And that’s what we did with wheat. We pressured it into becoming the more efficient, modern “dward wheat” common to, well, damn near anything that’s processed. Unfortunately, this selective pressuring seems to have had unintended consequences for at least some people’s health.
I do not think that the issue is what we (our ancestors) did to wheat, but the fact that it may be a more recent addition to our diet. It can take thousands of years to adapt to a new food.
It seems that people with a certain variant of the major histocompatibility complex—a component of the immune system—are susceptible to celiac disease. I think that it is analogous to the situation in which people who live in areas where milk is a major food have the enzyme lactase to digest the milk sugars, but people in areas where milk is not common cannot digest it. Many Asians cannot digest lactose—but Mongolians make milk a principle part of their diet, and have no trouble with it.