Yes, we will engineer a command brain, because technology is already arriving at this level of achievement. There will always have to be some kind of input. The brain will still have to be programmed to react to certain stimuli in a programmed way. To truly have it think on its own, would be creating life, which we will never do. But we can program a machine to make decisions, based on inputs.
Yes, we will engineer a "command brain", but only after we fully understand how our brains fully function. Research has taught us everything from the molecular structure of water to how to print in 3-D. Simply put, research and the indomitable spirit of the human brain will lead to its successful duplication.
Though scientists will try their hardest, and make may discoveries... I feel it will go the way of quantum physics; when you get to that level of complexity, it is all just too much for us as we are not the creators of this unimaginably complex universe (and mind!) Currently consciousness is just as befuddling to the best scientists as the Big Bang is - that time when all the known "lows" of the physical universe somehow did not apply.