Last night I was invited to a Seed dinner in Cambridge. The idea, I guess, was to throw together scientists from various disciplines and Seed contributors, and observe the resulting chemical reaction.
I had very interesting discussions with Drew Endy of MIT who is developing a molecular tool kit to engineer prokaryotes. Engineer? Well the idea is to reprogram bacteria to perform simple tasks such as turning on and off the production of fluorescent proteins over a regular time interval. These blinking bacteria are just the tip of the iceberg. Endy and others (such as Pam Silver) want to have bacteria and yeast that can count and do other nifty tricks. The programming language for these algorithms is a set of transcription factors and DNA elements. For now, the idea is to standardize the set of tools and get several groups from various institutions to use the tool kit to develop their own genetic algorithms. To get an idea about what Synthetic Biology is all about, here is a good place to start, also visit the Registry of Standard Biological Parts at MIT.
Another notable discussion was ... (more below the fold)
between Max Tegmark, Angelica de Oliveira-Costa, Irene Pepperberg and Dan Gilbert, two cosmologists, and two researchers of the mind (experimental psychologists, cognitive scientists? not sure what really applies, but you get the idea.) They were engaged in a lighthearted discussion on the idea of complexity - how to quantify complexity. To give you a flavor of the ideas floating around - What is inherently more complex, the universe, an organism, or the human mind? Interestingly the cosmologists pitched that life contains much more complexity than the universe (excluding the life that's in it), while the psychologists argued from the reverse position.
My thoughts on this? Perhaps we could use our current ability to use reductionalism as a metric for complexity. Now let me try to apply this without falling flat on my face. As we use reductionalism to deduce the workings of the universe we hit a barrier where reductionalism fails us, this barrier is at the sub atomic level - at Quantum Mechanics. Sure there are problems such as dark mass and dark energy, but much of our ignorance is contained with the primary properties of matter. Yes there are caveats ... like the recent discovery of geysers on Enceladus, but once these phenomena are discovered, my guess is that they are totally comprehensible using our own knowledge. As for life, reductionalism fails us (currently) at the cellular level. How and why cells behave the way they do is mostly a mystery. However I do believe that we can begin to understand what the basic mechanisms will be: protein interactions, molecular motors, gene control ... the details are not fully understood, and there are many surprises (like RNAi) waiting for us, but we can start to see how it's going to work. Then there is the mind. Now there we have close to nothing. We know it's complex, we understand some of the basic principles that must underlie sensory perception, memory etc. but how our neuronal connections induce various mental functions is way beyond us. And we don't even know how to approach some concepts such as consciousness ... so I think that the mind wins.
Another notable discussion was initiated when Jonah Lehrer from Seed was asked about what he thought was the most fascinating story that he had encountered in the past year. Neurogenesis. To find out more, read his article. Dan Gilbert explained that stress came in two forms: a positive stress that challenges us and that may enhance neurogenessis, and a negative stress (think despair) that actually inhibits neurogenesis. Animals in cages are under heavy negative stress, and as Gilbert explained "that's why no one ever observed neurogenesis in the lab."
Also another curious factoid: the number of former Montrealers in the crowd. According to one of the magazine's staff, Seed was conceived in Montreal. And as a former Montrealer, I'm not that surprised. The city is a haven for intellectual discussion, counter-culture thinking and a refuge from anti-intellectualism that is rampant in many sections of the American public forum. That's why many radical ideas are hatched in Montreal. The one problem with my hometown, is the lack of financial capital to keep us there. But who knows, some of us may go back one day.
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"geizers on Enceladus"???
Is that where old astronomers go to die?
You're spot on about Montreal. I'm not from here, but came for a postdoc at McGill. I doubt I'll stay here (way too cold for a Texas boy) but the intellectual atmosphere here is beyond compare -- and the effects it has had on my scientific growth are immeasurable. In terms of financial capital for biotech, it may pale in comparison to California and/or New England, but compared to the big cities of the midwest it seems to me that it is far superior. Perhaps if Quebec would finally seperate all the language silliness that seems to scare off investment would cease and finacial capital would catch up to intellectual capital. Just a thought...
Sorry about that typo - I'll fix it up.
Sounds like a stimulating evening! Thanks for the link to Lehrer's article, re: Gould, Duman et alia's research pertaining to neurogenesis. Interestingly, there are indications that treatment with lamotrigine (an anticonvulsant/mood stabilizer which modulates various ion channels) restores cognitive function in patients with bipolar disorder. Apparently, this doesn't happen overnight, and like treatment of major depression by serotinergic agents, takes time. So a neurotropic factor, and neurogenesis, may very well come into play.
But more importantly, where did you dine?
Oleana
http://bostonchefs.com/clients/Oleana/rest_page/index.html
Eastern mediterranean (Turkish, Syrian, Northern African). I had the venison with a pomegranate sauce. Excellent.
Gah. In my opinion, the systems biology types, especially at MIT, are just naive when it comes to the problems of your typical bench biologist. A standarized parts registry is great, but when ligation reactions at the bench fail more than half the time anyway, sometimes you have to wonder what the point is.
Some of the circuits they've made are also conceptually fascinating, but again, what's the point? It's a cool engineering tool, but the focus of biology at the moment is definitely more compreshension than engineering. Maybe someday, though...
I am olive green with envy. There's a dearth of decent restaurants in Princeton.
dlamming,
It's interesting that you mention Systems, Endy was into modeling untill about 5 years ago (or so he told me) but did not see where it was heading. What he's trying to do now is what we would call Synthetic Biology. The difference - Systems is trying to understand what is there in to-to (as Marc Kirschner wrote in Cell), while Synthetic Biology is trying to engineer what is not there, such as a cell that can count.
As for the DNA, Endy got a company to manufacture the DNA for free. All his students have to do is design the "circuit" get the DNA from the company and test whether the bugs behave as they would predict. Now not every tool in the toolkit is reliable, but it's trial and error. The better tools will get used more often and the less reliable ones will be modified or discarded.
You have to admit that the whole thing is worth a try.
"Also another curious factoid: the number of former Montrealers in the crowd. "
Like who? Or are all you Canadians undercover spies giving echother hand signals/joints? And do the joints have anything to do with radical ideas? I wonder.
If you're referring to Montreal exiles at the dinner - well at least two members of the Seed staff, myself and Steven Pinker (I had heard that he was a Montrealer and he confirmed it). Now if you are referring to radicals well that list can go on. There is Leonard Cohen, Pierre Trudeau (probably the most charismatic politician ... ever), Nick Auf der Maur (and his now famous daughter), the rock band Godspeed You Black Emperor, Robert Lepage (he may not be from Montreal), Michel Tremblay, Vitorio Rossi, Mordecai Richler, Annie Proulx (don't think she was born ther), Guy Lalibert (founder of Cirque du Solei), Alain Simard (founder of the JazzFest), Rufus Wainwright, William Shatner, the FLQ ... come to think of it Toronto has lots of radicals too, but I'll save that for another time.