The ones I'll remember

It's the end of a decade, which means a vast array of retrospectives for video games and movies and whatever the hell else. Assembling a "best of" list for games is a tricky and probably futile task, especially for a one-man show like this site. Games take too long to play, are too diverse in their experiences, and are spread across too many expensive platforms for one man to sample everything that might be a classic, or even everything that other people think is classic. Besides that issue, many games that are awesome experiences at the time trickle out of your mind to be forgotten until you see the case sitting on your shelf. So this is not the definitive best-of-the-decade list, nor is it even my best-of-the-decade list. This is my best-remembered list. These are the games I think about when I play other games, when I'm reading books, when I'm watching television. They are the games that have stuck in my mind long after I removed the disc from the tray, the games I think of playing again at least once a week. I'm not sure they're the best games of the decade, or even the best games of their respective years of release, but they're the games I'll remember.

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A single residue dictates a fold

Anfinsen's dogma — that the amino acid sequence of a protein uniquely determines its structure — naturally leads one to the idea that identity between amino acid sequences means identity between structures. This has proven to be a successful paradigm: sequence similarity reliably predicts structural and functional similarity. Evidence accruing in recent years, however, suggests that for small proteins, at least, this assumption may not be entirely safe. Adding to this view, in an article in PNAS this week (it's open access, so open it up), a research team led by Philip Bryan reports that they are able to generate significantly different folds with divergent functions from sequences that differ by a single amino acid.

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Non-native hydrogen bonds mediate structural transitions

A few weeks ago, I wrote that the goal of a structural biology research program ought to be to "characterize the conformation and energy of key, functionally-relevant members of the protein's structural ensemble and identify the pathways between them." The Nature paper last week, among other examples I mentioned in the preceding post, described functionally significant minor members of the native-state ensemble, and this is certainly an area where structural studies are making a lot of progress. But what about the other part of that statement, the transition pathways? How are we to study them, and what can we learn about them? Experiments alone are unlikely to tell us everything we want to know about the intermediates between different native structures. We can, however, use simulations validated by experiments to investigate the mechanisms of structural change. Today in Cell, research primarily performed by my coworkers Alexandra Gardino and Janice Velos demonstrates that the bacterial signaling protein NtrC  rapidly samples its active conformation even when it is not phosphorylated. Moreover, they confirm predictions that the intermediates between these two states are stabilized by hydrogen bonds not present in either one.

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Alternate structures and catalysis in cyclophilin

Of all the sources of structural variability in proteins, the hardest to pin down is side-chain conformational heterogeneity. Side chains aren't always easy to model into their primary conformation in the first place — you need excellent crystal diffraction or NMR data to do it. Even if you pulled that off, it's not always clear how (or if) side-chain fluctuations relate to a protein's activity. If we carefully examine our data for the faintest signals, however, we can sometimes find evidence of secondary conformations that play an important role in function. In an article in this week's Nature, James Fraser, myself, and others show that in the case of the proline isomerase cyclophilin A (CypA), alternative conformations of side chains play a key role in catalysis.

Previous experiments on CypA had established that the backbone amide groups of many residues were sensitive to a conformational fluctuation on the millisecond timescale. Under conditions where this enzyme is saturated with a peptide substrate, the fluctuation rate for some of these residues is very similar to the catalytic rate, suggesting that the dynamics and catalysis are linked in some way (2). Later experiments also showed that this fluctuation was an intrinsic property of the enzyme, continuing even in the absence of substrate (3). What we didn't know, however, was how the dynamics of cyclophilin were related to catalysis. We couldn't know, because we had no idea what the motion we were detecting was.

In the case of enzymes like adenylate kinase, there is a dramatic rearrangement of structural elements, and the population of conformations corresponding to the "end points" of that motion can be significantly enriched by altering the amount of substrate present in solution. In the case of CypA, neither of these things seems to be true. Supplementary Fig. 1a (freely accessible from the article page) neatly encapsulates the problem. For this figure, 48 structures of CypA, some with ligand and some without, were aligned, and the variation between them was determined. While there is some variability in the chain conformation, it is primarily limited to a group of residues known to undergo fluctuations that are not related with catalysis (blue chain). The residues involved in the catalysis-related dynamics don't seem to have much variability, even across this fairly large group. So we can't trap the unknown, minor state of CypA by adding substrate, and there's no evidence of an alternate state that explains the NMR data.

Knowing this, we suspected that some kind of side-chain motion accounted for the observed dynamics, probably involving an aromatic group of some kind. Our efforts to gather evidence for this, however, ran into some typical NMR problems — resonance overlap and poor sensitivity exacerbated by chemical exchange. Fortunately, the crystallographers came to our rescue, in the form of Tom Alber and his super-talented grad student Jaime Fraser. Jaime had determined a crystal structure of CypA at cryogenic temperature and analyzed the data using their algorithm RINGER, which examines electron density below the threshold typically considered "noise" in order to identify possible alternative rotameric states of side chains. He found evidence of multiple conformations for a few residues, but nothing that would explain the NMR results. Jaime had the bright idea to redo the experiment at room temperature, which Tom was convinced would result in nothing more than a radiation-damaged crystal and bad diffraction data.

What actually happened was that when Jaime examined the electron density from that experiment he could identify a group of side chains that had more than one conformation in the crystal, which you can see in Fig. 1. These residues included serine 99, methionine 61, and the catalytic arginine 55. Right in the middle of this group was phenylalanine 113, a residue with an aromatic side chain capable of causing changes in chemical shift at relatively long range. For context, the image to the left shows a structure of cyclophilin (PDB code: 1RMH) in complex with the model substrate we used in our own experiments (succinyl-Ala-Ala-Pro-Phe-p-nitroaniline), with the side chains of S99, F113, M61, and R55 in red. As you can see, F113 and M61 form part of the floor of the binding pocket, with S99 rather remote.

So here we have an alternative structure of CypA, hidden below the threshold typically considered when determining a crystal structure. It was certainly plausible that fluctuations in this ensemble of side chains could give rise to the NMR observations, but plausibility isn't proof. One way to address this would be to try and force CypA to adopt the less-populated conformation. If you look at Fig. 1d you can see that the two conformations of S99 lie at the standard rotameric positions, and that the less-populated rotamer of S99 would run into the more-populated rotamer of F113. So, if you replaced one of the side-chain hydrogens of S99 with a methyl group (i.e. mutated the serine to threonine), that might push the other residues of this group into their minor conformational state. So, that's what we did.

To the right you can see an overlay of structures for wild-type (WT) CypA (red) and S99T (green), aligned using structural elements on the opposite side of the protein from the active site. As you can see, the backbone traces match very closely, except for the helix and loop on the right. These elements are involved in crystal contacts in the S99T structure, but not the WT; a lower-resolution structure of S99T shows no differences here. Another key difference between these structures, of course, is the position of the side chains (thick neon); as shown here (and more clearly in Fig. 2c) they seem to have adopted the minor conformation from the WT structures. Although this mutation inspires widespread chemical shift changes (Fig. 3a) consistent with the hypothesis that this concerted side-chain rotation gives rise to the NMR observations, the structures seem very similar. Yet, S99T CypA differs from WT in two important ways.

The first difference is that the conformational fluctuations are dramatically slower, but only for residues that showed catalysis-related dynamics in WT (Fig 3d). In fact, this rate is now so slow that due to a quirk of NMR we can only determine the slowest rate of the process. At 10 °C, this fluctuation in S99T is about 60 times slower than the slowest process in WT.

The second key difference between the mutant and the WT is that catalysis is dramatically slowed. Because CypA does not consume its substrate (it acts on both cis- and trans- proline bonds) its activity can be assayed by NMR, as you can see in Fig. 4. As with any enzymatic assay, the net activity is proportional to the amount of enzyme added, so just glancing at these spectra (and knowing the enzyme concentration) you can estimate that S99T has at least 40-fold lower activity than WT enzyme. If you actually perform the fits, it turns out that the reaction velocity for S99T is about 240 times lower than that for normal CypA, but this includes a contribution due to the fact that S99T does not bind its substrate as tightly either. If you correct for this, it turns out that S99T has about 70-fold less activity than the normal enzyme. Not only is this similar to the change in dynamics, it's also quite comparable to another mutation, R55K, that removes a group that performs some of the chemistry.

These results indicate that a conformational change in a group of side chains including F113 is primarily responsible for the chemical exchange behavior observed in WT. The S99T mutation stabilizing the minor conformation dramatically and similarly reduces both the conformational fluctuation rate and the catalytic rate. This suggests that dynamics and catalysis are linked not by happenstance but by some direct relationship. Unfortunately, these experiments do not provide any direct insight into the mechanism by which dynamics contribute to catalysis. They do establish, however, that in CypA coherent fluctuations of side chains, barely detectable in protein crystals, nonetheless make a critical contribution to function.

1) Fraser, J.S., Clarkson, M.W., Degnan, S.C., Erion, R., Kern, D., & Alber, T. (2009). Hidden alternative structures of proline isomerase essential for catalysis Nature, 462 (7273), 669-673 DOI: 10.1038/nature08615

2) Eisenmesser, E.Z., Bosco, D.A., Akke, M., & Kern, D. (2002). Enzyme Dynamics During Catalysis Science, 295 (5559), 1520-1523 DOI: 10.1126/science.1066176

3) Eisenmesser, E., Millet, O., Labeikovsky, W., Korzhnev, D., Wolf-Watz, M., Bosco, D., Skalicky, J., Kay, L., & Kern, D. (2005). Intrinsic dynamics of an enzyme underlies catalysis Nature, 438 (7064), 117-121 DOI: 10.1038/nature04105

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Don't look for "the" structure

It surprises me how often I hear students, postdocs, and even professors talk about determining the structure of a protein. A singular structure has the advantage of being relatively easy to interpret, but the cost of this is often the loss of functional data. It's easy to understand how this terminology emerges from the discipline of crystallography, which after all only works when the protein molecules adopt only a small number of conformations. Yet even when it comes to NMR, a technique that should be very sensitive to the fact of structural multiplicity, the language of researchers and the structural tools available to them are too often oriented towards the idea of a singular structure. But any representation of a protein as a single conformation is a simplification — every protein exists in multiple structural states.

Trivially, we are aware that a given polypeptide chain can adopt a number of different conformations — the "folded state" of any given polypeptide chain covers only a tiny sliver of the possible conformational space. A protein that is "unfolded" occupies not a single, well-defined state but a vast multiplicity of states, and this kind of statement is not controversial because we tend to imagine unfoldedness as a messy chaotic jumble of conformations. The reality is less cut-and-dried: although unfolded proteins may have no regular structure, many still have a propensity to form particular secondary structures or interactions. The reality of denatured proteins is that they have a complex and varied energy landscape, not an array of possible structures that all have roughly equivalent energy. The flipside of the popular view is that the a protein's native state draws down to a sharp energy well, and this conception is also misguided.

The most dramatic counterexamples to the idea of a neat, punctate energy well come from proteins that adopt several different folds in the native state. One relevant case is lymphotactin, which freely interconverts between an α/β monomer and an all-β dimer under physiological conditions. Lymphotactin may be unusual, but the principal message from that study is one that ought be paid attention to in others, particularly when the protein in question has functional conformational diversity. Consider α-synuclein, a protein implicated in Parkinson's disease. In the presence of some detergent micelles this protein is known to take on an α-helical hairpin structure, with two helices laying down on the charged surface of the lipid headgroup. In solution, however, it seems to take on a number of different forms, and may interact with true lipid bilayers in a completely different way than it interacts with micelles. For proteins that interconvert between several different physiologically-relevant folds, one is never pursuing the structure, but rather a structure.

Of course, we don't expect most proteins or domains to regularly adopt alternate overall folds. However, reorientations of domains or monomers is a relatively common behavior, and one that poses a sticky challenge for structural biologists because incidental properties of a particular arrangement may bias our experiments towards observing it. A minor member of the ensemble, if it has favorable packing geometry, may exclusively populate a crystal. Similarly, NMR experiments to determine domain arrangement via residual dipolar couplings must always be undertaken with an eye to ensuring that interactions with the aligning media do not bias the results. No single structure of adenylate kinase can instruct us about its catalytic cycle, and structures of the unbound state do not capture the reality that the protein continues to open and close in the absence of ligand. Single structures do not capture motions of domains or monomers relative to each other and that often means an incomplete understanding of function.

Domain motions are also an overly dramatic example, because simpler rearrangements of the backbone take place in many proteins, even when regular secondary structures are evident. Fluctuations of the main chain play a functional role in several proteins — as, for instance, in the flaps of the HIV protease. Additionally, rearrangements of the backbone have a significant role in signaling, as in NtrC, which I'll talk about more in two weeks. Proteins where the main chain rearranges in response to ligand binding or post-translational modification generally cannot be described by a single structure.

Even if the backbone is rigid, every protein will have flexibility in the side chains of its amino acids. One of course expects to see this kind of behavior in side chains on the surface of a protein, where it is usually dismissed as irrelevant. However, we also know that side chains can rotate and move in the core of a protein, and that on some protein surfaces they can undergo coherent rearrangements. I'll talk a bit more about the functional relevance of side-chain motions next Thursday. For now, suffice to say that side chain rotations cannot be so easily ignored and sometimes have functional effects. Structural studies that do not capture these rotations may be missing something important.

My point here is not that single structures are stupid or useless. A structure can be very informative about about a protein's function, and often has great power to explain the effects of mutations and ligands. However, we should not mislead ourselves into thinking that any single structure will have all the answers, or indeed any of them. Every protein is a constantly interconverting ensemble of structures, and there are many layers of structural diversity within that ensemble, reaching from whole fold rearrangements to "mere" side-chain adjustments. Determining the structure of a protein is not a coherent goal for a research program. The successful structural biology study will characterize the conformation and energy of key, functionally-relevant members of the protein's structural ensemble and identify the pathways between them.

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Chosen at birth

Last post, I mentioned that the tendency to choose segregation as a means to solve problems was a feature of many societies in the world of Dragon Age. Another, related motif appearing in many Thedan societies is the existence of a rigidly-defined social order in which a person's status and even his occupation are set at the moment of birth. To varying degrees this kind of social rigidity appears in almost every social group in the game (except the elves). Through its dialogue and plot, Dragon Age: Origins repudiates these systems, but in its mechanics it supports them.

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Out of sight, out of mind

Playing Dragon Age gave me a relatively frequent sense of déjà vu. Although the game portrays a number of different nations and societies, there are recurrent features that speak to underlying ideas about the psychology of its inhabitants. One such motif is the tendency for its denizens to solve their problems through segregation. At several levels, the people of the continent of Thedas like to resolve issues by pushing problematic groups into isolated areas and pretending, as much as possible, that they no longer exist.

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A few things

I promise there will be actual content in essay form later this week, but I have to kick the week off with some housekeeping. Some of this is bad, and some of it is good (or I hope it's good).

Bad news first: I've been getting pretty regular comment spam on this blog for about a month now, at a rate of about one post every half day or so. I don't know why anyone's bothering — most of the posts affected are at least half a year old — but it's still pretty irritating to click back to the blog every day to delete internet pharmacy ads written in badly formatted bbcode. Blogger doesn't give me a lot of options for dealing with this, and I'm not in the mood to migrate to some other platform. So as a first step I am turning on moderation for all posts more than 90 days old. The only kind of comment I will refuse is an obvious advertisement, but comments will obviously show up slowly on those posts. My other options are to block anonymous comments, which I definitely will not do, or to use a CAPTCHA, which I find to be annoying and have evidence is only moderately effective. Hopefully this will resolve the issue.

On the good side, my friend Ben Abraham, proprietor of the SLRC blog and organizer of Critical Distance, is going to be visiting GDC. Michael Abbott and David Carlton have already gotten him a pass, but since Ben is in Australia and GDC is in America, there's a rather expensive plane ticket to deal with. On the right side of the blog you can see a little widget for donating money to help cover the cost of that flight. I'd appreciate it if you could spare a few bucks to give him a hand.

If giving money to Ben doesn't sound like something you want to do, then I hope you'll find space in your budget to give a few dollars to Penny Arcade's annual Child's Play charity drive. Child's Play buys toys, books, and games for children's hospitals throughout the world to help make the lives of children with serious illnesses much less miserable. I spent a lot of time in hospitals myself as a kid, and the only parts of those stays that didn't suck terribly was the time I got to spend getting my ass kicked by the original Legend of Zelda. You can donate money, plain and simple, or you can choose your local children's hospital and buy something from their Amazon wish list. There are items on those lists that cost as little as $10 and will make a big improvement in what is usually a horrible experience, so please donate something if you can.

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The uncertainty principle

Although it uses conventional horror tropes, Condemned: Criminal Origins takes an unusual approach for a survival horror game. Survival horror often generates tension through resource scarcity, limiting the player's ability to fight or heal himself, but because of its melee combat focus Condemned is necessarily limited in this respect. The relatively plentiful checkpoints mean that the player usually isn't punished excessively for failure. Yet Condemned is a frightening, tense game because it artfully keeps the player from knowing what is coming next.

Condemned has a significant advantage when it comes to generating fear because of its visceral combat. While a few guns can be found in almost every level of the game, its hero Ethan Thomas can't carry ammunition for any of them. As a result, he is forced to improvise melee weapons from the environment, and fight his enemies up close and personal. Moreover, he's not fighting fantastic creatures, but ordinary people who have taken on (in most cases) a subtly monstrous aspect. The close quarters and melee brutality make the combat intrinsically frightening, but if that were all that Condemned had going for it, it would not be a truly scary game.

Video games pose a special problem with regard to creating fear because any game is a system that can be mastered. If the designer wishes to evoke a fear response through an attack on the avatar, he must contend with the player's ability to manipulate a game's combat systems. If the player becomes proficient at fighting off the enemies, or lowers the difficulty to compensate for his incompetence, then the onset of a fight stops being frightening and starts becoming a problem to be solved. Similarly, if a cue or activity is known to precede a fight loses its power to develop fear. These moments cease to be tense and instead become a time where the player prepares himself for a battle he knows is coming. Knowing that a fight is about to happen lets the player feel in control of moments where he is meant to feel vulnerable. To be frightening, a game must re-weight the power relationship in favor of the designer, rather than the player.

Condemned presents just this kind of activity in the form of crime scene investigation tools that Ethan must use to track down the serial killer who has framed him. The player often must use the tools in order to find vital clues, but Ethan cannot hold one of these gadgets and a weapon simultaneously. Thus, every use of an evidence-collection tool leaves Ethan vulnerable to attack. In any number of games this would form the basis of a recurring sequence: see clue → collect evidence → get assaulted. The player would enter the state just described, in which starting to collect evidence would signify the onset of a combat sequence and allow the player to feel control. Instead, the developers of Condemned chose to attack the player during the course of evidence collection only occasionally. Sometimes Ethan gets attacked while he collects evidence, and sometimes he does not. The player cannot develop mastery because these sequences have ambiguous outcomes.

Condemned plays with this idea in other ways as well. Environmental sounds sometimes signify an imminent attack, and sometimes do not. In one level, some mannequins turn into enemies and others, often indistinguishable, don't. The levels occasionally rearrange themselves, without regular signifiers. Condemned avoids predictability, and this denies power to the player.

The finest articulation of the skillful design that went into Condemned comes in its penultimate chapter, in which Ethan must search the (apparently) empty house of the serial killer for clues. The killer has written trails of words that lead to important spots, but these can only be seen if the player uses Ethan's UV lamp. The whole house becomes an evidence collection routine, but the developers resist the urge to have enemies burst out of every door and window as Ethan searches. The occasional attacks they employ instead support the tension of the sequence without letting the player view it as a combat routine. This level is so memorable in part because of the exquisite suspense it generates.

The most interesting thing about choosing to attack at only some of these junctures is that it doesn't come at any cost. From studies of conditioning, we know that using a variable schedule of positive or negative reinforcement (i.e. not reinforcing every time) is no less effective at generating a desired response than continuous reinforcement. In fact, research has shown that conditioned responses created using variable reinforcement are more resistant to extinction than those created with continuous reinforcement. By associating the fear of a surprise attack with just some of these evidence-collection routines, the developers guarantee tension in all of them, without granting the player any feeling of power over the game.

Condemned ultimately falls down because of its last level, an uninteresting romp across a farm, beating down mutant hillbillies on your way to a dull and conventional final boss. Up to that point, however, Condemned cleverly steals power from the player by avoiding routine. Because the player can never be certain when an attack is coming, the intrinsic fright generated by the game's brutal combat is never diluted by the player's mastery. The player's uncertainty perpetuates his fear.

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Capsule: Nostalgia

Final Status: Story and most low-level side quests complete.

Put This on Your Box: At last, a game that ignores Britain's long history of brutal aboriginal repression!

Most Intriguing Idea: Evoking the 19th-century adventure novel in a game.

Best Design Decision: Near-ideal implementation of turn-based combat in the ground battles.

Worst Design Decision: Incredibly unbalanced and tedious airship battles.

Summary: Nostalgia unapologetically grabs for dated JRPG tropes, and for the most part succeeds in creating a pleasant experience. We have a chipper sword-wielding teen with spiky blond hair, a demure teenage girl with magic powers and amnesia, and two spunky orphans, all out to save the world from... well, it's a JRPG, so the story doesn't make much sense anyway. This time the hash is made with an inappropriate fusion of Norse and Greek mythologies, if you're keeping score. Battles proceed using a turn-based system similar to Final Fantasy X. The system is sharp, transparent, and perfectly executed (graphically appealing too: this is a quality game). On the ground, the difficulty curve is quite gentle and the battles are mostly easy. Even if you never take a single side-quest you will probably be perfectly prepared (or even over-leveled) when the end of the main story comes. The aerial battles are another matter: they are brutally difficult and often unwinnable. Players will frequently find themselves unable to either hit the enemy ship at all, or to escape. When victory can be achieved, it can sometimes take up to ten minutes to whittle down the massive life bars of enemy airships. Even at low altitudes, relatively frequent encounters with enemies that totally outclass the player's own Maverick airship occur well into the game, forcing frequent reloads. Nostalgia also appears to have the warm fuzzies for the British Imperium, but not a lot of time to spend on acknowledging what that meant for people who weren't white. To an extent this is excusable because the whole goal here is to evoke the feel of a Victorian adventure novel (the hero's parents have separate bedrooms), but it adds to the sense that this game is out of date — in this case, by at least a century.

If you can't say something nice... When it stays on the ground, Nostalgia is a fun little romp evoking pleasant memories of JRPGs past.

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Capsule: Mario & Luigi: Bowser's Inside Story

Final Status: Story finished.

Put this on your box: I HAVE CHORTLES!

Most intriguing idea: Leveling up your arch-nemesis to defeat your other arch-nemesis.

Best design decision: Constantly layering something new and interesting on the core mechanics.

Worst design decision: The unbalanced dodge mechanic and the tedious temporary invincibility in the boss fights.

Summary: Mario & Luigi: Bowser's Inside Story follows an established pattern for the Super Mario role-playing games. It combines light platforming action with turn-based battles that are supplemented with timing-based action to improve damage or defense. This has worked before and it works here, creating a perfectly competent RPG where Mario and Luigi roll around in Bowser's guts, powering up the big spiky turtle so he can take down the ludicrous Fawful, who has conquered both the Mushroom Kingdom and Bowser's domain. The gameplay is mostly solid, but the dodge mechanic is unbalanced. If you figure out the dodge for an attack, you'll never take a point of damage, but if you don't figure out what to do or the proper timing for it you will die constantly. Earlier RPGs in this series mostly used the dodge to reduce rather than eliminate damage, and that would have been a wiser choice here, as the ability to escape harm completely seems to have encouraged the designers to make enemy attacks very powerful. In addition, many of the bosses have some kind of invulnerability (Fawful, for instance, is effectively invincible for five turns at a time), which makes fighting them fairly tedious. On the plus side, every area inside of Bowser seems to have its own interesting twist, making sure the platforming never gets old, and powering him up uses some nifty rhythm games that I rather liked. The writing mostly works well, especially when you encounter the loopy dialogue of characters like Fawful, Sakon, or the doctor. Unfortunately, Bowser himself is pretty one-note, although his tough-love attitude towards his subordinates, and their adulation towards him, can be pretty funny. After a while, though, he wears thin, and there's so much of his dialogue in the game that it gets a bit tiresome. For me, the game overstayed its welcome a bit, but despite some minor design hiccups it's a high-quality experience that delivers both humor and gameplay depth.

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Blog of the Round Table: The denouement of the rings

The role-playing game, as a genre, owes much to the imagination of J.R.R. Tolkien. The same could be said for much of the fantasy genre in film and literature as well, but the diversity of approaches in these media reflects intricate linkages to multiple concepts of fantasy and folklore. Role-playing games, which build lengthy, epic storylines in fantasy worlds populated by multiple sentient races, follow in the footsteps of Tolkien's magnum opus. In terms of the time investment and the breadth of the imagined world, many RPGs are quite similar to The Lord of the Rings, but while that trilogy keeps going for several chapters after the climactic fight with the forces of Sauron, a game typically stops dead after its most intense battle, with ill effects for both character arcs and the closure of the story. Since they've taken so much from Tolkien already, perhaps games could look to his last chapters to find inspiration for gameplay beyond the climactic fight.

Let's begin by considering the case of Eowyn and Faramir, two characters who are slowly falling in love during the late phases of The Return of the King. Their stories effectively end with a scene in which Faramir confesses his love and asks Eowyn to consider him. It's not particularly realistic, but RPGs that have a particular focus on relationships and the use of conversation trees (Mass Effect, for instance) could take a cue from this. A relationship that has developed slowly over the course of the game could be realized in the aftermath of the final battle. Obviously, you could make this dependent on successful navigation of a conversation tree. In a game like Mass Effect that links conversational proficiency with actions and attitudes during the game, making this tree impossible for a particular alignment could be a way to emphasize the personal cost of the decisions that have been made.

As part of his closing arc, Aragorn, who is concerned about his ability to maintain Gondor in the future, is led by Gandalf into the mountains, where he finds a seedling offspring of the sacred tree Nimloth, symbolizing the rebirth of the nation. This is, essentially, the novelization of a fetch quest, and a gameplay denouement of this kind would require some extra elbow grease to be emotionally effective. However, if an appropriate symbol is developed throughout a game, then a mission to retrieve that symbol could be a good way to bring closure to an epic RPG. Having defeated the great enemy, you find an object that matters personally to the characters and implies hope for the future.

The hobbits have the most elaborate denouement, in the form of their journey back to the Shire, and the elimination of the forces endangering it. This approach has several advantages, which are shared between trilogy and game. Firstly, many interesting characters are developed at the beginning of the story who must necessarily be left behind when the journey at the core of it begins. Returning to those characters reminds the player (or reader) of the things that seized his interest back when he started. Additionally, seeing the central characters in the presence of the initial supporting cast again provides a yardstick for measuring their increase in maturity, confidence, and power. Because RPGs, particularly of the Japanese variety, are often concerned with the maturation of the hero as a parallel to his leveling up, this is an effective way to reflect on the implications of the game as a whole.

The triviality of the destruction of the forces of the Shire displays the newfound strength and leadership of the hobbits of the Fellowship, but it also points out another possibility for closing out a story. For some reason it is typical to have the final boss or the leader of the opposing forces be some immensely powerful warrior, but this need not be the case. You could set up a story where a relatively weak king is supported by an army of incredibly powerful soldiers. Defeating his minions could be tough, but the king himself could be a trivial boss. The climactic battle could come much earlier than the final fight, with the last battle in the game serving as an expression of a new power relationship in the world. Something along these lines occurred near the end of Final Fantasy X, where the real climax of that game is the battle against Yunalesca and the bosses within Sin constitute various moments of farewell, although admittedly some of these fights are not easy.

The final phase of The Lord of the Rings that I want to draw attention to is the departure of the ringbearers from the Grey Havens, symbolizing their passage into the next life. Characters in RPGs often die as a part of the story, or occasionally (as in the Fire Emblem games) perish permanently if they fall in battle. A journey to carry their spirits to the next world, or simply to return their bodies to their home villages, could provide gameplay that puts those losses in context. One could also make the bodies a physical burden in some way, making this journey more difficult in a Lonesome Dove kind of way.

Of course, these various approaches could also be combined in various ways to provide a closing chapter that follows the climactic boss. My point here is not that The Lord of the Rings is the apotheosis of effective denouement in fantasy storytelling. However, the way it ties up its character arcs contains a number of ideas for developing a more interesting closing to an RPG story than just a cutscene followed by a credit scroll. Extending the gameplay beyond the climactic boss offers the opportunity to put a satisfying cap on the character and world development, and thus make the whole story a richer and more rewarding experience.

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Not quite legendary

A music fan, particularly a fan of a musical style that has acquired additional cultural trappings, asserts individuality by membership in a group. The contradiction has given rise to familiar parent-teenager fight scenes in a hundred tired family dramedies. Though the story stays the same from decade to decade, the music changes, and understanding the fan means understanding not just the sense of community brought by any fandom, but also the vital energy of the musical style itself. The engine of Tim Schafer's Brütal Legend rumbles with the energy of heavy metal. Unfortunately, it never really roars to life.

More than enough has been said about the world of Brütal Legend, a land of heavy metal album imagery brought to life. The aesthetic is somewhat divergent, because metal has a fascination with both medieval fantasy and modern road machines. What unifies these interests is the desire for power and recognition, as articulated through archaic battle ideals and contemporary engine tuning. The game's protagonist, Eddie Riggs, plays into this idea because although he is an extremely capable roadie, he is forced to use his talents in unrecognized service to a particularly irritating faux-metal group of recent vintage. When he is transported to the world of real metal he has the opportunity not only to use his talents in service to his preferred kind of rock, but also to put down the forces that corrupted it in his life.

Although the world of Brütal Legend has dozens of opportunities for side missions, their repetitious nature means that the most interesting gameplay lies in the linear main story. Many of the encounters in that quest involve "Stage Battles", where Riggs commands a rock army fueled by the adulation of merch-hungry fans. This came as a surprise to me, as the demo had led me to believe that the game would be more in the vein of a third-person action/adventure. And, in all honesty, my utter incompetence at the stage battles eventually caused me to be thankful that I could change the difficulty mid-game. Still, the stage battles gave me the impression that they were meant to generate the feeling of individual and group empowerment that lies at the core of the metal experience. Giving the player control of an individual leading an army of headbangers and chopper-mounted warriors creates an opportunity to charge into battle at the head of a rock'n'roll army.

In practice, however, this doesn't work out. It's not that the stage battles are completely broken, it's just that the sum of a dozen little things makes them much less fun than they should be. Ordering individual units or groups of units to attack specific points is often advantageous but too much of a chore. Figuring out where you're being attacked, or where your troops even are, is often too difficult. If you distribute your forces across several different objectives or locations you will rapidly become overwhelmed by the task of trying to command them all effectively. Even when you hook up with them, actually charging into battle with them is a tough timing trick: your allies never quite seem to keep your pace, always running a bit behind or a bit ahead.

Beyond the mechanical issues, the problem with the stage battles is that nobody is on the stage. The internal fiction of Riggs as an unappreciated roadie falls apart because everyone, including the putative leaders of the human rebellion, takes orders directly from him. Thus, the late attempt to bring the story back around to the idea of Riggs as a behind-the-scenes player rather than an acknowledged hero feels implausible and unearned, especially given that his head prominently adorns a nearby mountain. Brütal Legend has the roadie, but not the band, and you need both if you're going to have a real rock concert.

Brütal Legend doesn't hang around for long, which is fine, but it cuts off abruptly, as if in mid-story, and that is not fine. More than half of the game's missions flesh out a conflict with hair-band avatar Lionwhyte, a relatively minor player, and most of those are tutorials to one degree or another. The rest of the game concerns a series of battles with the forces of the Drowned Doom, representative of the dramatic excesses of the goth scene. Then, within moments after their defeat, the player is dropped into the final boss fight against the demon lord Doviculus, leader of the Tainted Coil. Aside from the jarring shift to fighting a new, totally unfamiliar enemy, this smash cut into the final battle sells the whole conflict with the forces of the Tainted Coil short. The danger that Lionwhyte and the Drowned Doom pose to the world, and their relationship to real-life corruptions of the "metal" ethos, are pretty clearly developed, but Doviculus and the Tainted Coil get very little of this, and none of it is experienced through play. In essence it feels like a third of the game got cut out.

The story that remains is of uneven quality. The game's early segments are tightly written, and draw humor from the plausible behavior of well-realized characters. The excesses of heavy metal imagery and modern music are played for laughs, but not in a mean-spirited way. The writers know that we know that sometimes heavy metal takes itself too seriously, and play that angle up. Then the writers go and fall into the same trap, and start to focus less on the amusing adventures of Eddie Riggs and more on the serious business of the game's plot. This would be fine, except that Brütal Legend falls firmly into the class of stories where nobody says the few obvious and reasonable words that would solve all their problems, until the buzzer goes off and it is Time To Explain The Story before the final boss battle. The sharp comedic writing of the introductory segment slowly oozes out of the script, leaving only flaccid melodrama by the end. You can laugh at that, perhaps, but not with it.

For a fan, a musical style is an important part of an individual personality, but it is also a key way of identifying with a group. You can't really capture the essence of the allure of heavy metal without incorporating both those aspects, and Brütal Legend's curious mix of play styles may well be the best way to deal with this dichotomy in a game. Unfortunately, art that addresses contradictory ideas often turns out to be contradictory in its own right, and this is the fate that befalls Brütal Legend. The third-person action never sits quite right with the tactical elements, and the advantages of the game's open world are offset by the repetitive nature of the side-missions. The writing switches from self-aware comedy to self-absorbed melodrama, much to its detriment, and the game tries unsuccessfully to set Riggs up as both roadie and frontman. Despite these problems, there is much to praise in Brütal Legend, especially its bold gameplay choices and the striking realization of heavy metal imagery in its open world. While it fails to realize its full potential, it at least succeeds in being interesting, and that alone is worthy of recognition.

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The role of dynamics in catalysis

For some enzymes, dynamics on the millisecond timescale play a critical role in catalysis. I don't think this is a particularly controversial or unclear statement, but then, I know what I mean by it. In the process of communication, however, the intended meaning sometimes gets lost or transformed. A statement that addresses an entire catalytic cycle, for instance, might be interpreted as addressing only the chemical step. This seems to have happened in a pair of papers that concern the transfer of energy from conformational rearrangements to a chemical reaction.

Consider a reaction scheme in which an enzyme loosely associates with substrates (E.S), then "closes" to form a tight, catalytically-competent complex that then undergoes a reaction with the rate k_chem:

Pisliakov et al. (1) ask whether the closing process can accelerate k_chem. They ask this question primarily because a group from Harvard University proposed that this was possible in a paper printed last year in J. Phys. Chem. B (2). In that paper, Min et al. performed some simulations suggesting that such an acceleration was at least possible, and consistent with some enzymatic data. Pisliakov et al. approach the question with simulations of the reaction of the phosphotransfer enzyme Adk with 2 ADP molecules to form ATP and AMP. As part of the catalytic cycle, the enzyme goes from an open state (PDB: 4AKE) where the ATP and AMP binding sites are exposed to solvent, to a closed state (PDB: 1ANK) where the substrates are shielded from the surrounding solution by ATP and AMP "lids" that close down over the active site.


One can, perhaps, imagine that when the enzyme closes around the substrates, some motion will occur that promotes the transfer of a phosphate group from one molecule to another. Pisliakov et al. use a three-tiered system of simulations to address the question, as a way of trying to get around the difficulty of dealing with the long timescales required. Their simulations allow them to adjust the energy barrier to match the experimental rates or accelerate the reaction so that the whole pathway can be simulated. In general, they find that conformational fluctuations do not enhance the chemical reaction rate in this system.

I have two main concerns about the science that was performed here. The first is that the energy barriers in the long-timescale experiment appear to be improperly paramaterized. In estimating these barriers for the phosphotransfer reaction in Adk, Pisliakov et al. used 260 /s as k_chem. However, although the actual reaction carried out by Adk follows an extremely complex scheme, the analysis performed by Wolf-Watz et al. utilized a simplified scheme that combined all post-association steps into a single k_cat. This is why the concordance between k_cat and k_open justifies the conclusion that lid-opening is rate-limiting. In principle, the experiments used for that paper are incapable of separating the opening and closing steps from the chemical step. Therefore we have no experimental knowledge of the phosphotransfer rate, except that it is greater than 260 /s. This perplexing error appears to have originated with Min et al., but I am surprised Warshel's group did not catch it.

This is not a major problem because the bulk of the conclusions of the experiment were drawn from a different simulation in which the energy barriers were lower, but this leads to my second concern. If the structural transition involves a very smooth and coherent rearrangement of the protein, then simply manipulating energy barriers should not result in a serious error of analysis. In reality, however, ensemble motions of protein elements are not going to be so directed or uniform. Structural rearrangements are not highly singular steps, but involve a large number of intermediates and transition states. Motions in the late stages of the structural transition that promote catalysis may well be missed by simplified models, or accelerated beyond productivity by lowering the energy barrier.

That said, I'm not particularly surprised that Pisliakov et al. find that energy from the conformational coordinate does not transfer to the chemical coordinate, nor do I disagree with the finding. Despite what Pisliakov et al. appear to believe, the papers that have come out of Dorothee's group don't argue that the millisecond motions contribute directly to the chemistry. Doro doesn't believe that for a second. Neither do I. The importance of dynamics has little to do with shoving the reaction along the chemistry coordinate, but everything to do with getting substrates bound and into a state where chemistry is possible.

Dynamics allow an enzyme to reconcile incompatible functional requirements. To efficiently function as a phosphotransfer enzyme (as opposed to a hydrolytic phosphatase), Adk must expel water from the active site during catalysis. If the active site is inaccessible to solution, however, there is no way for the substrates to diffuse into it. It is difficult to create a single, rigid fold that can accommodate both these demands, but by fluctuating between two states the problem is resolved quite easily. So yes, the dynamics are essential to catalysis, but that does not imply that the conformational and chemical energy coordinates are coupled.

More perplexing is the discussion of the hierarchy of motion, which Pisliakov et al. take to mean that nanosecond motions somehow contribute to the chemical coordinate. As I discussed when that paper was initially published, the question being addressed was whether and how motions on the fast timescale (ps-ns) in Adk were related to the slower (ms) motions of the lids. In a hierarchy of motion, fast timescale fluctuations enable or promote slow timescale dynamics. In the case of Adk, this means that nanosecond flexibility at structural hinges allow the millisecond motions of the ATP and AMP lids. It was not implied, then or since, that the nanosecond motions in question make a direct contribution to movement along the chemical coordinate. This is not to say that there are no researchers who believe that ns motions contribute to catalysis — I've previously mentioned some work on hydrogen tunneling that makes precisely this argument. In the specific case of Adk, however, the contribution of ns motions to catalysis consists entirely in their enabling of the slower ensemble motions of the nucleotide binding domains, and nobody but the Warshel group has suggested otherwise.

There is an ongoing disconnect in the literature concerning the role of dynamics in catalysis. While it is true that in many cases rates of structural transitions correlate with rates of catalysis, this does not imply that the conformational transition coordinate is linked to the chemical reaction coordinate by direct transfer of energy. It is more likely that the dynamics of the enzyme contribute to catalysis by generating reaction-competent states from reaction-incompetent states. This is not to say that dynamics cannot possibly make a contribution to phenomena such as hydrogen tunneling, but it strikes me as unlikely that motions on the millisecond timescale will contribute to a chemical coordinate. Experiments, rather than simulations, will be the ultimate test of the idea. However, in principle, this hypothesis can only be tested experimentally on enzymes where the conformational changes do not limit the chemical reaction rate. Because the rate of the chemical step is unknown in Adk, it may not be an appropriate model system for addressing this question.

1. Pisliakov, A., Cao, J., Kamerlin, S., & Warshel, A. (2009). Enzyme millisecond conformational dynamics do not catalyze the chemical step Proceedings of the National Academy of Sciences, 106 (41), 17359-17364 DOI: 10.1073/pnas.0909150106

2. Min, W., Xie, X., & Bagchi, B. (2008). Two-Dimensional Reaction Free Energy Surfaces of Catalytic Reaction: Effects of Protein Conformational Dynamics on Enzyme Catalysis The Journal of Physical Chemistry B, 112 (2), 454-466 DOI: 10.1021/jp076533c

3. Wolf-Watz, M., Thai, V., Henzler-Wildman, K., Hadjipavlou, G., Eisenmesser, E., & Kern, D. (2004). Linkage between dynamics and catalysis in a thermophilic-mesophilic enzyme pair Nature Structural & Molecular Biology, 11 (10), 945-949 DOI: 10.1038/nsmb821

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A good way to spend a day and a half

My compilation of critical writing about Grand Theft Auto IV has gone up at Critical Distance. If you have a couple of hours to devote to reading some interesting writing about the game that was supposed to change everything then hop on over and get clicking. There's a lot to read, and I ended up including a pretty diverse set of posts, from straight essays to cross-blog dialogues, to one post from Corvus' site that ended up in there because of a really interesting comment. Also, because the game appeals to such a broad swath of gamers, I made an effort to dig into gamer-oriented blogging sites like Destructoid and IGN, with uneven success. I found plenty of posts, but many of those bloggers seem to be focused on producing their own reviews rather than a focused essay. Unfortunately, while everybody has an opinion, not everyone has an interesting idea.

One idea plenty of people had was to compare GTA IV to Saints Row 2. This was an easy thought to have because the folks at Volition kept pushing the concept that GTA IV had lost the fun of the sandbox while SR2 had expanded it. I must have scrolled through a dozen bullet-point posts about why SR2 was better (this seemed to be the prevailing opinion). I probably could have hacked together a section about it, but it would have required me to accept a painful quality dip. Instead, I linked copiously to Shamus Young's compare/contrast series on the two games, which I thought did a really admirable job of examining the competing design philosophies rather than just talking about how much more fun SR2 was.

Another subject that received a lot of coverage was the phenomenally ill-advised "Ladies of Liberty City" video IGN made and then retracted. This was a real problem because the people who responded to that video generally made reasonable points about the GTA series, but often didn't do a good job of GTA IV itself, mostly because they never played it. I seriously considered a secondary post or sub-section just on this subject, because there was a lot of interesting writing about it. Unfortunately, much of it was undermined by bad fact-checking; a significant proportion of these posts, even some of the better ones, included false information about the content of the game. The sad part is that most of these essays would have been just as compelling without the misinformation. After some internal debate, I had to conclude that making the section would only lead to drama I didn't want to deal with — in particular I felt that I might end up inadvertently turning those posts into flamebait.

Aside from these, most of the other main threads of commentary made it into the sections you see in the compilation. I feel like I did a little more synthesis in this compilation than previous ones. I tried not to come down on one side or the other of any particular case, but I did try to subtly draw out ideas that were somewhat nascent in the individual essays so that they might attract new writing. One of the ideas rumbling beneath the complaints about GTA IV's heavy emphasis on linear narrative is that the gameplay of Grand Theft Auto games is inherently transgressive: the game is about breaking the rules, the boundaries, the laws. In that kind of game, ludonarrative dissonance might be created just by having a linear narrative that denies the player significant input.

I also thought there was an intriguing idea percolating in a couple of pieces that Niko lies to himself about his sociopathic tendencies using the fiction that he has no choice but to be a murderer. Niko, and Rockstar's handling of him, engendered a lot of negative reaction, but my own feeling was that they did a reasonably good job of exploring a very bad person who, like many very bad people, sees himself as a fundamentally good guy with a functional moral code. But it was also interesting to me to find that there were a number of people who took Niko at face value, and consequently tried to play the game in a way that minimized property crimes and murders. The prevailing opinion is that GTA IV requires a lot of killing, but creative players have been exploiting the game's flexibility to draw the number of murders down to a surprisingly low level. Maybe that's ganking the system, or maybe that's buying in to one part of the system over others.

Whatever you think of the Pacifist Niko Challenge as an approach to rulesets generally, it does underline one key fact about GTA IV. The rules and systems created by Rockstar North allow for a huge range of behavior, but don't really require any more violence than is typical in any other gunplay-focused game. Popular attacks on the game interpret the most extreme activities that it permits as if they were actions the game requires, often as a consequence of (proudly proclaimed) ignorance. This strikes me as a case of shooting the messenger. If we're going to get upset about what happens in a game of GTA IV, we ought to worry less about the fact that people can do horrible things in a game, and more about the fact that they actually choose to do them.

One more thing. In order to comply with the FTC I will now list everything I've received for free from a game publisher:

That is all.

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Capsule: Dead Space: Extraction

Final Status: Game completed on Normal difficulty, some levels replayed on Hard.

Put This on Your Box: It's like Civil War medicine... in space!

Most Intriguing Idea: Converting a third-person precision-shooting horror experience into a first-person precision-based rail shooter.

Best Design Decision: Working the kinesis and stasis tools into the railshooter experience.

Worst Design Decision: Long, pattern-based boss monster battles that devolved into tedious chores.

Summary: Dead Space: Extraction is a prequel to Dead Space, which I found to be more interesting than Silent Hill: Homecoming, but hit some low points that eventually drove me off. Extraction introduces this story through the experiences of six (mostly temporary) survivors of the disaster on Aegis VII and the Ishimura. Combat, as in the original, depends on the player's ability to strategically shoot off the enemies' appendages; body shots are usually ineffective. The developers attempted to bring this precision-shooting idea to the boss fights, but unfortunately that created some excessively-patterned battles that went on far too long. Those fights, and some irritatingly long mob fights aside, the gameplay was solid and the atmosphere was good. Extraction unfortunately suffers from really abysmal performance. I saw slowdown and glitches on several occasions, and the game crashed on me five times. Two of those were hard crashes that forced me to turn off the console. It's a damn shame that the game was so unstable because...

If you can't say something nice... Dead Space: Extraction really does develop some very good tense and creepy sequences. For the most part it's a solid game and a good addition (or introduction) to the Dead Space franchise.

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Touch the void

In a curious way, maybe the climber stops living when he begins to climb. He steps out of the living world of anxiety into a world where there is no room, no time, for such distractions. All that concerns him is surviving the present... He leads a separate life of uncomplicated black and white decisions—stay warm, feed yourself, be careful, take proper rest, look after yourself and your partner, be aware. Be aware of everything until there is nothing but the present and there are no corrosive fears to eat away at confidence.

— Joe Simpson, This Game of Ghosts

Eric Simmons must climb a mountain. Not because it is there, not because it will bring him glory, but because up there in the snow and mist of Chomolonzo, something has gone terribly wrong. His brother Frank, sent to retrieve a sacred Buddhist terma from the peak, has gone missing. Angry and murderous ghosts have covered the slopes, somehow released from the bardo, a time between death and nirvana or rebirth. Equipped only with Buddhist implements he barely understands, Eric must reach the summit to find his brother and end the curse he unleashed.

Like climbing, Cursed Mountain requires the player to understand and manipulate the surrounding landscape. Survival horror games use atmosphere and resource scarcity to create tension and fear in the player. In Cursed Mountain, as in Resident Evil 4, the scarce resource is the space between Eric, whose best attacks require him to be motionless, and the enemies who are out to kill him. The awareness of space manifests in the player's tactical response to the ghosts: those that move rapidly or can harm you from across open ground will receive priority, because Eric moves so slowly and has no effective dodge capability. Spatial exploration and management are also key in the life-draining "ghost khorlo" segments, where the player must find and eliminate sigils while avoiding aggressive ghosts. Moreover, the healing incense sticks that can be used to replenish Eric's life are quite plentiful, but can only be used in specific places that are fairly rare. With even modest exploration of the game's world, Eric will always have plenty of healing items and unlimited "ammo"; what he lacks is open ground.

Although the areas the game requires you to traverse are very linear and generally require very little skill to cross, these features are disguised by their considerable verticality and mazelike design. There is only one way through, but that path is usually not obvious from a distance. Unfortunately the areas where Eric must actually climb the mountain are much less creative. Cursed Mountain is merely the best climbing game you could make based on walking. In the game, Eric uses his feet almost exclusively, except for some wall-climbing segments that differ little from those in Ocarina of Time. For the most part the mountain itself doesn't seem particularly devious: only a few spots require the player to do anything more than barrel straight ahead along an obvious linear path.

Even the strolling feels unsatisfactory. Eric's plodding pace works when you consider he's a man who's generally fit but who has built himself for considered motions in low oxygen environments rather than sprinting. Unfortunately, this characterization through motion falters because the walking animation stutters strangely on slopes and stairs, and Eric has considerable trouble stepping over tiny obstacles.

The gameplay also disagrees with the characterization when it comes to item discovery. Cursed Mountain depicts Eric as disbelieving, but respecting, the religion and culture of the Sherpas, as opposed to Frank who is openly contemptuous of them. Yet the game asks you very early on to smash pots to gain incense sticks, keys, and diaries that explain the events on Chomolonzo. This mechanic feels tired and stilted, of course, but more than that it is difficult to reconcile Eric's supposed uprightness with this degree of property destruction. The level design also fights against the character's central conceit: it's difficult to believe that an experienced, well-equipped mountain climber will be stopped by a relatively gentle slope or a low wall. Even the blocking potential of steep-walled chasms falters when Eric will be climbing sheer vertical rock faces in short order.

I feel such concern for the way the fiction plays because Cursed Mountain's narrative otherwise works quite well. It has rough and awkward moments, like any script, but the principal characters are convincingly drawn, and it efficiently juxtaposes several sets of interesting and compelling ideas. As a big brother myself, I felt empathy for Eric's conflicting feelings towards Frank and self-doubt of his own worth as a sibling. The script also sketches out a parallel between Bennett's quest for literal immortality through the terma with Frank's desire for figurative immortality through mountaineering history. A single, well-depicted near-erotic scene sets up a compelling and troubling connection between Frank's desire to summit the peak and sexual violence against the mountain, which the game's Sherpas see as a female goddess.

Yet the design constantly sells this narrative short, as best illustrated by its dull, prosaic depiction of the bardo as a darker rehash of an immediately preceding area, a sin compounded by the powerful explanation of this spiritual realm delivered immediately beforehand by a Lama. The level offers nothing resembling the test of enlightenment and understanding the Lama describes, just a simplistic prelude to a boss that doesn't seem to symbolize anything.

I cannot chalk this up to a general lack of ability, however, because some levels are masterful, including a maze of ice tunnels that can only be escaped with the help of radio direction from a man who may already be dead. Cursed Mountain shines when it uses isolation, a genuine uncertainty about where to go next, and hints delivered in ways that make you question whether Eric is even sane anymore. Part of the power of these sequences comes from the fact that Cursed Mountain merely makes you ask about sanity, and resists the temptation to provide an answer. Did you really hear Paul Ward? Did you ever really speak to Edward Bennett? Even the game's final moments concern an act of survival at once so implausible and believable you won't be sure of anything other than the scene's emotional authenticity.

Sadly, Cursed Mountain never embraces its core ideas fully enough to really succeed as a whole game. Greatness always seems just within its grasp, but the game is toppled from the heights by its unimaginative level design and mechanics, and its use of inappropriate gameplay tropes. In its best moments, however, Cursed Mountain truly inhabits the persona of a man whose entire existence relies on his understanding of space and distance, whose whole world is the howling wind and the biting cold and the lonely rock of a mountain that must be ascended, even if it means brushing up against the realm of the dead.

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The blunted blade

Japan's greatest swordsmiths, Masamune and Muramasa, were not contemporaries, but there are several legends involving both of them. One tells of a competition in which each one forged a sword and lowered the blade into a river. Masamune's sword seemed to be inert: fish swam up to it, the flowers floating in the river brushed by without harm. Muramasa's blade, in contrast, cut everything it touched. The fish were split in two, the flowers sliced to ribbons, and the very air hissed in pain as the weapon cleaved it. A passing monk saw the display and chided Muramasa, pointing out that Masamune's sword cut no undeserving thing, while Muramasa's blade killed indiscriminately. Time and legend have ascribed a bloodthirsty, evil aspect to Muramasa's swords, and it is this reputation that Muramasa: The Demon Blade aims to evoke.

Vanillaware, the creators of Muramasa, are probably best known for their 2007 role-playing game Odin Sphere, a game which was marked by a beautiful coherence of story, play, and symbolism. It would not be fair to expect another masterpiece of this quality, but I did expect the resemblance between the two games to be more than skin-deep. If you come to Muramasa looking for gorgeous 2D graphics and a fantastic score, you will not be disappointed. Unfortunately, the simplistic story and uneven design of Muramasa make it a hollow and repetitive experience.

Muramasa: The Demon Blade features two stories: that of the princess Momohime, possessed by the spirit of an evil swordsman, and that of the amnesiac ninja Kisuke. Unlike Odin Sphere, where the stories of the five main characters were intertwined in often surprising ways, these two tales have little besides backstory and a few shared characters connecting them. Moreover, the story is presented in very spare fashion, rarely offering anything more than a few lines of dialogue to explain why a particular boss must be fought or where to go next. There is no rich, textured narrative here, and as a result the game feels more like a quickie tour of Japanese folklore than a coherent story. The romance between Kisuke and Torahime is too understated, and Momohime's dedication to the reprehensible Yukinojyo is unmotivated and frankly sad.

The world of the game is, of course, feudal Japan, divided up into the provinces from the era of the Shogunate. These provinces appear in the game as a series of connected rooms (or zones, if you prefer), with some limited internal geography that must be traversed with light platforming. Sometimes these rooms are filled with enemies from the outset, in which case they can either be fought or bypassed. Random encounters also occur in these rooms, instead of in a separate battle stage, although when this happens the room no longer scrolls and the player must fight in the window onscreen at the moment of attack. Defeated enemies lose their souls, which can then be used to repair broken blades and forge new swords. Eating food (to provide "Spirit" to the character) is also necessary to forge additional weapons. The cooking element is very light, however, and most of the recipes rapidly become irrelevant because they have too small of a healing effect relative to the size of the life bar (which expands more than 50-fold over the course of the game).

The difficulty and complexity of combat, for the most part, depend entirely on the player's choice of "Muso" or "Shuro" play. In Muso mode, most battles can be won with sheer aggression, with the exception of some bosses and the random encounters I discussed in the previous post. In Shuro mode the fighting becomes more complex and tactical, although many enemies are still susceptible to a strategy of continual attack. Momohime and Kisuke have exactly the same controls and abilities, however, so the only real difference in gameplay between their respective stories is a few field enemies and the bosses. Even this disappears late in the game, when they gain the ability to fight each other's bosses. At that point the game reaches a repetitive nadir, but one that must be slogged through in order to level both of the characters up enough to wield the game's final sword and see the "true" ending. Leveling up the characters to defeat major enemies is generally unnecessary because your foes seem to scale with your level, particularly the bosses and the enemies leading up to them.

The troubling thing about these various components is that they all seem disconnected, or even opposed. The RPG elements, particularly the massive life bar, make the game's simplistic cooking system largely irrelevant. The scaling of enemies makes the leveling irrelevant, but at the same time, participation in the monotonous combat can only be justified by the need to level. The brilliant composers at Basiscape created a score that allows the battle music and field music to switch seamlessly between bars, and the battles take place without a screen swap, but the wonderful effect this has on the game's continuity is ruined by the scroll-lock and post-battle EXP screen. You run around collecting souls all game, but the story essentially ignores this grim task. Moreover, the need to do it has no real bearing on the gameplay — unless you consistently run from every battle you will have little trouble gaining the souls required to forge all the swords twenty times over by the end of the game. Muramasa is fundamentally incoherent.

I can't help but feel that Muramasa would have been better off if Vanillaware had embraced the brawler at the game's core and discarded the RPG elements (and Muso difficulty) entirely. The process of leveling up doesn't really add anything to the game, and the character development offers nothing for the player to do. Because the expanding life bar and experience screen notably interfere with other elements of the game, why not just get rid of them? Focusing the game on tactical combat, and the sword system on the selection of special attacks or abilities, would have made this a game about fighting smart rather than just about whacking things with a sword until you reach the next boss. Making Kisuke and Momohime play in noticeably different ways would also have made the game a more interesting experience.

Even those changes, though, would only somewhat ameliorate a fundamentally hollow experience. Muramasa: The Demon Blade reminds us of a famous swordsmith and his bloodthirsty blades, but the madness and viciousness thus evoked never really find their way into the gameplay or the thinly-presented story. Like its vast, fractured provinces, the various systems of the game never manage to form any coherent whole. Instead, the game comes across as a whole bunch of ideas thrown together willy-nilly and wrapped in as beautiful a package as possible. Muramasa has no secrets to reveal, no depths to plumb, no story to tell that equals its luxurious presentation. Like a ceremonial sword, it is glorious to behold, and better gazed upon than used.

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Muramasa goes to hell

Most of Muramasa: The Demon Blade is set in Japan, laid out on a map based on the provinces of its feudal period. In one act, however, the possessed princess Momohime jumps down a well in Kyoto (Yamashiro) and finds herself in a fiery underworld populated by demons. Although the game is suffused with elements from Japanese myth and folklore, this drop into a completely fantastic area represents a substantial break from the rest of the game's semi-historical motif. It represents a break in other ways as well, few of them good. Muramasa's episode in hell creates player frustration in almost every phase, to the detriment of one the game's most memorable sequences.

The stages set in hell involve a marked increase in difficulty. Most of the monsters encountered in this area are trivial little imps that have been seen all game and can be disposed of with a few strikes. Because they can launch projectile attacks if left alone, the best approach to deal with them is unbridled aggression. In the hell stages, however, these imps are accompanied by one or two hulking monsters that are very tough to kill. Not only do these oni take a great deal more damage, they also have an expanded arsenal of attacks that do significant damage to Momohime, and more importantly to her swords. Because a broken sword makes the player essentially incapable of offense or defense, these encounters can rapidly become very dangerous, and the player will spend much more time dodging attacks than is typical for a random encounter. Although the oni are vulnerable at every spot, fighting them requires a consideration for angle of attack and tactical retreat that goes beyond that needed for many of the game's bosses.

This is not an intrinsically bad thing, because the boss of this area, the Big Oni, also imposes tactical requirements that make it quite different from the preceding bosses in the game. It would have been clever to set the stage for this fight by making the oni enemies in the field have similar vulnerabilities and attacks to the big boss so that the player would be trained for the boss fight by the more ordinary encounters. Unfortunately, the oni from random encounters have only the slightest resemblance to the Big Oni in their attacks, and no similarities in vulnerability. So although they are in many ways much tougher to fight than the boss, the player takes nothing useful away from these encounters.

Irritatingly, the increased difficulty of these particular monsters does not seem to acknowledged in the experience yield from the battle. In Muramasa, the primary determinant of experience reward appears to be the monster level, which is in turn set by the player's level. This careless approach to the difficulty/reward dynamic is a characteristic flaw of Japanese RPGs, though not by any means confined to them. As Denis pointed out to me, the asymmetry between difficulty and reward appears in some Western RPGs as well. The foes introduced in Fallout 3's Broken Steel, for instance, give similar experience to their lower-level brethren, despite the steep increase in difficulty. At any rate, it's not unexpected to see this in Muramasa, though it is irritating, and it points to a larger issue I'll get into with my general critique later this week. Here, it merely accentuates the frustration of dealing with the more difficult enemies in the field, and helps turn the trip through hell, one of the least visually interesting areas in the game, into an annoying slog.

This means that the player arrives to the boss battle frustrated or even angry, which is a shame because the battle with the Big Oni is a really clever and interesting fight. The stage for combat is set by a pitch-perfect scene where Momohime convinces the Big Oni to swallow her whole, in classic trickster-hero style. The first phase of the battle then involves cutting your way out of the monster's belly, a classic epic trope that would in most other games have been played off as a cutscene. The main battle requires Momohime to attack the monster's horns, evoking the famous Japanese myth of Momotarō. Absent the cultural context, however, this resonance, and the accompanying hint about how to attack the Big Oni, are missing.

This again can easily become frustrating, because the target area on Big Oni is just large enough to be hit occasionally by attacking his body. Because every previous boss in the game is vulnerable at more or less every visible spot, the player might not even think this limitation on Big Oni is possible. Training the player to attack the horns with the randomly encountered oni would have been an ideal solution to this problem. Alternately, Vanillaware could have elected to have only the horns or head flash in response to damage, or to have shown the horns cracking and breaking as the battle progresses. However, the developers, being familiar with the myths about oni, simply might not have thought about how to convey that information to a Western audience. So, another possibility would be for the localization team to slip a hint into the dialogue boxes somewhere.

The journey into hell displays a set of outright mistakes and lost opportunities. Although the difficulty of this section is out of line with the rest of the game, the level of challenge is appropriate to the area being entered. However, because that challenge is not rewarded, what was merely tough becomes frustrating. The strategic requirements for dealing with the oni foes also break with the rest of the game, but it could have been used to prepare the player for a new wrinkle in the upcoming boss. Instead, the demons are dealt with using totally disjoint approaches: raw aggression for the smallest, careful dodging for their larger brethren, and targeted attack for the boss. That makes what could have been Muramasa's most striking and epic section into a frustrating and ultimately tedious slog.

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Capsule: Professor Layton and the Diabolical Box

Final Status: Story finished, most extra puzzles solved.

Put this on your box: A gentleman leaves no puzzle unsolved!

Most intriguing idea: You don't really need to make puzzles part of the story. You can just jam them in there any old way and people will still love it!

Best design decision: Moving the setting around to make each chapter's geography more varied.

Worst design decision: The tea set, a boring game of trial-and-error that doesn't fit the puzzle aesthetic or provide any entertainment.

Summary: Professor Layton and the Diabolical Box follows the same scheme as its predecessor — a mystery presents itself to the Professor, who then must solve puzzles to obtain clues, get around recalcitrant villagers, and just for fun. While some of the puzzles are directly integrated with story events, for the most part they are no more than tangentially related. Diabolical Box has a greater reliance on transfer and picture-scanning puzzles than Mysterious Village, in part because the latter form the basis for almost all the gameplay in the camera minigame. In addition there is a hamster minigame (cursed with appalling voice acting) that also has a puzzle component, in terms of arranging items in the hamster's play area to maximize the number of steps he will take. This pattern is broken with the tea minigame, in which the player must mix components to make particular teas. As mentioned above, the game would have been better without it. The story is little more than an excuse to tramp through environments looking for puzzles, with train-sized plot holes, but it does its job and is charmingly presented. The final twist is unintentionally hilarious, because it suggests that the Professor and Luke kept running into puzzles because they are puzzle maniacs. For the most part, it's more of the same, but when the original is so good, that's not really a problem.

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