Has crop ethanol met its Waterloo?

It should be obvious by now that I think today's is one of the best issues of Science in recent memory. This will be my last post out of this issue, but even these three posts don't come close to covering everything in there that I think is cool. If you don't work at an institution that has a subscription, you could do a lot worse for your brain than buying a copy online or at a newsstand or bookstore. So to wrap up my blogging on this one, I'll cover some papers that support my extreme distaste for biofuel mania, especially with respect to food crops such as corn and soybeans. A pair of articles today find that using food crops for ethanol is even worse in terms of carbon balance than continuing to use fossil fuels.

My regular readers will no doubt be aware that I positively loathe the idea of using corn for ethanol, and am somewhat dubious of the benefits of using even cellulosic ethanol as a biofuel. These are at best stopgaps on the way to fully clean energy sources, do not in general remove a great deal of carbon from the atmosphere, and may have significant adverse effects on the environment and carbon balance. So you should consider this post in light of the significant potential for confirmation bias. That said, these papers seemingly end the debate on the carbon balance benefits of corn or soybean ethanol, and raise serious questions about the benefit of any form of monoculture intended to replace petroleum, especially if they take over cropland or forest.

The fundamental problem with previous models of greenhouse gas reductions due to biofuels, according to the authors of these papers, is that they do not take into account the carbon debt incurred by altered land use. For instance, clearing land to allow the planting of biofuel monocultures has the effect of releasing all or almost all of the carbon presently fixed in plants in those areas (1). Moreover, forward-looking economic models were not previously employed to judge the likely effects of shifting food crops into fuel production. For instance, the increased cost of corn might induce clear-cutting intended to free up more cropland to grow the now more-profitable food crop (2).

What happens when you start taking those "carbon costs" into account? Searchinger et al. find that corn ethanol doubles greenhouse emissions versus petroleum over a period of 30 years and doesn't break even for 167 years. Fargione et al. predict that it takes 48-93 years, depending on what kind of source land is used, before corn ethanol pays back its carbon debt. And it's not even the worst: biodiesel derived from lands that used to be rainforest take more than 250 years to balance the carbon sheet, on average. Even cellulosic energy sources, if they are grown on viable cropland, produce more greenhouse gases over the next 30 years than petroleum does (2).

So, are we totally screwed? Not exactly. Both papers suggest that cellulosic sources grown on marginal croplands or prairie, or derived from existing biomass waste (i.e. inedible cornstalks) still end up on the right side of the carbon balance sheet. This is consistent with estimates from a study I discussed previously.

The ideal response to both global warming and oil dependence is to depress petroleum usage (by increasing fuel mileage and encouraging public transit) while transitioning to a completely green transportation system that doesn't rely on combustion at all. Stretching out oil and growing forests is the best option for slowing emissions short term, and does not require an additional construction of infrastructure to produce and distribute ethanol. If biofuels are unavoidable, however, then they should be derived from non-food crops grown on marginal land if at all possible.

It's still not clear that biofuels can replace petroleum, so they may not help us as much as we'd like. However, if they are not to hurt us, we must make sure that we make wise choices about what kinds of sources to use and where to grow them. The best evidence now conclusively indicates that ethanol from corn and soybeans (except for cellulosic derived from their spare biomass) is not the way.

1. Fargione, J., Hill, J., Tilman, D., Polasky, S., Hawthorne, P. (2008). Land Clearing and the Biofuel Carbon Debt. Science, 319(5867), 1235-1238. DOI: 10.1126/science.1152747

2. Searchinger, T., Heimlich, R., Houghton, R.A., Dong, F., Elobeid, A., Fabiosa, J., Tokgoz, S., Hayes, D., Yu, T. (2008). Use of U.S. Croplands for Biofuels Increases Greenhouse Gases Through Emissions from Land-Use Change. Science, 319(5867), 1238-1240. DOI: 10.1126/science.1151861

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Venter Institute synthesizes a bacterial genome

Continuing the banner day, Daniel G. Gibson and colleagues have published a rather subdued article in Science. In this truly impressive experiment, a group from the J. Craig Venter Institute synthesized and assembled an entire 583 kilobase-pair genome of Mycoplasma genitalium (1). Besides being a fairly cool piece of work all on its own, this outcome has profound implications for the future of bacterial research and the development of custom organisms

The stated purpose of the research is to investigate M. genitalium itself, which has the convenient property of possessing a very small genome. As the authors note (emphasis mine):

Approximately 100 of its 485 protein-coding genes are nonessential... it is not known which of these 100 genes are simultaneously dispensable. We proposed that one approach to this question would be to produce reduced genomes by chemical synthesis...

One might reasonably conclude from this passage that JCVI has a dearth of small thinkers: this is akin to proposing to light your yard by shifting the position of the moon.

Yet Gibson et al. pulled it off using a tiered assembly method. They synthesized 101 overlapping pieces of DNA ~6 kb long. Using in vitro recombination they assembled groups of these into 24 kb fragments and propagated them using bacterial artificial chromosomes. Using a similar strategy they managed to continue assembling fragments up to about 144 kb in size; beyond this, however, the in vitro method did not work. So they turned to the yeast Saccharomyces cerevisiae to assemble the larger "C" fragments into half-genome and even whole-genome constructs. They then checked the whole genome for errors using the famous "shotgun" approach. Amazingly, their first run produced only two errors, both human in origin. After some wrangling they ironed it all out and ended up with precisely the genome they wanted, complete with special "watermarks".

So they managed to construct an enormous hunk of DNA. What's the benefit? Well, they can do those crazy experiments that they're planning, for one thing. For another, assuming they can figure out how a mycoplasma works, they can design a new mycoplasma that does something special. For instance, they could design a new genome containing genes that allow the bacterium to eat toxic materials, or purify uranium out of the soil, or turn biomass into octane.

Granted, it is possible to get some of these genes into a bacterium using plasmids or BACs. However, what goes in can also go out—ejecting a plasmid is relatively easy, especially if it doesn't provide any selective advantage. Completely ejecting a genomic cassette, while possible, is much more rare. Moreover, if you can custom-design the genome, then the custom enzymes can be interspersed with essential genes, making deletion that much more unlikely. Thus, once the genome can be manipulated at will, the only limitation on what an organism can be made to do is the extent of our ability to find or design proteins that fulfill the desired function. Figuring out which of a hundred-odd genes from M. genitalium can be done away with is just an efficiency step to make space for new genes to do whatever we want.

This approach will be a powerful tool for other experiments as well, don't get me wrong. For instance, you could use the approach to place custom tags around certain genes so that they get excised at particular times or in a conditional manner, or you could swap sequences around to get a better idea how important gene arrangement is. But there's no denying the enormous advance that this success makes possible, despite the authors' decision not to speculate in the paper. The genome-synthesis technique is an essential step in the construction of a completely custom organism.

1. Gibson, D.G., Benders, G.A., Andrews-Pfannkoch, C., Denisova, E.A., Baden-Tillson, H., Zaveri, J., Stockwell, T.B., Brownley, A., Thomas, D.W., Algire, M.A., Merryman, C., Young, L., Noskov, V.N., Glass, J.I., Venter, J.C., Hutchison, C.A., Smith, H.O. (2008). Complete Chemical Synthesis, Assembly, and Cloning of a Mycoplasma genitalium Genome. Science, 319(5867), 1215-1220. DOI: 10.1126/science.1151721

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The Arty Party of Games

So, now that we've had a little fun with serious science, let's have a little serious discussion about fun. Gamasutra has two excellent features up about the relationship between games and art, and I think both of them have merit. EA producer Jim Preston's feature, "The Arty Party" prompted an impassioned response from E. Daniel Arey about "The Art of Games". Jim Preston has a really good comment on Arey's piece, and of course Arey's is a really good response to some of the limitations of Preston's article. Both pieces have merit, and I highly recommend reading both of them if you have the time.

Preston's article is primarily an indictment of arguments over whether games are art or not. He points out that often what defines art for people is context: the best violinist in the world playing the best violin music ever written may not be taken for an artist if he is pursuing this activity in a subway station. In this regard, the real criterion by which one can judge whether some object is art is whether people believe it is art. Consequently, Preston doesn't believe that engaging people like Ebert in a debate over whether games are art is worthwhile. This speaks to my own prejudices; as I have mentioned before, I think the best way for enthusiasts to regard this question is to treat the debate as won and start talking about and judging games as works of art. The earnest and articulate belief in games as art will do more than toppling a dozen Eberts in what Preston terms "essentialist debates".

Arey's piece is a response to what he perceives as a sort of self-satisfaction in Preston's article. He feels that Preston's attitude reflects a willingness to let games stand still, as it were, with respect to their artistic form. Arey, on the other hand, thinks that developers and publishers should be actively pushing the artistic boundaries of the medium. I'm in agreement on this point as well. While Arey believes there should be some push on the supply side, I've already argued that there should be pull on the demand side as well. Arey believes that, regardless of context, the idea of art still matters, and that people in the bright centers of publishing should do all they can to encourage innovation and growth in the artform.

As Preston notes in his comment, these views aren't really at odds with each other. Gamers ought to treat the debate as won, but both developers and gamers should want to win more, and win better. Talking past the essentialist debate is all well and good, but we shouldn't be content with that. Even if we've won or avoided the fight over whether games are art, we should still strive to bring to market something that can show up an Ebert and expose the argument that games "can never be art" for the vacuous nonsense that it is.

In keeping with my own prescriptions (and Preston's) I am going to try to finish some in-depth studies of games I've been meaning to post (similar to my post on Silent Hill 2). I hope I'll be able to have the first of these up by Sunday evening. Others will have to wait for refresher play and by the same token, for loaned-out games to return to me.

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Don't eat the white snow!

A bunch of really great stuff came out today, so much that I'm not sure I'll be able to get to all of it. We can start with the shortest article of interest, a paper in Science that's sure to interest mothers whose children stand around with their tongues out in a flurry. Brent Christner and colleagues have discovered that snow from pretty much anywhere contains bacteria (1). Well sure, you probably suspected that, but these bacteria didn't move up from the ground... they fell down from the sky.

Crystals generally form more readily when they have a nucleation point. Protein crystallographers are well aware that seeding their trays with microcrystals from a partially successful screen can significantly improve results. Non-scientists can see this as well, in the growth of ice crystals on certain surfaces or the popular home experiment of crystallizing sugar onto a string. The very rough string surface provides many more nucleation points than the smoother bowl surface, or the liquid, and so crystal formation on the string is preferred. A similar principle is at work in the formation of ice crystals in clouds. Any small particle can conceivably serve as a nucleation point: aerosols, dust, and even living things. And of course, once they form, those ice crystals can return to earth as snow or rain.

The authors aseptically collected fresh snow samples from various locations (France, Montana, the Yukon, and Antarctica) and melted them. They filtered the snowmelt and resuspended the filtrate in a smaller volume. They then assayed the freezing temperature between -2 and -9 °C. To prove that the ice nuclei (IN) were biological in origin they attempted to inactivate them using heat (to denature proteins) and lysozyme (to break up bacterial membranes). The experiment is pretty simple—in fact, except for the parts that explicitly prove bacteria are involved you could mimic this at home. The next part isn't so easy to try yourself: they used flow cytometry to identify particles in the snow containing DNA.

DNA-containing particles were found at all locations, as were IN that could be inactivated by heat. Several locations also had IN that could be inactivated by lysozyme. The authors chalk up the apparent discrepancy to incomplete hydrolysis or lysozyme resistance. The authors don't explicitly identify the bacteria in the article, but some of the points they make suggest that they may be species that are commensal or pathogenic towards plants. Of course there's no guarantee that the bacteria that land this way are still alive: the authors didn't assay motility or attempt to culture from the isolated IN. That lysozyme had an effect, however, suggests that the cells did not crack just from the conditions, and everyone who works in the biological sciences knows that even humdrum everyday bacteria like E. coli can survive freezing. The obvious implication is that it will be very difficult to control the spread of any species that can pull off the same trick. All they have to do is get blown up high enough and come down in the next rainstorm.

In spite of this news, it's probably not dangerous for your kids to eat a few snowflakes from the sky. This finding isn't so much a revelation as it is a reminder: bacteria are all around us and coat essentially everything we touch, eat, or drink. And that's true even if you don't drink anything but whisky and rainwater.

1. Christner, B.C., Morris, C.E., Foreman, C.M., Cai, R., Sands, D.C. (2008). Ubiquity of Biological Ice Nucleators in Snowfall. Science, 319(5867), 1214-1214. DOI: 10.1126/science.1149757

POSTSCRIPT: Tara Smith has good post on this, with a forum image for all you 4channers. Ed Yong also has a great post.

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If this teapot's a-rockin'...

Anonymous Coward (self-designated) at Bayblab managed to stir up a pretty little storm in the science blogging community today with a little article about "The State of Science Blogging". AC apparently believes that the science blogs at ScienceBlogs have too much blog and not enough science. Of course, several of the ScienceBlogs people are up in arms. Some well-reasoned responses can be found at Laelaps, Uncertain Principles, and Greg Laden's Blog. Dave Munger also has an excellent piece on the subject. You can even read the comment thread at Bayblab if you want, but I wouldn't advise it. It's altogether too much effort to catch the gems out from the flying monkey poop. As sole proprietor of a blog that's occasionally about science and almost never read by actual people, my opinion doesn't matter to any of the parties involved. However, I like seeing my thoughts in print, so I will share with you that I think that Anonymous Coward's argument is wrong-headed.

AC seems to think that blogs that self-identify as "Science Blogs" ought to focus primarily or exclusively on science as a topic. His stated reason for this is that people will get a false impression of what science is about, particularly with respect to PZ Myers' blog. I think, that AC's concern points to the opposite conclusion, however. Moreover, I believe that irrespective of true or false impressions of science, it is beneficial for those who blog about science on a regular basis to also post on topics that are of more general interest.

One of the problems that scientists face—in America, at least—is an anti-intellectual culture that stereotypes them as socially inept "eggheads" who ramble endlessly about esoteric subjects and cannot relate to normal people. While this may be true of me a few scientists, it's not true of that group as large. The "false impression" that scientists should be concerned about is the widespread belief that they are some weird breed of alterna-human that lives on tax dollars and has no experience of the "real world". Scientists who blog on politics, or their personal lives, or that great ham sandwich they had last night perform a valuable service for all of us by making it clear that scientists are just as (ab?)normal as everybody else.

So that justifies the occasional non-science post on a "science blog". Still, what about blogs that are mostly about non-science topics? Again, I'm not troubled. The simple fact of life is that most people don't come to the internet looking for good science. In fact, most people close off and actively avoid discussions of science. They visit blogs to hear about politics, or movies, or cookware, or diet tips, etc. and they won't be reached by blogs that only cover cell biology or rock formations. But if they come to somebody's blog because of a post about Rambo and there happen across a post that explains a scientific subject in an accessible way, then they might be drawn in. Blogs that cover a diverse set of subjects that includes scientific matters grow the audience for science and increase awareness of research in a way that exclusively scientific blogs won't. Why? Because the only people who read blogs that are only about science are people who are already interested in science.

Look, if somebody who loves video games comes to this blog because of my Professor Layton review (no representation is made that anyone other than Wlad and myself read that post), and while here sees the appendix post, or some other science post, or my post about science about video games, and becomes interested in and motivated about science, even if only for a couple of hours, does science win or lose by that? The game is worth the candle in my view.

The truth of the matter is that the science blogging community is a very tiny corner of the blogosphere. That little teapot will never turn into anything bigger than what it is if we restrict ourselves to fitting the image that popular imagination tries to stuff us into. Rather than stirring up a wee storm over whether everyone who blogs about science deserves to be called a 'science blogger', shouldn't we be encouraging as many people as possible to write good posts about science, whether that's one science post a year or one hundred?

POSTSCRIPT: After I had written this, but before I was able to edit it or post, Bayblab "revealed" that their initial post was a puerile, uncontrolled "experiment". Don't know if that's the truth or not. Maybe their second post is the experiment.

POSTPOSTSCRIPT: Coturnix has a really good post up as well. You might also re-check Greg's Blog and Drugmonkey for some reaction to the "experiment" post. My own feeling is that AC was trolling and got what he wanted.

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Nothing Spells Relief Like BOOM! Headshot!

Courtesy of Kotaku I learned of an article on the response of players to violent (and non-violent) video games out of a Finnish lab (1). The study has garnered attention because its results seem to contradict popular rhetoric that games encourage violence and desensitize their players to it. What Ravaja et al. found was that players of a first-person shooter had negative emotional reactions to killing or wounding opponents, and a positive emotional reaction to "dying" in game. These results seem odd, but I feel they're reasonable and hint at interesting avenues for future research.

First, the methodology. The authors of this paper used several physiological measurements in combination with subjects' reports of emotional experience and a personality test. In the case of the physiological measurements, skin conductance level (SCL) was used to assess general arousal, and EGM recordings of muscle activity determined positive (zygomaticus, orbicularis oculi) and negative (left corrugator) emotional valence. The researchers studied 36 students (70% male) aged 20-30 playing three (one "training", two "play") 5-minute sessions of James Bond 007: Nightfire or Super Monkey Ball 2. If I'm reading the "Event Scoring" section right some of these players had good reason to be frustrated: it looks like someone managed to die 8 times (although it's not clear whether this refers to a single 5-minute play session or a sum over both).

So, what did the Ravaja et al. observe? SCL appeared to increase after every kind of game event, though not uniformly so. This suggests basically that in-game events are stimulating, which is probably good news for the developers. Then the authors try to use the EGM data to parse exactly what kind of emotional response the player is having to various in-game events. The researchers find that zygomaticus and orbicularis oculi activity decreases in response to killing an opponent and increases in response to the death of the player. As one might expect, corrugator activity increases in response to opponent deaths and decreases in response to player death. The negative emotional valence was attenuated in players who had high Psychoticism scores on the personality test. Player self-reporting of emotional experience suggested that the primary emotion felt during play was fear, with lesser numbers reporting pleasant relaxation, anger, or depression (probably that guy who died 8 times). Players also reported strong feelings of joy. However, it is not clear whether these reported emotions come exclusively from the Nightfire test or include the Monkey Ball results. As gamers are well aware, different games can produce vastly different emotions.

What are we to make of all of this? Well, the first thing is to remember not to take this too seriously. The sampling here was very limited and included only a single day of play. Moreover, it did not involve anyone under the age of 20. So, we cannot gain any information here about long-term desensitization to violence, developmental effects, etc. It would be foolish to draw very general conclusions here. The games used do not sample all of the genre space and do not include extreme visuals. However, we can take away a few ideas that can be explored in future research.

First, it would seem that a player's reaction to in-game violence depends on his or her own personality. Negative responses to opponent deaths were slightly attenuated in individuals who had higher than average psychoticism scores (this does not indicate that they were psychotic). This suggests a common-sense idea, namely that whatever negative emotional effects games produce can be reduced by positive context. Similarly, negative contexts will exacerbate negative effects. Emotionally healthy people who play games will probably have emotionally healthy responses to them. However, again, this is something that needs to be examined more thoroughly in children and adults.

Second, these results may point to part of the nature of the entertainment experience. Remember that one of the primary emotions reported by players was fear. First-person shooters and other twitch-style games rely on a sort of catharsis for their emotional impact. Anxiety is developed and sustained throughout a level as danger is repeatedly encountered, often building to a fever pitch with a very difficult boss fight of some kind. The end of the level is accompanied by a quick easing of that anxiety, a release of the held breath, that may produce a positive emotional response. The authors suggest that a form of that relief may also be occurring when the player "dies", mitigating or overwhelming the negative emotions associated with failure. In this regard it is somewhat regrettable that the study limited the play time. It would have been interesting to compare the emotional response to successful completion of a level with the emotional response to "death". The authors also suggest that failure in a 'fake' context might be associated with a positive challenge. One caveat with the "player dies" result is that this was the least-sampled condition.

And what are we to make of the negative emotional response to the deaths of enemies? Well, it suggests that one of the central assumptions of the "murder simulator" argument, that games associate positive emotions with violent acts, is not necessarily true. One might also conclude that even digital people seem like people, and that some gamers therefore feel they have transgressed even when they kill an AI character. However, player attitudes towards virtual opponents are likely to be strongly determined by context. It would be interesting to see if these results would be recapitulated if the researchers were to, say, set the difficulty to a very high level and force the player to play until the level was completed. It would also be interesting to compare player responses between "killing" a standard enemy and a difficult boss. Also, it's important to remember that these techniques measure facial movements, not emotions themselves. Perhaps the players are just wincing as a reflex, without any higher emotional thought about it.

Ultimately, this study is too small and too limited to be ultimately probative as regards even the short-term emotional effects of playing video games (remember, the total play time for each individual game was only 15 minutes). The unexpected emotional responses to player and opponent deaths, however, suggest at least that there is a great diversity of emotional responses to video games. From a scientific standpoint it will be interesting to see how further research develops these findings into a more coherent view of response.

From a gaming standpoint, it will be interesting to see if developers try to calibrate games to play off these responses. In a certain sense this has already happened: Shadow of the Colossus is an example of a game that (occasionally) worked to inspire a feeling of guilt about killing your enemies. Will this research inspire designers to take that a step further, to actively try to make players feel unhappy about killing their enemies? Will players respond to such an approach?

1. Ravaja, N., Turpeinen, M., Saari, T., Puttonen, S., Keltikangas-Järvinen, L. (2008). The psychophysiology of James Bond: Phasic emotional responses to violent video game events.. Emotion, 8(1), 114-120. DOI: 10.1037/1528-3542.8.1.114

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Is Multiculturalism to Blame for Iraq?

Well, today I had the misfortune of reading an article so transparently silly it amazes me that editors at the Christian Science Monitor allowed it to be printed. I begin to wonder if its author, Lawrence Harrison even read what he was writing, or simply ignored the obvious contradictions of his position in order to serve his point. In the opinion piece, "The End of Multiculturalism", Harrison asserts that the two great failures of the Bush administration—Iraq and immigration—have their roots in multiculturalism. He goes on to prescribe some actions by the government to nip that there multiculturalism in the bud. The whole article is built on an inane straw man, and consequently its merits are nil.

Harrison stuffs his scarecrow relatively quickly. By his second paragraph he is saying:

But multiculturalism rests on a frail foundation: cultural relativism, the notion that no culture is better or worse than any other – it is merely different.

First of all, this sort of statement is primed to elicit a reaction, as it implies an attack on the reader (the reader is assumed to hold his own culture in high regard). However, the central tenet of normative cultural relativism is not the same as the central tenet of a multiculturalism, which is that every culture has some value. Because the multiculturalist seeks to construct a single coherent society out of diverse cultures he implicitly accepts a set of external norms. Without such norms a coherent multicultural society cannot be constructed.

This is not an insignificant difference: the multiculturalist is still in a position to, say, oppose female genital mutilation, while a bona fide cultural relativist is not. The normative cultural relativist must reject the notion that there are any external norms by which a given culture can be judged, while the multiculturalist is not obliged to such an extreme position.

Harrison acknowledges this non-equivalence as well when he asks:

What, then, are the implications for a foreign policy based on the doctrine that "These values of freedom are right and true for every person, in every society"? The Bush administration has staked huge human, financial, diplomatic, and prestige resources on this doctrine's applicability in Iraq. It is now apparent that the doctrine is fallacious.

The stated doctrine is an explicit rejection of normative cultural relativism. Yet Harrison attributes it to a multicultural worldview. If these words truly reflect some kind of multiculturalism (as Harrison claims they do), then multiculturalism cannot be the same as cultural relativism. Moreover, if the failures of this 'multicultural' foreign policy arise from this sentiment then they are a result of cultural aboslutism ("right and true for every person") rather than cultural relativism. Harrison seems to be arguing that the flaw of 'multiculturalism' in this case was the invalid application of external norms—in other words, his is the argument of a relativist. Of course, I don't mean to suggest that Harrison is a relativist; rather, I mean to suggest that he is an idiot.

The reality is that the Bush foreign policy is not 'multicultural' in any intelligible sense. And to be honest, its failures were not so much philosophical as practical. Examining the war policy in the light of multiculturalism is nonsensical because they are not related. This is probably why Harrison doesn't spend a great deal of time trying to explain why it is. Instead he skips on to immigration, which at least seems like it could be intelligently framed in terms of multiculturalism.

Once again, however, Harrison utterly fails to deliver. The best he can offer is to sloppily and inanely equate bilingual education with values that perpetuate underachievement. However, it is totally unreasonable to suggest that multiculturalism requires us to uncritically accept cultural values that are at odds with particular norms. One can legitimately argue that Mexican customs, language, food, and literature are worth celebrating in America without being committed to the idea that the educational failings of immigrants ought be tolerated or encouraged. Only a hard-line normative cultural relativist is bound to such an odd outlook, and, of course, multiculturalism is not the same as cultural relativism. Harrison triumphs over his idiotic straw man, but produces no arguments relevant to the stated topic. The delayed assimilation and continued poverty of Hispanic immigrants are of major concern to everyone, not just monoculturalists.

There are other reasons to despise this article—among them Harrison's creepy adulation for 'Nordic' values and 'Anglo-Protestantism'. However, the chief reason to reject his argument is that he isn't talking about multiculturalism at all. While acculturation and economic opportunity for the Hispanic minority are a pressing concern for the nation, Harrison's extreme and distorted views of multiculturalism do nothing to inform the debate.

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Arieh Ben-Naim's Mystifying Decisions

I recently read Arieh Ben-Naim's book Entropy Demystified, a book I feel would have benefitted greatly from being more somewhat more focused on the task of explaining entropy than it actually was. While Ben-Naim, as promised, does a good job of reducing the second law of thermodynamics to "plain common sense", he makes confusing decisions to include arguments better meant for experts and diatribes that serve nobody. As a result I feel the book, though largely useful, may ill-serve the lay audience for which it is apparently intended, especially as regards the areas where non-scientists are most likely to encounter the concept of entropy.

In my view, the purpose of a popular book on a scientific subject is twofold. First, it should provide readers with enough good science to understand the subject as it appears (if it appears) in their lives. Second, it should provide the lay reader with a framework that allows him to interpret the words of experts. That is, the reader should come away with an understanding of what scientists mean by (in this case) entropy. Thus, popular books on any subject are not a reasonable platform to argue for paradigm shifts. First of all, you're not talking to your target audience (i.e. experts) when you do this. Second of all, the lay readers that agree with you will now be thinking of the subject in a very different way than most of the scientists they will encounter. So not only do you fail at what you're intending to do in terms of serving your new paradigm, you also fail at one basic task of the popular science book. The unfortunate thing with Ben-Naim's book is that it fails at the second task and ends up with mixed results on the first, for no real reason. He could have done just as good a job explaining entropy without introducing the new paradigm at all.

Entropy, despite its importance, is not a topic that lay people encounter very often. The transfer of heat from warmer to cooler bodies is a common example, as is the diffusion of dye in a liquid, or the mixing of two liquids or gases. Ben-Naim does an excellent job of explaining the role of entropy in these processes, building up from relatively simple dice games to complex discussions about temperature and gaseous mixtures. However, he does not do any job at all of explaining the role of entropy in reactions. Consequently, he fails to explain how apparent counteractions to entropy occur. A layman reading this book will understand why a gas expands, but not why it was possible to compress it in the first place. Also, Ben-Naim's approach and focus on mixtures and the like will also leave the reader utterly unprepared to encounter discussions of entropy in connection to the hydrophobic effect. Could the framework here introduced be extended to explain micelle formation and protein folding? I don't doubt that this is so, but Ben-Naim doesn't do it, to the detriment of the book and its readers.

What's Ben-Naim doing with all this space that he's not using on talking about the role of entropy in chemical reactions? Well, he's arguing for a view of entropy based on information, specifically defining entropy in terms of "missing information". Although this position has some merits, this book is an entirely inappropriate place to make the case for it. Why? The most pervasive popular misuse of the second law of thermodynamics is in creationist canards about the thermodynamic impossibility of evolution. These misinterpretations often rest on ideas related to information (as colloquially used) or distortions of information theory. Although Ben-Naim repeatedly states (correctly) that information has a precise scientific meaning, he never graces his readers with it. I fear this leaves them more vulnerable to creationist distortions than before they started reading. That Ben-Naim says little to emphasize the meaning of "closed system" or the other parts of thermodynamics exacerbates the problem. The discussion of information was not strictly necessary to his overall point—his excellent introduction of probability would have sufficed—and it is easily misread and misused. In my opinion, he should have held his tongue here and allowed his book targeted at the academic audience (A Farewell to Entropy: Statistical Thermodynamics Based on Information) to make the case.

Ben-Naim also devotes pages and pages to complaints about other authors' (Atkins particularly comes in for criticism) presentations of entropy. These sections contain a few good ideas, but on the whole read like petulant complaints about more popular writers. That these pages serve any real purpose at all is debatable; that they weaken Ben-Naim's case is certain. No matter how much he disagrees with these authors it would be better for him to disregard them and focus on constructing his own case than deconstructing their books. I agree with him that science writers are too eager to portray entropy as mysterious, but clearing up the mystery is sufficient. His detailed rebuttals of their language are unnecessary.

It's a pity, because Ben-Naim really does pack in some useful and important concepts. Strip away the unnecessary information theory, and his book does an excellent job of reducing the law of entropy to common sense. Entropy Demystified explains what entropy actually means for certain physical systems, and excels at building this picture up from very simple games that anyone can intuitively understand and model. That said, Ben-Naim does not tie entropy into real processes nearly as well as he could, and his insistence on representing entropy in a way that has not yet gained mainstream acceptance may mitigate his readers' ability to apprehend what scientists are saying about the subject. Moreover, the fact that this alternative presentation is "entropy as missing information" is more likely to perpetuate misunderstandings about entropy (especially with regard to evolution) among the lay audience than to clear those misunderstandings up. As such, I cannot recommend this book, despite its virtues.

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Planes Flying on Plants? What's Next?

Virgin Atlantic pulled off an interesting little stunt the other day. They flew a Boeing 747 across the Atlantic. Well, that's not so interesting. What's interesting is that one of its four engines was fueled by biodiesel—in this case a mixture of oils from babassu nuts and coconuts. Ultimately, this act barely addresses any of the questions surrounding the future of our transportation system. But even though it's just a stunt, I don't disapprove, because I think it's important to raise people's awareness of the monumental challenge we are going to face in this century, one that has profound implications for our ongoing prosperity and the global economy.

Like I said, the trip itself accomplished little. As a practical matter it established that at least some biofuel blends remain liquid enough to use as fuel at temperatures and pressures experienced by airplanes. The concern in this case isn't just that the biofuel will turn into a solid or a gel; it's also a possibility that a biofuel could remain liquid but become too viscous for efficient jet engine operation. Fortunately, that didn't happen (the other three engines had conventional jet fuel in case it did).

However, that's about it. We have no particular reason to believe that the existing tracts of babassu and coconut will provide sufficient fuel to replace the hydrocarbon uses of airplanes. The current batch was produced in such a way that it didn't interfere with food production, but hey, it only powered a quarter of a single transatlantic flight. Does the world produce enough babassu nuts and coconuts in a year to supply fuel for a single day's worth of flights? This is a pervasive problem with the biofuels approach. The most optimistic estimates about switchgrass ethanol suggest that it would replace no more than 30% of current petroleum use. That means we are going to have a serious problem.

The increasingly global nature of the economy means that many goods travel a very long way. The raw materials must be shipped, often to a factory in a different country. Once assembled, the manufactured goods must be shipped to the US, often overseas. Once they reach the US, they must be distributed, a process that sometimes involves rail but always involves an 18-wheeler or panel truck at some point. This is a lot of shipping, and the feasibility of biofuels to replace the energy source at any point is completely unproven. I don't think anyone doubts that biodiesel can power a ship if you have enough, but there's no evidence that we can produce enough. Even if we manage to produce sufficient yields of biofuels they may be significantly more expensive than the present plentiful oil. Of course, they will eventually become more economical than oil, but this will not be through any virtue of their own.

Supplies of oil will become increasingly tight. In the past, spikes in oil prices were driven by speculation or market interference by OPEC. But within the next few decades we will start to see oil prices rising because of supply scarcity. And because the resource is not renewable, once those prices start going up they will never go down until demand collapses. What this means is endless inflation. Oil permeates our economy. It provides the raw materials for our goods from drugs to sneakers, and the for the plastic in which those goods are encased and protected. It provides the energy and lubrication for the machines that transport those goods to our markets, and for the machines that carry us from our widely distributed homes to those markets and back. Parts of the markets themselves are constructed from materials made from oil and they were built by machines that ran on petroleum. The effective price of goods will be inflated at every single one of those steps.

This will murder the economies of developing countries. The only way to keep prices down at US destinations will be to either re-industrialize America or treat already underpaid workers in foreign countries even more terribly than they already are. Neither bodes well for these developing countries. Stagnant economies will only add to the damage likely to result from global warming, resulting in enormous instability. Stagflation on a global scale will pound the last nail into the coffin of the already-tenuous pax Americana unless we do something.

The Virgin flight is valuable because it emphasizes the need to plan for petroleum scarcity now. Scrambling to replace oil once we're past peak production is a fool's game. Biofuels such as those used in this stunt will probably not be the answer, but we cannot even know that without further research. Research money from DoD, USDA, and DoE should be funneled into this field now to establish the most viable means of replacing petroleum and mitigating demand. Otherwise the global economy will run aground when the great oil tide recedes, with all hands lost.

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The Evolution of Protein Folds

Now online for next week's edition of PNAS is a commentary by Alan R. Davidson (1) about a paper in this week's edition of PNAS out of Matthew Cordes' group (2). Both are worth reading because they speak to a very interesting question: where do new protein folds come from?

The Roessler et al. paper doesn't address this question directly. Their initial intention was to identify the relationship between two distantly homologous proteins: P22 Cro and λ Cro. Though they both belong to the Cro repressor superfamily, these two proteins have just 25% sequence identity and significant dissimilarities in structure, as you can see on the right in the figure I have shamelessly stolen from the paper. P22 is an all α-helical structure that appears to be exclusively monomeric, while λ is an α/β structure that forms a dimer with nanomolar affinity. In an effort to bridge the structural gap between these proteins, Roessler et al. looked at group of proteins related by transitive homology. The idea, as they put it, is that

In this approach, two dissimilar sequences, A and C, are indirectly linked if a third "intermediate" sequence B exists with sufficient similarity to both A and C to imply homology with both proteins. The relationships between A and B and between B and C combine to support distant common ancestry between A and C.

Thus, they identify 3 intermediates, each with about 40% identity to its nearest neighbors, that bridge the sequence gap. Then they ask whether these sequence intermediates are also structural intermediates.

The answer is "yes", and in a somewhat surprising way. It is not the case that each step along the transitive pathway slightly increases β-strand content. Rather, while Xfaso 1 has an all-α structure very similar to P22 and is a monomer, Pfl 6—which is 40% identical (!)—has an α/β structure similar to that of λ Cro and dimerizes with ~1 mM affinity. This dissimilarity allows the authors to present some interesting ideas about the evolution of the Cro family which are summarized in their Figure 4. But what seizes Davidson's imagination is the conjunction of fairly high sequence similarity with structural dissimilarity. What makes this conjunction even more impressive is that the sequence identity is evenly distributed while the structural differences are not. The N-termini of these proteins contain structurally similar helix-turn-helix motifs, so they primarily differ in the structures of the C-termini. Yet amino-acid identity holds up across essentially the whole sequence.

Why is this such a surprise? Well, there are a variety of reasons, which Davidson outlines pretty well. It boils down to this—for a given sequence, it is generally possible to mutate a significant percentage of the residues without disrupting the fold. That is, the sequence overdetermines the structure. Consequently, proteins that have homologous or significantly identical sequences (and 40% identity would probably fall in this range) are expected to possess very similar structures. This poses a problem for protein evolution because it is expected that the initial pool of folds was rather small. If protein folds are highly resistant to disruption or alteration by mutations, it's difficult to imagine how the present enormous diversity of folds arose.

This impression is actually somewhat mistaken. It's typical to perform X→Ala mutations in these studies, and while this can occasionally produce significant cavities in a structure, it probably significantly underestimates the potential effects of a mutation at any given spot. For buried residues, size increases and the introduction of unbalanced charges (X→Trp, Asp, Lys, etc.) are mutations likely to drive the formation of new structure. For solvent-exposed residues, the introduction of bulky nonpolar side chains (X→Phe, Leu, Ile, etc.) would also be more likely to result in a novel fold than the typical approach. I have a feeling that these kinds of mutations are significant in this context, but I cannot check this because both 3bd1 and 2pij are still on hold and cannot yet be retrieved from the PDB. I may elaborate on this point when the coordinates are released to the public. For the time being I should point out that though the quantity of identity is similar between the two termini is similar, the quality is not: identical residues in the N-terminus almost all appear together, while in the C-terminus they are spread out. However, it is worth noting that what groupings of identical residues can be found in the C-terminal region tend to occur within the structural features that changed.

Davidson bears out this point when he refers to some experiments that have shown that a few mutations in key spots could change a protein's fold significantly. He seems to be unaware, however, of natural instances in which highly similar sequences produce dissimilar folds. As I have mentioned before, the upper limit on sequence identity producing dissimilar folds is known. Structural studies that Brian Volkman's group published in 2002 (3) demonstrated that the maximum sequence identity that allows for the adoption of a completely different structure is 100%. That is, given reasonable changes in solution conditions a single peptide sequence can produce two entirely different folds.

The last time I blogged on lymphotactin I discussed the implications of Brian's findings for the protein folding and protein structure prediction crowds. In the context of sequence similarity, however, the lymphotactin story also has implications for evolution as well. To a certain extent it suggests that we have been somewhat blinded by Anfinsen's dogma, in particular the assumption of the unchallenged minimum. The lymphotactin result indicates that context can be extremely important—a sequence that stably folds into one structure in one set of conditions will not necessarily maintain that structure under different conditions. In an elementary sense, we know this already, since we are aware that high temperatures and high concentrations of cosolutes such as guanidine and urea tend to unfold proteins. The important idea is that conversions between Anfinsen-like folds (i.e. folds that conditionally dominate the energy landscape) can occur within the range of conditions that can be achieved physiologically. Because the relationship between sequence and structure is not truly one-to-one, fold diversity may be much easier to achieve than we have suspected on the basis of existing structural studies.

In the end, the results of Roessler et al. provide a powerful counterpoint to conventional expectations about the relationship between sequence identity and structural homology. It appears that Cro proteins group into two kinds of structures, underscoring the well-known stability of protein folds to mutation. However, the structural discontinuity, not hinted at by sequence comparison alone, reinforces the point that fold diversity may be significantly easier to achieve than alanine-scanning mutagenesis experiments have led us to believe. Davidson nonetheless still has a significant point. In this case, it appears that transit to the new structure was relatively short, and Cro is functionally a dimer in both forms—Xfaso 1 Cro forms a dimer in the crystal, and all Cro repressors are expected to dimerize on DNA. But what happens in the transit to a completely novel structure? Can function be maintained as the protein navigates the molten-globule strewn sequence space between stable folds, and if so, how? These are questions that we will have to answer as we develop a greater understanding of the evolutionary history of biomolecules and de novo protein design.

1. Davidson, A.R. (2008). A folding space odyssey. Proceedings of the National Academy of Sciences, 105(8), 2759-2760. DOI: 10.1073/pnas.0800030105
2. Roessler, C.G., Hall, B.M., Anderson, W.J., Ingram, W.M., Roberts, S.A., Montfort, W.R., Cordes, M.H. (2008). Transitive homology-guided structural studies lead to discovery of Cro proteins with 40% sequence identity but different folds. Proceedings of the National Academy of Sciences, 105(7), 2343-2348. DOI: 10.1073/pnas.0711589105
3. Kuloglu, E.S. (2002). Structural Rearrangement of Human Lymphotactin, a C Chemokine, under Physiological Solution Conditions. Journal of Biological Chemistry, 277(20), 17863-17870. DOI: 10.1074/jbc.M200402200 OPEN ACCESS

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Dear gamers: please stop buying crap

Yesterday Kotaku put up an article about Barack Obama's line in which he says people "...are going to have to parent better, and turn off the television sets, and put the video games away, and instill a sense of excellence in our children..." The particular editor at Kotaku clearly overreacted by seeing this as Obama using games a metaphor for underachievment. That's clearly not the point. But if it were, it would be a largely valid point, and more importantly a point with which most Americans would agree for mostly correct reasons. Anyone who has read this blog for more than a week knows I am not saying this because I believe games to be devoid of artistic content. Quite the opposite: I earnestly believe games have the power to convey stimulating stories and emotions in a uniquely powerful way. Unfortunately, most video games, and especially the video games that have the most impact on popular culture, fall far short of this ideal. True video gaming enthusiasts are not the only ones to blame for this problem. However, they are well-placed to do something about it.

The main features supporting Obama's (and the larger public's) view are pretty obvious. For the most part, games are not a physical activity, although the Wii is changing that to some extent. They generally do not convey enlightening or even interesting stories. Because they divorce themselves so totally from the science, history, or mythology on which they occasionally claim to be based, the vast majority of games are not even slightly educational. Indeed, in this regard they are usually so far off base they aren't even wrong. It is at least possible, even likely, that shooters and gory games desensitize their players to violence (though not necessarily uniquely so), especially if those players are young. The majority of television and movies are at least as bad and probably worse. However, video games shouldn't make a negative case versus competing media; they should try to stand positively on their own. This, at present, they cannot do, particularly not as they are perceived in the larger culture. Given what the average person knows, a parent promoting any alternative activity, be it reading books or playing with sticks, over video games would be acting reasonably. At least the sticks won't make your kids dumber.

What makes this so upsetting to me is that it need not be so. Many games rely on critical thinking and problem solving skills. Games largely do not possess the "quick cuts" common in commercials and film that are suspected to adversely affect attention span and concentration. In fact, most games reward concentration and careful observation. And despite the generally grim situation, there are many games that include interesting and stimulating narratives. Even the first-person shooter genre, justifiably reviled for its generally awful writing, recently developed entries that featured a genuinely interesting story (BioShock) and an extremely clever and novel mechanic (Portal). Games like these, that favor inventiveness and storytelling over crystal-clear graphics of aliens' heads getting blown to bits, are rare gems to be celebrated.

But why? Why is BioShock the revelation, instead of being the status quo? Why is Shadow of the Colossus the exception rather than the rule? The reason is that the low (intellectual) quality muzzle-flash-and-gore spectacles sell. They sell spectacularly, and the simple fact is that companies have not just a desire, but an obligation (to their shareholders) to maximize their profits. If cow manure sold like candy bars, you'd never see another Snickers vending machine. The reason gamers don't get candy is that they're willing to buy crap.

Why are there great artistic movies, despite the triumphant profits of summer blockbuster pablum? Because there are people that believe in movies as an art form, who support artistic movies, who tell their friends about the emotionally moving films they see and encourage those people to support them. Some of these buffs also enjoy the occasional schlock film, and there's nothing intrinsically wrong with schlock films or watching them, as long as you don't confuse Transformers with Citizen Kane. Look, Halo isn't art. It's got art—perhaps even really good art—in it, but hey, Face/Off had some great cinematography and set design. That doesn't mean Face/Off isn't schlock—nobody in film confused dual-wielding Nic Cage with Nic Cage in Leaving Las Vegas. Halo is great fun, but the perception of the broader culture is that we see Halo and Gears of War as the pinnacle of the gaming artform, while I think the genuine perception of gamers is that these are the easily-discarded summer blockbusters.

Game publishers appear to be content to let the public perception stand. Thus, it falls to the enthusiasts to help elevate the form. We can do that in many ways. The most obvious, and the one most likely to directly impact the choices made by publishers, is to shift our purchasing habits. When you come across a game that makes an artistic statement, buy it; when you want to play a game that doesn't, rent (or ignore) instead. Stop pre-ordering games—require publishers to demonstrate quality and artistry before you buy. When it becomes favorable to a company's bottom line to push artistry over flash, they will do so. Why? Because they love money.

In that same vein, reward reviewers (with your traffic) if they focus their greatest attention on the artistic merits of games. I know the initial reaction to this is to say that reviewers should review games for "what they're trying to be" rather than focusing on the artistic aspects. That's a bunch of crap. Roger Ebert, Leonard Maltin, and that funny-looking guy from the Today show could all pan the hell out of the next entry in the "Michael Bay Blows Up" series (Michael Bay Blows Up Alcatraz, Michael Bay Blows Up Asteroids, Michael Bay Blows Up Your Childhood, etc.), and it will still make hundreds of millions of dollars. Game publishers and designers, as well as the purchasing public, need to develop a similar attitude towards bad reviews of schlock games, instead of insisting that review scores reflect popularity or ultimate sales. If Halo is bad art, give it an F, even if it's a good time. There's nothing wrong with doing that as long as the audience is aware of your angle, as they are with Ebert.

The final thing to do is for enthusiasts ourselves to talk about games as art, and to focus on artistic games when gaming comes up in casual conversation. Enthusiasts must get in the habit of talking (or writing) about games as art, rather than purely entertainment. The earnest, well-articulated, public attitude that games are art will do a great deal to promote this view in others, even if they have no direct experience of artistic games.

Obama was right to say what he did, and the next politician to say it will be right, and the next one after that, up to the day you lose your teeth and your mind. Games will always be a juvenile, inferior medium unappreciated by the public at large unless those who love them most put real pressure on developers, publishers, and reviewers to transform the motivations and attitudes that inform game creation and media response. If dollars support the best art instead of the best gloss, better art will be made and supported by the industry, and if the public at large gets used to seeing games discussed as art, criticized as art, and publicized as art, they will get used to thinking of them as art.

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It's official: HD-DVD = Betamax

To be honest, this took a little longer than I thought it would. Toshiba has decided to halt production of HD-DVD players, although the company claims that it will continue to support existing products through maintenance, etc. It will take a little time for this to shake out on the larger stage—studios that had committed to HD-DVD will probably face a little uncertainty. In the end though, Sony is like every other company: it loves money. So I would not expect any more than the standard amount of groveling to be required. The Sony executives have to be feeling good, seeing as they managed to win this format war. Coming on the heels of favorable January sales numbers for the PS3, this makes for a wonderful February for them.

It will be interesting to see the effect of this development on the console wars. The presence of Blu-ray on the PS3 may have aided that format's ultimate triumph. However, in this generation, only the PS3 is truly positioned as a multimedia center. You could get an HD-DVD player for the XBox 360, but it was an add-on. Given that Sony is a major supporter of Blu-Ray, it's unlikely that they will produce a Blu-Ray peripheral for Microsoft's benefit, though nothing in principle prevents MS from developing code to support 3d-party Blu-Ray peripherals. Because the PS3 is not that much more expensive than a good Blu-Ray player, it becomes a more secure 2-for-1 proposition. But that's something the XBox never really was anyway. The PS3 might get a minor boost from people who were holding back because of a perceived potential for Blu-ray to fold, but this was probably never a significant portion of the console-buying public. And the simple fact is that unless some significant changes occur in the PS3's game library, it won't attract anyone who currently isn't in the market for a console.

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