I'm not making much progress on revising the USS manuscript, I think partly because, deep down, I'm worried that our logic is a bit weaker and more circular than I'm happy with. So I'll try to lay it out below.
Our goal for our USS research is to find out whether these sequence motifs are abundant simply because of the molecular drive caused by the biased DNA uptake machinery, or because natural selection favours cells that take up DNAs from closely related cells/species. This latter explanation arises from the common assumption that cells take up DNA because recombination generates benefits, and is inconsistent with our proposal that cells take up DNA simply as food.
We seem to be trying to discriminate between these explanations by finding out whether the bias of the uptake machinery matches the motif accumulated in the genome. But I think this is not a good test, because such a correspondence is consistent with both explanations. Furthermore, the DNA uptake data in the manuscript aren't compelling enough to push this very weak argument.
But why am I thinking of doing a big rewrite at this stage? Why don't we just make the minimum improvements necessary to satisfy the reviewers and send the damn thing back in? Now that I've reread the whole manuscript and reminded myself of what we said, I guess I'd better reread the reviews, and the responses suggested by the post-doc author, and see if I think we can do this.
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