Acquisition of scientific reasoning is one of the big challenges in education. A popular educational strategy advocated for acquiring deep knowledge is inquiry-based learning, which is driven by emerging "good questions". This study will address the question: "Which design features allow learners to refine questions while preserving student ownership of the inquiry process?" This design-based research has been conducted over several years with advanced high-school biology classes. The results confirm the central role of question elaboration as an interactive process that leads from vague to complex and adequate. To make this happen, the inquiry process must extend over a long time, learners and teachers should share a knowledge improvement goal, and text produced by students should be structured by question-answer pairs addressing a single concept using authentic resources. Further features are discussion with peers, teacher feedback with respect to answer elaboration and conceptual differentiation, and finally, teacher guidance that should fade out in successive inquiry cycles to ensure student responsibility.