Diagramming the Atari Pathway

Okay, it was an outside speaker at work who planted this seed in my brain, and now I can't shake the image -- but perhaps by writing this I will (but also perhaps I will infect my loyal readers with it).

The stated observation was that some biological pathway diagrams "look like Space Invaders". Now, I hold such games dear to my heart -- they were quite the rage in our neighborhood growing up, though we didn't own one & I was never very good. Nowadays one can buy replicas which play many of the old games -- except the entire system fits inside the replica of the old joysticks. My hardware-oriented brother loves to point out all the interesting workarounds which are now fossilized in these players -- such as limits on the number of moving graphics ("sprites") which could occupy a scan line.

But which video game seems to be the model for some of these diagrams? Space invaders is an obvious candidate (or one of the knockoffs or follow-ons such as Galaga), but my old favorite Centipede (or its successor Millipede) is even closer -- they even had spiders trying to spin webs.

It would be a pretty funny visual joke -- saved for precisely the right time (the wrong time could be disaster!) -- to have a pathway display morph into a game. The transcription factors start moving about and crashing into the kinases which in turn blast away at the receptors.

Versions of the reverse have sometimes occupied my mind -- what if we could make scientific programs more game-like? The notion I most commonly ponder is a flight simulator for protein structures. Even that could be taken to another level -- your X-wing is flying down a canyon of the giant structure, ready to unleash a boronic warhead to destroy the evil proteasomic death star!