Cut the beef chuck roast into 1-inch cubes and season thoroughly with sea salt and black pepper.
Heat the ghee in a heavy Dutch oven over medium-high heat until shimmering.
Sear the beef cubes until a dark, savory crust forms on all sides, then transfer the meat to a plate.
Add the diced onion, carrots, and celery to the same pot and sauté until the onions are translucent and slightly caramelized.
Stir in the minced garlic and tomato paste, cooking for 1 minute until the mixture is fragrant and darkened.
Pour in the red wine to deglaze the pan, using a wooden spoon to scrape up all the flavorful browned bits from the bottom.
Return the beef to the pot along with the bone broth, thyme sprigs, and the bay leaf.
Cover tightly and simmer on low heat for 2 to 3 hours until the beef is fork-tender and the sauce has thickened.