Have you seen Dr. Harris's interesting recent viewpoint concerning the gut and our immune response, on Melissa's blog? Here's the argument, blow-by-blow, paraphrased for brevity, and sometimes for humorous effect.
Paleo didn't fix my digestive problems. "Good" and "bad" foods are defined relative to your individual biology and current situation. The line is blurry between "good" nut and coconut flours and "bad" grain flours. Also, I eat foods that taste good and that sometimes includes grains. If you don't like that, you're a stupid baby.
Many (all?) plants have antinutrients, and picking an "evolutionary template" is misguided. MiRNA in rice may have been a news item, but it's not necessarily unique.
Right on bro. I'm the guy who brought you "varying levels of macronutrients are not going to kill you". Now allow me to blow your mind with some more tasty joojoo. Avoiding bad guys like gluten may relieve symptoms, but the core problem is often immune dysregulation. Guess what? You can eat a 100% perfect paleo diet, but the root problem may not be food.
Immune dysregulation? I have so many questions on this, I don't even know where to begin. What's up with the GAPS diet? You're saying helping your gut flora is not the ultimate purpose in life? The microbiome is so crazy!
Let me entrap you in my lyrical flow...The bacterial component is very important but there is very little you can do to change it once you are older than a toddler. This is what my reading of the literature so far shows. Yogurt and Kimchi and probiotic pills and eating dirty veggies are all peeing in the wind if you have any serious immune dysregulation going on. How to improve the immune system? That's the big question. Maybe...WORMS! Yes, consider the helminth. Don't be a dummy though, parasites can kill. Don't go willy-nilly eating dirty veggies and walking barefoot in the swamp.
Obi Kurt Kenobi, you're our only hope! What do you think of the use of pseudocommensals?
If you're reading this, you should also read this... http://paleohacks.com/questions/107257/is-paleo-a-band-aid#ixzz1qMw36TFg