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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What's that appendix for, anyway?

Well, it keeps coming up, doesn't it? Famous cdesign proponentsist Dembski brought it up again recently in his list of ID "predictions" (click for epic fail). While his point was nicely deconstructed by Afarensis, I think it's worth examining the paper that attributed a function to the appendix. Just what did Bollinger et al. say about its function? On what basis did they draw their conclusions? And, I suppose most exasperatingly, what does the paper mean for evolution? Is the appendix vestigial or not, and if not, does that vindicate ID, evolution, or both?

The paper in question is an elaborately stated hypothesis, premised on the idea that

The occurrence of the appendix sporadically throughout phylogeny might suggest that the structure is evolutionarily derived for a specific function rather than merely a vestige of a once important digestive organ.

The emphasis in the above is mine, and included primarily to demonstrate that regardless of where the paper takes us it cannot be a successful unique prediction of ID, because the rationale behind the search for a function was evolutionary in the first place. But what exactly is it that the authors think the appendix is doing?

Well, they believe that the appendix is a site at which bowel biofilms are created, and a reservoir for commensal bacteria. What does this mean? Well, as we all ought be aware, we share our bodies with a significant number of bacteria who live on what we fail to digest and occasionally assist us by breaking down what we cannot and feeding bits of it to us. In recent years, as we have generally developed a greater appreciation for the role of the extracellular matrix in various aspects of biology, it has been demonstrated that our intestinal flora are to some extent supported by a rich layer of polysaccharides coating our intestinal surfaces. Bollinger et al. premise a role for the appendix in the support of this biofilm on the basis of three main pieces of evidence.

1. The appendix is located at the proximal end of the colon, where the greatest density of biofilm can be found.
2. Bowel biofilm is known to be associated with mucin and IgA, and the lymphoid tissue of the appendix could abundantly produce these molecules.
3. The position of the appendix protects it from the fecal stream.

Given that biofilms benefit the host organism (us), the idea that the appendix promotes the formation of the biofilm and serves as a reservoir of friendly commensal bacteria in the event that the colon was flushed out in response to a pathogenic event (e.g. diarrhea) is an attractive attribution of function.

There are several reasons one might not find this convincing. The first of these is that biofilms are likely to be a ubiquitous feature of mammalian digestive systems. While this does not disprove the idea that the appendix promotes the formation of biofilms, it does suggest that the observed relationship between biofilm presence and the appendix might be coincidental. Similarly, success of bowel biofilms in such organisms would suggest that the abundance of lymphoid tissue in the appendix is not necessary to populate the film with the requisite immune molecules. Given the propensity for the appendix to suffer a blockage (with resulting appendicitis), one might also find proposition 3 to be tenuous, though I would welcome a rebuttal on this point from a professional gastroenterologist or anyone who studies peristalsis rigorously.

In general this hypothesis is difficult to test due to the fact that direct analogues to the human appendix in other organisms are rather rare. However, there are some experiments that can be performed, the most obvious of which is to take some animal that lacks an appendix (a carnivore of some kind?) and examine the distribution of biofilm in its colon. This would likely address whether point (1) represents a causative relationship or coincidence, and an examination of the molecular composition of the biofilms of these animals would give us good information about whether (2) is a valid reason to attribute this function to the appendix. A comparison of biofilm distribution and composition between human subjects who possess an appendix and those who lack one (at least 6% of the population, it would seem) would also indicate whether removal of the appendix deranges biofilm formation. Comparative studies of biofilm regeneration and intestinal recolonization by commensal species following diarrhea in normal and appendix-free individuals would also be of value in assessing the function of the appendix. So there are further experiments to be performed which can speak to this hypothesis.

But, let us assume for Mr. Dembski's sake that all of these experiments have taken place and yielded results which cast the best possible light on this hypothesis. Would it establish that the appendix was not vestigial? Well, no, not if you genuinely understand what vestigial means. Again, Afarensis makes some good points here, and there is also an interesting discussion of vestigiality on the appendix page at TalkOrigins. The fundamental point that you must appreciate is that vestigial does not mean useless. The word "vestigial" describes a particular kind of evolutionary history of a feature, specifically that a given physiological construct has lost the purpose it possessed in ancestral species. Vestigiality implies nothing about present function. Thus, even if it has a function in humans, the appendix would still be vestigial unless we could use it to ferment all those cellulose-laden tree leaves we eat. So it simply isn't true that the discovery of a function for the appendix means it's not vestigial—indeed, the presence or absence of a modern function doesn't speak to the vestigiality of the appendix at all.

Supposing that the hypothesis proves to be valid, it doesn't pose a real problem for evolution. Remember that the reason Bollinger et al. claim to have developed this hypothesis is to find an evolutionary rationale for the preservation of the appendix. If it turns out to provide a benefit, even in the form of a marginal improvement in biofilm robustness, then this might provide an explanation why the organ has not been lost completely. On the other hand, such an explanation is not strictly necessary; our anatomists may just be catching the appendix on the way out.

And actually, given the ubiquity of biofilms, validation of this hypothesis would represent a(nother) philosophical disaster for the intelligent design conjecture. If the appendix truly provides a significant benefit to biofilm formation, then it seems logical to ask why the designer included it in so few mammals, of such disparate kinds. Why not put it in all of them? If it's not important for that, then why put it in any? The apparently random distribution (and dissimilarity) of appendices in mammals is consistent neither with a purposeful insertion of elements known to be of benefit, nor with a purposeful trimming of elements known to be useless. Evolution, on the other hand, is perfectly at home with this kind of convergent funny business. In this sense, it doesn't matter whether a function is ever found for the appendix or not. Vestigiality aside, the existence of the appendix cannot be explained by the design conjecture if it is useless, nor can it be explained by design conjecture if it possesses a function, as this hypothesis suggests, that would be of benefit to all animals, including those that lack one.

Bollinger, R.R., Barbas, A., Bush, E., Lin, S., Parker, W. (2007). Biofilms in the large bowel suggest an apparent function of the human vermiform appendix. Journal of Theoretical Biology, 249(4), 826-831. DOI: 10.1016/j.jtbi.2007.08.032

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I Love Layton

I have just finished playing Professor Layton and the Curious Village, a game I cannot recommend highly enough to anyone who has ever enjoyed thinking. The combination of straight-up puzzle solving and adventure game, charmingly presented in 2D, will leave you wanting more and wondering why nobody did this before. Brain game shovelware may well be doomed. The Professor puts that genre to shame and begs the question: "Why didn't anyone do this before?"

The premise of the game is simple enough—well-known puzzle-solver Professor Layton is summoned to a village to solve the riddle of a hidden inheritance. With his assistant Luke in tow, he heads off to the town of St. Mystere (sigh), where it rapidly becomes obvious that the missing "Golden Apple" is the least of the mysteries confronting him. The townspeople have a strange penchant for posing puzzles and riddles (which can get annoying), and soon enough crimes ranging from a murder to a "doze-and-dash" are plaguing St. Mystere, demanding Layton's attention. The story is pretty entertaining, even though you'll probably figure out most of the mystery about the time you finish the easiest of the bonus puzzles.

Resolving most of these mysteries, and sometimes even moving around the town, requires you to solve several riddles. The simplest one is to the right—some of the puzzles, like this one, require nothing more than clear tracing of lines. Others require some pretty subtle thinking. I have seen some complaints about the difficulty, and I cannot entirely give these credit. The puzzles of the game generally don't require any more knowledge than typically possessed by a fifth grader. The difficulty comes from a requirement for creativity and mental discipline. A child playing this game may need assistance from adults in spots, but then again, an adult playing this game may need a childlike outlook to achieve some of the necessary lateral thinking. In short, if you have kids, play this game with them. You will all have a great time. And don't worry; if you don't have a 10 year old to help you, a limited number of hints are available.

The tale of Professor Layton is conveyed through 2D animations and drawn backgrounds. The character design is excellent, with endearingly wacky villagers that are full of personality. The game features a substantial amount of voice acting, which actually works out quite well, though I suspect it cut down on the amount of music available. The soundtrack is passable, and works to help set the tone, though having some more variety would have been nice.

The game isn't perfect. Although the touch control is essentially seamless, the movement system seems unnecessarily elaborate. The village mostly runs out of puzzles before the game runs out of story. As I mentioned the mystery itself is a little easy to get (though it requires a little leap), and also more or less solves itself. A little more involvement from the player in solving the larger riddles would have been great. The game is also a little short—the 15 bonus puzzles and additional downloadable content should provide your fix until Level 5 delivers the sequel that the bonuses page promises is coming. There are already 3 Professor Layton games out in Japan so this will mostly be a matter of localization. A longer story might also have helped get the player a little more emotionally involved; as is the story ends just as you're really starting to fall in love with the characters.

Professor Layton and the Curious Village is a pleasant little game with a story and characters just wacky enough to make the numerous brain-teasers seem a natural part of the world. The puzzles themselves aren't crushingly difficult, though a few can get a little frustrating. The story and presentation makes it much more engaging than the standard brain-game shovelware. Cute enough to engage a child, smart enough to stump an adult, Professor Layton is charming fun anyone who loves thinking can enjoy.

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Cowardly Democratic Candidates Punt on FISA

The ancient Romans famously covered up the governmental shortcomings of their empire by the distribution of free bread and the holding of spectacles, including gladiatorial combat and the races in the circus. It's a cynical strategy that works, as we can see in our own country today. Recently we've had bread—in the form of the hastily-passed economic stimulus bill—and we've sure had a circus—the pathetic and hilarious hearings about Roger Clemens' butt. And amidst that clamor, as quietly as it could manage, the Senate passed the extension to FISA, including the provision that grants immunity to the telecommunications companies that complied with the totalitarian demands of the Bush administration. McCain voted in favor of telecom immunity. That was the wrong decision, but at least it was a decision. And what did Hillary Clinton and Barack Obama do? Those agents of change, those defenders of our liberties, those brave voices against theose who would turn our country into a dicatorship of the paranoid, didn't cast a vote at all. Clinton didn't even bother to show up.

No narrative of the telecom surveillance makes unqualified immunity a good idea. On the one hand, if these companies eagerly agreed to hand over the records of their customers without threat, then they clearly deserve to be held civilly (if not criminally) liable for the loss of privacy. If the companies were blackmailed or threatened into taking this step by overzealous agents of the government, then it seems a little less fair to expose them to liability. However, it is every citizen's duty to resist unlawful action of the state. The companies had an obligation to blow the whistle when confronted with this unlawful demand, not cave in to it like some spineless Democratic Senator. If they failed in this duty, then they deserve to get punished. Moreover, granting this blanket immunity greases the wheels for further abuses.

If the companies can prove that they believed themselves to be acting in good faith in compliance with a legitimate court order, then they should of course not be held liable. This, however, is a matter for the courts to decide, not the legislature. Including provisions of immunity for future cases where the FISA court orders the handover of such information is legitimate (the involvement of the court should not be optional), but granting immunity for past cases where the handover of data was not proper is not. At any rate, the propriety of the order ought be proven in court, not assumed by the Congress.

Even if you disagree with me on the issue, the fact remains that Obama and Clinton have been very loud about the abuses of the Bush presidency, and how they will change the way that Washington works. This vote belies those claims. It was a pure and simple act of political calculation. Obama and Clinton must have known that voting against FISA wouldn't help them politically—it would only get them points with people who already hate the current administration and its policies, a group of people unlikely to vote Republican in November. A "Nay" would almost certainly come up in the main election, framed by McCain as a vote against national security. Voting for the bill, on the other hand, could seriously dampen the enthusiasm of liberals, and would provide an opening if, say, Clinton voted for it and Obama either did not vote or took the chance of opposing. As a cynically calculated political strategy, only refusing to vote made any sense. But haven't both these candidates claimed to be different?

Clinton is the worse offender. Obama at least went in and consistently voted in favor of amendments to limit the more egregious provisions of the bill. At least he registered some kind of disapproval, even if ultimately he didn't speak up when the vote counted most. But when the issues came up, Clinton, who loudly attacked Obama for his number of "present" votes in the Illinois legislature, apparently didn't have a damn thing to say. Where was her leadership? Where was her devotion? What was she doing on February 12th that was more important than your civil liberties? Well, she was giving a speech in Texas, saying:

I believe that we need a president, starting on day one, who's going to roll up his or her sleeves and get to work.

Well, I guess it depends on what your definition of "work" is. Apparently, Clinton's doesn't include defending our liberties or performing her elected duties.

Liberals, lovers of the Constitution, haters of the Imperial Presidency, this vote is the sign that you are being taken for granted. This is the sign that this man and this woman are not who they say they are. They are the same spineless fools that ceded authority to Bush time and time again, and they are still afraid, still cowering in fear that they will be called weak on national security. Understand that these people would rather be known as enablers of tyrants than defenders of liberty. Understand that they are so afraid of the preception of weakness that they have lost their moral courage. Understand that all their pretty talk about change is just that—talk. They are the past. They are politics as usual. They are the problem they claim they'll solve.

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"There's a great future in plastics..."

There's a deeply disturbing article up at Best Life (hat tip to J. Jacquet of Shifting Baselines, check her page for a nifty link to ORV Alguita's blog) about the pervasive presence of plastics and plastic waste products in the ecosystem, particularly in the ocean. I can't really add anything to the description of the disaster: the article and Alguita blog do a more than sufficient job of that. The problem is daunting, and seemingly insoluble. The particles that cause the most danger are too small to be sifted from the sea, and the use of plastics themselves is pervasive in society. What can we do to fix this mess?

Much like the global-warming problem, two main steps must be taken. Less plastic needs to go into the environment, and we need to be taking plastic out of it as well. Reuse and recycling of plastic are good ideas that will eventually be forced on us anyway by the disappearance of readily-available petroleum. More effective means of recycling will be a must as the supply of raw materials becomes more constrained and expensive. In addition we will likely be forced to complement and then replace the existing petrochemical syntheses and their products with alternate methods and end-products. These should be designed with an eye to biodegradability, either on their own or with the addition of some non-toxic catalyst.

Removing the existing plastic from the environment (and mitigating the damage from future releases) is a significantly greater challenge. Even if we managed to clean up the gyres in some way, degraded plastic appears to be a ubiquitous presence in the water and soil. Supposing that we managed to clean up all that was visible we would still be leaving a substantial fraction behind in the form of highly-degraded particles. It is unlikely that we will ever be able to clean it all up using conventional means. What we really need to do is to enable some creature or set of creatures to digest the stuff.

This would not be a small challenge: even natural polymers are notoriously hard for most creatures to digest. However, as I commented in the Orgel post, we know of bacteria that can digest petrochemical waste products. Given sufficiently masticated plastics, it should in principle be possible, perhaps through directed evolution, to develop proteins appropriate to degrade the polymers and digest the subunits thus produced. The natural solution to the degradation of cellulose as a food source involves perhaps as many as 200 species of bacteria and protozoans; it is unlikely we could produce anything nearly as efficient with a single microbe. However, it may be sufficient to produce just a rudimentary digestive reaction. Once that is good enough for plastic digestion to get started, efficiency is likely to evolve on its own, since the ability to utilize such a food source could constitute a significant selective advantage. Obviously one would want to use an obligate anaerobe or perhaps some kind of plankton for this purpose, to diminish the chances of a "gray goo" problem.

Given a few million years or so, it's likely that microorganisms will evolve that can digest plastic, or help some other organism digest it (as in the case of termites). Regrettably, we do not have millions of years to solve the problem. Of course we should try to come up with some mechanical means of harvesting the larger chunks of plastic from the ocean, but in the absence of significant penalties for dumping, on an international level, such steps will only provide temporary amelioration. Moreover, they will constitute only a partial solution to the problem. In this case, it may be wise for us to try and give evolution a nudge in whatever way we can, lest the prediction of a 'plasticene' geological stratum come true.

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FFXII: Superficially Epic

As I started writing that review of FFXII: Revenant Wings, I realized that I'd never taken out my notes on its predecessor and arranged them into a review. So, I decided I would go ahead and do that. I've played through the game twice now, and I feel it likely that I'll play it again at some point in the future. Final Fantasy XII walks an interesting line: compared to recent entries in the series it seems very much like a new direction. I felt, however, that it actually hearkened back to older entries in many ways. This synthesis had many strengths, but the game did not play to them as well as it could have. For all its epic grandeur, FFXII never really connects emotionally, in the end producing a superficial experience.

The battle system garnered the most attention, because it was the largest departure from Final Fantasy X. A turn-based system with a separate battle screen was replaced by "real-time" encounters in the field. However, the "real-time" system is something of an illusion, and in fact is a throwback, because it is essentially a partially-automated version of the active time battle system that series veterans are familiar with. The real difference here was the elimination of the battle screen, a move that made sense in terms of firmly rooting the action in the world, but which highlighted the oddity of having only half your party involved in a fight. The advantage of the change is most evident in terms of scaling. Giant enemies seem truly enormous in this system, and it also accommodates swarms of enemies that can be a drag in a turn-based system, as anyone who has sat through a Dragon Quest battle with 8 or more slimes can attest.

The removal of discontinuities and transitions between the overworld and battle screen adds a greater sense of immediacy as well, and creates some interesting moments—your characters might end up running through the desert with an enormous dinosaur on their heels, for instance. This engagement is adversely affected by the "Quickenings", rather inexplicable special attacks that seem to take place on some other plane. It would have been better, and achieved more to differentiate the characters, if these had been replaced by in-field special techniques.

The price of all this is the control afforded by a turn-based system. While it is possible to manually direct all your characters, it is more efficient to use the rudimentary AI system (gambits) so that they control themselves. There was some grousing about this, and also the "license" system that forced you, in the early stages of the game at least, to pick and choose what weapons and abilities your character could use. In the end though, these aspects of the system, however controversial, were secondary, because the real selling point of the Final Fantasy games has been presentation and story.

The story was quite a departure. While many of the popular FF entries were highly personal stories intertwined with a traditional fantasy epic, FFXII is much more distant from its characters. In FFX, Tidus repeatedly states "This is my story," but FFXII is emphatically not the (supposedly) main character Vaan's story, nor even Princess Ashe's. The player's characters are all very small relative to the conflict being played out, and for the most part they are unable to affect its course. Only at the very last do the efforts of the characters amount to a thrust against the march of their history. Even then, they affect only the superficial aspects of the moment (i.e. who wins the battle); the great task, the toppling of the Occuria, has already been achieved.

The presentation matched the epic focus in several ways. Full-video cutscenes seemed slightly less textured than they were for FFX—compare Tidus' skin and hair to Vaan's, for instance. Full-video also seems to be used somewhat more extensively for establishing shots than in FFX, and the main characters get rather less screen time in the action shots. Thus, in general, the full-video cinematics feel more remote from the characters. Similarly, the soundtrack is very grand and highly orchestrated. Horn and string ensembles take the lead here, rather than the solo instruments that dominated most tracks of FFX. As a side effect, the music is less intimate, and at times feels almost superficial, like it came out of a fighting game. Although some themes get repeated, the music has nothing like the coherence of FFX. These features work with the nature of the story presented.

So too does the general vastness of the landscapes involved. Entire regions of FFX could fit into single screens of FFXII, and the exterior landscapes are generally quite distinct. Interiors are something of a problem for the game, however; the differences between the various mines in the game mostly amounts to pallette work. Also, in some instances the scale seems very odd—particularly in the corridors of Imperial ships, which are too wide, too purposeless, and have improbably high ceilings. In general, however, the scaling of the environment works to the advantage of the game's approach, emphasizing how large the world is relative to the characters and their story.

This is not to say that there is no personal conflict motivating the story, but it does not play out nearly as intimately as in some other entries. Vaan (the protagonist) and Vayne (the principal antagonist) see each other briefly at the beginning of the game and do not meet again until a few brief moments before the end, but the story tracks their movements and the development of their opposing ideals. Curiously, both wish to be free of oppression: Vaan from the Empire that Vayne represents, and Vayne from the godlike Occuria who try to control history. That Vayne and the Occuria both view their respective rule as benevolent does not impress those who endure it. Despite their key similarity, Vaan and Vayne are presented as physical and emotional opposites, with very different reactions to the resented oppression. Vaan wishes only to be free, and his own master, while Vayne wishes to take the godhead himself, by manufacturing his own version of the magical stones that the Occuria use to distribute power (and with it, control). The problem with this dichotomy is that while Vayne is the unquestioned leader of his side of the argument, Vaan is not a leader nor seemingly even essential to his.

As the story progresses it sounds two main thematic notes: a suspicion of power and the powerful, and the futility of revenge. Criticism of current events could easily be read into either of these if one wished, though the tale of small nations caught in a conflict between two great empires seems more directly analogous to the Cold War. Intertwined with the theme of vengeance is the resolution of loyalties—familial and political. In general the characters choose to be loyal to the future rather than to memory, which could also be read as a political statement.

One interesting feature of the story is that Vayne and Doctor Cid both have a habit of talking to thin air, seeming to be insane. Yet the "Venat" they speak to, a renegade Occurian god, is actually present (invisibly). The obvious note sounded about the ease of confusing religion and insanity may obscure larger questions about how we can distinguish a good God from an evil one, and whether any God that relates to the world purely through power can be truly benevolent. Is Venat good or evil, or both?

These threads are interesting, but through them we ultimately learn very little about the characters. FFXII spends so much time building up the enormous supporting cast that we never get to connect very completely with or truly understand the putative main players. At the end of the tale, we know that they have done certain things, but we understand very little about why. Nor does the story end with any resolution of tensions or personal transformations. Most of the characters (except Penelo, who is practically a non-character) reconcile with their past, but the significant transformations that Yuna and Tidus underwent in FFX find no echo here. Vaan, Ashe, and Basch are somewhat less bitter at the end of the story, but otherwise not significantly changed. The relationships between the characters of the party never seem to develop or change—at times it's not at all clear why they're even still travelling together. Rather, it is the secondary characters, Larsa especially, who are transformed by events of the story, and their relationships that develop and change. In that respect, FFXII resembled some of the earlier FF games to its detriment.

The only remedy to this weakness would be a change in the narrative. A narrowed focus would have helped—Penelo and Fran could have been excised or relegated to supporting-cast status without much of a loss. Fran and the Viera in general felt like an indulgence of puerile sexuality—the village full of scantily-clad bunny girls was almost fatal to the tone. Vaan should either have been excised or built up significantly—for long stretches of the story he seems like a supporting character who got stuck to the main plot by accident, which is not a problem unless (as here) the events of the story seem as insignficant to him as he is to them. Trimming some of the fat and refocusing the story could draw out Vaan's developing leadership and responsibility, and Ashe's resolution with her past, to a much greater degree. It would also allow more space to play on Ashe's relationships with Vaan and Balthier. At several points the Occuria seem interested in using Vaan somehow, or pushing Ashe towards him. Again, allowing more space for this to play out would also have been wise.

As an epic, FFXII mostly works, and the vastness of the landscape, the massiveness of many of the enemies, and the sweeping score help reinforce this property. However, while the political and military tale is compelling, the personal story is not: the main characters are never developed adequately, their relationships do not seem to evolve, and for all their epic scope the events of the story do not seem to greatly change them. The automation of your allies, the vastness of the world, the remoteness of the score, and the two-dimensionality of the characters creates a fundamentally alienating and impersonal environment only partly ameliorated by the engagement of the continuous-field battle system, and this only weakens the emotional impact further. Ultimately, FFXII is grand but not touching—all glorious gilding, and no lily.

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Revenant Wings doesn't play up to its presentation

Final Fantasy XII : Revenant Wings for the DS opens with some really beautiful video sequences, accompanied by lovely music. Immediately, the top-notch presentation that Final Fantasy games are known for asserts itself. Yet, as is so often the case with FF spinoffs, the actual game doesn't live up to the polish. Despite its production values, Revenant Wings is an uninspired game with merely passable mechanics.

The box promises a version of the FFXII battle system, and Revenant Wings more or less delivers that with its real-time action and skill charging, though the context is quite different. Each of the characters commands a group of monsters in most parts of the game, making it more of an RTS, though there really isn't any resource management going on. This isn't to say that there's no micromanagement—you'll be doing plenty of that, because the AI does not make good decisions and cannot be stopped from making bad ones.

You have no option with the AI other than setting a single "gambit" (automatically used skill). So you cannot, for instance, tell a group of creatures to stand their ground. Ranged creatures especially have a tendency of getting into trouble this way, but any of your creatures might chase after an enemy against your orders. It's also difficult to respond quickly to problems, in part because your creatures move so slowly, but also in part because your units have a hard time moving around one another. In fact, it will not be at all uncommon to see melee and flying units wandering aimlessly through the ranks long after you have ordered them to move to a particular spot, especially when you have lots of relatively stationary ranged units. As you might guess, units have no AI that commands them to stay together, which will occasionally result in a lone member of a platoon charging hopelessly into the mouth of death while his comrades mill stupidly about in your lines.

Other than the traffic jam problem, the touch control works pretty well. Unit selection is straightforward, and never caused a significant problem. Unfortunately, it's not always easy to get units to do what you want—your units and the terrain can obscure opposing units, preventing you from ordering an attack. Also, especially on screens where there is significant variation in altitude, it's not always clear where you are telling your units to go, or even where you can tell them to go. Once you successfully order them, they'll take a while to actually get moving; your commands always seem to take a backseat to whatever the units are doing at that moment.

As a strategy game, Revenant Wings is run-of-the-mill. There's a standard revolving set of weaknesses (flying creatures weak to ranged creatures weak to melee creatures weak to flying creatures) and the requisite elemental strength/weakness setup. It's generally more important to exploit the former than the latter when you choose what creatures and leaders you'll take into battle, but here too you are overly limited. For much of the game you have no real choice about what attack mode your leaders will use. Later on, you have somewhat more flexibility, but in the end you will have only one healing leader (Penelo) and four ranged combat leaders (with two each of flying and melee leaders).

Despite all the limitations, however, the game is not terribly difficult or strategically challenging. Most maps can be solved with a tenacious advance or simple distract and destroy tactics. The exceptions are one ill-advised stealth mission, a few missions involving allies (who apparently long for death) and the final mission, which is somewhat insulting in that you are essentially confronted with a gun that can only be destroyed by attacking the mouth of the barrel. It is doable, but tedious and frustrating, and made more so by the tendency of characters whom you have told to remain in a safe area to wander into the path of the shot (due to the aforementioned AI issues). Naturally, enemy troops are never damaged by the enormous laser blast. In short, difficulty is added in lazy ways—useless allies, massive enemy respawns, over-leveled opponents, and silly terrain effects—rather than more subtle approaches like truly coordinated enemy attacks or realistic competition of strategic goals. This feeling of laziness is accentuated by the interminable recurrence of bosses, especially the Judge of Wings and Ba'Gamnan's crew.

The presentation, as I mentioned, is top-notch. The music is especially notable. Although almost all of it is cribbed directly from the original, it was ported to the DS without a significant loss of sound quality. The result is a really enjoyable audio experience, though some of the sound effects are obnoxious. The in-game graphics of course don't match the detail and beauty of the pre-rendered cutscenes. However, they're perfectly serviceable in most instances. The environments are nice, and the map of Lemures is very pretty (this is less true of the Ivalice map). The monster designs have a lot of personality for their size, though I feel that the art department stretched themselves a bit too far on some of the larger espers—these are sometimes too detailed, resulting in an complex yet uninteresting blob.

This description could also apply to the plot, which hits many of the same notes as the original FFXII and adds some Kingdom Hearts-style rambling about hearts (anima). It's interesting to know what happened to some of the minor characters of FFXII, but it's striking that the main characters appear to be totally unimproved by previous events. Penelo is sent to video-game writing purgatory with stock jokes about her bad cooking, and at one point devolves into a sobbing useless wimp. This isn't anything original: I note it only because Penelo's backbone and sass were her only distinguishing characteristics in the previous game and here they are eviscerated for no apparent reason. None of the other characters do much to distinguish themselves—oh wait, one is an emotionally closed-off pretty boy, a novel concept for SquareEnix writers. Cameos by the several of the original FFXII cast amount to just that: cameos, with no additional character development.

Pretty cutscenes and pretty music achieve nothing if they're applied to a run-of-the-mill game with a lame plot. Regrettably, that's exactly what happened here. Revenant Wings' uninspired mechanics, oversimplified strategy, and limp story waste the value applied in the graphical and audio departments. It's not a terrible game, but those who expect a play experience as vivid as the opening videos will come away disappointed.

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What was Leslie Orgel saying?

Well, my first impression on reading Leslie Orgel's recent (posthumous) essay in PLoS Biology was that it was just the sort of rich quote-ore that creationists and cdesign proponentsists cannot resist mining. Indeed, it was not long before famous cdesign proponentsist Casey Luskin began distorting the article in a way that served his personal beliefs. Others have dissected the failures of Mr. Luskin's analysis, and of course volumes were written about his putative misuse of the Research Blogging icon. In all the clamor condemning Mr. Luskin, Orgel's actual paper seems to have gotten lost. I thought I might write about it.

Orgel's article itself doesn't contain any new research, and those who are keeping track might notice similarities to a previous essay on the same topic from 2000. The issue at hand is the origin of life, which owing to our inability to travel back in time is one of the most difficult subjects in biochemical research. It is almost impossible to know exactly what chemicals were present in the prebiotic milieu, what minerals and surfaces were available to perform catalysis, and which of the many possible environments was the one in which life actually arose. As such, the field is highly speculative. Orgel's essay is something of a reaction to this.

It is popular to speak of an "RNA world" of primitive organisms in which most or all of the functions currently performed by proteins were instead performed by RNA. This model has the advantage that RNA can have both informational content and catalytic activity, but it demands the question of where the RNA came from. Some elements of nucleic acids can form nonenzymatically from simple chemicals likely to be present in the prebiotic milieu, but the transition from adenine and ribose to a diverse oligosaccharide with a phosphate backbone is not trivial. If, however, enormous autocatalytic cycles existed on the prebiotic Earth, that would resolve many of these objections.

In his essay, Orgel seemingly meant to quell enthusiasm (I use the term in its pejorative sense) for this idea, not because he believes it is intrinsically false, but because it doesn't really make things easier for us. He takes as an example the reverse citric acid cycle, pointing out that although it is extremely useful, and moreover is autocatalytic, it requires numerous and diverse chemical activities, many of which could go awry if the wrong substrate were used for a step. The assertion that this cycle underpins the existence of life requires appropriate colocal catalysts acting with sufficient efficiency to keep the cycle running. Moreover, it requires that unproductive (or toxic) side-reactions not drain away the reactants at any step. That is, the catalysts present must discriminate between different possible reactants, so as not to break down components inappropriately before they advance in the cycle. It is not immediately apparent that this is possible (certainly it does not appear to be probable), and Orgel was not convinced by several of the attempts to justify prebiotic catalytic cycles. This article summarized his reasons for skepticism.

This attitude has been misrepresented as meaning that Orgel believed (A) that prebiotic autocatalytic cycles were impossible, and (B) that important life cycles are irreducibly complex. Both propositions are false, and it is also false that Orgel believed them.

Part of the rebuttal to proposition A is referenced in Orgel's paper itself, when he mentions Arthur Weber's recent work in which a reaction of various trioses with ammonia gave autocatalytic products. Although the cycle at work in that instance is not yet understood, Orgel points to it as being particularly promising, in part because it requires no additional catalyst, and in part because it yields high-energy carbon compounds of a kind that might be useful substrates for life.

Granted, the reactions of the Weber experiment may not be directly analogous to anything observed in modern organisms, but I feel that this should not be seen as a problem. After all, why would a primitive organism evolve an activity to perform catalysis already occurring naturally? Rather, one would expect that primitive organisms, whatever their informational and structural characteristics, used the products of autocatalytic cycles as raw material for more exotic activities, which were later repurposed to the production of raw materials as a way to gain a competitive edge or to respond to resource scarcity. If, additionally, very complex abiotic cycles similar to the TCA cycle existed to produce more exotic or useful substrates, it ceases to be quite as problematic if they are not highly efficient or specific. Indeed, these sorts of shortcomings would likely serve as a basis for establishing selective advantage for those organisms that evolved compensating protein catalytic activities.

It is not necessary that abiotic cycles intended to serve as a metabolic origin of life work perfectly, or even that they involve products and intermediates similar to those used by contemporary organisms. They need only be efficient and specific enough for life to get started, with intermediates and products that are useful enough for primitive organisms to benefit from them. Orgel's objection is not that this latter situation is impossible; rather he feels that it is sufficiently implausible that actual evidence is needed, rather than hopefulness and modeling.

The sharp-eyed will (hopefully) note the influence of Orgel's rules in the above, especially the First Rule: "Whenever a spontaneous process is too slow or too inefficient a protein will evolve to speed it up or make it more efficient." The rebuttal to proposition B, of course, comes in the form of Orgel's Second Rule: "Evolution is smarter than you are." The belief that any biological systems are irreducibly complex results merely from a failure to understand the enormous problem-solving potential of selection combined with random mutation and millions upon millions of years of time to work. Certainly Orgel would never have accepted that evolution could not produce these complicated cycles once given a chance, or that these cycles could not be broken down in a useful way for primitive organisms. Orgel's point is not that any of this is impossible, it is that it must be shown to be plausible:

The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own.

Orgel's paper does not rule out the possibility of autocatalytic cycles, nor does it assert or even imply that some mystical intervention is necessary to explain how life came about. Orgel's paper is a demand for evidence. It is not enough to say that autocatalytic cycles solve the problem of biogenesis, nor even that they are more plausible than other explanations. Negative arguments do not suffice; a positive argument must be made and backed up by simulations, reconstructions, and experimental evidence. Orgel points favorably to several promising avenues of research in this regard.

Intelligent design is not among those avenues, and it is certain that Orgel would reject it. Having only a (flimsy) negative case in its favor, lacking even the virtue of plausibility, and ignoring his second rule, ID must be seen as weaker than any extant metabolic or genetic theories, which at least are not based on magic. Orgel's overall point is a valuable one. It is disgusting and disgraceful that, with flagrant disregard for his thinking, Orgel's essay should be misrepresented as supporting "if pigs could fly" views of the origin of life.

Primary citation:
Orgel, L.E. (2008). The Implausibility of Metabolic Cycles on the Prebiotic Earth. PLoS Biology, 6(1), e18. DOI: 10.1371/journal.pbio.0060018 OPEN ACCESS

Other peer-reviewed articles referenced:
Orgel, L.E. (2000). Self-organizing biochemical cycles. Proceedings of the National Academy of Sciences, 97(23), 12503-12507. DOI: 10.1073/pnas.220406697 OPEN ACCESS
Roy, D., Najafian, K., von Rague Schleyer, P. (2007). Chemical evolution: The mechanism of the formation of adenine under prebiotic conditions. Proceedings of the National Academy of Sciences, 104(44), 17272-17277. DOI: 10.1073/pnas.0708434104
Weber, A.L. (2007). The Sugar Model: Autocatalytic Activity of the Triose-Ammonia Reaction. Origins of Life and Evolution of Biospheres, 37(2), 105-111. DOI: 10.1007/s11084-006-9059-9

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Dynamics and tunneling in soybean lipoxygenase

Because even the simplest case of enzymatic catalysis involves multiple steps (i.e. association, chemistry, and dissociation), semantic issues have obscured the question of what role protein structural dynamics play. For instance, the opening of the lids in Adenylate kinase appears to be rate-limiting, but there is as yet no evidence that dynamics play any role in the phosphotranfer. Thus, one can argue that dynamics are critical (because they are rate-limiting) or irrelevant (because they contribute nothing to the chemical step). Some authors, Arieh Warshel for example, have argued that the latter finding is general—that the highly successful transition-state stabilization model leaves no place for dynamics in chemical catalysis. Some researchers, however, believe that dynamics may play a significant role in chemistry when catalysis proceeds by other routes, especially hydrogen tunneling. In this vein, Matthew Meyer, Diana Tomchick, and Judith Klinman presented evidence in last week's Proceedings of the National Academy of Sciences that protein dynamics play a significant role in the chemical step of catalysis for the protein soybean lipoxygenase (SLO-1).

Hydrogen tunneling refers to the idea that a hydrogen may in some instances "tunnel through" an energy barrier, going directly from substrate to product without wasting any time or kT in actually surmounting that barrier. A reaction that primarily reflects tunneling should have three properties. The reaction rate should vary only weakly with temperature, because tunneling mostly divorces the rate from kT. Using an Arrhenius plot, this translates to a low calculated energy of activation. Replacing the reactive hydrogen with deuterium should enormously inhibit the reaction—a large kinetic isotope effect (KIE)—because the doubling of mass makes tunneling less likely. Nonetheless, the difference in the energies of activation (ΔE_a) for hydrogen and deuterium calculated from an Arrhenius plot should also be small, if tunneling is the main mechanism. Conceivably an enzyme could enhance the rate of such a reaction by using dynamics to promote favorable vibrational modes for the tunneling to occur, or to temporarily adopt a disfavored structure that puts reactive groups at a better distance for tunneling.

SLO-1 exhibits all three features, and so Klinman's group has used it as model system to try and understand whether and how enzymes promote tunneling reactions. In this case they have performed a series of mutations of isoleucine 553. In addition to existing data on WT and I553A, they analyzed the KIEs, crystal structures, and activation energies of I553L, I553V, and I553G mutants. They find that the protein as a whole is not much distorted by any of these mutations, nor do any of them appear to have significant effects on the binding pocket or substrate dissociation constant—the K_d for each mutant is around 3 μM, while WT is around 10 μM. Yet as the bulk of the mutated residue decreases, the ΔE_a increases significantly. In addition, the kinetic isotope effects decrease much more sharply with temperature than for WT. Again, the magnitude of this increased temperature dependence appears to vary inversely with the bulk of the side chain at I553. From these features, and a decline in the magnitude of the pre-exponential factor, the authors argue that dynamics play an important role in encouraging the tunneling reaction.

Well, you know how I love long-range dynamic effects in proteins. But I don't quite buy it here. An argument based on negatives is never very satisfying in any case, and here we have a lot of questions. For one thing, to say that the structure hasn't changed significantly seems overly simplistic to me. The lowest-energy structure may not have been seriously deformed, but absent crystal packing and with a little extra kT around, the average structure might be different. Additionally, these structures were obtained in the absence of ligand. Even though the energetics of binding do not appear to differ significantly for these mutants, the structure of the enzyme or ligand may have changed in the bound state. Even if I accept that the existing structures argue for a completely identical binding site in the free state, and this could realistically be debated, that's no guarantee that the same is true of the bound state.

I'm not denying that the evidence is strongly suggestive, and getting direct data may be difficult given the size of the protein. However, almost all of these side chains are methylated. That means that perdeuteration of the protein in concert with specific side-chain labeling could be especially fruitful in directly observing the dynamics of the pocket during catalysis. It should also in principle be possible to label other side chains in the region to determine how mutations affect the whole area. It is likely that the substrate can also be labeled, possibly with a nucleus or tag that is poorly relaxed. T₂ is likely to be a major challenge here, but not necessarily an insurmountable one, especially since the enzyme appears to be folded and active up to around 50 °C. The presence of the iron is certainly a complicating factor; however, the dynamics should be the same whether catalysis is occurring or not, so possibly it could be substituted with a non-paramagnetic metal. It wouldn't be the easiest project in the world, but it should be doable.

I think these results are intriguing, and I'd love to hear Warshel's take on them. Nonetheless, I feel I have to reserve judgment at least until dynamic changes in the pocket that seem to correlate with the kinetic observations are directly demonstrated by NMR or some other method.

Meyer, M.P., Tomchick, D.R., Klinman, J.P. (2008). Enzyme structure and dynamics affect hydrogen tunneling: The impact of a remote side chain (I553) in soybean lipoxygenase-1. Proceedings of the National Academy of Sciences, 105(4), 1146-1151. DOI: 10.1073/pnas.0710643105 - OPEN ACCESS ARTICLE

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