Why don't USS accumulate in our model?

The undergraduate is working at home, making improvements to the use-ability of our Perl model of USS evolution, while I'm here doing some test runs with the slightly unwieldy version we have now.

This is the version that incorporates the first major improvement. Instead of a single "best-score" fragment recombining with the genome in each cycle, each of the scored fragments can recombine with the genome, with a probability proportional to its score. In principle this should allow the recombination to introduce new USS-like sequences faster than they are lost from the genome by mutation. But in practice the USS-score of the genome drifts up and down but doesn't consistently increase.

"When in doubt, run more controls."

So I've made a modified version of this program that has the same feature as our PositiveControl.pl program (it's name is PositiveControlv2.pl). Instead of mutating random fragments and recombining them back into the genome, it replaces their sequences with perfect USS cores. Of course the fragments need to be the same length as the core.

OK, this positive control tells me that the program is doing what it should. 10 fragments are recombining into the genome each cycle, which is what should happen to the 10 fragments the program considers each generation. Now I'll test PositiveControlv3, which puts in an imperfect USS instead of a perfect one. If the program is doing what I want, on average 8 of the 10 fragments will recombine each generation, and the genome score will not get as high as with perfect USSs.

OK, that worked too. So I think the problem may not be with the implementation of the code, but with the design of this version of the model. Back to the drawing board... (literally, back to the big whiteboard in the hall outside my office).