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I haven't used Facebook in a while, so maybe things have changed, but don't they show you a permissions page where you agree to give the developer access to your information?

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Yes, but the problem is that Facebook's API also allowed lax access to your friend data, so people who had not consented to the collection of their data through this app ended up with their data harvested as well.

Also, there are various ethical issues with the users consenting to provide data under the guise of academics and then the data being turned over to commercial and political interests.

Yes, and it always has been the case. The issue here is the scope of data requested, and what that data is being used for.

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