Hi John,
I understand your problem and I wish to share my experience with you. My worst failures in getting the students involved were a general mathematics class for computer scientists in Italy and a linear algebra class for future school teachers in Germany. In the first case, most people just weren't interested in understanding the theory, the philosophy, the general idea behind the concept of algorithm, of computer program etc. In the second case, the (alas!) future teachers were not interested in understanding a mathematical method, rather than just learning some separate topics, which they would eventually repeat to their future pupils. I have tried everything: the sweet understanding educator, the strict threatening tutor, comedy on stage, a little dance...(see the Neil Raz's post in the conversation Why do people teach?): nothing. There is only this one thing that seems somehow to pass through the wall of students' indifference: the enthusiasm of the teacher. Reading the feedbacks given by my students and reading their facial expression, I've learnt that if they see that you love what you are doing, sometimes they let you carry them with you, or, in the the worse cases, they take pity on you and try to pay attention for your sake only...which is a bit sad, but still is something (the goal justifies the means in this case, I believe).

I would also add that there is simply a huge amount of inertia which has to be overcome. Most people would rather passively absorb than actively learn. There is a very comforting feeling, for many people, in sitting back and letting waves of information wash over them. By contrast most beginning students associate producing answers in class with tests. Very few of them listen in any kind of active way, i.e. trying to jump a step ahead, or guess where the argument is going, or doing calculations or approximations in their heads.

If you cannot provoke people to respond simply by questioning (and this is hard to do when they feel strongly that you know the answer and all they have to do is wait) then it is perhaps a good idea to address this problem directly. You can try to explain how you think productive learning happens, or you can simply observe that there is a very high correlation in your experience between students who regularly ask questions in class and students who make As in the course. If you are more of an authoritarian, you might base a portion of the section grade on "participation" and find some reasonable nonjudgmental way to judge this (i.e. a binary 1 or 0 points awarded each week simply on whether a question is asked). 

You might also try restructuring your sections a bit. Sometimes quizzes at the beginning put people into a more active mode; sometimes quizzes at the end encourage prior participation as everyone tries to get up to speed. Small group work is also a nice possibility, though for a science class it might require some time spent arranging well-thought-out problem sets.

Here's one I recently heard: at the end of each class, ask students to write on a piece of paper short anonymous answers to 2-3 simple questions. Questions can be: what did you/didn't you like about the class? What didn't you understand? How would you answer this short, simple and concrete question (insert a question that that reveals whether you as a student understand a basic concept), etc.