What to discuss in the Discussion?

The postdoc gets back from his Christmas break tomorrow, and I plan to have a revised version of his uptake-bias manuscript waiting for him.  I've been working through the last part of the Results, and it's looking pretty good.  Not finished of course, as there are still two analyses to add.  One is the experimental test of the positional interactions predicted by his analysis, comparing uptake of DNA fragments containing single or double mismatches from the consensus USS.  I think he's going to do this experiment as soon as he gets back.  The other is analysis of out-of-alignment uptake sequences in fragments that were taken up despite lacking a good in-alignment uptake sequence.  This issue arises because some fragments contained small insertions or deletions that caused their uptake sequence to be misaligned in the original analysis, and some other fragments may have substitutions that created an uptake sequence at a new location in the fragment.  There aren't very many of these out-of-alignment uptake sequences but sorting them out helps clarify some other issues.  He's already done the analysis (at least most of it) but we still need to incorporate it into the Results.

The bigger problem is what to say in the Discussion section.  Right now it's a shambles, with lots of interesting points and good sentences and well-written paragraphs all jumbled together.  I need to get a better perspective on this - to think about what actually should be discussed.

One place to start is the Introduction.  Issues we raised there should be addressed and ideally resolved in the Discussion.  Unfortunately, our lovely work doesn't really resolve these.

Well, so much for working on the Discussion...  I'm now back to asking myself (and, in absentia, the postdoc) questions about how we interpret his analysis of interaction effects:  Do interaction effects explain the discrepancy between genomic motif and uptake motif?  Do interaction effects support the hypothesis that uptake bias is intrinsic to the mechanism of uptake, and not the effect of a single dedicated recognition protein?  And more questions I've added to his lovely figure, so I remember to ask him them tomorrow.

And now, I've got two manuscript reviews (both overdue) and a book review to do.