Field of Science

Two steps forward, one step back?

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.

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