He was primarily a zoologist, but he also made significant botanical collections from San Diego to Fort Mohave, Arizona in 1861. Cooper was active in the California Academy of Sciences, eventually becoming Director of the Museum.

[1] In 1860, he returned west and joined the Blake Expedition that went from St. Louis up to the Missouri River and into Idaho and Washington.

He worked as a contract surgeon for brief periods with the US Army and Josiah Whitney, the chief of the California Geological Survey.

He wrote on his difficulties in a letter in 1870 In this country, like most others, the pursuit of science as a private business is a losing game ...

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