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.

Read the rest...

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.

Read the rest...

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

Read the rest...

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.

Read the rest...

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.

Read the rest...

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.

Read the rest...

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.

Read the rest...

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.

Read the rest...

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.

Read the rest...

Chase fixing

Well, the dust has settled at Richmond, and my favorite driver is out of the hunt for the Sprint Cup. Of course, Clint Bowyer was definitively out of the Chase after his poor showing at Atlanta last week. It's been a tough, up and down season for Bowyer, who I like because he's talented, unassuming, and gets no respect, not even from his own employers. They rewarded his great showing the past two years by giving his team and owner points to somebody else (Casey Mears, of all people) and sticking Clint with a brand-new car and crew. The overall implosion of RCR has been a major disappointment this season, but Bowyer's performance, even with the greenest team, has been the best of a mediocre bunch. Still, with Bowyer definitively out of the Chase, and my beloved football starting up again, the question for NASCAR is: what's to keep me watching racing on Sunday afternoon?

Of course, Bowyer isn't the only driver I root for. I've always liked Stewart, and I'm also partial to the international contingent of Montoya and Ambrose (technically, the most Southern of all the drivers). If I'm going to go with the "no respect" theme, then I should also think highly of the Biff, which I do. And of course there are some drivers I root against. I don't like to see anybody wreck, of course, but I might let out a small cackle of glee when the Busch brothers, Hamlin, or "cousin Carl" turn in a poor effort. So I have some interest still in how the Chase plays out. The problem is that due to its structure the Chase is played out long before it ends. As I recall, the Homestead race has only had a real chance to decide the championship once, and the past few Chases have been effectively decided by the time the green flag waved in Phoenix. Most Chasers are eliminated from contention long before that: last year Kyle Busch was through after Dover, and Talladega dramatically thinned the list of possible champions.

The other problem, of course, is that Jimmy Johnson seems to always win this thing. It would be unfair to deliberately calibrate the Chase to specifically stop him, although not without precedent. After all, the Chase was basically invented to prevent Matt Kenseth (or a similarly consistent non-winner) from ever taking home the Cup again. Johnson just does too well on most of the Chase tracks for anyone to catch him. He's not magical, of course, but he's unflappable, and as I've mentioned before, almost fatally unmarketable.

One way to shake things up would be to alter the track selection, especially to thin out the intermediate tracks. Some of those certainly ought to be kept: a Chase without a stop in Texas or Charlotte would be a strange beast, and Kansas always seems to produce an interesting race somehow. New Hampshire's flat oval is just funky enough to stay. Still, there's no good reason to ever race at Fontana, and much less reason to go there in the Chase. If the series is going to hoof it out to Cali, then the Chase should visit Infineon. A road race would diversify the Chase tracks and make it a more complete test of the drivers. I think the racing is actually more entertaining at Watkins Glen (or even rainy Montreal), but the fall weather up north might be too much of an issue. Homestead is also a really uninspiring track, a race nobody would watch if the champion weren't crowned there, and seemingly selected for no better reason than the climate. I think the Chase ought to end at Nascar central in Charlotte, and Homestead's spot given to a more unique and interesting track. Since we're talking about my fantasy here, I'd put a Chase race in Darlington again.

Another way to address the Chase's boring side would be to alter the scoring. This might sound more radical, but the Chase already makes a pretty artificial change to the points. Moreover, the goal of the Chase is not necessarily the same as the season points, so there's no particular reason to keep that scoring system for the Chasers. With that in mind, here are three alternatives.

Option 1: Not enough pie

Chase scoring comes with a simple scale: 10 points for 1st place down to 1 point for 10th place, no points for lower. I would foresee two improvements from this approach. First, because the number of scoring spots is less than the number of racers in the chase, there will be a desperate fight for every position. Second, because the spread of points is so narrow and there's no more penalty for coming in 43rd than 11th, one or two bad races will not completely eliminate a contender. The compressed dynamic range should make it easier for those who are behind to catch up with a few good performances, keeping the Chase drama alive until the checkers wave in Miami. The Chase would be "seeded" by treating regular-season points as a race (so 11th and 12th place Chasers get no points) plus one point per regular-season win. The weakness of this approach is that it gives the non-Chasers a lot of spoiler power, and might de-emphasize Chase wins.

Option 2: "Winning isn't everything, it's the only thing."

Chasers are supposed to be champions. So in the Chase you get 1 point for winning, and 0 points for anything else. Regular-season wins and points, in that order, serve as a tie-breaker and nothing more, except that the regular-season points champion and the winner of the most regular-season races would get one Chase point each. Again, non-Chasers would have a lot of spoiler power, but that would fit in with the organizing scoring principle. More problematic, though, is that the drama could easily be sucked out of this system. In theory the only way to clinch a Championship would be with six wins in this system (maybe less if you started with a bonus), but in practice, and assuming relatively strong competition, three wins might be an insurmountable lead, with other drivers splitting up the other races. So, a strong showing early on could kill the drama.

Option 3: Only racing against each other

Use any points system you want, but in scoring the championship, only consider a driver's position relative to other Chasers. Again, this has the effect of compressing the dynamic range of scoring, meaning that the championship points race will be closer all the way up to the end. It would certainly mitigate the influence of a team being taken out of the championship due to somebody else's wrecks. On the other hand, a team's own errors would also become less damaging, and the whole thing smacks of grading on a curve.

The Chase has done a good job increasing the drama of the last couple of regular-season races and the first few Chase races. The problem continues to be that the system hasn't elevated the season's final few races above their traditional status as irrelevant epilogues to an essentially settled championship run. Shaking up the track selection to emphasize a broader range of skills, and compressing the points range so that the issue remains in doubt all the way to the end, might make the Chase more compelling and interesting to those who, like me (and all those Jr. fans), don't have their favorite driver in the mix.

Read the rest...

We didn't come for the rocks

I wonder if science fiction is really so easy to misunderstand. If sci-fi is just men in tight outfits scrambling across fake plaster rocks until the one in a red shirt gets killed, then of course the whole enterprise is ludicrous. But that's never been the draw. It's not "new stars, new gas giants" that the Enterprise seeks, but "new life, new civilizations". Kids might tune in for the guy in a plastic lizard suit, but adults stayed for the idea of a man without emotions. Could you really live like that? What would it be like? These are the real voyages of the Enterprise in particular and sci-fi in general: not out into space, but inward into the lives of the people out there. Nobody cares that Tatooine is an arid terrestrial with a surface rich in silicon oxides that suffers from persistent dust storms; they care about Luke Skywalker, Han Solo, and what they do in that vast desert. Surely the talented writers at BioWare understand this. Yet, though they set up an intriguing story about people in their sci-fi epic Mass Effect, they inexplicably delivered a game about the rocks.

Mass Effect, in its fiction and its science, clearly belongs to the same genre of space opera as Star Trek and Star Wars. Although the game gives somewhat more consideration to real physics than the other titles, its handling of biology rests at the same level. Most alien species, with the exception of the agreeably freaky hanar, look more or less like us, right down to the mammae, with various kinds of funky head designs to disguise the fact that they have relatably human faces and bodies. This isn't necessarily a bad thing. Although it is true that the medium of videogames frees the developer from the practical limitations that make such "aliens" necessary in live-action, actually implementing a radical design in a believable way (for instance, constructing a set of conversational mannerisms) would be incredibly difficult and would not be guaranteed to yield a creature human players could relate to. Anyway, an exploration of biological possibilities is every bit as much beside the point as the exploration of rocks. What the best sci-fi really explores is ideas about other ways of being — exploring people.

Mass Effect grabs hold of this possibility early on when we are introduced to the Citadel, an enormous space station of mysterious origin that serves as the seat of galactic politics and culture. Here dozens of races butt up against one another, and we are offered glimpses of intriguing new cultures: the libertarian militarism of the turians, the intensely political salarians, the religious hanar, and the slow-speaking elcor who preface every statement with a description of its emotional underpinning. Not all of these races are so interesting (the plight of the quarians quotes far too literally from Battlestar Galactica), but I found the possibilities exciting, especially given the relatively weak position of humanity in this milieu. I thought that the powerful conversation system and the generally well-written characters could be leveraged into an exploration of this rich society. Instead, I was given the 2183 equivalent of an ill-handling dune buggy and sent on the Johnny Shepard Good-Times Tour of the galaxy's most desolate shitholes. Bouncing across the tenth absurdly craggy moonscape to the fifteenth identical base, I wondered why I was still playing.

The answer should be the story, which is a very standard space opera, delivered with just enough cleverness and originality to stay interesting despite its scenery-chewing villains and reliance on played-out fantasy tropes. The player must track down the turncoat galactic agent Saren, who has forged an alliance with the Reapers, an serially-genocidal machine race from the depths of space. He and most of his organic allies have had their minds corrupted by Sovereign, an enormous ship which at first seems to be merely connected to the Reapers. At least in the order I played its missions, the game seemed to time its revelations well and develop them properly.

Yet I came to have three main problems with this tale. The first, a minor point, is that the Conduit spits its passengers out inside the Citadel structure. We are told that a mass relay works by nullifying the mass in a corridor between it and its terminus. The troubling implications of this process for the intervening matter — station, spaceships, and lovely Asari maidens — are not discussed, but I presume the sentient components of that matter would object. The second problem, more concerning, is that the Reapers' behavior is fundamentally inexplicable. The writers eventually give up on explaining their motivation, dismissing the question by telling us that evil metal gods work in mysterious ways.

The final problem, which might be fatal, is that there is no logical reason anything in the story should happen at all. Consider that Mass Effect carefully demonstrates that (1) the Citadel Council trusts Saren completely (Citadel mission), and (2) it is possible to sneak geth soldiers, tanks, and artillery emplacements past the galaxy's most advanced weapons scanners (Noveria mission). Would it not have been considerably easier for Saren to just import a couple thousand geth to the Citadel, walk into the control chamber, and let Sovereign in, relying on the Council's trust for the element of surprise? The only thing that prevents him from doing this is that he showed his hand in the player's first mission on Eden Prime — that is, Saren only needs the Conduit because he was trying to find the Conduit. Hiding the terminus in plain sight on the Citadel was a clever move by the writers, but it ends up being too clever by half, because it only delivers Saren to a place he could have easily reached anyway, were he and Sovereign even half as intelligent as the game wants us to believe.

Nonetheless, the writers managed to hold my interest up until this last, unsatisfying reveal, thanks in large part to solid characters underpinned by excellent voice acting. While some of them have one-note personalities, that single note is played very well, and others show unexpected depth. Codex entries and his own early actions prepared me to see Wrex portrayed as a low-rent Klingon clone, so the elaboration of his backstory as a thoughtful civic leader really worked. Sadly, the ultimate payoff for exploring these stories always seems to be yet another trip to yet another prefab base on yet another hunk of lifeless rock.

The strength of Mass Effect is not its larger plot or barren worlds but its characters and societies. The problem is that although the game's best mechanic is ideally suited to explore that angle, it's left hanging in the wind in favor of a standard power fantasy reliant on wobbly systems. As a shooter the game is merely passable, and the mechanics only get worse from there. The exploration and vehicular combat are irritating, the inventory and party management is trash, and the AI seems only marginally better than that used in DOOM. The hacking / surveying / finding artifacts minigame is a boring, mindless chore. In contrast, the conversation system and the cinematic presentation shine almost every time they appear, making for the most satisfying in-game discussions I've ever seen. Why not take that system and run with it? Why should the most interesting parts of the game be trapped in the completely non-interactive Codex?

I believe BioWare can get this right; they are halfway there already. They have created a universe which, like the best science fiction, is ripe for the exploration of new ideas and new ways of living. Unfortunately, all Mass Effect let us explore was the plaster rocks.

Read the rest...

Proteins stick together when it's crowded

One of the many ways that a living cell does not resemble a test tube is in the degree to which its internal environment is crowded. Cells are crammed full of massive protein complexes, vesicles, organelles, carbohydrates, peptidoglycan, and other assemblies that occupy a great deal of space. The tubes and cuvettes used for biochemical experiments, in contrast, typically contain nothing more than a few proteins and small molecules of interest along with a relatively dilute set of salts and buffering agents. Because many complexes appear to be stabilized by crowding, and excluded volume effects are known to favor compact, folded protein chains, there is considerable interest in estimating how protein behavior changes in the spatially-restricted environment of the cell. In some cases this is approached using NMR to study changes in dynamics and structure inside cells. In a recent issue of Biophysical Journal, groups from Florida State University and Rehovot University, in separate papers, address how crowding affects protein-protein interactions.

Both groups perform biochemical experiments in vitro to examine this question. In order to crowd the solution, they add reagents such as ficoll, polyethylene glycol (PEG), and dextran, and compare the changes in binding and kinetics to solutions that have merely been made more viscous (through the addition of glucose, for instance). Batra et al. study the association of two components of the E. coli DNA polymerase III and find that the presence of crowding agents slightly stabilizes the complex. However, as the size of the crowders is increased, this stabilization is diminished. Batra et al. develop a relatively simple mathematical model that suggests this observation results from the fact that larger particles pack less efficiently, leaving larger "holes" in which the protein complex sees something more like dilute solution.

Phillip et al. study several protein complexes. Similar to Batra's group, they find that crowding with dextran modestly increases the binding affinity of two of their protein pairs, but that this is not replicated for crowding with PEG. Particularly for PEG-1000, there was a clear decrease in affinity, although a non-crowding viscogen (ethylene glycol) had an even greater effect. Phillip et al. also measured the kinetics of binding, and found that the association rates were significantly lower in crowded solutions, as compared to buffer. However, when the rates were corrected for the effect of viscosity, it appeared that the crowding agents slightly increased the association rate. The authors attribute this to excluded volume effects in the binding transition state. The dissociation rate was also slightly reduced in crowded solutions, which the authors explain by the longer lifetime of the encounter complex (allowing a larger fraction of complexes to fall back to the lower-energy bound state).

Given that crowding appears to have a profound effect on the function of certain complexes, the relatively small effects observed in these studies might seem confusing. Batra et al. argue that although each individual binding interaction is only modestly stabilized, the effect should be cumulative. As a result, multi-subunit complexes will experience a greater effect than small heterodimers. Additionally, the most famous examples of crowding enhancement involve very large complexes — the ribosome, decameric assemblies, hemoglobin polymers, etc. In comparison, the complexes formed in these model studies are quite small. It may be that the stabilizing effect of crowding depends to some degree on the size of the complex to be formed. While similar size is difficult to achieve in strictly heterodimeric systems, it should be possible to monitor the assembly of large complexes like GroES/GroEL under crowded conditions. A study of the relationship between the size or number of components in a complex and crowding stabilization may prove instructive.

Batra, J., Xu, K., Qin, S., & Zhou, H. (2009). Effect of Macromolecular Crowding on Protein Binding Stability: Modest Stabilization and Significant Biological Consequences Biophysical Journal, 97 (3), 906-911 DOI: 10.1016/j.bpj.2009.05.032

Phillip, Y., Sherman, E., Haran, G., & Schreiber, G. (2009). Common Crowding Agents Have Only a Small Effect on Protein-Protein Interactions Biophysical Journal, 97 (3), 875-885 DOI: 10.1016/j.bpj.2009.05.026

Read the rest...