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The word "whole" refers to the fact that all of the berry is used and nothing is lost in the process of making the flour, rather than referring to the complete berry in its natural grown state. Because the flour contains the remains of all of the berry it has a textured, brownish appearance.
"Brown" bread made from whole wheat flour is more nutritious than "white" bread made from white, refined, flour even though nutrients are added back to the white flour. Thus, brown bread is more natural than white because it is less refined and retains more of the naturally occurring vitamins and minerals. This is important to nutrition because while we have identified many of the vitamins and minerals occurring naturally in foods, there remain doubts that we have identified them all. Much less confidence attends our understanding of minimum daily requirements of these vitamins and minerals and any such published numbers can only be used as guidelines.