1. Let the short ribs sit at room temperature for 15 minutes. Season generously with salt and black pepper on all sides. Heat a large, heavy-bottom pot or Dutch oven over medium heat. Add enough vegetable oil to just coat the bottom of the pot.
2. Working in batches, sear the short ribs really well, about 3-4 minutes on all four sides. Transfer each batch of meat to a foil-lined sheet pan or plate once seared.
3. To the pan drippings, add the onion, carrots, and celery. Season with salt and black pepper. Sauté the vegetables for a few minutes until tender and caramelized. Stir in the garlic and cook for another minute.
4. Stir in the flour and let cook for a minute or so, stirring continuously. Deglaze the pot with the red wine. Bring to a simmer, scraping the bottom of the pan to release all of the flavors. Let simmer for another minute.
5. Stir in the crushed tomatoes, tomato sauce, bay leaves, thyme, sage, and another pinch of salt. Let the tomatoes simmer for 5 minutes.
6. Stir in the beef stock. Add the short ribs back to the pot. Bring the liquid to a simmer. Cover the pot, leaving a small crack open to allow some steam to escape.
7. Turn the heat all the way to low and let the short ribs braise for 3 hours, stirring occasionally.

To Assemble:

1. Prepare of large pot of boiling, salted water.
2. After 3 hours, remove the short ribs from the pot. Strain the sauce, using a wooden spoon to really press and release all of the flavor from the vegetables and herbs.
3. Pour the sauce back into the pot. Using a folded paper towel, blot as much fat off the top as possible. Bring the sauce to a simmer over medium-high heat. Reduce the heat to medium-low and let the sauce cook and reduce for about 20 minutes.
4. Meanwhile, use your hands and a pair of gloves to shred the meat, discarding any large chunks of fat, bone, and connective tissue. At the same time, drop the spaghetti into the boiling, salted water and cook for 2 minutes less than the package’s instructions.
5. Once the sauce has reduced and thickened, whisk in the butter, one tablespoon at a time. Stir the shredded meat back into the sauce. Taste and season with more salt and freshly cracked black pepper as needed.
6. Drain the pasta and toss it with the sauce. Alternatively, ladle the sauce over the spaghetti. Serve with the parmesan cheese and herbs on top.