Nornagest comments on The Octopus, the Dolphin and Us: a Great Filter tale - Less Wrong
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That's a version of the "chimeric theory", one of a few for the origin of eukaryotic organization: see Wikipedia's article. The DNA of the host cell would have migrated into the encapsulated bacterium or archaeon, through processes that I'll admit I'm a bit fuzzy on.
(Wikipedia links several papers in support of this theory; the only un-paywalled one I could find, however, is Margulis et al. 2000.)
Huh. I've skimmed this a few times and it's pretty hard to understand... so they are saying that the nucleus ancestor was a fast swimming oxygen avoider, and it basically chose to avoid oxygen by hiding inside another cell like a hermit crab - and in exchange, pushing the "shell" cell around...and eventually fusing genomes with it?