We invest a lot of time and energy acculturating the students to the real scientific enterprise, and our book is crafted to support these efforts. As a result of explicitly addressing these issues, after a few weeks most students buy into our approach. This problem of student expectations and perceptions is not unique to our course. When we first taught this new course, we did not recognize how serious this problem can be, and it is likely that some students went through the entire course without understanding what we were trying to do. Now that we understand the problem, we are very explicit right from the beginning and continually throughout the course in explaining what we are trying to do and why, and this has essentially solved the problem.
Most students now respond very well to being asked to think for themselves.
We had a student who during the first few weeks of the course appeared to be exceptionally weak and definitely headed for failing the course. Just before the first exam, she came to office hours to ask for clarification of some points. It was puzzling to find that she did seem to understand the main concepts. In previous science courses the teacher told me what I needed to know, but in this course you wouldn't tell me anything. She got one of the highest scores on the exam.