Pat beef chunks dry with paper towels and season generously with salt and pepper. Heat 1 tablespoon olive oil in a large Dutch oven over medium-high heat. Working in batches, add beef and sear until deeply browned on all sides, about 3-4 minutes per side. Transfer browned meat to a plate.

Reduce heat to medium. Add remaining 1 tablespoon olive oil to the pot. Add onion, carrots, and celery, and cook, stirring occasionally, until softened and lightly golden, about 7-8 minutes. Stir in garlic and tomato paste and cook for 1 minute until fragrant.

Pour in the red wine, scraping up all the browned bits from the bottom of the pot with a wooden spoon. Simmer until the wine reduces by half, about 3 minutes.

Return the seared beef and any accumulated juices to the pot. Add crushed tomatoes, beef broth, bay leaves, thyme, and Parmesan rind if using. Stir to combine. Bring to a boil, then reduce heat to a low simmer. Cover partially and cook for 2 to 2.5 hours, stirring occasionally, until the beef is fall-apart tender and reaches a safe minimum internal temperature of 145°F (63°C).

Remove the bay leaves, thyme sprig, and Parmesan rind. Use two forks to shred the beef directly in the pot into bite-sized pieces. Stir to incorporate into the sauce. If the sauce seems thin, simmer uncovered for 15-20 minutes until thickened to your liking.

Taste the ragu and adjust salt and pepper. Let it rest off heat for 10 minutes. Meanwhile, cook pappardelle according to package directions until al dente. Drain, reserving 1/2 cup pasta water. Toss the pasta with a generous amount of ragu, adding a splash of pasta water if needed. Serve in warm bowls topped with Parmesan and basil.