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A while back I spoke to Vipassana teacher Joseph Goldstein about his event at InsightLA, which takes place tomorrow. A few years back Joseph was generous enough to answer reader questions about practice and had this to say about "what to do with our minds during vispassana practice":
The response to your question about what to do with the mind during vipassana practice will depend on what method you are practicing. If you are continuing with the method taught by Goenkaji, I think it would be recommended to stay with the sweeping, paying closer attention to the sensations in the body. If you are interested in experimenting with other techniques, you might try becoming mindful of the thought itself, acknowledging that it is there either with the note "thinking" or simply by being aware of the thought as the present moment object of mindfulness. We don't need to be in a struggle with thinking. It is a natural function of the mind. Our practice is not to stop thinking, but to be aware of thoughts as they arise so that we're not carried away by them. As Suzuki Roshi said, "Don't be bothered by your thoughts. Let them come and let them go.
The audio of our short talk is below. Read more about the InsightLA event here.