Permutation City

Instead, she zoomed in closer, switched to atomic colors (but left the pervasive aqua molecules invisible), temporarily halted time to freeze the blur of thermal motion, then zoomed in still further until the vague specks scattered throughout the workspace sharpened into the intricate tangles of long-chain lipids, polysaccharides, peptidoglycans. Names stolen unmodified from their real-world analogues -- but screw it, who wanted to spend their life devising a whole new biochemical nomenclature? Maria was sufficiently impressed that Lambert had come up with distinguishable colors for all thirty-two Autoverse atoms, and unambiguous names to match.

She tracked through the sea of elaborate molecules -- all of them synthesized by A. lamberti from nothing but nutrose, aqua, pneuma, and a few trace elements. Unable to spot any mutose molecules, she invoked Maxwell's Demon and asked it to find one. The perceptible delay before the program responded always drove home to her the sheer quantity of information she was playing with -- and the way in which it was organized. A traditional biochemical simulation would have been keeping track of every molecule, and could have told her the exact location of the nearest altered sugar almost instantaneously. For a traditional simulation, this catalogue of molecules would have been the "ultimate truth" -- nothing would have "existed," except by virtue of an entry in the Big List. In contrast, the "ultimate truth" of the Autoverse was a vast array of cubic cells of subatomic dimensions -- and the primary software dealt only with these cells, oblivious to any larger structures. Atoms in the Autoverse were like hurricanes in an atmospheric model (only far more stable); they arose from the simple rules governing the smallest elements of the system. There was no need to explicitly calculate their behavior; the laws governing individual cells drove everything that happened at higher levels. Of course, a swarm of demons could have been used to compile and maintain a kind of census of atoms and molecules -- at great computational expense, rather defeating the point. And the Autoverse itself would have churned on, regardless.

Maria locked her viewpoint to the mutose molecule, then restarted time, and everything but that one hexagonal ring smeared into translucence. The molecule itself was only slightly blurred; the current representational conventions made the average positions of the atoms clearly visible, with the deviations due to bond vibration merely suggested by faint ghostly streaks.

She zoomed in until the molecule filled the workspace. She didn't know what she was hoping to see: a successful mutant epimerase enzyme suddenly latch onto the ring and shift the aberrant blue-red spike back into the horizontal position? Questions of probability aside, it would have been over before she even knew it had begun. That part was easily fixed: she instructed Maxwell's Demon to keep a rolling buffer of a few million clock ticks of the molecule's history, and to replay it at a suitable rate if any structural change occurred.

Embedded in a "living" organism, the mutose ring looked exactly the same as the prototype she'd handled minutes before: red, green and blue billiard balls, linked by thin white rods. It seemed like an insult for even a bacterium to be composed of such comic-book molecules. The viewing software was constantly inspecting this tiny region of the Autoverse, identifying the patterns that constituted atoms, checking for overlaps between them to decide which was bonded to which, and then displaying a nice, neat, stylized picture of its conclusions. Like the handling rules which took this representation at face value, it was a useful fiction, but . . .

Maria slowed down the Autoverse clock by a factor of ten billion, then popped up the viewing menu and hit the button marked RAW. The tidy assembly of spheres and rods melted into a jagged crown of writhing polychromatic liquid metal, waves of color boiling away from the vertices to collide, merge, flow back again, wisps licking out into space.