Also, I do not know if your distinction between experiment and theory takes into account the whole picture. First, I do not think that “decoupled” is a fair characterization of their situation in physics. As you recognize, any physist who goes off into the woods is only able to make any progress because of the prior accumulation of data and theory. The same is done by any experimentalist when interpreting their data. Both are forms of interpretation of experimental data, and I think to make a strong semantic distinction by saying that the former is decoupled from experimental data can be problematic because it does not fully appreciate the interpretive process. I would suggest this may be more problematic by focusing on the established base of theory as central to the decoupling, when what may be more important is the established base of data (which neuroscience also lacks) which enables the establishment of a base of theory.

Second, I would say that the Gedankenexperiment is an example of just how coupled experiment and theory remain in physics. Einstein revolutionized physics, but he could not have done so without his resort to mental experiments. Not only are the equations and theories with which he is working the results of the large established base of data, but he provided his additional experiemental frameworks. Further, take as an example someone such as Bohr (who also revolutionized physics, although this is often not fully appreciated, because of the equivalance made between his complementarity principle and Heisenberg’s uncertainty principle, despite the truly significant difference between the two, with the former having ontological implications compared to the latter’s mere epistemological understanding). Bohr was meticuluous with his thought experiments, carefully diagraming their precise measurements as a way to fully appreicate the inseparability of a scientist and her resultant data, as well as theory and experiment. This focus of his enabled him to understand his work to change the very foundations of our understanding of being, in ways that Einstein could not have appreciated (and even actively fought against). Bohr’s work, especially his attention to experiemental detail and the affect of the scientist on the experiment, enabled the exposing of the faults in our dominant ontological framework, the metaphysics of individualism. (These topics are developed in Barad’s Meeting the Universe Halfway.)

Finally, I think that the distinction between Plato’s and Descartes’s “pure introspection and phenomenology” and Cajal’s “real live data” is a further problematic symptom of the harsh distinction between experiment and theory (and also one reason why so many scientists don’t respect philosophers, despite their complete dependence on philosophy when interpreting their data). I do not think that you can deny Plato and Descartes were dealing with “real live data” even though their scientific method was not as rigorous or established as it is today. To claim that only neuronal data is “real live data” requires the presupposition that brain is all that really matter and that everything is just “in the head.” I believe that there is plenty of support to the contrary, holding that meaning is not in the head, but out in the world.

The dominant empiricist framework largely disparages theoretical work (hence the importance of philosophers like Quine and Sellars who point out the problems with that framework). Rigidly separating out the experiment from the theory of theoretical work does a disservice to that work. It also leads theoretical scientists and philosophers to overlook experimental data and experimentalists to ignore theory and philosophy.

Once last thought: I think that questions such as “Why does it consistently seem that roughly 90% of neurons are inactive?” are extremely laden with unexamined presuppositions (e.g., what does “inactive” even mean within a holistic, dynamic system such as the brain/mind). I do not think that we are going to be able to develop any truly insightful understandings of the brain/mind without confronting such questions as the hard problem of consciousness. Every neuroscientific experiment has implications for consciousness, and only by recognizing that inseparability will true progress be possible. That does not mean that we should jump right into explaining consciousness, thought, love, etc., just as we shouldn’t try to explain these tiny anomalies separate from their broader context. Rather, any approach is going to be far more complex and is going to include constant reconfigurations of the framework within which work is being done.

With any work we do, we must recognize and appreciate its ontological and ethical implications. We should be constantly engaged in the unending struggle to reconcile the particular within the general and the general within the particular, and through that ceaseless friction, we will develop greater insight.