Monday, May 22, 2006

SB 2.0 report

Came back this morning [on another red-eye flight, aaargh] from Synthetic Biology 2.0. Overall, it was a pretty nifty conference, with talks covering a lot of different topics. Thankfully, several people have saved me the trouble of trying to remember details from each talk by blogging about the conference: Mackenzie Cowell has a bunch of short posts giving high-level summaries of all the talks, whereas Oliver Morton [an editor at Nature] and Rob Carlson have slightly longer posts about various "meta" bits surrounding the conference. With that, my personal take:

Favourite phrases/words from talks:
- "Cyanobacillus generates ugly cells at low frequencies": from a talk by the author of a paper I've written about before. Apparently, beauty is only cell-deep.
- "Retrosynthetically": I still have no idea what that means, but it sounds cool.
- "Aza-ylide": an intermediate of an apparently well-known reaction [well-known to a segment of the population I am clearly not a part of]. What I liked about this word is its pronunciation: "eza-illid", [where the initial "e" is pronounced like the "a" in "age"] which makes it sound like Snoop Dogg's contribution to science.
- "What we're doing here is preposterous": from David Baltimore's talk about the Grand Challenge in Global Health that he's involved with. This statement referred to the fact that they're trying to do gene therapy, stem cell therapy and immunotherapy all at once, and none of those three therapies has worked [satisfactorily] yet, in any other setting.
- "Counting to 2 in a scaleable manner": one of the "Future challenges" listed in the concluding slide of a talk.
- "Don't laugh, Drew, if you had a pair of silk underwear, you'd be a lot less irritable": [slightly paraphrased] from Chris Voigt's talk about getting Salmonella to secrete spider silk, and why silk is such a wonderful material.


Moment of Zen
-
Craig Venter showing a video [from the Discovery Channel, I think] whose main theme was "Craig is cool. He is travelling around the world in his yacht, collecting seawater and trying to sequence the DNA of critters he finds in it." As entertaining as the idea is, and as much as I'd like to be trawling around the world on a yacht, the video contributed absolutely nothing to the actual scientific content of his talk [as far as I could tell, but maybe I'm missing something]. At first I found it cringe-inducing, as in "Is he really so oblivious that he's showing an ad for himself ?", and then I transitioned to a state of awe at the sheer Zen-master chutzpah of the man.

Moment of "wha' happen ?"
-
Jef Boeke talking about his lab's plans to rebuild chromosome III in yeast, and generating "genome swarms" of lots of yeast strains with different genomes. This is exactly what I was working on doing last year [based on an idea supplied by Drew], as described here and here. I eventually ended up bailing on this project because I couldn't figure out how to generate lots of genome variations via synthesis and/or come up with a good enough reason to ask Drew to spend the money it would have taken to do this project. Boeke has figured out a high-throughput way of generating genome variations, and figuring out what variation has been created, which isn't that surprising, given that:
1. he's been working with yeast since the mid-80's
2. he's published a bunch of papers on large-scale yeast genomics
3. he's an expert in transposon biology, and transposons are one way to generate variation in a genome
4. he's associated with the Hopkins High Throughput Biology Center
In other words, if somebody was going to figure that bit out, he'd be a bad person to bet against. However, he hasn't quite solved the money and "why do this ?" issues: he estimated that it'd take about $10 million over 5 years (!) to do this project, and he didn't really have any more "Wow, that would be so cool/useful !" ideas for what modifications to make to the yeast genome, and why, than I did. He's taking an interesting tack on gathering input, though: he issued an invitation to the yeast community to give him feedback on what sorts of changes they'd like to see made to the yeast genome; one good place to get those kinds of suggestions will probably be the 2006 Yeast Genetics and Molecular Biology meeting.

All that said, I still think it's a really, really cool idea and one I'd love to work on, so I plan to talk to him some more about it and see whether there's room for a collaboration. Of course, the thesis idea that I used to gather my thesis committee has exactly zero to do with this, so that might lead to needing to do some "cabinet reshuffling".

... and that's all, folks.

Addendum: as I mentioned above, one of the speakers was David Baltimore, an insanely accomplished man -- he helped to organize the Asilomar conference on recombinant DNA, is now the president of Caltech, was president of Rockefeller University for a while, helped to found the Whitehead Institute at MIT, and, oh, by the way, won a Nobel Prize when he was 37. I think I can be forgiven, then, for the fact that the [slightly juvenile, granted] thought that kept going through my mind as we stood shoulder-to-shoulder at the urinals in the men's bathroom was "I'm peeing next to a Nobel laureate ! I'm peeing next to a Nobel laureate !". It's not often you get to say that ;-) I considered telling him that I thought he was a pretty cool guy, but that might have been a bit ... awkward, given the circumstances.

Addendum #2: one other thing that struck me was the breadth of biological systems that were talked about, and being used, to build synthetic circuits. The bit that I still don't quite understand is how the folks that described working with multiple different genetic sub-systems from other organisms knew about the existence of these sub-systems in the first place. Did they just do tons of literature searches, hoping to stumble onto something that was appropriate ? Was there a serendipitous conversation with somebody working on something totally different who said "Oh, I've got just the thing you need" ? As we start to think about building more complicated circuits, or circuits with wider functionality, that knowledge of what "parts" are available is going to become more and more important. The Biobricks Registry is an attempt to provide such a parts list, but it requires community contribution to really be useful, and I wonder whether its emphasis on "standardized" parts is going to turn away contributors who don't feel like doing the work necessary to make their genetic circuit standards-compatible. It would be a shame if synthetic biology became as lore-based as much of [experimental] biology is, requiring expert knowledge of the literature, word-of-mouth etc to know what parts are available to build a functioning circuit, instead of having a more systematic way to retrieve this information.

2 Comments:

Blogger Mackenzie said...

Dear Alex, I'm the author of cis-action, and I was hoping you wouldn't mind changing my name to "mackenzie cowell" - Davidson is the school I just came from. Thanks! See you around sometime; we should get together and talk shop over coffee or something. I just moved to Boston earlier this week, and I'll be working in Jim Collins' / Tim Gardern's labs this summer. Thanks!

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