

For those interested in synthetic biology, check out the new DARPA call for proposals: Living Foundries: Advanced Tools and Capabilities for Generalizable Platforms (ATCG) - Federal Business Opportunities: Opportunities

And check out the "teaming" site trying to bring together groups and people with diverse backgrounds and interests. Kudos to Alicia Jackson at DARPA and DARPA in general for recognizing the importance of synthetic biology.

I note - Alicia Jackson's announced this push at the Synthetic Biology meeting at Stanford earlier in the summer:

• Twitter / Jonathan Eisen: Alica Jackson from DARPA announcing DARPA is getting into synthetic biology in a big big big way w/ "Living Foundries Program
• The Tree of Life: Some quick notes on #Synbio5: Synthetic Biology ...
• Check out video from the Synthetic Biology meeting where this was announced:

For some other information about this see:

• DARPA's Living Foundries Concept
• DARPA Wants Artificial Lifeforms - Technology Review
• SOLICITATIONS - Defense Advanced Research Projects Agency
• DARPA's Microsystems Technology Office launches Living Foundries

Some quick notes on #Synbio5: Synthetic Biology 5.0 at Stanford

Well, just got back from Synthetic Biology 5.0 at Stanford.  I don't really have time to do a thorough job with a blog post but I will try to fill in some details here.

1. Got invited by Natalie Kuldell in April to participate in an education workshop for the meeting.  Eventually said yes, but only after deciding to not go to the Earth Microbiome Meeting in Beijing. I said yes in part b/c it was close by home but also b/c of the people Natalie invited to be on the panel.  She wrote in the invitation email:

Other panelists who have confirmed their participation in this session are from Understanding Science/Understanding Evolution (Juday Scotchmoor), Nature Education (Ilona Miko), Science for Citizens (Darlene Cavalier), GenSpace (Ellen Jorgenson), and Hong Kong University of Science and Technology (King Chow).

And well, of the ones I knew on the list, they all were great.

2. Had a conference call (very brief) in June to discuss the session.

3. Headed out to Stanford very late Tuesday night - and thus missed the Slam session that night.  I got to my hotel at about 1:30 AM.

4. I woke up early enough to hop on my bike and ride on over to the meeting.  I was a PhD student at Stanford and had brought my bike in the hopes of going for some rides around town.  I took some pics on the way in:

Do you get permission to engineer your microbe?

Well, lots of researchers manipulate microbes in various ways in the lab. They delete genes. They make mutants They insert genes. Sometimes, they insert antibiotic resistance genes to help with the genetic manipulations they are doing.

Do researchers always think about the potential risks of what they are doing? Well, probably not. Most of the time that is OK as the risks are negligible. But some of the time, there are real risks to consider. One example of a real risk is the introduction into some pathogen of genes encoding a form of antibiotic resistance not seen normally in that pathogen. If that strain escapes from the lab, it could, in theory, spread into the real world and make treating infections by that pathogen more difficult.

All Things Considered had a very interesting story on "Making Drug-Resistant Germs In The Lab" about exactly this issue a few days ago where they discussed how one researcher submitted to an NIH oversight panel a request to carry out this type of experiment. It seems as though very few researchers actually submit requests to carry out these experiments, even though many are doing it. NPR also discussed how the CDC reviews requests to manipulate certain really nasty pathogens and that most of the requests have been granted. Unfortunately, I cannot find a transcript for this story to quote, but it is really worth listening to.

Venter on Colbert

Craig Venter was on Colbert last night, talking mostly about synthetic biology and using microbes to make various things (e.g., energy). Colbert kept trying to egg him on in various areas, but Craig played the straight man again (like the last time he was on Colbert) through most of it. Although I should note, Craig seemed much more relaxed this time.

First Ever Synthetic Organism Patent?

Wired is reporting that the Venter Institute has applied for a patent on the first fully synthetic organism (i.e., they synthesized the genome in the lab ... I am sure that the organism had to be "booted" up in some way using a living organism).

Wired reports:

Scientists at the J. Craig Venter Institute have applied for a U.S. patent on a minimal bacterial genome that they built themselves. According to the patent application, it's "a minimal set of protein-coding genes which provides the information required for replication of a free-living organism in a rich bacterial culture medium."

What do people think? I for one find the patent system completely incomprehensible. I think most biotech. related patents recently have been overly broad and/or represent something that should not be patented. But in this case, I do not know enough detail to really judge but it sounds like at least they did some real work here, which is more than the case for many genome sequence related patents from the past. Given that many places now have patents on mice and other organisms with single genetic knockouts, I do not see how the patent offices could reject a fully synthetic organism. This is not to say whether it is a good idea to synthesize an organism, but I think we are past that point anyway as clearly people will do it.

Synthetic Biology (faculty job available at U. C. Davis in the Genome Center)

Just heard another talk by Drew Endy about Synthetic Biology and his attempts to make the field work more like Engineering than Biology. Basically, what he is trying to do is to make biological parts (e.g., Biobricks) at the DNA level that would work like circuitry board parts do for making computer chips and related devices. As they get more biological parts, more people will be able to treat synthetic biology in an abstract way - that is they will not need to know per se how the biological parts work, just that they have particular properties.

My favorite part of the field of Synthetic Biology is IGEM, the The international Genetically Engineered Machine competition. Students compete to make cools things from their biological parts. Among the more interesting items that have been made is a bacterallawnthat work as a camera.

In general, I like synthetic biology and the potential it has to produce major benefits for the world, although I wish some of the practitioners were less flippant about the potential risks in the field. And, this minor blog would not be complete without the self interest. THe UC Davis Genome Center has just announced a new faculty position in this area (specifically in cmputational and experimental approaches to network and synthetic biology). So if you are in this field and want to join a great collection of faculty working in diverse areas of genomics, please apply.

Job at Davis

Kofi Annan urges restrictions onf biotechnology

Reuters is reporting on a speech by Kofi Annan, Secretary General of the United Nations, in which he

warned of “catastrophic” results if recent advances in biotechnology, including gene manipulation and work with viruses, fell into the wrong hands.

He also said

“We lack an international system of safeguards to manage those risks,” he said. “Scientists may do their best to follow rules for responsible conduct of research. But efforts to harmonize these rules on a global level are outpaced by the galloping advance of science itself.”

He even suggests that the time is ripe for international governing bodies much like was done for nuclear energy in the 1950s. Is this a ploy to use the current animosity towards biotechnology in Europe to give the UN something new to do? Clearly, the US would not sign on to such things with the current administration (or probably any administration). But I certainly find it interesting that he is pushing this. I wonder if he is specifically worried about synthetic biology too or if this is just more concern for genetic engineering in general.