Blitz the onion, carrots, celery, and garlic in a food processor in separate batches. Making sure they are as close to a ½-inch dice as possible. Heat a Dutch Oven or heavy-bottomed saucepan over medium low heat, add the olive oil reheat for 30 seconds and then add the onions, carrots and celery and season generously with Kosher sea salt and fresh cracked black pepper. Cook stirring often with a flat bottomed wooden spoon, until the vegetables start to sweat out some of their liquid about 10 minutes. Keep in mind low and slow, we don't want color, we just want to soften the soffritto.
Toss in the garlic, oregano, fennel seeds, basil, thyme, and red pepper flakes stir to combine, cover the pot and cook, stirring every 5 minutes (total of 20 minutes), until the vegetables are soft and savory. Reduce the heat if you notice the vegetables start to brown. Turn up the heat to medium and add the sausage, breaking apart into bite sized pieces, and cook for 5 minutes.
Now pour in the tomatoes, chicken stock, beans, and bring to a medium boil (not super aggressive) gently stirring and add Parmesan cheese rind and bay leaves. Reduce the heat back to medium-low for a gentle simmer. Cover the pot so the lid is slightly cracked and cook until the beans are very tender. Anywhere from 1-3 hours depending on if you used soaked or canned beans. Remove the Parmesan cheese rind after cooking is complete.
While the soup cooks, bring a pot of heavily salted (Kosher sea salt) water to a rolling boil. Cook pasta till al dente, according to package directions. Drain and set aside. Don't be tempted to cook the pasta in the soup, unless you want a thick and gummy outcome! Cook them separately and save yourself the heartache of a ruined soup.
Divide pasta among bowls and top with soup, garnish with fresh grated Grana Padano, a drizzle of olive oil, fresh basil and Herbed Crackers or crusty bread for dipping if desired.