SilasBarta comments on Is it rational to be religious? Simulations are required for answer. - Less Wrong
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I think that underscores the crucial difference about doing simulations in this context: You're simulating a being that can itself do simulations, and this is the defining aspect of that being's cognitive architecture.
No, it is not particularly relevant to run such simulations where the entities have sufficient technology to run advanced simulations themselves. Almost all that we'd want to find out in this context we can use simulations of entities of a limited technological level for.