The post-doc working on how and why cells lose competence has some very interesting data, but it makes us realize that we haven't yet spelled out clear hypotheses for this data to address. It's tempting to try to come up with the true explanation of why many cells/strains/species lose competence while others retain it, but that's not what we need at this stage. Instead we just need some clear overly-simplistic statements of the different possible causes and their consequences, to guide our thinking.
So here's one possibility:
Maybe cells take up DNA only because the genetic changes this sometimes causes are occasionally beneficial. (Most people think this is true, though I think the DNA=food consequence is much more important.) These benefits will be rare. So most competent cells will go for long periods taking up DNA but getting no benefit. When mutations that reduce or eliminate gene function arise in genes needed only for DNA uptake, there may be no selection against them for very long times. Depending on the particular mutations, these cells will have an advantage because they won't waste resources taking up DNA that's doing them no immediate good. So the frequency of competent cells in the population will be gradually decreasing.
(I write 'may be' because mutations that mess up one component of a complex machine may cause harm in ways that eliminating the whole machine wouldn't (like the difference between a car with no brakes and no car at all). For example, knocking out the secretin pore but keeping the rest of the DNA uptake machinery messes up the membranes of competent cells in ways that knocking out the ability to turn on competence doesn't. But lets not worry about this right now.)
But once in a while a cell that takes up DNA gets a good genetic change, one that lets it outcompete its relatives. This cell and its immediate descendants all have fully functional competence genes, so the frequency of competent cells in the population has increased.
The long-term outcome depends on how often DNA uptake produces good changes and how often deleterious mutations arise in competence genes and how harmful or beneficial these mutations are in the short term. If the good changes happen often enough, this could give populations that always contained lots of competent cells and some recently arisen non-competent ones. But if the good changes are less frequent, the cells with mutations causing loss of competence could completely take over. And once this happens there's no going back.
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