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Step 1
Preheat the oven to 325F.
Step 2
Pat the short ribs day and sprinkle the pepper, sea salt, and thyme leaves on top of them. Rub the seasoning in to fully coat the short ribs on all sides. Heat the olive oil in a dutch oven or medium heat, then add the short ribs to the pan (do this in batches if they don’t fit in a single layer). Brown the short ribs on all sides, about 2-3 minutes per side, until a nice, caramelized brown crust has formed on the exterior of the ribs. Remove the browned short ribs to a plate.
Step 3
Drain the rendered fat from the pan, reserving only 1 TBS of fat in the pan. Return the pan to the heat and lower the heat to medium-low. Add the chopped onions, carrots, celery, garlic and bay leaves to the pan. Saute until the vegetables are tender and translucent, about 5-7 minutes.
Step 4
Add the red wine, port wine and balsamic vinegar to the pan with the vegetables. Bring to a simmer and scrape up any browned bits stuck to the bottom of the pan with a wooden spoon. Simmer the wine until it has reduce by one third, which should take 5-8 minutes.
Step 5
Add the beef broth to the reduced wine and stir to combine, then place the short ribs back in the pan. They should fit snugly in the pan and be just barely covered by the liquid. Tuck the parsley in to the pan around the side of the ribs. Cover with a lid and transfer to the preheated oven. Roast the short ribs for 2 1/2 to 3 1/2 hours, checking every 30-45 minutes and turning the ribs over in the pan at least once. When finished, the ribs should be completely tender, such that you can easily pull the meat apart with a fork. Remove them from the oven and let cool for 20 minutes. For best results, cover and transfer them to the fridge overnight before serving.
Step 6
When ready to serve, remove the ribs from the fridge. Skim off and discard the hard white fat on top of the dish (there will likely be a lot of this). Preheat the oven to 400F, and return the ribs, uncovered, to the oven for 15-20 minutes – this is to both reheat the ribs and to gently brown the exterior. Before serving, ladle the sauce and vegetables out of the pan and strain through a fine mesh strainer. Discard the vegetables. Serve the ribs on mashed potatoes, gnocchi, or buttered egg noodles, topped with the strained sauce.