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The Professor is clearly a physicist and inventor. Is it ever shown why he is running a small scale shipping company with only a handful of employees, instead of (for example) working in a government lab or university research center?

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  • Even if the professor claims to be a physicist, not much of what we see him do in the show is actually physics. The technical term is "mad scientist" (or some would say "engineer") :-P – David Z Dec 2 '16 at 7:04
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For the money

Fry: This is awesome! Are we gonna fly through space fighting monsters and teaching alien women to lurve?

Farnsworth: If by that you mean "transporting cargo" then yes. It's a little home business I started to fund my research.

Space Pilot 3000

You may wish to note that the Professor does maintain an office at Mars University, something of a sinecure given that no-one ever takes his classes.

Farnsworth: No, I need it shipped to my office at Mars University. It's a little experiment that may well win me the Nobel Prize.

Leela: In what field?

Farnsworth: I don't care, they all pay the same.

...

Fry: Oh, I don't know. Hey, Professor, what are you teaching this semester?

Farnsworth: Same thing I teach every semester: The Mathematics of Quantum Neutrino Fields. I made up the title so that no student would dare take it.

Mars University

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    Also he'd never be able to work with anyone elses... (cf. A big ball of garbage) – k_g Nov 28 '16 at 3:42
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    Curiously, a common plot device is that the company is going bankrupt or has to officially reclassify everyone as slaves instead of as employees, etc. – zibadawa timmy Nov 28 '16 at 7:51
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    @Zibadawatimmy - Because the company is incompetently run. When Fry and the Professor disappear into the future, you can see the success Leela makes of it. – Valorum Nov 28 '16 at 8:04
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    I beleive I will now watch every episode of Futurama again. – Daft Nov 28 '16 at 14:23
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    @Daft Again? As in you weren't already? Does not everybody live their life in an endless cycle watching the entire series over and over again? – Dason Nov 28 '16 at 18:51
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Professor Farnsworth may have started the company to fund his research (see Valorums answer), but he also sees it as cheap source of labor for his projects (similar to a research group in a lab):

Farnsworth: This is not a business. I always thought of it more as a cheap source of labor, like a family.

from Future Stock

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    And spare blood in Amy's case, albeit she's one of his students, not a member of the crew. – Valorum Nov 28 '16 at 11:06

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