Heat to boiling a large pot with 4 quarts of water in it. Once the water is boiling, salt it with 1 Tbsp of salt. Once the water returns to a boil add the pasta to the pot. Leave uncovered, let cook on high heat with a vigorous boil. Put the timer on for 8-10 minutes, or whatever your pasta package says is appropriate for al dente (cooked but still a little firm). Drain.
Once you've started to heat the water, start working on the sauce. Heat olive oil in a very large skillet on medium heat. Add the chopped onion, Italian seasoning and red pepper flakes. Cook for 5 minutes, stirring occasionally, until the onions are softened. Add the garlic, fresh thyme, season with salt and pepper. Cook for an additional minute, until the garlic is fragrant. Remove from heat and set aside.
Heat a large cast iron pan on high heat. Salt the bottom of the pan generously. Once the pan is hot, break up small chunks of ground beef and add them to the pan, without stirring. (You may need to work in batches; do not crowd the pan.) You want the meat to get well browned. If the pan is too hot and the meat is burning, not browning, take the pan off the heat for a little, and reduce the heat to medium high. On our coil electric stove, it takes the high heat setting for the meat to brown sufficiently, but your stove may be different. Once the meat is browned on one side (a couple of minutes), use a metal spatula to flip the meat over to brown on the other side. At this point, assuming you are using a cast iron pan, you can remove the pan from the heat. The residual heat in the pan will finish cooking the meat.
Use a slotted spoon to lift the meat from the cast iron pan and add it to the pan with the seasoned onions. Add tomato sauce. Use the edge of your metal spatula to break up the bigger chunks of meat into smaller pieces. Add basil. Add a teaspoon of sugar. Bring to a simmer on low heat, let cook, uncovered, for 15 minutes.
Once the sauce has simmered for 15 minutes, adjust seasonings. Add salt and pepper to taste. Add a little more sugar if the sauce is too acidic. Add more tomato sauce if the sauce is a little dry. Stir in the cooked penne pasta. Sprinkle with chopped parsley. Serve immediately.