Today's paper was : 

Pernitzsch SR, Sharma CM (2012) Transcriptome complexity and riboregulation in the human pathogen Helicobacter pylori. Frontiers in cellular and infection microbiology.

It's a quick review of sRNAs in H. pylori, a species once thought to use very little RNA-based regulation (AKA riboregulation). The presumed lack was based on observations that H. pylori lacks the RNA-binding protein Hfq, generally thought to be a requirement for riboregulation. Turns out that's not the case. H. pylori may regulate plenty of cellular activities using sRNA, including the stress response and flagellum biogenesis.

A chamber, made

So, Antichamber. I finished it recently. Spoilers may follow. It's not a monumental challenge, but I'm fairly sure it's not intended to be one. It also hasn't lost much of its spark for me despite an original release date of more than a year ago. Games get spoiled so easily these days. Portal, this game's obvious inspiration in both design and technical matters (despite not sharing the same engine, but that's just a technicality in the grand scheme of things) certainly didn't have such a stable shelf life. That may just be due to cake and lies.

Yes, Antichamber. I won't describe the details and I'll assume you've either tried it out already, are planning to play it, or will never do so. It's a minimal game with an ambient background. The visuals are predominantly white or a few colors at a time. The soundtrack is a collection of chirping birds, rushing wind, and distant thunder. The goals are straightforward: go where you haven't been, open closed doors, collect new equipment and learn all the neat things you can do with it. Every stage is summarized in a tidy aphorism, the presumably obvious lesson gently restated in a single sentence and a napkin-sketch cartoon.

Antichamber is ostensibly about life. That's an ambitious goal and probably a bit too much for any one creative work to concern itself with. Instead, I think it provides an excellent example of minimal gaming. It's certainly not minimalist gaming, though that's a popular and valuable trend in and of itself.

Rather, Antichamber deconstructs modern gaming into some of its most dominant elements: confusion, movement, and surrealism. All three of these elements are particularly well suited to gaming as they benefit from interaction. A film can confuse us, make us feel like we're moving, or even present impossible images (indeed, every film is made of impossible images, or it would be theater). Only an interactive experience can make us feel like the world isn't responding to us in the way it's supposed to. It's also the only way to simulate control over one's own movement and to do it in a way that's realistic enough to be convincing and responsive but unreal enough to retain a patina of fantasy and unlimited possibilities.

The paths in Antichamber are circuitous but eventually require pursuit of a floating, dark, ghostly mass. The mass sounds like strangers congregating in an art museum lobby* and looks like a glitch.** By the end of the game, it's fully within the players control, ready for release until just the last few moments. Before that point, the ghost does many of the same things the player does as far as opening doors and wandering around an illogical maze goes. We could almost recursively view this black mass as the game's player or even just the concept of a player. Players make games what they are, but they'll all have different experiences in the process.



*Or, um, maybe an antechamber. Anterooms are pretty critical to congregating and to the hanging of coats, though neither happens in Antichamber.

**It's kind of like this recent art project.

A brief, hopeful rant about Powerpoint

The "tools of the trade" are little more than iconography for most trades. In science, no matter the field, one of those tools is usually Powerpoint. It doesn't look as good on a flag as a hammer or sickle or even a cutlass* but it's still the reliable sidearm of any scientist with conclusions to present and an audience to hear about them. Despite -- or perhaps because of -- its popularity, Powerpoint is widely abused. It's less of a tool and more of a drug. Many scientists just can't get through a presentation without loading up a stack of slides and letting 'em fly.

Lets break the cycle, folks. Some physicists are abandoning the slides in favor of whiteboards and direct conversation. Even better, we can avoid the bullet-point habit entirely and adapt to specific audiences. Presentations should be about expanding upon ideas, not glossing them over! I can't claim to be a presenting expert and certainly haven't had a long career. Even so, I can hope for numerous chances to present my research outside the bounds of Microsoft's glowing rectangles.


*I once saw a version of the University of Virginia logo specially prepared for their department of Biology. The sabres had been replaced by micropipettes, the actual tools of the molecular biology trade.

It's tough to stay focused. There's always something requiring more attention than it's ever going to get, and in the odd times when it gets nearly the required amount, it's probably due to the sacrifice of some limited resource. Time is a limiting factor, certainly. Motivation is another one. If the end result of a project looks dim and distant, I can only imagine how it will look when it's within reach.

I suppose there's a lot to be said for having a concrete idea of presumed context. I've often found this to be an irritant in fiction: the author provides just enough detail for me to get a good mental image of the characters and their context, but just when it's relevant, new details emerge. This isn't along the lines of "she saw the reflection of her blue eyes in the pooling rainwater" when all along I had thought the character had brown eyes. It's more like having the rainwater appear in the first place when I had understood the weather to be clear. Is this the fault of my own assumptions, or can I reasonably expect authors to provide me with enough detail to minimize assumptions?

The same issue is true with writing scientific manuscripts. That's what I'm doing now. It's a collaborative job, so at any point a fellow author may add or remove details and data. The collaboration is helpful when it works toward the same goal but that goal often remains blurry, a granite crag looming in the distant hills.

Dysfunctional uncles and luminous oncology

I've been trying to remember a particular film all afternoon and was totally stumped about it. I knew it was from the 90's and involved someone dying of cancer, but beyond that, all I could remember was finding it inordinately sad -- a real heartstring-gripping jerker-of-tears. I remembered that and the keywords "Jewish packrat uncle." Those three words were enough for Google identify the film: 1995's Unstrung Heroes. This was a validating result as I had already tried searching for "Unsung Heroes", though this is actually a North Korean spy film series and an unrelated short mockumentary about superheroes.

Andie McDowell looks awfully cheery on that movie cover for somebody dying of cancer. Franz Lidz, whose memoir was the distant base material for Unstrung Heroes, later wrote about the subject, finding that "...the terminal sappiness of cancer movies is probably beyond remedy."