In the late 1800's, Paul Ehrlich discovered, quite by accident, the <blood brain barrier>, which protects the delicate brain from all the provocative compounds in our blood stream. Only the small, lipid soluble molecules such as oxygen and carbon dioxide flow through the barrier. Even sugar, i.e. glucose, doesn't pass, and since that is the primary fuel for the brain, an active transport mechanism has evolved to ferry sugar across the divide.
The barrier is not a physical structure. I mean, the brain isn't wrapped up in a plastic bag. Instead, the barrier is implemented in the walls of the blood vessels that traverse the brain. They are functionally different from the arteries and veins that nourish the rest of the body. It's an imperfect analogy, but the holes are smaller. The brain is a fragile organ, and it must be protected. Even the lowly fruitfly has a blood brain barrier, though it is structurally different from ours.
Jack Samuels, an expert in glutamate sensitivity, offers a compelling theory. Perhaps John's blood brain barrier is just a bit leaky. It still blocks the macro molecules that would kill a person outright if they entered the brain, but it allows some of the smaller molecules through. These include glutamates, and other impurities found in 20th century food. This genetic variation would have been harmless just a century ago. There has been no evolutionary pressure to oppose it. So we should not be surprised to find that some of our children react, behaviorally, emotionally, or mentally to these novel compounds. None of this explains problem #2, but it does explain problem #1 perfectly.
Finally, Jack offers a ray of hope. In some cases children "outgrow" some of their sensitivities as they enter puberty. Perhaps the blood brain barrier completes its development as we reach adulthood. Continuing our imperfect analogy, perhaps the holes tighten up. I dare not count on this, but it would be wonderful if true! John can look me straight in the nose, as he approaches his teen age years. Manhood is just around the corner. We will continue to watch his diet; but someday, if we're lucky, we can lift some of these restrictions.