The following is an argument presented based upon research and investigations into diet, physiology and human history. This article will allow you to piece some things together and develop your own opinion.
Basically, there is a huge difference between traditional methods of processing grains, which yield our breads, pastas and pastries, and conventional (and more recent) method of processing.
Traditionally, Man understood how nature operated and would pass that wisdom down the line. The wisdom of soaking nuts, seeds, grains and legumes goes back thousands of years, and rightfully too. Our ancestors, who left their paleolithic lifestyle and settled down in farms to seasonally plow the soil, had recognized that these sources of nourishment had protective mechanisms, designed to ensure the survival of the pod until such conditions that favored germination arrived.