The immune system is designed to swiftly remove foreign proteins in the bloodstream because for the most part, foreign proteins in the bloodstream usually means overwhelming infection. Non-self proteins are never supposed to be in the bloodstream. They are not absorbed that way from the intestines.

Most viral or bacterial infections do not lead to any viral or bacterial proteins in the bloodstream. Much of the time the immune system is reacting to infections on the surface of the mucosal layer, which is the lining of the nose/mouth/throat, and the lung. The main immunoglobulin here is IgA. The mucosal layer does an admirable job of restricting the infection to this surface area and therefore keeping the foreign proteins out of the bloodstream.

One problem with exposing the bloodstream to proteins is that the immune system develops such a brisk immune reaction to them that the next time the immune system is exposed to these proteins, even if they aren't in the bloodstream, the immune system activation can be so brisk that it is life threatening.

Prior to the increased use of immunizations in the 20th century, accidental overwhelming activation of the immune system was seen infrequently enough that it didn't even have a name. But once people developed the technology to inject proteins directly into the bloodstream and therefore prime the immune system, we began to see this phenomenon more and more.

First termed "aphylaxis" by researcher Richet in 1902, and then changed to "anaphylaxis", Richet found that the first time he injected sea anemone toxin into dogs, they tolerated it fine -- but this first exposure of course primed the immune system, such that the next time he injected sea anemone toxin, they had such an overwhelming immune system response to the protein that they died. Thus his term "a-phylaxis" meaning "the opposite or against protection", as his line of research was to see if by injecting the proteins into the bloodstream he could make the dogs immune to the toxin, and obviously the dogs dying much quicker than the actual toxin could kill them was the direct opposite of the protective effect he was trying to achieve.

It is always possible for an immune response against a protein the immune system is exposed to to accidentally cross react with other proteins -- be they proteins in food, the environment, or even the human body. Rheumatic fever, for example, is a well known condition where the human body builds antibodies against streptococcus bacteria that accidentally cross react with heart and joint proteins, such that the antibodies do damage to the joints and heart valves.

So what are the chances that the mounting number of vaccinations are priming immune systems to accidentally react against environmental proteins, and thus be partially to blame for the increasing number of kids suffering from asthma and atopy, as well as the increasing number of food allergies? It's exactly what we would expect if we understand the physiology, and it would be the same phenomenon as the auto-immune destruction of the pancreas this post talks about.

The rate of anaphylactic reactions is increasing -- in the 1980s it was 20/100,000, one decade later it was already up to 50/100,000.

But most vaccine advocates have no conception of this because for the most part they don't actually understand how the immune system works.