Classic Red Wine-Braised Beef Short Ribs

bone-in short ribs, about 10-12 oz each (3 lbs. total)

freshly ground black pepper

coarse sea salt

fresh thyme leaves

olive oil

onion, peeled and finely chopped

carrots, peeled and finely chopped

stalks of celery, finely chopped

garlic, peeled and finely chopped

whole bay leaves