Season the beef chunks thoroughly with the sea salt and black pepper.
Heat the ghee in a heavy-bottomed pot or Dutch oven over medium-high heat until shimmering.
Sear the beef in the hot pot until a deep brown crust forms on all sides, then remove the meat and set it aside.
In the same pot, add the onions, carrots, and mushrooms, sautéing until the vegetables soften and the mushrooms release their moisture.
Stir in the minced garlic and tomato paste, cooking for one minute until the paste turns a deep brick red.
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 and add the bone broth, thyme sprig, and bay leaf.
Lower the heat to a simmer, cover tightly, and cook for 90 minutes or until the beef is tender enough to break with a fork.
Discard the bay leaf and thyme sprig before serving the stew in warm bowls.