Ken G said:
Yes, I think the next class of physical theories, those that go beyond the latest new particle, are going to combine theories of dynamics with theories of cognition. We are getting close to the place where we can no longer pretend we are not involved in our own knowing about reality. The device of separating ourselves from our questions got us pretty far, but we had to always know it was a fundamentally bogus approach. I think Douglas Adams had it right-- at some point knowledge looks not like figuring out the right answers for our questions, but rather figuring out the right questions for our answers.
Connecting back to the OP, one of the dangers is that QM seems to have something to do with observers, and so something to do with human consciousness. It is a slippery slope of speculation.
And even talking about cognition is problematic if we have no good theory of cognition.
Theories of cognition are in fact where I started out. Theoretical neurobiology. The computational model was obviously flawed (not untrue, but clearly not the whole (or holistic) story). And the dynamical systems approach was equally, somewhat true, yet also fundamentally missing something.
Looking for the right ontological grounding, I found that theoretical biology had been through the same issues in the 1960s and 70s. As a result, in the 80s and 90s, theoretical biologists were realising that the grounding theory for them was some more sophisticated model of thermodynamics. One that gave primacy to the idea of development and gradients - to the kind of open systems thermodynamics of Prigogine rather than the static, close realms of early statistic mechanics.
Then in the 1990s, theoretical biologists made a connection to semiotics (or the Peircean kind) as a way to talk about meaning as well as information in a thermo perspective.
So there is definitely a movement in biology and neuroscience, if not yet a revolution, that sees thermodynamics in some rounded systems sense as its natural basis. The "physics" that grounds the sciences of life and mind is not the one of particles, fields, and other simple material stuff, but the physics of systems.
Then looking around, it seems obvious that even physics and cosmology are attempting to be more systems-based - more holistic and self-organising, less atomistic and background dependent. Which again means that the proper metaphysical grounding would be something a thermodynamic modelling of causality.
So forget "qualia". That simply is the extension of atomism into phenomenology. The claim that consciousness is constructed from collection of subjective atomistic shards just does not fly with anyone who actually has studied neurocognitive processes. It is a fiction that gives some philosophers a respectable career - they look like they are doing good reductionist thinking. But it is a construct as lame as philogiston or aether or other things we now laugh about.
But Jambaugh's point about the boolean observation is right. We need an atomism in the sense that we need a definition of the smallest, or simplest, system-forming action. And there is also something new here because that "atom" is intrinsically dichotomistic. There has to be an observer and the observed in some sense. A meaningful relationship.
But we also have to find the language to describe the "atom of a system" in ways that don't have false connotations. And thermodynamics would seem to be the place to find a jargon that is both neutral enough to apply equally well to physics or mind science, and yet also having the right kind of causal or ontological connotations.
Myself, I find that the dichotomy of degrees-of-freedom~constraints is very useful. A system is in general where you have some set of global constraints that act to particularise a set of degrees of freedom. This is the top-down~bottom-up view of hierarchy theory. A coupling of levels of causality in which the larger scale "observes" the smaller scale - that is, it resolves a broad number of degrees of freedom into the select few which are actually building the system (so it can continue to "observe" and so persist as a system).
So the atom of a system is this dyadic relation between degrees of freedom and constraints. In QM, for example, it would be the interaction between the experimentalist's set-up and the indeterminacy contained in some prepared initial conditions. In mind science, you get the interaction between global anticipatory state and localised sensory "surprises" or salient events.
(If you want the best current neurocognitive model, check out the Bayesian brain work and note how it is based on the very thermo concept of minimising a system's free energy -
http://en.wikipedia.org/wiki/Bayesian_brain).
To sum up, thermo is the physics of systems and so is naturally the foundation for complex systems science (such as biology and neurology). And I would argue that it has to be the foundation for "foundational" physics too. What is missing from the current modelling is the "observer" - a theory of the global constraints. And then we need an atomistic model of systems. But this is going to be an intrinsically dyadic story in which we find both observer and observed in their simplest possible form. Some version of the idea of emergent constraints in interaction with (sub)mergent (or otherwise constrained and directed) degrees of freedom.