>Dean, what qualifies a protein as foreign?

A foreign protein would be any protein your body doesn't recognize as eiher
one of its own or properly identify as harmless food.

A good way to define foreign proteins is also to suggest that any form of
protein which is significantly different from a protein that would have
been in the ancestral human diet is probably foreign.  For example, there
is no evidence that humans ever ate wheat prior to about 10,000 years ago,
and most humans have been eating it for considerably less time.  Wheat
contains glutens, forms of protein which are larger and more complex than
the those found in meat, nuts, and fruits.  There is considerable evidence
that these proteins cause a number of autoimmune reactions because the body
doesn't know what the hell they are.  Thus it launches immune attacks on it
(resulting in allergies), or even worse, it gets confused by them.  There
is some research indicating that eating wheat proteins causes some of the
body's mechanisms to become confused and lose the ability to distinguish
the body's own tissues from foreign invaders, so the body starts attacking
itself, as seen in rheumatoid arthritis and apparently mulitple sclerosis.

Grains are known already to cause a number of diseases, and it appears that
the glutens are probably the primary causative factor in much of that
(although there's also argument that the high carbohydrate content of
grains is also a cause of problems for many people who eat a lot of them).

The overwhelming body data suggests that all the beans we commonly eat
today (including soy), all the grains we eat, and most dairy products
contain proteins which are quite different from any protein forms we would
have encountered during the millions of years of evolution our species
underwent before the advent of agriculture.

If you want to look at this in evolutionary terms, the "safe" proteins
would be meat (including insects), eggs, nuts, and the minor amino acids
found in fruits.