Preheat the oven to 400 degrees F. Line 12 muffin cups with paper liners, or coat with cooking spray. Set aside.
Sift the flours, baking soda, salt, and cinnamon into a large bowl. Stir in the brown sugar, wheat germ, and raisins, and make a well in the center of the dry ingredients.
Lightly whisk together the yogurt, oil, egg, orange zest, and juice. Pour into the well and stir only enough to moisten.
Spoon into the muffin cups. Bake until the muffins are golden brown and the centers are firm when gently touched, about 15 - 20 minutes. Leave muffins to cool in the tray for 2 - 3 minutes, then turn them out onto a wire rack. The muffins are best eaten fresh, preferably still slightly warm from the oven, but may be cooled completely and then kept in an airtight container for as many as 2 days.
For carrot and spice muffins, add a dash of nutmeg, stir 2 small grated carrots into the flour mixture with the wheat germ, and reduce the amount of raisins to 1/4 cup.
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