Genes are sentences and genomes books

It’s really a pleasure to talk to smart people who don’t have any idea what you’re talking about.  I think it forces you to come up with the best analogies and metaphors.  The most essential explanations.  It turned out that Sally read my post on watching the Long Now synthetic biology debate, and so she went and watched it too.  We talked about it on and off over a walk today, and I ended up making this analogy, which I liked a lot.

Every gene is like a sentence.  It’s the smallest unit of biology that expresses a meaningful biological idea, in the same way that it’s hard to say something interesting without constructing a whole sentence.  Of course, more complex ideas require many sentences to convey, and similarly, metabolic pathways require many genes to encode.  A genome is like a whole book, conveying a large system of interconnected biological ideas into a coherent entity.

Synthetic biology is the business, or art, of writing new biological books, using only sentences that you copied from somewhere else.  It’s as if you were given the complete works of Shakespeare, and told to write a new play, using only his own lines, but reorganized however you saw fit.  With a big enough library of books, it would be possible to pick and choose sentences, paragraphs, or entire sections or chapters, to convey pretty much any idea of your own, in someone else’s words, especially if your idea had anything to do with love, or loss, or war, or the human condition in general.  As it is now, we’re just making variations on a theme, inserting whole chapters from Moby Dick into some tract by Nietzsche or a poem by Lao Tze, but we’ll get more subtle and creative as time goes on.

Continue reading Genes are sentences and genomes books

How inevitable is synthetic biology?

I love watching talks and seminars online.  It is in so many ways superior to watching them in person.  You can pause the talk to discuss it with your friends out loud, or to look something up online.  You can skip the boring introduction.  You can stop watching the talk if it’s lame, and try another one, and keep trying until you find a good one.  Maybe best of all, there are vastly more talks available online than even at a large and diverse institution.  The one plausible weakness is the lack of interactivity – you can’t ask questions.  But it turns out that the Q&A part of most public talks (and even departmental colloquia) kind of suck.  You can mitigate this weakness by watching the talk with other people who are thoughtful and intelligent, and talking to them about it during and after.

Rene, Michelle and I sat down last night and watched this excellent debate between Drew Endy from Stanford/MIT and Jim Thomas, put on by The Long Now Foundation.  The formal presentation/debate portion is an hour long, and is followed by another hour of discussion.  Endy is in favor of an open source type model for synthetic biology, with the technology being available to basically anyone.  Thomas thinks it should be controlled, and kept out of the hands of potentially dangerous actors: the military, the corporate oligarchy, etc.  Their positions are of course more subtle and well thought out than that, but you can only fit so much into a nutshell.

Continue reading How inevitable is synthetic biology?

Shared Links for May 5th

  • How David Beats Goliath – When the rules are stacked against you, the intelligent thing to do is break them. (tagged: strategy law war insurgency guerilla gametheory basketball lawrenceofarabia )
  • Continuous bankruptcy – Bankruptcy as it stands now is a discontinuous process. Your legal solvency is binary: either you are bankrupt, or you are not. It doesn't have to be that way, and I think you can make a good argument that it's better if it isn't. Continuous processes work themselves out in small steps, with lots of information flow along the way. Discontinuous ones are like explosions. It's easier to muster resistance to an explosion once you see it coming, and delay it. But how much better to start getting signals early on, and avert it altogether? (tagged: finance policy economics bailout banks bankruptcy discrete continuous )
  • Digital Recovery of Moon Images – Ahh, NASA. Your data management has improved over the years, but that's not saying much. 20 tons of magnetic tape in an abandoned McDonalds houses the only extant copy of the pre-Apollo analog imaging of the Moon (still the highest resolution available in most places). It can only be read by one machine on Earth, which was recently rescued from a chicken coop, and refurbished by a man who is about to die. You can't make this stuff up. (tagged: information technology space nasa archive data moon )
  • Will the Future Be Geo-Engineered? – The future is already geo-engineered, and has been ever since we started burning coal on a large scale more than 200 years ago. The question now is whether we back off, and try to let the system return to the quasi-equilibrium that allowed our civilization to arise, or introduce new and exciting perturbations, with completely unpredictable non-linear effects. I know which one I'm hoping for. (tagged: geoengineering technology non-linear climate policy environment )
  • Hacking Scalia – Law professor gives class an assignment to dig up as much "private" info as possible on Justice Scalia, a notable anti-privacy force on the SCOTUS. This irritates Scalia. Exactly! (tagged: law privacy scalia scotus )
  • No new coal: what real direct action looks like – The $10 million spent on violently policing the "climate camp" protest outside Kingsnorth is absurd, given that a single motivated saboteur, capable of advance planning and actually willing to risk arrest and injury, can walk into the power plant and shut down 500MW of coal fired power generation. If governments fail to deal with greenhouse gas emissions effectively, and remain in thrall to the carbon lobbies, it seems likely that soon this kind of action will become more common, and truly disruptive. All it takes is a few thousand people who actually care, and our infrastructure can be brought to its knees. (tagged: energy environment green coal climate protest kingsnorth directaction )

Shared Links for Mar 6th

Shared Links for Feb 28th

The Edge’s Annual Question for 2009

From the Edge, and their annual “World Question Center” for 2009.

What will change everything?  What game changing scientific ideas and developments do you expect to live to see?

Many thoughtful answers, including a particularly good one about climate, likening potential abrupt state changes to unpredictably soundly sleeping giants that we do not want to awaken:

Unfortunately, we are discovering more giants that are probably lighter sleepers than the thermohaline circulation (THC). Seven others — all of them potential game-changers — are now under scrutiny: (1) the disappearance of summer sea-ice over the Arctic Ocean, (2) increased melting and glacier flow of the Greenland ice sheet, (3) “unsticking” of the frozen West Antarctic Ice Sheet from its bed, (4) rapid die-back of Amazon forests, (5) disruption of the Indian Monsoon, (6) release of methane, an even more potent greenhouse gas than carbon dioxide, from thawing frozen soils, and (7) a shift to a permanent El Niño-like state. Like the THC, should any of these occur there would be profound ramifications — like our food production, the extinction and expansion of species, and the inundation of coastal cities.

We’re wallowing in the fat tails.

Wall Street’s Game of Risk

A relatively thoughtful piece from The New York Times Magazine on the risk metrics used by Wall Street, especially the now notorious Value at Risk (VaR).  However, it still seems like neither the author nor the risk managers they interviewed really get what Taleb is saying.  Or possibly they’re just not willing to admit the implications of what he’s saying: that market outcomes, especially when investing is focused on the short term, are dominated by so-called “rare” events.  And that the consequence (as one of the managers even says outright), is that a lot of the investment banks don’t really have a business model.

Except, of course, for the fact that they can count on the public coffers if they all arrange to go bankrupt simultaneously.  Better, in this case, to fail in a conventional way along with everyone else, and be bailed out, than to play your own game for the long term, like Warren Buffet, and either succeed unconventionally, or have to take responsibility for your own failures, which are then likely not to take place at the same time industry wide.

We’re playing the same game of fat-tails chicken with Earth’s climate, and that story will eventually have the same ending if we are unable to generalize the lessons of this relatively innocuous financial disaster.

We need more Dionysian Science

Michelle and I just finished reading The Botany of Desire by Michael Pollan. It was good. He can get a little rambling at times, but overall it was entertaining and enjoyable. The book follows the relationships between people and four plants, through history. The four plants are: apples, tulips, cannabis, and potatoes. It pairs with them four desires, respectively: sweetness, beauty, intoxication, and control. The connections are more than a little tenuous, but the histories are certainly worth examining. The apple chapter in particular has inspired me to learn more about hard cider (since it turns out that’s largely what Johnny “Appleseed” Chapman’s apples were used for, all across 19th century America). And who can resist an examination of cannabis’s relationship with humans, written at least partially while stoned?

One theme Pollan has touched on repeatedly, in this book and his others, is the competition between Apollonian and Dionysian impulses in nature and society. Apollo representing order and control, Dionysus wildness and chaos, both being utterly necessary for civilization to be dynamic and persistent, for knowledge to increase and broaden through time. E.g. our Apollonian monocultures of Russet Burbank potatoes are vulnerable because of their uniformity, but are also productive and economically efficient. The Andean potato farmers of antiquity grew dozens of different varieties in different micro climates, all the while allowing the plants to hybridize with the local wild potatoes, maintaining a possibly less productive, but certainly more diverse and robust system of potato cultivation, in which new biological innovation was constantly taking place, and in which the farmers were well protected against catastrophic collapse in any one year… unlike the potato farmers of Ireland in the 1840s. The potato chapter in particular focuses largely on a very recent interaction with the potato: the introduction of a genetically engineered variety called the “New Leaf” by Monsanto, that produces Bt toxin to guard the plant against the Colorado potato beetle and other insect pests. Continue reading We need more Dionysian Science

The Two Mile Time Machine by Richard B. Alley

I just finished reading Richard Alley’s little book The Two Mile Time Machine. It’s by far the best climate change book I’ve read so far. More information, less polemic. Personally I would have loved more plots and fewer long complex sentences explaining the relationships between different climatic variables, but maybe that’s just because I’m a scientist. Continue reading The Two Mile Time Machine by Richard B. Alley

Freeman Dyson on Climate

The futurist and physicist Freeman Dyson wrote a piece for the New York Review of Books on Climate Change. He’s a very (very) bright guy, but I think he is wrong. Actually, I think that the whole framing of the climate issue in the media, in the government, and possibly in many scientific circles, is wrong. Continue reading Freeman Dyson on Climate