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In Google Summer of Code, they use the phrase 'flip bits, not burgers':

provide students in Computer Science and related fields the opportunity to do work related to their academic pursuits during the summer (think 'flip bits, not burgers')

Doing a Google Search only turns up results which talk about this and not meaning of the term.

I think its used in computer science too...

What does it mean?

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Flipping bits refers to manipulating computers usually in low level memory and so is not exactly an accurate term for doing Summer of Code programming, but is just a way to twist the burger flipping metaphor. Fast food service usually being considered an entry level position requiring little skill, and presumably inferring that programming voluntarily for Google would be a more worthwhile endeavor.

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    ...and a job working at a fast food place is often described as "flipping burgers." And working at fast food joints is a common summer job for students. – Kit Z. Fox Aug 1 '12 at 17:19
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    ...And most programmers would rather a job flipping bits than burgers... You're making me hungry! – American Luke Aug 1 '12 at 17:27
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    ...And most programmers working at a fast food restaurant would probably end up programming something using burgers as physical bits anyways... Maybe. – Casey Kuball Aug 1 '12 at 19:14

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