Intuition is the mix of conscious and unconsious thought, but, thought it still is. The brain stores an unimaginable number of bits of information in its nureons. The interconnection between those nureons is more complex than any set of supercomputers hooked up in parallel in existance. The general process of how relationships between inputs and outputs is pretty well understood now, but the specific processes, which can lead to "intuition" are not.
The bottomline is, however, that the brain is simply adding 1 + 1 to get to 2 or the aggregation of all the science and mathematics Einstein absorbed prior to whichever "insight" he had that led to E=MC squared ... in this case, a realization that Time wasn't a constant in all situations.