Traditional realists would project our knowledge today backwards in time and say that quarks always existed, even for Aristotle. He just didn't know, poor fellow. But there is little justification for that move. It's a kind of intellectual arrogance to assume that what we understand today is absolutely true and always has been true and always will be true. There is no logic that requires that assumption.
History speaks against it.
This example is similar to the brain example. We might want to say that while the theory of quarks is a socially contingent reality, the quarks themselves are not. However, by projecting the theory of quarks backwards in time to Aristotle, we see that it is more difficult to maintain a separation between theory and fact, and more difficult to insist on the absolute mind-independent reality of quarks. Generative Realism says there was nobody alive in Aristotle's time whose subjectivity was juxtaposed to anything like quarks. Therefore there could not have been any quarks by definition.