Just thought today's comic was pretty amusing -- even if "an archaeon" would be more grammatically correct. Also, the phrase "primordial soup" is actually from Alexander Oparin's 1924 work, although Darwin's comments in regard to a "warm little pond" suggest he subscribed to a similar heterotrophic beginning of life.
But Darwin did encounter archaea even if he didn't know them by name -- in "The Voyage of the Beagle" Darwin describes a salt lake in Chile where "parts of the lake seen from a short distance appeared of a reddish colour, and this perhaps was owing to some infusorial animalcula." -- in other words he was observing haloarchaea.
