Go Ahead and Let Them Eat Dirt
Part of a parent's job description is constant control over their young child's eating of the world around them. Every parent has witnessed their child eating dirt, paper, sand, little pebbles, small toys, marbles, rubber bands, paper clips, and even little bits of snot. I know, you're really grossed out now, but the truth hurts. There are even disease conditions that have everything to do with eating improper things, such as Pica, the main symptom of which is eating dirt. But if you step back and take a broader view of this, you will notice that there may be more to this than a crazy, gross habit. There is a growing body of evidence that children's ingestion of certain things actually is a way to develop immunity.
It has long been thought that geophagy (eating dirt or the earth) seems to be most common in children during times of high susceptibility to parasites and in pregnant women in hot, moist climates. Research by Cornell University showed that 30-60% of pregnant women in parts of Africa reported craving dirt during pregnancy compared to .01% of Danish women. It soothes the digestive tract (similar to the ingestion of various clays) and protects the body from viruses and bacteria that enter through the gut, while increasing nutrient absorption.
We seem to have forgotten how important it is to expose ourselves to the world. The development of immunity seems to be a direct result of ingesting our environment. Throughout history from ancient Egypt to colonial America, grains were ground with stones that would slough off minerals into the flour. It might wear down the teeth over time, but it might have had a strong effect on the development of immunity. This is why many Egyptian children that live along the Nile can swim in the bacteria-filled water without getting sick, while a European tourist would require a trip to the hospital after a cooling dip. This may also explain why many children are developing celiac sprue, because their gut immunity has never developed.
Warning: more grossness ahead... We chastise our kids about picking their noses, but if you realize the amount of pollen, dead bacteria and other airborne pollutants that are present in nasal mucous, then you can imagine how this might go a long way to programming the immune system to recognize challenges from the environment. Now granted, eating local organic honey is a much nicer way to do this, but if we interfere with every attempt by a child to subconsciously build their immunity without offering an alternative, then we are setting our children up for a fall into disease later on.