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I do not recall him working as a scientist in the movie but he was there to replace his brother who was a scientist to begin with.

EDIT: Actually, Jake was replacing his brother because he had the same DNA as his brother because they were twins, so he could use Tommy's expensive avatar because they could not afford to replace it. Jake did not have the same occupation Tommy was originally assigned before his death, though. Jake was working as a bodyguard for the Avatar Team.