> The encrypted file – if The Register understands the paper correctly – embeds actions that are permitted on that file (for example, the ability to read and write to parts or all of the file. The Evaluate function is able to use the combination of the public key and permitted actions (described as circuits) to operate on the file without decrypting it.

I'm pretty sure that this has nothing to do with permissions. Homomorphic encryption maintains certain properties of the plaintext (through some isomorphism) to allow pre-defined operations (operations that the isomorphism are designed for).

Also, why theregister? Why not link to the actual article (http://eprint.iacr.org/2011/277) or the github project (https://github.com/shaih/HElib) They're much, much more informative.