Bear,

I, too, have been following up on the mitochondrial theory put forward by HK and find it very credible.  One aspect of many of the inflammatory diseases is that the mitochondria undergo 'metablic reprogramming' and switch to glycolysis and gluconeogenesis under non-hypoxic conditions.  This metabolic shift is, in turn, associated with 'trained immunity' in cells of the innate immune system.  Trained immunity is under, guess what, epigenetic control - a very complex interacting system of histone and other protein methylation and acetylation.  Busy now but will post references later. 

Jupe