Initial Permutations in DES posted January 2014

I have to code a whitebox using DES encryption in a class. Which is pretty cool (I would have prefered doing it with AES but the other group got tails and we got heads).

Here is where the Stanford course I passed on Coursera shines. The explanation of DES on it is brilliant. I was wondering about the initial and final permutations that occurs in the algorithm though and Dan Boneh doesn't really talk about it besides saying it's not for cryptographic purposes.

I found a solution on a new sub-stackoverflow dedicated to Cryptography : http://crypto.stackexchange.com/questions/3/what-are-the-benefits-of-the-two-permutation-tables-in-des