I had this thought while scrubbing shampoo out of my hair.
I know what makes pumpernickel dark these days: most professionals add caramel coloring to their dough, and homebakers will add either instant coffee or cocoa powder. I've used both methods in a bakery and at home. But pumpernickel is an old, eastern European bread, and, as far as I knew, they weren't adding coffee or caramel dye to their bread back then. So, what used to make pumpernickel dark?
My co-worker at Philly Bread, David, had my answer, and it has to do with both the ingredients and how the bread is baked.
Pumpernickel has relatively high sugar content for a traditional bread. Not only do you add molasses to the bread, but the rye grain itself--and pumpernickel is mostly rye, not wheat--has quite a bit of sugar. So you take this higher sugar dough (not sweet compared to the sweetened pastries we eat now), and you bake it very, very slowly in a bread pan. Just as the sugar in onions will caramelize and brown if you cook them slowly, the sugars in pumpernickel dough caramelize in the low heat of the oven and the whole loaf browns through.
I've been baking pumpernickel in my wood-fired oven, just as it was done traditionally. After my pizza has been baked at 750 degrees, my loaves at 500, my veggies at 400, my chicken at 350, only then does the pumpernickel go in. It bakes in the last of the heat, somewhere in the 250 to 300 degree range. Although I'll be honest with you: I always put the pumpernickel in too soon because it just feels wrong to bake something at such a low temperature!!