The main difference between the brain and a CPU is that the brain runs at a much lower, variable clock speed (10-100Hz) to reduce switching costs and makes up for this with extensive pipelining and parallelization when possible. The high node count and necessary connectivity is then possible due to the use of directed self assembly.
At any rate, it is quite likely that the neocortex of the brain simply computes a function(s) recursively upon sensory input (see Chomsky's minimalist program for suggestions on what it could be). What is unclear is what this function is, and how it comes about - for this reason the approach by some has been to attempt to simulate an entire brain to see what it does. But without the necessary abstractions, this will be inherently wasteful and generates nothing new other than validating your experimental data.
At any rate, it is quite likely that the neocortex of the brain simply computes a function(s) recursively upon sensory input (see Chomsky's minimalist program for suggestions on what it could be). What is unclear is what this function is, and how it comes about - for this reason the approach by some has been to attempt to simulate an entire brain to see what it does. But without the necessary abstractions, this will be inherently wasteful and generates nothing new other than validating your experimental data.