It doesn't even need to be that there are "souls," we just need to find a way to explain what Thought is. Saying it's the lights on an MRI aren't good enough - all the MRI tells us is that blood goes to certain parts of the brain during certain thoughts. Just like a radar gun displaying 50MPH isn't the car actually going 50MPH, so too do we need a way to explain what a Thought or Mind actually is.

So far this hasn't happened. If it had, it would be breaking news, because consciousness would be "solved."