The work and ideas underlying the US variation manuscript are getting better, but the manuscript itself is getting farther from completion, not closer.
Advance #1: Realizing that I can use a log scale for the x-axis to see if runs have really reached equilibrium.
Retreat (the opposite of advance?) #1: Realizing that runs I had thought were at equilibrium aren't, so that conclusions I had thought were solid are not, so I don't really know what the true results are!
Advance #2: Realizing that I should think of/write about the elevated fragment mutation rates as degrees of divergence.
Advance #3: Remembered that the Introduction says that the goal of the work is to evaluate the drive hypothesis as a suitable null hypothesis for explaining uptake sequence evolution. Our results show that it is; the accumulation of uptake sequences under our model is strong, robust, and has properties resembling those of real uptake sequences.
Progress: Going through the Results section, annotating each paragraph with a summary of the all of the relevant data, annotated by whether this is solid equilibrium data (fit to use) or not. This is taking a lot of time, because I have to identify and check out (and sometimes enter and graph) the data, but the results aren't as bad as I had feared. Runs that have already finished fill some of the new-found gaps, and others are already running but won't finish for a few days (some longer). So I'm going to finish this annotation, queue whatever runs I think are still needed, and then maybe spend a few days on the optical tweezers prep work (at long last) while the runs finish.
8 hours ago in The Phytophactor