Caporale's latest work, The Implicit Genome, covers a lot of cool mechanisms for the generation of variability within genomes. One interesting mechanism is through contingency loci.
A contingency locus is an area of the genome which has a high mutation rate, which is associated with a frequently-changing environment. A typical reason for contingency loci is to get around the immune system. The contingency loci in many bacteria are for their outer coat proteins, which is what the immune system recognizes. Bacteria and single-celled eukaryotes can evade the immune system by rapidly mutating their outer coat.
Now, usually the relationship between microbes, hosts, and immune system is discussed in terms of warfare - this fights this, this evades that. But what if this was instead a mechanism that wasn't nearly as much about warfare as it was about adaptation?
For example, Opa proteins on N. meningitidis are surface proteins that are encoded by contingency loci. Different versions of these proteins adhere to different types of cells. So, what I'm wondering is - are mutations in these contingency loci associated with mutations elsewhere, or expression changes elsewhere? For instance, might certain microbes alter their biochemistry in coordination with their surface proteins so that they assist the right cell type in the correct way? In other words, instead of "evading the immune system", might it instead be trying to find a biochemistry which is helpful to the organism, and using surface proteins to advertise to the immune system what sort of tissue the organism is best configured for. The immune system, rather than "combating" the antigen, might be just cleaning up good microbes which are just in the wrong place, or perhaps in the wrong configuration in the wrong place.
Anyway, it's an interesting possibility, but I'm not sure how it might be investigated. But it might make a good research project for a budding Creation PhD student somewhere.
I'm not quite sure how this question would be investigated, but it's sure worth asking.