In a small bowl, combine 3 tablespoons warm water, 1 tablespoon of the sugar and the yeast (which should be stored in the freezer for best use). Let the mixture rest until a faint froth appears on the surface, 10 minutes.
In a medium bowl, mix together 5 cups warm water, the remaining 1/2 cup brown sugar, the whole wheat flour, oats, wheat germ, butter and salt. Add half of the yeast mixture and mix until combined. Add the rest of the yeast and again mix until combined. Then add the all-purpose flour, a cup at a time, mixing between each addition.
Turn out the dough onto a well-floured surface and knead for 7 to 8 minutes. Lightly grease a large bowl with softened butter. Shape the dough into a ball and set it into the greased bowl. Cover lightly with a piece of plastic wrap or cloth. Set the bowl in a warm place and allow to rise until the dough has doubled in size, about 1 hour.
Once the dough rises, turn it out onto a floured surface and slice into 4 equal portions. Take each section and, using a rolling pin, roll the dough into a 9- by 20-inch rectangle-- use the length of your loaf pan as a guide for how wide to make your rectangle of dough. Tightly roll the dough into a log that is about 9-inches long, making sure to not stretch out the middle of the dough as you roll. Pinch the seam with your fingers to seal it.
Rub a 9-by- 5-inch loaf pan generously with softened butter. Set the log of dough in the pan, seam-side down, making sure to fill the pan evenly. Cover with a kitchen towel and set in a warm place to rise until doubled in size, about 1 hour.
Place an oven rack in the bottom third of the oven. Preheat the oven to 350 degrees F.
Bake the loaf until the top is a deep golden brown, 30 to 35 minutes. Cool for 10 minutes in the pan, then turn out the loaf onto a wire rack to cool completely, about 1 hour. Once cool, wrap well in plastic and store at room temperature for up to a week.
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