I was reading Gene Conversion in the Rice Genome, and noticed this:
Pseudogenes in the rice genome with low similarity to Arabidopsis genes showed greater likelihood for gene conversion than those with high similarity to Arabidopsis genes.
While arabidopsis is probably a different created kind than rice, it got me wondering - what if, when two species enter into symbiosis, one species transfers pseudogenes to another, which are then used in gene conversion to set up the biochemical pathways for the symbiosis?
Thus, pseudogenes might act like a symbiosis integration script, giving a template for interacting with it. The other organism then takes that template, and, through gene conversion, uses pieces out of it to alter its own genome to match the symbiosis?
Anyway, that might be an interesting path to look down.