January 07, 2009

Synthesizing biofuels

Carl Zimmer is one of my favorite science writers. And while I was in the Peruvian Amazon over the holidays, I enjoyed reading his book on parasites Parasite Rex. This way, if I managed to pick up malaria while I was there, at least I'd now know what a beautifully well adapted parasite I would have swimming in my veins.

But this post isn't about parasites, or even about Carl Zimmer. It's about hijacking bacteria to do things we humans care about. Zimmer's most recent book Microcosm is about E. coli and the things that scientists have learned about how cells work (and thus all of biology). And one of the things we've learned is how to manipulate E. coli to manufacture proteins or other molecules desired by humans. For science, this kind of reprogramming is incredibly useful and allows a skilled scientist to probe the inner workings of the cell even more deeply. This potential helped the idea gain the label "breakthrough of the year" in the last issue in 2008 of Science magazine.

This idea of engineering bacteria to do useful things for humanity, of course, is not a new one. I first encountered it almost 20 years ago in John Brunner's 1968 novel Stand on Zanzibar in a scene where a secret agent, standing over the inflatable rubber raft he just used to surreptitiously enter a foreign country, empties a vial of bacterium onto the raft that is specially engineering to eat the rubber. As visions of the future go, this kind of vision, in which humans use biology to perform magic-like feats, is in stark contrast to the future envisioned by Isaac Asimov's short stories on robots. Asimov foresaw a world dominated by, basically, advanced mechanical engineering. His robots were made of metal and other inorganic materials and humanity performed magic-like feats by understanding physics and computation.

Which is the more likely future? Both, I'd say, but in some respects, I think there's greater potential in the biological one and there are already people who are making that future a reality. Enter our favorite biological hacker Craig Venter. Zimmer writes in a piece (here) for Yale Environment 360 about Venter's efforts to new apply his interest in reprogramming bacteria in the direction of mass-producing alternative fuels.

The idea is to take ordinary bacteria and their cellular machinery for producing organic molecules (perhaps even simple hydrocarbons), and reprogram or augment them with new metabolic pathways that convert cheap and abundant organic material (sugar, sewage, whatever) into fuel like gasoline or diesel. That is, we would use most of the highly precise and relatively efficient machinery that evolution has produced to accomplish other tasks, and adapt it slightly for human purposes. The ideal result from this kind of technology would be to take photosynthetic organisms, such as algae, and have them suck CO2 and H2O out of the atmosphere to directly produce fuel. (As opposed to use other photosynthetic organisms like corn or sugarcane to produce an intermediate than can be eventually converted into fuel, as is the case for ethanol.) This would essentially use solar power to drive in reverse the chemical reactions that run the internal combustion engine, and would have effectively zero CO2 emissions. In fact, this direct approach to synthesizing biofuels using microbes is exactly what Venter is now doing.

The devil, of course, is in the details. If these microbe-based methods end up being anything like current methods of producing ethanol for fuel, they could end up being worse for the environment than fossil fuels. And there's also some concern about what might happen if these human-altered microbes escaped into the wild (just as there's concern about genetically modified food stocks jumping into wild populations). That being said, I doubt there's much to be worried about on that point. Wild populations have very different evolutionary pressures than domesticated stocks do, and evolution is likely to weed out human-inserted genes unless they're actually useful in the wild. For instance, cows are the product of a long chain of human-guided evolution and are completely dependent on humans for their survival now. If humans were to disappear, cows would not last long in the wild. Similarly, humans have, for a very long time now, already been using genetically-altered microbes to produce something we like, i.e., yogurt, without much danger to wild populations.

From microbe-based synthesis of useful materials, it's a short jump to microbe-mediated degradation of materials. Here, I recall an intriguing story about a high school student's science project that yielded some promising results for evolving (through human-guided selection) a bacteria that eats certain kinds of plastic. Maybe we're not actually that far from realizing certain parts of Brunner's vision for the future. Who knows what reprogramming will let us do next?

posted January 7, 2009 08:19 AM in Global Warming | permalink | Comments (0)

May 25, 2008

On climate change

Sometimes I'm haunted by the feeling that I'm studying the wrong things in life. That while networks, evolution and terrorism are interesting, they're only peripherally related to the central problems that face our generation. That is, sometimes I wish I worked on climate change and, in particular, on sustainable development and carbon-neutral energy sources (like solar cells). Fortunately, there are a lot of people working on this problem, and there's even a climate change summer school this year, run by the Mathematical Sciences Research Institute (MSRI) in Berkeley CA [1]. If you can't make the event, MSRI recently published an online book that gives a good introduction (in relatively accessible terms) to the science, called Mathematics of Climate Change.

It's hard, of course, to really get your head around how big a problem the energy-question is. We all know by now that we should use less oil, that we should buy more fuel efficient cars, that we should have better insulated houses, lower-power refrigerators, etc.; there are lots of shoulds floating around in the media. And then there are the sky-is-falling types, who say that if we don't do all these things immediately, then the planet is going to overheat, the oceans will rise 100 feet, and civilization will be cast 4000 years back to the Stone Age. Fear can be a powerful motivator, but only when it's clear what the right reaction is. Unfortunately, for an average person who wants to have a positive impact, to do their part in saving the world, it's not at all clear what can be done, or even how much urgency is really warranted.

Last week, Prof. Nathan Lewis (CalTech) visited SFI as our colloquium speaker. Lewis has been trying to get his head around just how big the problem of sustainable growth is, and then translate it into understandable terms. I wasn't that thrilled with the style of his presentation, but the content itself was great and the message was rather clear.

First, there's the question of what are the consequences of climate change. If the consequences are small, then maybe it's okay to ignore the whole problem. Unfortunately, the last time we know for a fact that carbon dioxide (CO2) levels were close to what they are approaching now, 90% of all life on the Earth became extinct. This catastrophe happened about 251.4 million years ago (for comparison, dinosaurs died out about 65.5 million years ago), and is called the end-Permian extinction event. To put it in more clear terms how big an extinction this was, it's the only time in all of Earth's history that cockroaches almost became extinct. This is not, of course, to say that 90% of all life on Earth (possibly including us) will become extinct over the next few centuries or millennia because of the increased (and increasing!) CO2 levels we're experiencing, but that we have very little experience with or expectation about what happens when CO2 levels are this high, and the only data point we do have (the end-Permian event) suggests that things could be very bad. So, it might be useful for us to try to avoid venturing into such unknown territory. We only have one planet to experiment with, after all.

So, if we're resolved to avoid end-Permian-like CO2 levels, what can we do? If you think that human-generated CO2 makes no significant contribution to the global CO2 levels, then you don't have many options that don't involve actively extracting CO2 from the atmosphere (e.g., planting lots and lots of trees). On the other hand, if you, like the vast (vast!) majority of climate scientists, think that human-generated CO2 is the main culprit of rising CO2 concentrations (and temperatures), then we have lots of options, since we theoretically have control over how much CO2 we as humans emit [2]. Unfortunately, one of Lewis's points is that, given the scale of the problem we face and how much time we have left to solve it, simply reducing CO2 output is not going to be enough. That is, being green enough to save the planet as we know it is going to require a major reallocation of our civilization's resources; business-as-usual, or even a half-assed attempt, is not going to make a big enough change in atmospheric CO2 concentrations to prevent the planet from being irrevocably changed (heated) for the next 3000 years or more.

To keep CO2 levels from approaching end-Permian levels, we basically have to eliminate almost all CO2 emissions from human industrial activities, everywhere on Earth, within the next 50 years. That's a huge task, especially considering that China recently became the world's largest emitter of CO2, and, along with the US, shows little interest in reducing its emissions. (Scare-tactics go both ways, and the usual argument against doing anything is that it will hurt hurt economic growth, cost jobs, etc. This is ridiculous, of course, since there are huge economic gains to be won by being successful at creating clean, abundant energy.)

Fortunately, there's a good solution at hand: solar energy. Unlike other sources (wind power, tidal power, geothermal power, biofuels, etc.), solar energy is incredibly abundant (1000 times more abundant than wind power), and could satisfy the energy demands of the entire planet using today's technology. Some estimates say that enough sunlight falls on the southeast quarter of New Mexico to power the entire United States. In fact, solar energy is so abundant that covering only something like 1% of the Earth's land with solar panels would give us plentiful power in perpetuity. And, as a bonus, solar power emits basically no carbon dioxide.

The hurdles to a solar-powered future are twofold (there are others, too, but these are the big ones). First, there are the political problem with getting all of civilization to embrace this solution now, rather than in 50 years when it's too late (that is, in 50 years, if we've done nothing significant, CO2 levels will already be at their end-Permian levels). The political climate does seem to be changing a little, but the inertia in the direction of ignoring the problem and burning our way back to the end-Permian is very very strong. The second problem is that energy from the sun is still a lot more expensive than energy from oil and coal, so there's not yet an economic incentive to get behind solar power. For the average citizen, then, there's not much to do that won't cost (possibly a lot) more money, and this severely limits the ability of the populace to use their economic leverage to drive the switch to solar power. This last part is where carbon taxes or a cap-and-trade system can change the balance, by making oil and coal more expensive relative to solar. If these systems can be put in place relatively soon, and the political climate continues to become more favorable to large-scale changes to where we get our energy and how we use it, we may be able to avoid end-Permian-level CO2 concentrations. Plus, if we solve the energy problem (and with it the CO2 problem), there are other important problems (e.g., water, food, etc.) that we will, in principle, also be able to solve. It's a bright future, if only we can find it in ourselves to collectively get there.

Update 27 May 2008: In the comments, "diarmuid" points out that David MacKay, a well known expert on learning algorithms, inference and information theory, comes to basically the same conclusions above about how to solve the energy-climate problem. MacKay has even written a book "Without Hot Air" about it, for those interested in more. (It looks like a draft of the book is available for free download.)

Update 29 May 2009: Bela Nagy tells me that there's another summer school on climate change, with the impressive-sounding name The International Graduate Summer School on Statistics and Climate Modeling. This one is being run at CU-Boulder by the National Center for Atmospheric Research (NCAR) and the Institute for Mathematics Applied to Geosciences (IMAGe). It runs August 9-13, and they'll be accepting applications up until June 15th. The organizers are Stephan Sain (NCAR), Doug Nychka (IMAGe, NCAR), Claudia Tebaldi (NCAR), Caspar Ammann (NCAR), and Bo Li (NCAR and Pudue).

Update 14 June 2008: Carl Zimmer, science writer and author of a number of best-selling popular science books, now also has an essay on the end-Permian extinction and its relationship to the current warming trend, which says much the same thing about the threat life on Earth faces from increased CO2 levels.


[1] Climate Change Summer School July 14th - August 1st, 2008

Organized By: Chris Jones (UNC Chapel Hill), Inez Fung (U.C. Berkeley), Eric Kostelich (Arizona State University), K.K. Tung (U. Washington), and Mary Lou Zeeman (Bowdoin College).

[2] A nice paraphrasing of what the industrial revolution has done to the atmosphere is this: burning coal and oil in our factories and cars has had a similar effect on the atmosphere as if a massive volcano had been erupting continuously, with ever increasing ferocity, for 200 years or so.

posted May 25, 2008 09:24 AM in Global Warming | permalink | Comments (5)

July 31, 2006

Criticizing global warming

Dr. Peter Doran, an antarctic climate resesarcher at UIC, was the author of one of two studies that the polemicists like to use to dispute global warming. Although he's tried to correct the out-of-control spinning on the topic that certain deniers are wont to do, he's been largely unsuccessful. Politics and news, as always, trump both accuracy and honesty. In a recent article for the Amherst Times (apparently pulled mostly from his review of An Inconvenient Truth, which he gives "two frozen thumbs up"), he discusses this problem, and the facts. From the original:

...back to our Antarctic climate story, we indeed stated that a majority -- 58 percent -- of the continent cooled between 1966 and 2000, but let’s not forget the remainder was warming. One region, the Antarctic Peninsula, warmed at orders of magnitude more than the global average. Our paper did not predict the future and did not make any comment on climate anywhere else on Earth except to say, in our very first sentence, that the Earth’s average air temperature increased by 0.06 degrees Celsius per decade in the 20th century.

New models created since our paper was published have suggested a link between the lack of significant warming in Antarctica to the human-induced ozone hole over the continent. Besides providing a protective layer over the Earth, ozone is a greenhouse gas. The models now suggest that as the ozone hole heals, thanks to world-wide bans on harmful CFCs, aerosols, and other airborne particles, Antarctica should begin to fall in line and warm up with the rest of the planet. These models are conspicuously missing from climate skeptic literature. Also missing is the fact that there has been some debate in the science community over our results. We continue to stand by the results for the period analyzed, but an unbiased coverage would acknowledge the differences of opinion.

Tip to onegoodmove.

posted July 31, 2006 04:18 PM in Global Warming | permalink | Comments (0)

June 25, 2006

An Inconvenient Truth

Tip to onegoodmove.

posted June 25, 2006 02:28 PM in Global Warming | permalink | Comments (0)