The scientific method is a core element of all science. Yet, its different implementations are remarkably diverse, based on the varied concepts and protocols required in each specific instance of science. For experienced scientists, coping with this diversity is second nature: they readily and continually ask tractable questions even outside their expertise, and find the process of forming hypotheses, designing tests, and interpreting results fairly transparent. At the secondary school stage, the scientific method is often introduced as a series of clear steps in a pre-planned lab activity. In between these two stages comes the essential step of abandoning the supports of a step-by-step approach, and instead learning how to work through the scientific method to generate and answer one's own questions. In our experience, this process is rarely taught explicitly. Yet, undergraduate students (even strong students) can have difficulty translating their initial questions into testable hypotheses, and designing and interpreting appropriate corresponding tests. To combat this difficulty, we have developed a conceptual framework that distinguishes the fundamental concepts of pattern and cause. This framework guides undergraduates directly to posing tractable questions, formulating testable hypotheses (descriptive or mechanistic), and designing clear tests (surveys or experiments). Anecdotal evidence, including our in-course assessments and student feedback, suggests this approach leads to improvement of students’ scientific abilities. The benefits are noticeable when students apply the scientific method to their own questions and also while interpreting science reported in biological literature.