consciousness?

[Neo-Scholastic]

That is the other side of neuroscience - psychology and psychotherapy. The ideal theory would meet somewhere in the middle, but right now, we are starting from both ends.

I do not disagree with this statement. Neuroscience deals with material properties and physical causes that are quantitative. Psychology deals with mental qualitative ones. Where I think we differ is that you want to reduce one set of properties to the other, in such a way that describing one is just another way of describing the other. They may be two sides of the same coin, but they have distinctly different properties. I question the assumption that a model of reality with only four forces and a handful of constants can meaningfully account for the appearance of mental properties.

As you said, an ideal theory would meet somewhere in the middle. I believe that middle ground includes something equally fundamental to the structure of the universe to account for qualia and all the mental properties built from them. That something need not be supernatural in the traditional sense, it would just extend our understanding to include all the basic features of the natural world.

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...whether you view an item as a collection of atoms being held together or you analyze it as a single entity - say, a ball - you are talking about the same thing.

Not from my perspective. A ball could be composed of any number of different substances. A collection of atoms can assume multiple shapes. Even if they happen to co-exist in a single entity they are still very different in a way that makes a difference.