We build models of the universe that have many different levels of description. But so far as anyone has been able to determine, the universe itself has only the single level of fundamental physics - reality doesn't explicitly compute protons, only quarks.
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This post is part of the Rerunning the Sequences series, where we'll be going through Eliezer Yudkowsky's old posts in order so that people who are interested can (re-)read and discuss them. The previous post was Qualitatively Confused, and you can use the sequence_reruns tag or rss feed to follow the rest of the series.
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