Until recently I thought that no matter how advanced human/computer interfaces become, they will stop well short of direct control of thought. But recently I learned about the relatively new field of optogenetics, which allows neurons to be switched on or off by infrared light.
In particular, researchers have figured out how to insert a light-sensitive gene from algae into brain neurons. This essentially makes the neuron function as an externally controllable switch: one kind of IR stimulus turns it on, another turns it off.
Why is this so significant? Because human tissue, while fairly opaque to visible light, is translucent to infrared light. The further into the infrared spectrum, the more transparent human tissue becomes. Which means that genetically modified brain neurons could be switched on or off non-invasively — no nasty surgery required.
In the short term this won’t have much impact. But eventually, certainly sometime in the next half century, technology will have advanced sufficiently to enable real-time computer generated infrared holograms that target specific neurons and clusters of neurons from outside the skull.
Which means direct control of thought, for better or worse.
As I’m sure you already realize, there are both very good and very bad scenarios here. And it’s not really a question of whether this will be used. As with all technologies, inevitably it will be used. The question is what we will choose to do, as a society, once we can directly stimulate — and therefore simulate — sensation, experience and thought itself.