The primary mission of the Beagle was to map the coastline of southern South America and take oceanographic measurements (currents, bathymetry, etc) as well. Darwin's job as the ship's naturalist was to observe everything, write it all down and collect as many specimens as possible. It was his job to record the weather, geological features, plants, animals, fossils, rocks, minerals, indigenous people and anything else that he saw. It was through this voyage that Darwin's innate ability to observe in great detail and think "large" began to assert itself.
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