How soon you forget

If you played the demo for Enslaved, you have already been through the sequence. On a flying prison ship of some kind, a young woman, Trip, breaks out of her cell. She sets off an explosion that accidentally frees the player's avatar, a man named Monkey. She flees through the ship, cutting off Monkey at every turn, until he finally encounters her again just as the vehicle is about to crash. He clings to an escape pod as she ejects it, falling unconscious when they crash. While he is knocked out, Trip fits him with a headband that will kill him if he disobeys her. The sequence is exciting, visually memorable, and pretty fun to play. It is also at war with the story Enslaved seems to be trying to tell.

I haven't used a reminder like this in some time, but the game has only been out for a few days. So, look up at the title of the blog and carefully read the two words underneath it before you proceed.

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Costridium virulence: What's essential?

Clostridium difficile is an intestinal pathogen that causes diarrhea in hospitals and other healthcare settings (including nursing homes). Present as a commensal bacterium in a significant fraction of the population, C. difficile is usually rather harmless, its numbers suppressed by competition with the intestinal flora. When its competitors are decimated by antibiotics, however, C. difficile flourishes, releasing toxins that cause inflammation and diarrhea, which can be dangerous because the individuals suffering these effects are often already ill. There has been conflicting information, however, as to which of C. difficile's toxins are necessary to cause disease. A paper in the recent Nature (1) aims to resolve the question.

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From Masyaf to Firenze

If you believe Metacritic, Assassin's Creed II is a major improvement over its predecessor. The Metascore jumped 10 points between games, which would seem to suggest it solves a major problem, or at least a good number of smaller ones. I played the games out of order, going through Ezio Auditore's adventures in the sequel before I experienced Altaïr's adventure in the original Assassin's Creed. I can clearly see some areas where the latter game improved on the former, but I wouldn't say that the quality was dramatically greater. In some ways, it felt like the series lost as much as it gained going from one game to the other.

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Capsule: BioHack

Status: Complete, most challenges met.

Put this on your (nonexistent) box: Play Biochemistry 101!

Most intriguing idea: Modeling a puzzle game after natural regulatory systems.

Best design decision: Keeping things simple in these complex systems.

Worst design decision: The visually confusing quantitative and rainbow modes.


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Capsule: Professor Layton and the Unwound Future

Status: Complete

Put this on your box: Walk with the Professor! Feel the burn!

Most intriguing idea: Sorry, fresh out.

Best design decision: The super hint for times when you just can't figure out what the puzzle wants you to do.

Worst design decision: The world is much too large and the subway doesn't have nearly enough stops.

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Crime isn't just shooting people

Mafia II borrows so much from GoodFellas that 2K Czech probably ought to give Scorcese and Pileggi co-writing credits. Direct references to the film appear in a couple of specific scenes, but the real influence is more fundamental. GoodFellas depicts the mafia as a group of buddies, and Mafia II is built around the same idea. Although family matters motivate the game's protagonist, Vito, when it's convenient for the plot, the real impetus for his journey through the Empire Bay underworld comes from his friends. Unfortunately, the game's vision of mafia life falls apart because of its ill-considered adherence to gaming convention. Mafia II devolves into a series of increasingly ludicrous and bloody shootouts, even though a realist mob drama in the vein of GoodFellas would be an amazing game.

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Capsule: Prince of Persia: The Forgotten Sands

Status: Completed X360 version.

Put this on your box: In Persia, no pot is safe.

Most intriguing idea: Allowing the player to change, rather than just use, the environment in the course of a platform run.

Best design decision: Requiring precision timing with the environmental powers.

Worst design decision: Putting the rewind and combat powers on the same magic gauge.


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Zombie cyclophilins catalyze HIV capsid isomerization

If you're going to study the role an enzyme plays in a biological pathway, it's often useful to "kill" it with a mutation. For example, the proline cis-trans isomerase cyclophilin A (CypA) needs a particular arginine residue for its chemistry, so mutations that remove or alter that functional group, like R55K and R55A, should destroy the protein's function and have effects on the related pathways that help illustrate its role. The hydrophobic pocket it uses to bind substrates is made by residues like H126, F113, and W121. Growing or shrinking those residues should alter the shape of the pocket and change binding or activity, leaving the enzyme "dead".

Using model reactions and various binding assays, researchers have previously examined a number of these mutants (4,7) and found that they diminish isomerase activity and alter inhibition. However, a detailed study of the effects of the mutations on CypA's catalytic cycle has not been performed. Former Kern lab members Daryl Bosco (now a professor at UMass Medical) and Elan Eisenmesser (now at UCHSC) examined these mutants in greater detail to see how they really behaved. I also contributed some data at the last minute, when the third reviewer requested we study an additional mutant, prompting a scene that I promise was not too much like that Downfall parody. In every case we found that these enzymes, although significantly impaired, weren't as dead as they had seemed.

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The curious case of Kainé

The strength of Nier is the friendship between its decidedly odd cast of characters. The western release features a burly and frankly ugly man, a rare choice of protagonist for a JRPG. His principal companion is a pompous talking book that grants him magic powers. Also magical is their young comrade Emil, the sunniest character in the game and the one most constantly dumped on by its world. Then there is the possessed warrior Kainé, whose picture I have tucked beneath the fold because her appearance is arguably NSFW. That design is one of my main reservations about the game.

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New game minus

I recently wrapped up my time (for now) with Nier, a game I hadn't been planning to play. On the strength of Trent Fingland's extremely positive review, I decided to give it a spin, and now it has a place on my Game of the Year shortlist with BioShock 2, Red Dead Redemption, and Trauma Team. As Trent pointed out in his review, Nier doesn't really do anything new. Instead it picks and chooses from existing influences ranging from text adventures to twin-stick shooters. One strength of the game is that each of these play motifs surfaces at just the right moment and feels completely appropriate. The other main strength of the game is impeccable characterization, which can be attributed to solid writing and excellent voice acting. Nier's unique "new game +" mode expands on the characterization of a major character in an interesting way, but in my opinion this worked ultimately to the game's detriment.

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Capsule: Trauma Team

Status: Complete

Put This on Your Box: House meets ER meets CSI meets Ghost Whisperer!

Most Intriguing Idea: Fusing multiple styles of medical drama into a single coherent story.

Best Design Decision: The diagnostics segments.

Worst Design Decision: The mechanics for endoscopy.

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Capsule: Singularity

Final Status: Complete.

Put this on your box: One of the first games to combine ideas from Half Life and BioShock!

Most intriguing idea: Aging and regressing the environment to progress.

Best design decision: The seeker.

Worst design decision: Monsters.

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