Trim the short ribs. Depending on where the short ribs come from, they may have a thick layer of fat on them. Use a sharp knife to cut off that fat layer leaving only ¼ of an inch of fat. Set aside.
Place the kosher salt, garlic powder, pepper, thyme, red pepper flakes, and dark brown sugar into a bowl and mix.
Sprinkle the dry rub over the short ribs. Massage the spice rub into both sides of the short ribs and let them sit in the spice rub for 15 minutes.
Sear the short ribs. Heat a large dutch oven over high heat. Add olive oil.
When the olive oil is fragrant, add the short ribs to the dutch oven without crowding the pot. Sear the short ribs for 2-3 minutes on each side. You may have to do this in batches depending on the size of the ribs and dutch oven.
Place the short ribs into the slow cooker and turn heat to low.
Continue heating the dutch oven on the stove top but turn the heat to medium.
Deglaze the pan with beef broth and scrape the brown bits from the bottom of the pan.
Add the diced onion and garlic to the pot and let the onion cook in the broth for 1-2 minutes.
Next, add the red wine, tomato paste, anchovy paste, Worcestershire sauce, and diced tomatoes to the dutch oven and whisk until combined. Bring to a gentle simmer.
Pour all of the ingredients over the short ribs in the slow cooker.
Add the fresh thyme to the slow cooker and cook the short ribs on low for 8 hours.
Halfway through the slow cooking of the slow cooker, swap the short ribs on the bottom of the pile to the top of the pile.
When you are about 30 minutes out from the short ribs being done, bring a big pot of salted water to a boil and add the pasta to the pot.
Cook the pasta until it is cooked to al dente.
Strain the noodles and set aside.
Prepare the short ribs for the pasta. Remove the thyme sprigs from the slow cooker and discard.
Remove the short ribs from the slow cooker and place them on a baking sheet with edges.
The meat should fall off the bones if it hasn’t already. Discard the bones and any large pieces of gristle.
Shred the short ribs into chunks and place them back into the slow cooker and toss the meat into the sauce.
Serve the short ribs and sauce over the pappardelle.
Top with shredded parmesan cheese and fresh thyme.