Zaine comments on Seeking examples of people smarter than me who got hung up - Less Wrong Discussion
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B.F. Skinner and the humans as a 'black box'. A subtle shift in the field from Behaviourism to Cognitive Psychology, which has led to the establishment of neuroscience.
My memory fails me, but from recollection I believe Noam Chomsky criticised a 195X paper by Skinner, asserting Skinner's models were inaccurate and not psychologically real. Chomsky thought the behaviourist approach insufficient to fully comprehend the brain, and called for an alternate approach.
Apparently Noam Chomsky criticising B.F. Skinner was a big deal, and the disagreement entered the mainstream news. I cannot recall if they furthered the debate.
I'm not sure if this qualifies.