Plainly put there's nothing natural about a fast food diet, and since your body was designed to break down caveman foods (fruits, vegetables and cooked meats), these new chemical foods just don't mesh with your body's "food breakdown" systems.
For instance, trans fats are artificially hydrogenated fatty acid chains. Your body understands who to take apart and use normal fatty acid chains, but gets lost trying to break down trans fats. Unbroken chains of fat in your body are extremely unhealthy.