How does people, for example scientists, lets say come up with so many complicated names, are they in Latin or something, things like Eukarya, protista etc...

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Yes, they're usually based on Latin (or sometimes Greek) since as a "dead" language, Latin doesn't change its meanings.  English, for example is a "living" language, so words can change their meanings over time.  For example, back in the early 1900's, if you called a person "cool" or "hot," you were describing their temperature.  Now, you're probably describing how attractive they are.Kary means nucleus, Eu means true or good, so Eukarya means something with a "true(real) nucleus"