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Combine the onion, carrot, garlic, tomatoes, tomato paste, parsley, rosemary, thyme, and oregano in a blender. Blend on high to liquefy all ingredients.
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Season the short ribs with salt and pepper and dredge in the flour. Shake off excess flour.
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Heat the oil in a large dutch oven or heavy soup pot over medium heat. Cook the pancetta until crisp. Use a slotted spoon to transfer pancetta to a plate.
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Add the short ribs to the pot and brown on all sides, about 7 to 10 minutes. Transfer the short ribs to the plate with the pancetta.
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Carefully add the blended tomato mixture to the pot (it may splatter). Add the beef broth, wine, bay leaf, and pancetta to the pot. Stir to combine.
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Add the short ribs to the pot and turn to coat with cooking liquid. Bring to a boil then reduce heat to a simmer. Cover and simmer for 2 hours.
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Remove the lid and stir. Simmer uncovered for 1 1/2 hours, stirring occasionally.
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Check the short ribs for tenderness. If the meat does not come apart easily, cover and simmer until it does (30 minutes to 1 hour).
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Remove the meat and bones from the pot. Shred the meat from the bone. Discard the bones and any fatty tissue.
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Return shredded meat to the pot and stir to combine. Taste and adjust seasoning with salt and pepper.
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**For maximum flavor, cool the meat and sauce to room temperature then refrigerate overnight. Reheat in the pot prior to serving.
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Cook pasta according to package instructions. Reserve 1 cup of the cooking liquid if combining with meat and sauce (Serving method 1).
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Serving method 1: Add the cooked pasta to the meat and stir to combine. Add reserved pasta water, 1/4 cup at a time, if needed. Transfer to a serving bowl or platter and garnish or serve with parmesan cheese if desired.
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Serving method 2: Place the cooked pasta on a serving platter. Top with meat and sauce. Garnish or serve with parmesan cheese if desired.