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And they struggle to understand us.

Permutation City and Diaspora by Greg Egan are great and at times touch on ideas like this.

I loved the irony of the virtual citizens of a polis travelling physically to another star system and the first creatures they encounter are inside the "natural" simulation hosted by the chemical evolution of the Wang carpets.

Count Zero and Mona Lisa Overdrive by William Gibson (sequels to the more famous Neuromancer) have this idea. AIs obtain independence from humans in cyberspace (VR) and eventually make contact with AIs from elsewhere.

Cool! Will check em out

Disclaimer: this stuff is mostly just hinted at, while the plot is mainly about people working within this context. But so awesome. Blew my teenage mind in the late 80s.