First Chantry Flats S24O

Michelle and I went on our first S24O (sub-24hr overnight) bike trip last weekend, up in the San Gabriel mountains, above Chantry Flats on fire roads.  Despite some ill-timed road maintenance in Santa Anita Canyon, everything went wonderfully.  We got checked out by a fox near the ranger station for like half an hour, as little as 6 feet away, and had a beautiful full moon ride all alone the whole way.  Our dynamo powered headlights were plenty bright too, even for the dirt road, which I’d been worried about.  Read the full post for photos (and my first attempt at embedding a Flickr set in a post…)

Room With a View

Continue reading First Chantry Flats S24O

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

Shared Links for May 12th

  • Forecast: On Climate Change, Cooler Temperatures Bring Hotter Air – Augh, we are prisoners to so many perceptual fallacies. Recency and narration loom large among them. It turns out that the average temperature of the last 12 months is a reasonably strong predictor of whether or not people think they'll personally experience the effects of climate change (a multi-decade to century-scale process). We are failing to deal with problems we didn't evolve to perceive clearly. (tagged: climate statistics fallacy propaganda science )
  • In German Suburb, Life Goes On Without Cars – Ah, the New York Times has discovered Vauban! Now if only it had happened when gas was $4/gallon, we might have had a chance. We desperately need more experimentation in urban design, so we can have working examples to look at and build on. (tagged: sustainability green urban design bicycles germany transportation parking architecture )
  • Spuds in a Box – Build a box whose sides you can progressively remove from the bottom up, plant potatoes in the bottom, and fill with dirt as they grow. Remove lower slats to harvest spuds. I've certainly heard this suggestion from other people too. Will be interesting to see how well it works for these guys. Seems like you could also do this with some kind of bag, and if you sewed in sleeves/tubes periodically, that you could tie off, and then untie when you wanted to reach in and root around for a spud, you wouldn't have to worry about soil falling out when you pry off the boards. Others are supposedly reporting 50kg of potatoes from 0.5 m^2 area. (tagged: gardening green sustainability agriculture food urban design potatoes )
  • How Much Do You Earn? – A great annotated visualization of income distribution in the US as of the year 2000. It would be awesome to see an animated version of this, and see how it evolves through time. Turns out I make just about the most likely income in America ($20k), which is far below the mean (and the median). As a "household" though, I suppose we're right about at the median ($40k). Interesting. (tagged: economics wealth taxes government policy visualization )
  • The Capitalist Threat – Geoge Soros on Karl Popper's Open Society, from the mid-90s. He rails against the West's failure to extend a helping hand to the post-Soviet nations. He acknowledges that Truth may not be a strong enough motivator for most people, and that within a society that has decided to be Open, there are still many other choices to be made, but somehow fails to mention the way these two things end up pushing an Open Society closed with propaganda, apathy, and misinformation. Political evangelism – the process of deciding what (arbitrary) values your society is going to have – creates huge incentives for those who do not highly value truth to assert authority. I guess that's part of his point though, to robustly inoculate society against those assertions of perfect (authoritarian) knowledge. (tagged: economics politics popper society philosophy )

Shared Links for May 11th

  • Where can you get Cheap Natural Fertilizers and Soil Amendments? – A nice concise list of natural sources for garden nutrients, when your compost pile just isn't quite enough. (tagged: gardening food organic fertlizer compost biology )
  • Pinko bastion spawns capitalist solution to solar financing – Boulder city/county passed the same kind of property-tax based financing of energy efficiency (and solar) improvements on the Nov. ballot too – modeled on Berkeley, but with enabling legislation at the state level (to avoid the kind of lawsuit Berkeley had to fight over whether or not they had the power to issue such bonds). The biggest worry I had in reading the Boulder initiative though, was that they had not yet come up with a good mechanism for ensuring that the improvements which were being proposed (more insulation, solar hot water, whatever) would necessarily save enough energy in order to justify the value of the bond being created. Hopefully they’ve fleshed that metric of value out much better by now (in both Boulder and Berkeley) and it’s not possible to abuse it… otherwise I suspect you’ll get deployment of faddish fixes (e.g. sexy-sexy PV instead of solar hot water, or better insulation, or super-windows, etc) instead of the best energy improvement per dollar invested. (tagged: finance capitalism investing energy efficiency sustainability green solar berkeley boulder bonds )
  • Campaign for a Car-Free Lincoln Park, Pt. 2 – A lack of car-free options for arriving at Lincoln Park, coupled with poorly lit, unsafe parking far away from the park's main attraction means everyone just drives their cars all over the park, on the grass. Across the street, the DMV has a huge parking lot which is totally unused after business hours, which is when the park gets the overwhelming majority of its use. Why not (gasp!) timeshare the DMV lot? Hopefully no small children have to get crushed by the marauding death machines for someone in the state and city government to take this idea seriously. (tagged: cars parking transportation urban planning design )
  • FlyingConcrete – Beautiful biomimetic architecture. Curving vaulted ceilings and stairways. Rounded sleeping nooks and pillars like trees. Traditional rectilinear construction is so boring. This is lightweight concrete (cement with perlite, pumice, and other lightweight filler added instead of sand and gravel) laid up on a mesh that's been shaped such that when the cement hardens, it's a load bearing compressive structure. (tagged: architecture art concrete design construction buildings sculpture )
  • Drew Endy and Jim Thomas Debate Synthetic Biology – An unusually good discussion about the future of biotechnology, and maybe the only time I've ever really seen the "debate" format work, and elicit relatively thoughtful interaction. I think they're both dancing around the fundamental question though, of to what extent (if any) society even *gets* to make a choice on this topic. (tagged: biology biotech genetics technology science future debate longnow engineering )

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 )

A Letter to Richard Rhodes

Dear Richard Rhodes,

Thank you for writing The Making of the Atomic Bomb.  It was beautiful, and terrible, in the way I imagine a nuclear detonation might be.  It deeply changed the way I think and feel about history, about technology, and about the role and limitations of human volition and foresight in the making and potential unmaking of our world.  Somehow you made these people human, and independent of the roles they played.  You made the science beautiful, and the history engaging.  Given that books like yours exist, I am appalled that I was not required to read them in the course of my scientific education, and instead have had to stumble across them on my own.  I think science and engineering students deserve to have some understanding of the potential scope and consequence of our work, for better or for worse, before we are turned loose on the world.  Too often the ethical and philosophical impacts of technology are left completely unaddressed, or even shunned as irrelevant by scientists, until after the effects are widespread.  I doubt this kind of education would have much substantive impact on the overall course of history, or technological development, but I once attended a talk at Caltech by Hans Bethe on the Manhattan Project, and even after half a century he broke down into tears on stage.  He said he didn’t regret having helped create the bomb — that it had to be done — but that he felt guilty for having enjoyed it.  I would prefer that we were better prepared for the possibility of bearing that kind of responsibility, and for taking it on knowingly, as I think Oppenheimer and Rabi did, instead of only realizing our roles after the fact.

Continue reading A Letter to Richard Rhodes

Reading Afghanistan

I’ve been doing some reading on Afghanistan.  I am so glad I wasn’t born there.  I’m going to read more, but ugh, I need a break.

The first book I read was A Thousand Splendid Suns, by Khaleed Hosseini, who also wrote The Kite Runner.  It reminded me a little bit of One Hundred Years of Solitude.  It’s intergenerational, it’s about a community, and it’s discontinuous – there are large spaces in time between the salient events which are conveyed.  The style is also a little bit like the magical realism of Garcia Marquez, except that all the events really happened, and what makes them seem magical is how surreal they are.  How surreal and awful.

Continue reading Reading Afghanistan

Shared Links for Apr 30th

  • Transparency means nothing without justice – Government transparency is necessary, but not sufficient. If police violence is recorded and publicized, and nobody cares, it doesn't matter. This is in come sense emblematic of the coup in western propaganda. You don't need to control the media as the Soviets did or the Chinese do, if your population is comfortable enough not to care what's happening out there to someone else, and if their voting patterns are firmly tied to other issues (especially social issues like abortion), the idea of a democratic revolt becomes fairly abstract. I think this where a lot of the government's fear of economic recessions comes from. When people are out of work, or even hungry, suddenly they become a lot more excitable. (tagged: transparency law police politics technology internet )
  • Condensing steam without water – Concentrating solar thermal power stations are ultimately designed to run a steam turbine, just like a gas-fired power plant. That means they need water (to turn into steam). Problematically, most such plants use water as a condensing coolant (70% of Caltech's water usage is as coolant for our 14MW worth of gas-fired power)… which is going to be hard to come by in the desert, where CSP will be built. Thankfully, there's a way to recondense steam without using a water coolant – but it does require a huge cooling tower. Not so great in Pasadena, but probably fine in the Mojave, next to acres and acres of mirrors. (tagged: solar energy technology sustainability green electricity water )
  • Rousing a Latent Defense Mechanism to Fight HIV – It turns out there is a gene in humans that produces a protein which inhibits infection by HIV, but it has a mutation – a premature stop codon – which prevents it from being effectively synthesized. This mutation doesn't exist in most Old World monkeys (and that's apparently why they can't get HIV). Undoing the mutation allows the protein to be synthesized, and grants HIV immunity to human cells. I imagine that undoing bad mutations like this, and our inability to synthesize vitamin C, might be the first place we see human germ-line engineering outside of disease avoidance (preventing e.g. cystic fibrosis). Really, these mutations are hard to distinguish from genetic diseases – they're just diseases that we, as a species, have learned to live with. (tagged: genetic engineering hiv aids biology science research plos medicine )
  • Anna in the Middle East – Anna Baltzer is a Jewish American who got a Fulbright fellowship to live in the West Bank in 2005, and document the experiences of Palestinians. She's been giving presentations about it ever since. Some parts of her presentation are available via YouTube too. From the 15 minutes I watched she seemed like a level headed critic. She's speaking in Boulder and Denver in May. (tagged: israel palestine politics fulbright peace war )
  • Twitter + Stimulus = Humans are Gullible – A wonderful demonstration of the power of the confirmatory bias. Twitter is the perfect platform for the injection of random falsehoods. Too short for citations. Instantaneous distribution. Make sure your followers are predisposed to agree with what you say, and you can get them to believe just about anything – within that constraint. Too bad the author seems to think this only applies to conservatives. (tagged: politics twitter statistics propaganda )

Support AB 1186 for transparent parking costs

Dear Assemblymember Portantino,

I would like to urge you to support AB 1186, an effort to enhance the transparency of parking costs for easing the enforcement of California’s parking cash-out legislation.  This bill has been introduced by Assemblymember Bob Blumenfield (District 40), and is due for a hearing in the Assembly Transportation Committee on May 11th.  The cost of parking is enormous, generally hidden, and heavily subsidized, producing significant distortions in the transportation choices made by Californians.  Making the price of parking transparent, and enabling those who choose not to drive to recoup those costs, removing the hidden subsidies, is in the best interest of business, transit authorities, the citizens, and California in general.  For instance, at my own institution in Pasadena, the California Institute of Technology, we are forced by city regulations to provide what would constitute a vast oversupply of parking were employees and students required to pay the true price of providing those spaces, wasting $3 million each year (approximately $1000 per person on the campus), that could be better spent on our core scientific research and education mission.  While this bill unfortunately would not directly address this waste, it is a step in the right direction, and I strongly encourage you to consider other such steps.

Sincerely,

Zane Selvans