Heat a large pot of salted water on high to bring to a boil.
Meanwhile, add olive oil to the skillet and heat to medium. Add onions and saute for 2-3 minutes until transluscent. Add garlic and saute another 30-60 seconds.
Add penne pasta to the boiling water and set a timer for 7 minutes (or 1 minute less than the instructions state. If using fresh pasta, see recipe notes).
Add artichokes, tomatoes, and salt and pepper. Saute for 5 minutes, stirring occasionally. After 5 minutes the tomatoes should be soft enough to gently smash with the back of a wooden spoon to release their juice into the sauce. Do this for a majority or all of the tomatoes.
The pasta should be done cooking by now. Drain and set aside - but save to of the pasta water and DO NOT rinse the pasta!
Add miso paste, capers, pasta water, oregano, basil, and 1/2 of the Parmesan to the skillet. Mix well so that the miso paste mixes in and the Parmesan melts. Add the pasta and turn the temp up to medium-high. Let simmer to finish cooking the pasta another 1-2 minutes stirring often to coat the pasta in the sauce.
Finish with remaining Parmesan cheese and top with fresh parsley. Seve and enjoy!