Inflammation is the basic problem.
Our modern day nutrition sets us up for that inflammatory model.
Once the gut lining is weakened, it allows material and chemicals into the system that would normally be repelled. I think that the ongoing irritation over a long time sets us up for a raft of autoimmune and allergy responses.
This article by Dr Justin Marchegiani explores the topic further.
If you want to know how the combination of sugar, refined carbohydrate and polyunsaturated oils create the inflammation then come across to