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Put the bacon into a cold 10-inch cast iron pan and cook over medium heat until the fat is rendered and the bacon bits are crisp. Do not let burn. Remove the bacon to a paper towel lined plate. Keep the bacon fat in the pan and set aside.
In a large bowl, whisk together the cornmeal, flour, sugar, baking powder, baking soda, and salt. In a separate bowl beat the eggs with a whisk until foamy; whisk in the milk. Add the wet ingredients to the dry ingredients and stir just until combined. Fold in the bacon bits, chipotle, and chives. Pour the batter into the cast iron pan. Bake until a toothpick inserted in the center comes out clean, about 20 to 25 minutes.