Persona 3

The MegaTen games have always taken a sort of gleefully perverse approach to the RPG format. Some have been centrally based on the idea of cannibalism, and others represent a sort of bizzaro Pokemon where the cute, cuddly creatures are replaced by soul-swallowing demons. By comparison, the most provocative feature of the latest entry in the Persona series practically seems tame. The controversy over "evokers" aside, Persona 3 is a very good game.

The conceit of the game is that manifestations of human emotion, called shadows, appear during a "Dark Hour" that occurs at midnight. During this time most people are encapsulated in weird coffins, but occasionally a person lacks this protection and his soul is at least temporarily consumed by the shadows. Fortunately, some teenagers have a special ability to release their own emotions in the form of "personas" (using the evokers) that can combat the shadows. Most of the characters in the game have only one persona, but the (unnamed) main character can carry and release up to twelve at a time, with a total variety of about 200. Some of his personas are acquired after battles, and additional ones can be made by "fusing" them with the assistance of a creepy old man in a secret room.

The powers and abilities of the personas the user is carrying are advanced by experience, as is typical for RPGs. However, the abilities of newly-fused personas are determined by "Social Links" or friendships between the main character and other characters in the game. Developing and maintaining these links is a significant part of the gameplay and a major factor in your combat ability: by maximizing these links you can create increasingly powerful personas to use in combat.

The social link system is very robust, and one of the best game features I have seen in years. Most games that feature a friendship system rely very heavily on the giving of gifts and such, but in Persona 3 most of the effort of developing a friendship lies in spending time with your friends and saying the right things to them at critical junctures. The difficulty involved varies greatly and appropriately -- an old couple running a bookstore are generally just happy to see a friendly young man like yourself, while the teenage girls of the school are conversation minefields, easy to offend or just put off. The numerous social links and extensive scripting to go with them provides an immense quantity of gameplay. The main character can also devote time to improving his intelligence, bravery, and charisma; bringing these to certain levels is necessary to initiate some social links.

And then there's the combat. Because it was the location of a secret lab that caused the shadows to appear, the high school is transformed at night into a devilish tower called "Tartarus". In the spirit of roguelikes, the many floors of this tower are randomly generated on each visit, which means that in most cases if you go to the same floor twice in one night it will not look the same. These floors are densely populated by the shadows, and your primary task is to prepare yourself for significant monthly confrontations with "boss" shadows by training inside Tartarus.

The combat has a number of features that will feel familiar to MegaTen fans. Although it does not feature the devilish and unforgiving "Press Turn" system of Nocturne or DDS, combat in Persona 3 is dominated by elemental strengths and weaknesses. If an enemy strikes at your character's weakness, you will be knocked down and your defenses weakened. To add insult to injury, the enemy who successfully struck your weak point gets an additional turn. This is true for the characters too, of course, and if they are lucky enough to knock down all their enemies, your party can carry out a punishing "all-out assault" that significantly damages your foes. Thus, it is imperative to learn and remember the weaknesses of all the enemies you encounter.

The major problem with the combat is that your allies are not under your control. I understand why this was done -- a major theme of the game is that you cannot control others but grow stronger from understanding them. Unfortunately, the conceit of this theme relies on a successful illusion that your allies are people, and this illusion is shattered by the fact that they are dumb, dumb, DUMB. Their choices are frequently inscrutable, they waste energy on pointless spells, and they will repeatedly attack downed enemies (knocking them back onto their feet) rather than trying to knock down those that are standing in order to carry out a punishing assault. The player has limited control over the AI, and can tell them to prioritize knocking down enemies, but the AI setting is not carried over from battle to battle, and must therefore be reset every time. Even when the priorities are successfully set your allies will sometimes ignore them, and the priorities sometimes result in paralysis, with an ally opting to skip its turn even when a profitable action is available. Allies are also prone to casting buff or debuff spells when offense is in order, and curiously failing to use buffs or debuffs when offense is impossible. More subtle AI options were desperately needed here.

The other downside to this choice is that the combat amounts to a round-based system, which disengages the player. Early in each month, when new floors of Tartarus become available and the shadows are relatively strong and novel, this is not a serious problem. As each month progresses, however, the relative strength of the shadows falls so that no combat is a serious danger. At this point combat is still necessary, but becomes fairly dull and repetitive. The choice to disengage the player for the majority of the combat round then becomes an obstruction to enjoying the game.

As you might gather from this description, the combat in this game is "extremely easy" by MegaTen standards, which means it is "moderately difficult" by the standards of any normal game. You'll probably only die 6-7 times unless you're extremely careless and/or unlucky. By contrast, I died 10 times on a single boss battle in DDS 2. Some of the joint attacks that become available to the main character late in the game make the final battles extremely easy, if you wish them to be.

Other gameplay problems include the fact that the player has very few things to do during the "evening" period of the game "day". The options, especially early on, are basically just three -- fight, raise attributes, or go to sleep. Later on, one gains the option to develop a social link on certain evenings, but by this time the player may have raised his attributes to their max, further constraining the actions that are worthwhile. The result is that the player either fights, which has a tendency to lead to in-combat boredom and over-leveling, or sends his character straight to bed, which is dull. This will probably be exacerbated in a second play-through, as the academics, courage, and charm attributes are carried over. Sundays are a little hinky in terms of the day progression. The available social links are severely constrained in the period just before an exam at the school.

Equipping your characters and checking their status is also a bit of a hassle: you must speak to them to find out what equipment they have or how close they are to leveling. This is actually fairly necessary, because the experience derived from combat is extremely dependent on the character level and the number of characters in the party. The number shown after combat applies only to the main character himself, and is not the experience received either by the party members or even his own persona. This can make it somewhat difficult to determine if the experience yield from combat is actually sufficient to balance the time investment.

The other main weakness (for me) is that the game is too long. One could easily spend 100 hours on it in a normal playthrough. That's something I don't mind when I'm making a serious push for a complete game, but if I spend that amount of time just experiencing the main events then it becomes a pretty major investment. On the other hand, some people really are looking for that length from a game. This is a matter of personal taste, but you should be aware of it. On the upside, because the game time is so discretized, it's easy to pick up Persona 3 and play it for just an hour or so, and then go do something else. You don't have to invest a lot of time in any single play session, even though the cumulative length of the game is significant.

Graphically, the game is nice, though nothing special. Most of it is presented in a 3-D cel-shaded look, and character interactions are accompanied by well-drawn 2-D images. The character designs are done well, though some costume options were odd. The environments are attractive and sufficiently variable to remain interesting over the great length of the game -- a nifty feat given that there are probably only 40 or so different "rooms" outside of Tartarus, of which maybe 15 are regularly visited. Tartarus itself is something of a disappointment. Although the different "regions" of the tower all have distinct looks, they all have the distinct feel of a building, which doesn't seem quite appropriate for an enormous hell-tower. The artbook also suggests that the journey into Tartarus is intended to symbolize a trip into the human psyche, but this does not come across in the design at all. More could have been done, though I understand why it was not, given the constraints of keeping this all on a single disk.

Most of the personas the main character can get are essentially recycled artwork from previous MegaTen games, although the personas of the secondary characters all have excellent designs, as do the novel personas for the main character. The shadows are new artwork, but these designs are internally recycled quite a bit. In some cases there is a noticeable redesign to go with the repetition, but a number of the enemies are clear palette-swaps. The unique bosses have intriguing designs, however, and the final 'real' boss manages to twist a friendly character's face into an interestingly ghastly rictus of evil.

The cutscenes that are not in the game engine are presented in anime format. The art in these scenes is passable, but has nothing to especially recommend it. The story they are used to convey is powerful in spots, and the mini-narratives that are built into the social links are heartwarming in most cases, and in some are really moving. There are some genuinely funny moments, but the script does not pussy-foot around. One of your friends is facing a terminal illness, several are dealing with divorce or family trouble, and alcoholism and student-teacher affairs appear as well. The problems presented in these narratives feel very real and have realistically ambivalent outcomes. Unfortunately, the main story is much more standard, featuring the by-now-obligatory "twist", and characters who realize, "All this time I was just running away!". Now there's a phrase I'm tired of seeing in video game scripts. The central narrative could have used some work, but this game deserves a favorable rating on the basis of the social link stories.

The audio in the game is alright, but nothing to particularly rejoice at. The voice-acting is a little rough and sometimes doesn't flow well from sentence to sentence, but the voices are mostly appropriate. The music is mostly appropriate and pleasing, but unfortunately you hear all of it a little too much over the course of the game. Most of the sound-effects are good, but frightened shadows running away from you make a terrible noise that will have you reaching for the mute button.

All in all Persona 3 is an excellent game that deserves major kudos for its robust social link system and the accompanying narratives, and for being the only MegaTen game that a normal person is likely to finish without destroying a controller. It's a little long, and the central story is a little weak, but it's mostly engaging and well worth your while, especially if what you're looking for is a long RPG that's long but can nonetheless be played in short sessions.

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Two articles you should read...

A good review of the biofuels situation is now in BioScience (a subscription is required). Steve Nash (not the basketball superstar) breaks down the serious problems and misconceptions surrounding our growing infatuation with biofuels, as well as areas of research that are actually showing some promise. Thanks to the fine fellows at Deep Sea News for pointing it out.

For those who like NFL football, Sports Illustrated's Paul Zimmerman has a really nice column up at the SI website about the state of the game. It's not about whether 3-receiver sets are in; Dr. Z is more concerned about how the league portrays itself and is sabotaging itself. There's a little bit of (possibly misplaced) nostalgia in the piece -- I'm not sure I'd agree that we should go back to the days when the players had no option but to befriend the press in order to keep their careers going. However, his attacks on the inanity of the close-mouthed coaches and hoot'n'holler broadcasting really resonated with me, as did the anecdotes about the appeal of football at the end of the piece.

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Light and peppery, with a finish reminiscent of an archaeal cytochrome P450...

As will be reported in this week's Nature, French and Italian scientists have completely sequenced the genome of the common pinot noir wine grape (subscription required). As most wine connoisseurs would expect, the vitis vinifera genome is fairly complex, containing about 30,000 genes. While this is several thousand more than human beings, it is significantly lower than the number of genes noted in some earlier plant genomes, such as the poplar or rice. The most relevant comparisons cannot yet be made because the grape is the first fruit plant to be sequenced. However, some aspects of the annotations that can be made stand out noticeably. Relative to known genomes, the grape has a large number of stilbene synthases (responsible for the synthesis of resveratol) and terpene synthases (which produce compounds that give rise to wine's complex flavors).

For the present, this sequencing effort is unlikely to produce any great revolutions in the wine industry—a significant body of work is required to relate flavor profiles to genetics, especially so considering the influence that soil chemistry, water abundance, and climate have on grapes and the resulting wines. As this research develops, however, it may prove possible by transplanting cassettes of synthetic genes from one grape to another, to introduce flavors currently unique to poorly-dispersed or finicky strains into hardier grapes that can be grown anywhere. Moreover, this research may provide a means to protect grape monocultures from diseases or climate change by identifying (and possibly correcting) genetic weaknesses.

The thing that strikes me is how overdue this kind of research is. I've already written in this space on the importance of agricultural research in the context of climate change; this is particularly true with regards to fruits. Most grains are grasses, and while this does not mean they are invincible, it does mean they're likely to be relatively hardy—this is part of why they became so widely cultivated in the first place. By contrast, fruits and vegetables can be difficult to cultivate even in relatively good conditions. While grains are sufficient to sustain life, to ensure proper nutrition it will be important to make fruits and vegetables available. Understanding the genetics of these organisms is essential to that task.

It's important to emphasize that sequencing a genome is only the beginning of understanding an organism's genetics. Knowing what the genes you've sequenced produce, what stimuli control their expression, and what can be safely done to manipulate those stimuli or genes is the true aim of a genetic study. In this regard, plant studies lag significantly behind those in animals—the fact that many animals are significant models for human illness is a major reason for this. However, plants are the basis of our entire food supply, and therefore understanding their biochemistry may be of much greater importance in the near future. Research funding bodies, especially at the government level where the results will not be proprietary, should begin putting a greater emphasis on crop plant research in order to ensure the integrity of the food supply in light of climate change, declining diversity, and other challenges.

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Merck HIV vaccine trial fails

Bad news today from the fight against AIDS: the Merck STEP trial has been discontinued due to evidence that the vaccine neither prevents nor attenuates HIV infection. This is a serious setback, as the trial was utilizing a new strategy and had sufficiently promising results two years ago that it was actually expanded. While this doesn't mark the death-knell of the CTL approach by any means, it is certainly a major disappointment and will probably send a number of approaches in development back to the drawing board.

The classic approaches to vaccination in humans have failed for HIV for a variety of reasons. Part of the difficulty is that HIV has such a high degree of variation. There's no guarantee that any single vaccine could protect against every strain for any length of time. Moreover, vaccination using the virus itself is incredibly risky — even a virus that is missing the essential Nef protein from its RNA can damage the immune system. Experiments in SIV show that a damaged or attenuated virus only confers protection if it reproduces at low levels in the host, but at the same time this gives it a greater opportunity to revert to pathogenic status. For this reason, chemical inactivation, which truly kills the virus, doesn't produce a viable vaccine because the virus does not stimulate sufficient antibodies to protect the patient.

The Merck vaccine used a different approach entirely, based on the idea of activating cytotoxic T lymphocytes. Rather than using inactivated HIV, the Merck team transplanted three HIV genes into an adenovirus (one of the viruses that produces the common cold). The idea was that these genes would get expressed into protein and displayed on the cell surface in the major histocompatibility complex. This would train T cells to attack any cell that the HIV virus had infected. Thus, the approach would not be to immobilize the virus with anitbodies, but rather to destroy any infected hosts cells before virus production really swung into gear. Even if it failed to prevent infection per se, it was hoped that this approach would arrest the development of an HIV infection into AIDS.

Unfortunately, this clever tack seems to have failed, at least in this application. It may take some time to understand why things did not work out, and maybe there was just an unfortunate choice of which HIV proteins were used or some other idiosyncratic issue with Merck's particular formulation of the approach. Until a detailed post-mortem is complete, however, CTL-stimulation approaches will have to be evaluated in a harsher light, with a little less hope.

NOTE: IAVI probably won't have the study status updated until Monday.

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Hot alien lesbian sex!

The disclosure that Bioware's upcoming XBox 360 game Mass Effect will feature nudity in a sex scene has actually dulled my interest in the game, which is sad because that interest was substantial. Although Bioware wasn't promising to do anything deeply revolutionary, Mass Effect promised to be an important step towards the maturation of video games as a interactive storytelling format, as well as a key iteration in the continuing fusion of the FPS and RPG genres. In both these respects it was similar to presumptive Game of the Year favorite Bioshock, though Mass Effect promises to come down more towards the RPG side of this fusion genre. It's discouraging that a game that has the potential to advance the artistic level of the medium has also set itself up to be a key exhibit in the conservative case against video games.

My concern is not that the scene will be especially gratuitous or exploitive. For one thing, Bioware itself has not attempted to draw significant attention to the scene's existence or use it as a selling point. Contrast this with BMX XXX, which had no other selling points, or even the God of War games, which had robust gameplay and graphics but included nudity and sexual content for additional shock value. Although the news about Mass Effect's content has made some waves in the internet community, it did not to my knowledge originate from Bioware, nor has it been talked up by anyone associated with the company. Based on their reputation and the quality of their previous work, I fully expect that the scene will fit into the game as a plot event, and that those who object to it will be those who object to sexual content per se, with a little bit of extra offense due to the possibility of having a lesbian encounter. Nor am I particularly troubled by the fact that a male/male encounter is not apparently possible, except to the extent that it reveals the reasons the scene was included at all.

Not being especially gratuitous does not mean the scene won't be gratuitous, which sex scenes almost always are. This is not a complaint unique to video games — it is rare to find a sex scene in any medium that serves a narrative end that would not be as well or perhaps even better served with a mere indication that intercourse took place. The actual depiction of sexual intercourse mostly just titillates and rarely contributes to plot or characterization, though it may fit in with them.

I acknowledge that there are exceptions to this generalization; a very unromantic sex scene in Gohatto comes to mind. And a sex scene can serve some other purpose, as in Hot Shots! where Top Gun was parodied almost viciously. For the most part, though, a sex scene in a movie ends up more like the case of Highlander, where we learn less from the sex we see between MacLeod and Brenda than from what is implied by the ominous exchange between the Kurgan (Clancy Brown) and a prostitute ("I'm Candy"/"[chuckle] Of course you are"). Perhaps it is too much to expect high-minded content from a movie about immortal men lopping each others' heads off with swords, but the same can be said of sex scenes in almost any movie or book.

The problem with a sex scene is that the audience expects to be titillated by it, and this tends to distract from any narrative purpose it could serve. Graphic depictions also suffer from the fact that not everyone is aroused or even interested by the same things as the scene's creator. Those who aren't titillated will view the scene as something to be suffered through, rather than appreciated. This puts the creator in a double bind: nothing of value to the narrative can be depicted in a sex scene if it titillates the audience, but the audience is likely to be bored or repulsed if the scene is not arousing. At least in the latter case the story can be developed or advanced, but at the cost of making some viewers turn away or lose interest.

For Bioware, the answer to this latter problem is, as always, choice. Bioware has produced several games that are the epitome of the western RPG — you get to decide almost everything about your character, down to the gender, and you are given considerable control over outcomes in the game, often including whether the main character is good or evil. As a result the participants in the scene will be decided by the player, within limits.

It is somewhat curious that a male/male encounter is apparently impossible, though I could not say with certainty whether this reflects the biases or preferences of the programmers or intended audience. I'm inclined to believe either that the developers (keeping in mind that the industry skews strongly male) included only options that turned them on, and that if a gay option was suggested that it was rejected due to a perceived lack of interest or perceived negative outcomes. Bioware must be sensitive to, if not directly partaking of, a double standard in society which is more accepting of female than male homosexuality, especially among the male demographic that dominates videogame purchases.

Regardless of the reasons for the possible exclusion of male homosexuality, the very mutability of the scenario makes it difficult to believe that the scene has a strong narrative purpose. One of the characters in the scene cannot produce any honest revelations, because in this style of RPG the main character is a direct player avatar. The fact that the other character can be selected in some way by the player suggests that the intention of the scene is to arouse. That the selections all feature humanoids supports this view. If the scene is intended to titillate, then not only would it be more difficult for the developers to use the scene to advance the plot, it is less likely that they would even try. I would have been more intrigued to learn that the intercourse scene involved something utterly alien, that wouldn't be arousing (or at least not arousing to most).

I doubt most people will share my reaction (after all, what normal person boos boobies?), but the difficulties of incorporating such a scene into a solid narrative make me almost certain that Bioware didn't succeed at it. Yes, the primary features that sell Mass Effect will be the gameplay, graphics, and perhaps the overarching story, and yes, I've always had doubts about its western RPG narrative method. Still, what I hoped for from Mass Effect was a high-minded, interesting story (and yes, a game can have one), and it's disappointing to learn that something detrimental to such an experience has been built in.

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Tanford's Top Model

Of course, as soon as I criticize PNAS, something interesting comes out in it, although what interests me often has nothing to do with what interests people generally. In this case I am talking about protein folding, so Elan, you can go browse some other site. More specifically, I am talking about the unfolding of proteins, and how it is accomplished by urea, the lovely little molecule over to the right. Chemical unfolding (also called denaturation) of proteins using urea or guanidine hydrochloride has been a popular method of investigating protein stability and the kinetic determinants of folding pathways. My own work with Drew and Marshall made use of guanidine denaturation to determine the stability of eglin c, but Dave Shortle's examination of residual structure in denatured eglin c used urea. Blindingly useful as this little molecule is, experiments with it have been plagued by one niggling little question: exactly how does it work?

More than 40 years ago, Charles Tanford proposed a model of urea-denaturation energetics based on the individual contributions of the protein backbone and side chain, and the assumption that all these contributions were additive. From this excellent work, it was thought that the side-chains contributed significantly to the transfer free energies (ΔG(tr)) for each amino acid, and that interactions between urea and the side-chains were therefore substantially responsible for urea's denaturant capability. The observation that the m-value of a given protein — which essentially measures how good urea is at unfolding it — correlates with the surface area exposed on unfolding was taken as support of this proposition.

Looking at urea, it is difficult to see why this might be so. Urea is incredibly soluble in water (up to 10 M), on account of its ability to form numerous hydrogen bonds. That ionic or polar side chains such as D, E, K, R, Q, N, S, and T might prefer interactions with urea to interactions with other side chains is easy to understand, but these residues tend to be on the surface of the protein anyway. Even if urea occupies the hydrogen-bonding sites of these side chains, it's difficult to understand why this would lead to anything other than the destruction of loop-loop interactions. When we come to hydrophobic side chains the idea that urea solubilizes them becomes even harder to fathom. What sort of interactions would this very polar molecule enjoy with nonpolar side chains?

This has led some to claim that interactions with the backbone are equally (or more) important in urea denaturation, a proposition supported by some simulations. In this regard, however, simulations are always questionable because the progress in replicating the properties of water alone in simulation has been slow, let alone water acting in concert with a solute like urea.

Auton, Holthauzen, and Bolen claim to have now perfected Tanford's work by correcting the ΔG(tr) that underlie the energetic predictions for the activity coefficients of glycine, which are elemental to the predicted ΔG(tr) for all amino acids. They find that, given these new ΔG(tr), the Tanford model can be used to predict the m-values of a number of proteins. More significantly, they find that the primary contributor to the denaturation effect of urea is the peptide backbone, not the side-chains. In fact, they propose that the contribution of the backbone has been underestimated by as much as 40 (kcal/mol)/M.

They convincingly demonstrate their claim in Figure 3 of their paper (left). I would have preferred a different scale for this graph (a glance at Figure 2 will explain why they used the one they did), but even so the linear correlation between their predictions and the observations is fairly compelling. The dashed red line I've added here is roughly along the correlation you get if you use Tanford's original values (if you're curious this can be found in the paper's Figure 2). The upper and lower bounds pointed out here refer to the degree of residual structure in the denatured state. The implication from this figure is not only that the backbone is the primary determinant of the m-value, but also that most proteins have neither a fully random coil (lower bound) or a compact denatured state (upper bound). According to Auton et al. the central line actually approximates a self-avoiding random coil. Deviations from this line may reflect the existence of more or less residual structure in the denatured state of the various proteins.

Another implication of this paper is that the perceived relationship between m-value and exposed surface area in the denatured state is actually standing in for a simpler relationship. The analysis here suggests that although the exposed surface area is dominated by the side chains, the energetics are dominated by the backbone. However, the surface area should be roughly correlated with the number of peptide moieties available for interactions with urea. Thus, the length of a protein chain may be the most significant determinant of the m-value. If the argument of the paper is correct, the m-value should be directly correlated with the number of hydrogen-bonding-competent groups exposed in the denatured state.

This paper is not as clearly written as it could be, and will be a little difficult to digest for those who haven't thought seriously about chemistry in a while. Nonetheless, with a dedicated effort it should be possible for even a non-expert to follow the argument. I'm not sure about the delay, but I think PNAS makes articles open-access after 6 months, at which point you might want to check it out.

Auton, M., Holthauzen, L.M.F., and Bolen, D.W. "Anatomy of energetic changes accompanying urea-induced protein denaturation." Proc. Nat. Acad. Sci. 104 (2007) p. 15317-15322.

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Stew and circuses

Recipe for "Bolivarian stew":

6,600 pounds of chicken
4,000 pounds of beef
tons of vegetables
1 evil motherf***er

In an effort to prove that there really are no food-supply issues in his country, Venezuela's soon-to-be dictator for life Hugo Chavez has cooked the world's largest pot of soup. At a hefty 3,960 gallons, Chavez' effort has outdone the previous record by 2,500 gallons. A spokesman estimated that the enormous vat held enough to feed more than 60,000 people, surely a relief to those Venezuelans facing a shortage of basic staples that has led to protectionist measures while the currency falters on the global market. Chavez also took the opportunity today to warn private schools that they must either submit to government control or be nationalized. Soon, too, he'll be meeting with his 'communist' compatriots in FARC, ostensibly for the purpose of negotiating the release of their hostages, but maybe he's just going to buy them a beer. Truly a banner day for the leading lord of South America.

The soupvat is only part of a larger celebration to prove that Venezuela's economy is in good shape, even though the nation's oil boom is playing out like a bust for the average citizen. Of course by now I should be getting used to examples of Chavez' royal intentions, and to the fact that they're apparently invisible to the masses in his country. On the other hand, the arrogation of regal authority by the Bush administration in response to the terrorist threat was met with far too little and too faint protest until only recently. Other examples include Putin's Russia, which has clearly returned to Imperial ambitions (he's even anointed a successor), and the disastrous state of affairs in Zimbabwe under Mugabe. Almost everywhere, it seems, legislatures of nations facing real or perceived threats have abdicated their authority in favor of the executive, with uniformly disastrous effects.

This demonstrates both the key strength and the major failing of republican governments. A republic only ever works because the corrupting influences and petty concerns of individual representatives are held in opposition to the corrupting influences and petty concerns of other representatives. For every Tom DeLay there is a Barney Frank, so to speak. Unfettered from this secret system of checks and balances, you get screwballs like Chavez and Mugabe running their countries into the ground, or Bush and Putin draining their treasuries on pointless military development and adventurism.

The main failing of republicanism is that it relies heavily on having these same divisions within the electorate. When the electorate unites in confrontation of a threat, a failure of the Republic is likely. Sometimes the danger passes without too much ill effect, as with WWII in the United States, for instance. However, when a threat, real or perceived (like American Imperialism, terrorists, or white people), is exploited by a charismatic leader with popular support, then freedom is almost certain to suffer, as in America, or perhaps perish entirely, as has happened in Zimbabwe and seems likely in Venezuela. There is never any greater threat to liberty than unity of the electorate, particularly unity behind a popular leader. The love affair doesn't even have to last very long... just long enough for the leader to consolidate authority, as Chavez did (and Bush very nearly did). Once the leader is strong enough, he can dismantle his enemies and then even after the situation deteriorates (as in Zimbabwe) he can be relatively secure behind the apparatus he has assembled.

If you think we couldn't go down the road that Zimbabwe, Venezuela, and Russia are on, you should ask yourself what would have happened if Bush hadn't made the mistake of attacking Iraq. Without that quagmire destroying his popularity, would Democrats, even moderate ones, have taken power last year? Would the few voices of discontent that were raised against the Patriot Act and the Guantanamo prison have gained any traction had they not been united with those raised against the unjust and wasteful war? Despite the lives and treasure wasted in Iraq, the Republic is fortunate that Bush and the neocons made this mis-step. Otherwise Bush might even now be anointing his successor, while Chief Justice Harriet Miers writes decisions cementing the power of an Imperial Presidency that might take decades to reign in.

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Mr. Excitement

Clint Bowyer finished the season-opening race at Daytona upside-down and on fire, and didn't finish any higher than third for the rest of Nascar's "regular season". But Nascar's points system has always been forgiving to a fella who just can't win a race, and the driver of the 07 did well enough in all those races to put himself in the Chase for the Nextel Cup, something significantly more popular drivers such as Mark Martin (who was semi-retired and voluntarily sat out several races), Dale Earnhardt junior (who sat out several races involuntarily because the engines his evil stepmother Teresa gave him blew), and Kasey Kahne (whose cars for most of the season just plain blew) couldn't manage. Of course, being the only driver in the 12-man Chase without a single win meant he went in dead last, and I'm sure there was a contingent of fans who hoped he would stay there as a stark argument that Nascar's championship system is still fluky. Not me, though -- from the moment I saw him step out of his flaming car and calmly stare at it, I figured he was a good man to root for. He rewarded that optimism at an opportune time.

Today's win at New Hampshire was not only Clint Bowyer's first win of this season, it was his first win on the Nascar Nextel Cup circuit period, and it couldn't have come at a better time. Beyond merely moving him up from 12th to 4th (a byproduct of the new Chase scoring formula which grants 10 points for every regular season win), it proved that he deserved to be in the Chase at all. That was especially needed coming off his disappointing performance at Richmond, where he challenged early only to spin out while trying to pass Carl Edwards for the lead. Though he managed to fight back to 12th in that race, and the quality of his run suggested his team was getting stronger, the spinout looked like a rookie mistake. A number of people were saying he didn't belong in Nascar's idiosyncratic little "playoff", but a win answers a lot of ills.

After a weekend full of surprises -- Mississippi State's big win over Auburn, somebody managing not to lose the ND-UM game, and 'Bama's stirring comeback over Arkansas -- it was nice to see the only contender who never won before take a trophy home in the first race of the Chase. Bowyer's only 15 points behind the leaders (Johnson and Gordon, with Stewart in third at -10), and though it doesn't seem possible that he could win it all, here's hoping Mr. Excitement has another surprise or two hiding somewhere in the 07 Chevy.

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The marriage thing

Recently released data from the Census bureau reports a surprising jump over the past 6 years in the percentage of people aged 20-29 who have never been married, for both males and females. This is not an entirely unexpected development, but rather serves as an exclamation point over a trend that has been developing for many years. People are getting married and having kids later and later, postponing these events until they are settled and have stable careers. The corollary to this is the increase in the occurrence of cohabitation before marriage.

This may not be anything to get particularly worked up about. Although the trend may lead to delayed childbirth, there's nothing intrinsically wrong with waiting until your 30s to get started on a family. People with a few more years as a single may have more time to find that special someone.

On the other hand, the decline of marriage may contribute to the existing trend of professional women waiting later and later (in some cases too late) to have children. The increasing cost of childcare makes single-motherhood almost completely untenable for women in some advanced professions (a young postdoc's salary will barely cover daycare in some places). Of course many cohabiting couples are models of fidelity notwithstanding the lack of vows, and a responsible father will contribute his fair share to the family. However, the formal arrangement probably brings some sense of security and commitment with it.

Of course there are factions that will react with utter terror and alarm to this situation, namely the family values pundits. The trend toward increasing cohabitation (living in sin!) is taken as a sign of moral decline; this will be added to that weight. They are likely to be most affected in this regard by anecdotes of people choosing cohabitation as a way to avoid the messiness of divorce. Probably divorce is a contributing cause to the current trend; witnessing their parent's travails may have put some of the twentysomething population off the idea of marriage. The irony here is that the "Focus on the Family" crowd have been frothing after the wrong culprit for so long. The real danger to the institution of marriage isn't gays who want it; it's straight people who don't.

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A Program for Response to Climate Change

The recent news that polar bears might disappear by 2050 shouldn't really shock anyone, but it does serve as a reminder that the global warming policies being proposed by our political elites are failures-in-waiting. That the Republicans have presented a suite of jokes as policy proposals is par for the course, but the Democratic approaches are equally weak. Most of them advocate cuts in greenhouse gas emissions, but that ship has already left port -- no cuts made over the next 40 years can prevent global warming, they can merely limit it. That's still a noble goal, and carbon cuts should be made, but the belief that we can do something to stop warming and then all will be well is fundamentally misguided. What we need and deserve to see from our candidates is not just their promises to reduce emissions, but their plan for mitigating global warming's impact.

Climate change will alter the temperature schedule and rainfall levels in many agricultural regions, producing novel climates in some portions of the country. Water may become scarce in some areas of the country now thickly populated. Sea levels will probably rise, threatening coastal regions. As supplies are exhausted, petroleum prices will begin to increase, making the modern suburban lifestyle less tenable for the middle class, especially when those price increases percolate through every other sector of the economy.

The response has to be multifaceted and nimble -- years of effort have not yet yielded any certainty on the precise effects of warming on the environment. So it would be a mistake for anyone to plan on the basis of any particular model. However, there are general steps that could be taken for preparedness.

Agricultural research and readiness: The United States has a plethora of agricultural universities, and now is the time to strengthen their research programs, with the aim of producing hardier, more efficient strains of our workhorse foods. Make use of the powerful techniques developed in the study of human health and bend them to the study and improvement of plants. Technical development should also be a focus: particular attention should be paid to the devising of more efficient irrigation systems. Pest control and topsoil management should also be priorities. Existing technologies should be pushed into use wherever possible; agricultural schools should be used as distribution centers to help local farmers put novel techniques into use. The government should take an active role in helping farmers adapt to the changes in local climate. The Department of Agriculture, in conjunction with local agricultural universities, should help farmers change what they grow and when they grow it so as to maximize productivity. This will have to come at the expense of tradition, and I'll miss Chilton County peaches if they have to go, but it's better for the food supply and better for the farmers if they're growing crops suitable for the climate they're experiencing.

Alternative fuels: By which I do not mean biofuels. In fact, biofuel initiatives should be abandoned immediately, not only because cutting forest to make way for biofuel monocultures is harmful to the environment, but also because biofuels will not substantially help carbon balance or warming in the long term. The simple fact is that burning biofuels is still burning something, and the additional CO2 and NO2 released during their cultivation will seriously diminish their potential to affect global warming. A recent (non-research) article in Science (subscription required) points out that sequestration of carbon in forests is superior to the use of biofuels from the pure greenhouse-gas perspective. Moreover, using arable land for biofuel monocultures will be a losing proposition when climate change stresses the food supply. Food prices in the United States and Mexico have already suffered some disruption from the proposed use of ethanol; when food itself starts being difficult to come by, the growing of corn for fuel (or even animal feed) is likely to be untenable.

If biofuels are to be used, then it ought only be when they can be produced exclusively from the refuse of existing food crops (cellulosic ethanol from cornstalks, for instance). Barring this, the government should enforce increasingly stiff fuel-efficiency requirements while pushing forward on research into non-carbon fuel sources for transportation. Simultaneously, every effort should be made to reduce the amount of automotive traffic required in everyday life...

Re-urbanization: Cities are crowded, messy, polluted, and filled with crime, but suburbs sprawl, destroy forests, promote excessive use of automobiles, and spread vile environmental impacts over a large area. As forests are our best friends in the fight against warming, anything that destroys them must be anathema. However, there is no way that any mandate of the government could shove everyone back into the cities. Rather, the government must work diligently to support the cities in their efforts to call people back by reducing crime and producing more family-friendly spaces. At the same time, the cities themselves must be revamped so that they are more environmentally friendly. "Green" buildings must be economically encouraged or enforced by statute. Public transit must be made as attractive and efficient as possible. Suburban sprawl must be curtailed, by inviting the nation back into the cities if possible, by forbidding further development in wooded areas if necessary. Increased property taxes encourage living in small spaces while providing additional revenues to support urban redevelopment.

Water Policy: Water management beyond the local level has largely been ad hoc up to this point, but with increasing populations in some major urban areas stressing the water supply of multiple states or large regions, a comprehensive higher-level policy must be put in place. The government should provide assistance to those wishing to move away from areas experiencing significant strains on the water supply, and help develop economic opportunities in areas where water is plentiful in order to make such moves desirable.

Disaster preparedness: One likely consequence of the development of novel climates is the destruction of the previous climates. In cases where temperatures rise and rainfall decreases, this will probably take the form of extensive forest fires. Even now it seems like every year brings a record number, and it's probably not because so many kids are playing with matches these days. The government will need to come up with a comprehensive plan for dealing with these fires without completely exhausting the men and women who fight them on our behalf. Trying to imagine and then plan for every possible contingency is a good way to get completely lost in details, but nothing DHS and FEMA have done since the Katrina disaster suggests that they have grown more nimble or capable. These agencies should be shaken up from top to bottom, and if necessary FEMA should be removed from the bloated and apparently completely ineffectual DHS.

This isn't everything that such a plan needs by half, and by this time next week I may have 3-4 more headings of components that are necessary. But it's telling that even the most environmentally conscious candidates seem to have only thought of one.

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Mr. Deeds goes to town

I hate the idea of submitting a paper to Proceedings of the National Academy of Sciences because if you get rejected you feel especially bad. Despite its relatively high impact factor, PNAS puts out a fair amount of garbage, and sometimes you feel like you're reading a dumping ground for the bad ideas of big names. Case in point is a paper from the lab of Eugene Shaknovich that just showed up in pre-publication form. Shaknovich is famous for performing simulations of proteins that rely on a reduced or "lattice" representation, and in the interest of full disclosure I'll admit that I'm highly dubious of this method. In this case, however, I'm relatively certain that the simulation produced a correct answer, for reasons that should become obvious as we go along.

Deeds et al. are out to address what seems like a fairly interesting problem of specificity in protein interactions. Most experiments performed in biomolecular laboratories make use of highly overexpressed proteins in relatively pure environments. This allows us to obtain quality information about the details of particular proteins and their interactions. However, what happens when we put these proteins into the cell at relatively dilute concentrations? If we consider a particular pair of interacting proteins, A and B, we know that their specific binding is strongly energetically favored. However, A and B probably have the potential to interact nonspecifically with many other proteins. If A and B are at relatively low concentration, and the cellular milieu is crowded with millions of these potential nonspecific interactions, can we be sure A and B will find one another?

To address this question, Deeds et al. construct their typical lattice models with two "proteins" that have a designed interaction, and simulated a situation in which up to 90% of a 3d space is populated by random "proteins" that have a small potential to interact with the targets. They let the systems equilibrate, and then take a look at the kind of interactions that are occurring. The findings are truly revolutionary, as you can see from the figure below. At low temperatures (A), the random interactions (blue) predominate when nonspecific-binding proteins are the larger component of the system. As the temperature increases slightly, to a point above the 'melting temperature' of random complexes, the designed, 'specific' interactions (black) begin to play a larger role, even at low 'concentrations' of interacting proteins. Finally, as the temperature really climbs, the specific interactions start to dominate the milieu.


So basically what Deeds et al. have discovered is that when the energy available from heat is enough to break random interactions but not specific interactions, then at equilibrium specific interactions are highly favored even if there is an awful lot of opportunity to bind randomly. On the other hand, if the temperature of the system is too low to break up random-binding events, then random binding dominates when most of the proteins are nonspecific binders. This is not a surprise, and hardly qualifies as a conclusion at all, even less so when you consider that this is a simulation (and thus that unsurprising results are likely to result directly from the assumptions used) and not an experiment on real proteins. This seems more like a control for some other experiment using this same system that derives some surprising conclusion.

Deeds et al. go on to make some important predictions from their discovery that energetics dictate binding (who knew kT could be so important?). For instance, they point out that in crowded protein-protein interaction experiments like the yeast two-hybrid screen there may be a lot of false positives, which must come as shocking news to any yeast two-hybrid researchers who have never read any papers or protocols about yeast two-hybrid screens, nor even Wikipedia. They also recommend using techniques that don't rely on overexpression, but the fact is that almost any molecular biologist would prefer it if he could answer questions using experiments that involved no overexpression. None of this is new, and to treat the insight as novel because some simulation showed it is just insulting.

In the end, this is a paper about a control, and not even a particularly well-written one. Don't get me wrong; it isn't bad for what it is, and I don't blame Shaknovich for trying to get it published in the best journal he could find for it. This is not bad science, but it doesn't tell us anything new, doesn't present a novel technique with wide application, or really provide any other reason to appear in a broad-based journal. I can and do blame PNAS for allowing in something that really ought to have been relegated to a specialized journal. And I will blame Shaknovich for the condescending tone of the discussion, in which he descends from his lofty computational height to tell us poor experimentalists "interesting implications" that we already knew. Too often, simulations get a bad rap from experimentalists, but this sort of paper, which will leave a bad taste in the mouth of anyone unfortunate enough to spend time reading it, makes that attitude seem justified.

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Oh damn that is so freaky

There's a lovely little article in this week's Nature about how moray eels eat their dinner (subscription required). Like nearly all fish, the moray has a second set of jaws in located in its throat, called pharyngeal jaws. The vast majority of fish use suction to transport food from the outer part of the mouth to the pharyngeal jaws. In morays, however, the suction is known to be weak, raising the question of how these particular predators manage to eat large prey. The answer, as it turns out, is a strange alternative mechanism: the pharyngeal jaws lunge forward to seize food in the moray's mouth and pull it into the throat, as shown in the radiographs below (arrow indicates pharyngeal jaws).


This unique approach to the problem is a fascinating story in biological structures. I, however, could not help but be reminded of another organism that has a mouth inside its mouth:

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Spongiform theology

I have just finished reading a couple of books by John Shelby Spong, once Episcopal Bishop of Newark and long a voice against the literal interpretation of the Bible. Spong's viewpoint really appeals to those who, like myself, view the Bible as containing principles of virtue rather than recitations of fact. The unfortunate thing about Spong's writing, besides his preacher's penchant for repetition, is that it appeals to those who, like myself, view the Bible as containing principles of virtue rather than recitations of fact. For very different reasons, Spong's books probably will not convince an atheist that there is anything of particular value in the Bible, and they certainly will not convince a Biblical literalist that it should be read as the epic myth it is.

The second point I take first because it is easier. Spong spends a fair amount of time in Rescuing the Bible from Fundamentalism going over some of the easiest-to-find contradictions in the Bible, and he repeats some of these in The Sins of Scripture. It's fair to point these out, but mere contradictions will never compel fundamentalists to change their approach to the Bible. Nor will their minds be changed by some of the "terrible texts" Spong quotes in Sins. Nobody ever remembers that Lot offered up his daughters to the mob as a gang-rape alternative, or that he later through incest fathered two nations with them. No, all anyone ever remembers is that God destroyed Sodom for being home to a bunch of gays, and then they go on about how Lot and his family were spared because he was moral. Nor will the fervent quoter of Old Testament purity laws feel any compulsion to renounce his wool-blend suit. And when he tries to get out of that by saying that the New Testament eliminates the old laws (a position he did not hold two minutes earlier when he called homosexuality an abomination), he will nonetheless admit to no obligation to tell his wife to shut up each time they enter a church. Consistency is not a thing fundamentalists require of themselves; thus they are unlikely to require it of their holy book.

In fact, Spong does plenty in both these books to alienate the literalist, not least his contention that Paul was gay. I regard his case for this as interesting but not compelling; the literalist will probably regard it as deeply insulting. Spong takes it as inspiring, and I can see how some literalists could view it that way, but my impression is that the typical fundamentalist uses the Bible as a post hoc justification for existing homophobia, and thus would regard the theory as entirely negative no matter what it implies about the saving power of Scripture.

So much for the fundamentalist. Spong's approach is almost entirely a loss. He comes closest to speaking to them when he points out that figurative or symbolic speech is a significant feature of Jesus' teachings. If the literal words of God are to be understood figuratively, shouldn't we look at "the word of God" the same way? But Spong doesn't do much with this point. He also in a few spots implies that viewing the Bible as inerrant and all-truthful makes it a part of the Godhead and is therefore idolatry. Again, he does not build on this point. Perhaps these aren't very strong (though I find them pretty compelling), but I feel that isn't his reason for shying away from them. The real reason is that his target audience is not fundamentalists who might be swayed by this approach. He's targeting people who already question their faith, or who have lost it by exposure to the fundamentalists. But does his work actually speak to these people?

In the end, I think it does not, or at least it will not call anyone to religion. Indeed, Spong makes it clear that what he seeks is a "religionless Christianity" or a "Christian humanism". He wishes to strip away the idea of a corporeal resurrection, a literal creation of the world, and a unique set of religious laws handed down through time. But without these things, what is Christianity? What are you stating when you say "I am a Christian, but I don't believe in the resurrection of Christ or that he was really the son of or consubstantial with God or that he died for my sins"?

Spong thinks it means something to say that, but what? That you agree with most of the things Jesus says in the gospels, except for the ones that are about God? If that's it, then you're just reading the gospels as third-hand philosophical dialogs, like a copy of a copy of some illiterate fisherman's recollection of a reading of Phaedo. Jesus takes the role of Socrates, dispensing wisdom and ultimately getting killed by his enemies for no good reason, and why bother? Reading the Bible as philosophy just makes you a worse Humanist, because there's no derivation of the New Testament's truly revolutionary principle other than to say it comes from God's love.

If you are coming to Christianity from without, what does believing in this add to your life other than useless dogma? If you are fleeing Christianity from within, what is there in this approach to bring you back into the embrace of the church? Nothing and nothing. There are better places to find a message of love for one another, undiluted by the racism, sexism, and absurdity that mar the pages of the Bible. If you already believe in loving your neighbor, why clutter that up with the baggage of Christianity? And if you feel that a logical derivation from first principles doesn't support loving your neighbor, what about Christianity will convince you? Spong's approach doesn't give anyone a reason to join Christianity or even just stay. Whoever you are, there's nothing in it for you.

Spong is right about one thing: Jesus had a revolutionary message for his day, one even most Christians today barely acknowledge and almost never put into practice. And the more loudly they proclaim their Christianity the further away from this message they usually are. This idea, running very much against the prevailing thought of the day, so transformed those who adopted it that they dressed his life up in the raiment of myth. That myth has swallowed the reality, and grown so large that the original message is suffocating to death beneath a blanket of hatred and mindless dogma and dead-hearted "Christians" carrying signs that say "God hates fags".

If you take it literally, the story of Jesus is a superstitious morass no self-respecting empiricist could really believe. Taken figuratively, it is a story about how the enormous power of Jesus' message can transform a person, not only in his dealings with others but also in his feelings about himself. Does the message have this power because God was within Jesus, or because God is within us? Does the resurrection mean that a dead man rose up, walked on water, and flew off into the stratosphere, or does it mean that God and Jesus are reborn within us every time we accept the message and live it out?

Spong doesn't seem to answer these questions, and really, I'm not sure he wants to try. In the end, these books are of value, because they illustrate that a man can hold on to faith while acknowledging that his holy texts are human documents that exist in time, not divine writs that exist beyond it. He does much to explain the historical context of the different books of the Bible, and their role in the evolving story of Judaism and Christianity. But Spong's vision for the future of Christianity is a road down which no true believer will go, nor any non-believer need go.

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What are you keeping that for?

Analyzing the conservation of DNA and protein sequences has proven to be an incredibly valuable approach in structural and molecular biology. The fundamental principle underlying the use of conservation data is the idea that conserved sequences are invariant for functional reasons. Changing the amino acid or base at these conserved sites, it is assumed, would lead to a catastophic structural disruption of a protein, eliminate an important functional group, or (in the case of DNA elements) substantially distort expression levels or splicing. If this is so, genetic elements that are ultraconserved (>200 bp segments that are 100% conserved between human, mouse, and rat genomes) should be positively essential to the survival of an organism. However, a recent study published in PLoS Biology (open access) indicates that removing at least some of these ultraconserved elements (UCEs) has little or no effect on development or longevity in mice.

Ahituv et al. knocked out four ultraconserved elements in C57BL/6J mice, none of which are known to code for protein. This is normal; more than half of these ultraconserved regions (481 have been identified) are not transcribed into RNA. It's thought that these non-coding regions are important for gene regulation, and some preliminary experiments suggested that this would be the case for these four. But homozygous or hemizygous (some of these genes were on the X chromosome) knock-out mice developed normally, for the most part, and were born in roughly the ratio one would expect from a Punnett square. Gender ratios and litter sizes were also normal -- this is particularly compelling in the case of the 2 UCEs located on the X chromosome. If losing these UCEs were fatal or even mildly problematic, we would expect to see some evidence of this in the gender ratio of the pups.

Element deletion was not entirely without effect. Knocking out one of them caused a very low incidence of male mice born with only one kidney. Another had a slight effect on the expression of a gene called Sox3 in the developing brain. However, the genes flanking these deletion sites have much more serious effects when they are deleted or otherwise disrupted -- several of these cause embryonic lethality. So the UCEs have enormously reduced effects compared to the flanking genes.

If they're not important, why are these regions conserved? That's a tough question, and in a way hinges on a false impression. This particular disruption of these regions did not adversely affect an extremely inbred pool of mice that were well-fed and kept in controlled climates. That is, these organisms are genetically abnormal and face little stress. Their responses to these mutations may not be indicative of mice in general, or even of other strains of laboratory mice. Moreover, these regions may only be important in stress conditions that are nonetheless ordinary -- development under conditions where some nutrient is absent or rare, for instance. Or the effect may only be felt after many cumulative generations.

Another possibility is that of redundancy or subtlety of phenotype. Some other element may be acting to do the job once performed by these UCEs. There is a similar story with growth factors, expressed proteins that are essential but nonetheless seemed not to produce a phenotype in mice unless several were knocked out of the genome simultaneously.

And finally, there is a possibility that the reason UCEs do not mutate is not that they are essential but that they can easily gain function that is fatal. That is, mutations turn the UCE into a toxic piece of DNA, but some minor function keeps them in the genome. This interpretation is not as well supported by existing data, however, which suggest that it is specifically the loss of these elements that reduces fitness.

As usual, this interesting work raises more questions than it answers. Understanding the reasons why UCEs are preserved with such high fidelity through various species will likely contribute a great deal to our understanding of expression dynamics and evolution.

Ahituv N, Zhu Y, Visel A, Holt A, Afzal V, Pennacchio, L. A., Rubin, E. M. "Deletion of Ultraconserved Elements Yields Viable Mice" PLoS Biology Vol. 5, No. 9, e234

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That's a spicy cupcake

Condolences to Katie for her school's embarrassing loss to 1-AA (or whatever they're calling it now) Appalachian State, a devastating failure that has effectively ended their title hopes for the year. Even if Michigan never loses again, the poll voters are never going to forget that they dropped to a lower division school, and even if they are struck by collective amnesia the computers will punish Michigan in November for their showing today. To be fair, it was not an easy win for App. State (a 2-time 1-AA champion) by any means, and Michigan could have won it. But bad coaching decisions and subpar play gave the day to a school better known for taking an annual early-season drubbing from UNC's basketball team than for their excellence in lower-division football.

This is the time of year when pundits complain about the cupcake schedule that many teams employ in the early part of the season. The advantage of scheduling these games for the big Division I schools is not the easy win per se, but the opportunity to get your team tuned up under fairly low-pressure conditions. In essence, these are the equivalent of preseason games, and there are a lot of reasons to dislike them. From a selfish perspective, they are unhelpful and potentially dangerous to a title bid, particularly when the computer rankings have a go at them. In a larger sense, they do a disservice to the sport by dampening enthusiasm. Who can really get worked up for the college opening weekend when presented a barn-burner like Texas A&M vs. Montana St., or Michigan vs. Appalachian St. for that matter? But today's experience brings up another selfish reason to avoid the cupcake: unlike the NFL preseason, your cupcake game counts. What happens if that puff pastry actually manages to win?

Well, we have the answer in this case: Michigan's title hopes are over. And congratulations to Appalachian State for it.

The only pity is that almost nobody saw the great game App. State put on except in highlights, thanks to the Big Ten's ill-conceived and inconsiderate decision to put all their lower-tier games onto their own special network that, incidentally, almost no cable subscribers can receive. The reason for this is that the cable networks (rightly) refused to put the channel on the basic tier, and the greedy bastards at the Big Ten decided that if they couldn't get what they wanted then they weren't going to play. Games that used to be broadcast by ESPN Plus, ESPNU, or regional broadcast teams like Jefferson Pilot Sports have now been relegated to an obscure channel almost nobody gets. The victory might be their karmic reward for their selfishness.

Originally that last sentence included a truly ghastly pun. Perhaps I'm learning restraint?

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