Season shanks with salt and pepper and dredge in flour. Place onion, carrot, celery and garlic in a food processor and pulse until very finely minced, but not yet puréed.
Heat oven to 350°F. Coat a Dutch oven with olive oil and place over medium-high heat. Sear shanks until deeply browned on both sides. Remove to a plate. Add a little more oil and add minced vegetables. Cook until vegetables red so$ and browned, 5–7 minutes.
Add wine to pot, scraping up browned bits as wine reduces. Add tomatoes, stock, thyme, and shanks. Bring to a boil, then cover (with lid or foil) and place in oven.
Check shanks after two hours; they’re done when the meat easily pulls away with a fork, and the sauce has mostly reduced to a thick coating (add more stock if liquid cooks down too far). Before serving, stir in one tablespoon of gremolata. Divide shanks among 4 plates with risotto, passing additional gremolata at the table. Serves 4.
*To make gremolata, combine 1/4 cup finely minced parsley, 2 grated or minced garlic cloves and the grated zest of one washed lemon.