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Hmm.. I do not think that is what I mean, no. I lean towards agreeing with Searle's conclusion but I am examining my thought process for errors.
Searle's argument is not that consciousness is not created in the brain. It is that it is not based on syntactic symbol manipulation in the way a computer is and for that reason it is not going to be simulated by a computer with our current architecture (binary, logic gates etc.) as the AI community thought (and thinks). He does not deny that we might discover the architecture of the brain in the future. All he does is demonstrate through analogy how syntactic operations work.
In the Chinese gym rebuttal the issues is not really addressed. There is no denial by Searle that the brain is a system, with sub components, through which structure, consciousness emerges. That is a different discussion. He is arguing that the system must be doing something, different or in addition to, syntactic symbol manipulation.
Since the neuroscience does not support the digital information processing view where is the certainty of the community coming from? Am I missing something fundamental here?
Well, that would run counter to the Church-Turing thesis. Either the brain is capable of doing things that would require infinite resources for a computer to perform, or the power of the brain and the computer is the same. Indeed, not even computers are based on symbolic manipulation: at the deepest level, it's all electrons flowing back and forth.