Season the beef: Pat the chuck roast dry. Season all over with the salt and pepper.
Sear for extra flavor: Heat olive oil in a large skillet over medium-high heat.
Sear the beef on all sides until well browned, about 3–4 minutes per side. Transfer to the slow cooker.
Sauté the aromatics: In the same skillet, add onion, carrots, and celery with a pinch of salt. Cook 5–6 minutes until softened and lightly golden.
Stir in garlic and tomato paste; cook 1–2 minutes until fragrant and slightly darkened.
Deglaze with wine: Pour in the red wine, scraping up browned bits. Simmer 2–3 minutes to reduce slightly. If not using wine, add 1/2 cup beef broth instead.
Build the sauce: Transfer the skillet mixture to the slow cooker.
Add crushed tomatoes, tomato sauce, oregano, basil, thyme or Italian seasoning, bay leaf, and red pepper flakes if using. Stir to combine and nestle the beef into the sauce.
Slow cook: Cover and cook on Low for 8–10 hours, or on High for 4–5 hours, until the beef is very tender and shreds easily.
Shred the beef: Remove the bay leaf. Transfer the beef to a cutting board and shred with two forks.
Return the beef to the sauce and stir.
Finish and balance: Taste and adjust seasoning with more salt and pepper as needed. Add sugar or balsamic vinegar, 1 teaspoon at a time, to balance acidity.
Serve: Toss the ragu with hot cooked pasta, thinning with a splash of pasta water if needed. Top with chopped herbs and plenty of Parmesan.