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One big key is for the organizers/leaders of the seminar to be willing to set the tone by asking frequent and sometimes stupid questions. If the audience gets into a low-question equilibrium rather than a high-question one then you're in trouble. You want people in the audience to feel like they can and should understand everything that happens, and should hassle the speaker until they do understand everything. So make sure that there are enough people in the audience who are willing to do this.