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Maria displayed a histogram of mutations occurring in the bacteria's three nutrose epimerase genes; the enzymes these genes coded for were the closest things A. lamberti had to a tool to render mutose digestible -- although none, in their original form, would do the job. No mutants had yet persisted for more than a couple of generations; all the changes so far had evidently done more harm than good. Partial sequences of the mutant genes scrolled by in a small window; Maria gazed at the blur of codons, and mentally urged the process on -- if not straight toward the target (since she had no idea what that was), then at least . . . outward, blindly, into the space of all possible mistakes.
It was a nice thought. The only trouble was, certain portions of the genes were especially prone to particular copying errors, so most of the mutants were "exploring" the same dead ends again and again.
Arranging for A. lamberti to mutate was easy; like a real-world bacterium, it made frequent errors every time it duplicated its analogue of DNA. Persuading it to mutate "usefully" was something else. Max Lambert himself -- inventor of the Autoverse, creator of A. lamberti, hero to a generation of cellular-automaton and artificial-life freaks -- had spent much of the last fifteen years of his life trying to discover why the subtle differences between real-world and Autoverse biochemistry made natural selection so common in one system, and so elusive in the other. Exposed to the kind of stressful opportunities which E. coli would have exploited within a few dozen generations, strain after strain of A. lamberti had simply died out.
Only a few die-hard enthusiasts still continued Lambert's work. Maria knew of just seventy-two people who'd have the slightest idea what it meant if she ever succeeded. The artificial life scene, now, was dominated by the study of Copies -- patchwork creatures, mosaics of ten thousand different ad hoc rules . . . the antithesis of everything the Autoverse stood for.
Real-world biochemistry was far too complex to simulate in every last detail for a creature the size of a gnat, let alone a human being. Computers could model all the processes of life -- but not on every scale, from atom to organism, all at the same time. So the field had split three ways. In one camp, traditional molecular biochemists continued to extend their painstaking calculations, solving Schrödinger's equation more or less exactly for ever larger systems, working their way up to entire replicating strands of DNA, whole mitochondrial sub-assemblies, significant patches of the giant carbohydrate chain-link fence of a cell wall . . . but spending ever more on computing power for ever diminishing returns.
At the other end of the scale were Copies: elaborate refinements of whole-body medical simulations, originally designed to help train surgeons with virtual operations, and to take the place of animals in drug tests. A Copy was like a high-resolution CAT scan come to life, linked to a medical encyclopedia to spell out how its every tissue and organ should behave . . . walking around inside a state-of-the-art architectural simulation. A Copy possessed no individual atoms or molecules; every organ in its virtual body came in the guise of specialized sub-programs which knew (in encyclopedic, but not atomic, detail) how a real liver or brain or thyroid gland functioned . . . but which couldn't have solved Schrödinger's equation for so much as a single protein molecule. All physiology, no physics.
Lambert and his followers had staked out the middle ground. They'd invented a new physics, simple enough to allow several thousand bacteria to fit into a modest computer simulation, with a consistent, unbroken hierarchy of details existing right down to the subatomic scale. Everything was driven from the bottom up, by the lowest level of physical laws, just as it was in the real world.
The price of this simplicity was that an Autoverse bacterium didn't necessarily behave like its real-world counterparts. A. lamberti had a habit of confounding traditional expectations in bizarre and unpredictable ways -- and for most serious microbiologists, that was enough to render it worthless.
For Autoverse junkies, though, that was the whole point.
Maria brushed aside the diagrams concealing her view of the Petri dishes, then zoomed in on one thriving culture, until a single bacterium filled the workspace. Color-coded by "health," it was a featureless blue blob; but even when she switched to a standard chemical map there was no real structure visible, apart from the cell wall -- no nucleus, no organelles, no flagella; A. lamberti wasn't much more than a sac of protoplasm. She played with the representation, making the fine strands of the unraveled chromosomes appear; highlighting regions where protein synthesis was taking place; rendering visible the concentration gradients of nutrose and its immediate metabolites. Computationally expensive views; she cursed herself (as always) for wasting money, but failed (as always) to shut down everything but the essential analysis software (and the Autoverse itself), failed to sit gazing into thin air, waiting patiently for a result.
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.