That our brains are more complex that hydrogen atom is a fact, but that does not invalidate scientific method. It simply means that we need much more time, more research, more data and more complex theories to understand brain than we need for an atom.
Psychology today reminds me the state of medicine before bacteria were discovered: we do some semi-magical rituals that sometimes work, but they do not produce predictable results, because we are yet to discover the real underlying mechanisms of human mind.