Some comments about my Evo-WIBO talk plan from a reader:

...what I'm really curious about is the sense I get that you feel a phenotype must be some sort of evolutionary goal (i.e., why would we have an a priori expectation that enzymes would evolve to accomplish homologous recombination?) Gender doesn't seem to pop onto the Natural History landscape full blown and ready to be appreciated. So why should HR? I really like the notion that HR might proceed from a DNA replication and repair background. 

I didn't mean to imply that phenotype is a goal, neither generally or with respect to homologous recombination (HR).  But most other microbiologists and molecular biologists have been assuming but not rigorously evaluating) that HR exists because of selection for its sometimes-beneficial consequences. 

And is it not possible that natural competence is currently an orphan process that exists for food uptake but was once a piece of a primordial sex process that developed further in other lineages but was cast aside in bacteria? (photosynthesis may have been cast aside in oomycetes in favor of parasitism).

That seems backwards to me, because selection for the food benefit is so straightforward and selection for sex so problematic.

To me, HR has to be more beneficial than horizontal gene transfer for a lineage to find it worth the trouble. When organisms are extremely simple the selective disadvantage of maintaining DNA that isn't carrying its weight should lead to its elimination. The notion of an allele implies the existence of a gene - but a gene not in the sense of a capable ORF but in the sense of two or more ORFs in a population that perform the same function in manner that the environment will influence and that selection can act on. If said variant ORFs come to be in the same cell, then HR can go to work on them.

Homologous recombination isn't really any 'trouble', to the extent that it happens as an accidental (i.e. unselected) consequence of enzymes selected for their effects on DNA replication and repair and of accidental transfer of DNA fragments by genetic parasites or of DNA uptake for food.  And in bacteria there's very little evidence that it ever occurs any other way.

The value of taking a different tack on a problem is prescient. And physics offers a host of tools and a philosophical background that could really help. To me the challenge of the 15 minute presentation is to illustrate how having data that describe the physical process of DNA uptake should allow mathematical model development for the process which then allows development of testable hypotheses. There are "big organism" examples of this approach bearing fruit.

I don't think that the phenomenon of natural competence needs mathematical models at all (nor do any other of the phenomena that sometimes lead to to recombination in bacteria). My point for the talk is that many hypotheses can be directly evaluated by more thorough investigation of the phenomena in question.