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Re:ECDSA smartphone key extraction using $2 magnetic probe by TickleSteve on Friday March 25, 2016 @08:50AM (#11359718)
There is a dedicated authentication coprocessor, to which the communications will be authenticated, so yes.
Re:ECDSA smartphone key extraction using $2 magnetic probe by ctz on Friday March 25, 2016 @10:39AM (#11360285)
The thing you're talking about ("secure enclave") is not present in the phone the FBI are trying to attack.

Also, the Secure Enclave co-processor is on-die, so there will be no need to authenticate or encrypt communications with it.