I’m not familiar with “holonomic” so I did a search:
It sounds like Pattee wants simply wants these macromolecules and genetics to have a stronger causal role in evolution but I'm not sure exactly what he's getting at. Perhaps you could start a new thread regarding Pattee and his contributions to philosophy and science.
Sure, Baranger's paper is pretty basic, but it clearly makes the point that chaotic systems are deterministic given precise initial conditions, which is relevant to the OP. I think it’s important also to separate out chaotic systems that are classical (and separable) in a functional sense, such as Benard cells, from systems that are functionally dependant on quantum scale interactions. Our present day paradigm for neuron interactions is that they are not dependent on quantum scale interactions, so it seems to me one needs to address the issue of how one is to model these “non-holomonic” properties (classical or quantum mechanical influences) and whether or not such a separation should make any difference.
This is a good example of what confuses me about everything you say about this "systems approach". Are you suggesting these "top-down constraints" are somehow influencing and subordinating local causation? That is, are you suggesting that causes found on the local level (such as individual neuron interactions) are somehow being influenced by the top down constraints such that the neurons are influenced not only by local interactions, but also by some kind of overall, global configuration? Or are you merely referring to how boundary conditions act as local causal actions at some 'control surface' such as we use in multi-physics approaches that use FEA to model physical phenomena in engineering and the sciences? Note that FEA and similar approaches are simplified versions of the underlying philosophy surrounding the more conventional “systems approach”, that nonlinear differential control volumes must be in dynamic equilibrium over time. It’s this dynamic equilibrium between local causes that might somehow be misconstrued as there being some kind of genuine downward causation which of course, isn’t a mainstream concept. Being an engineer, I’d readily accept that boundary conditions act on any given system, but the underlying philosophy of how those boundary conditions act on any classically defined, separable system, does not allow for nonlocal causation and thus does not allow for downward causation in any real sense of the term.
After rereading his paper, I’d say that he does in fact try to separate mental states (phenomenal states) from the underlying physical states as you say, but that mental states are epiphenomenal isn’t an unusual position for computationalists. Frank Jackson for example (Epiphenomenal Qualia) is a much cited paper that contends exactly that. So I’d say Farkus is in line with many philosophers on this account. He's suggesting mental states ARE physical states, and it is the mental properties that are "causally irrelevant" and an epiphenomenon (using his words) which I’d say is not unusual in the philosophical community. Not that there aren’t logical problems with that approach. He states for example:
That says to me, he accepts that neurons only interact locally with others but we can also examine interactions at higher levels, those that are defined by large groups of neurons.
There are some areas in his paper I’m not too sure about. Take for example:
If he’s suggesting that this “higher level” is not determined by the interactions of the lower level (their interactions) in a deterministic way based only on the local interactions of neurons, then that sounds like strong downward causation which is clearly false. Certainly, there are people who would contend that something like that would be required for “free will” or any theory of mental causation. But I’m not sure that’s really what he wants.
In another questionable section he states:
In the part emphasized, I’d say he’s trying to suggest that a person is somehow “immediately” and “simultaneously” affected by a “global state” on entering this classroom which I picture as being a zone of influence of some sort per Farkus. Were the same person to enter the same room and was blind and deaf, would these same “global states” immediately and simultaneously also affect that person? Sounds like Farkus wants his readers to believe that also, but that sounds too much like magic to me.
I suspect that the punchline to all this is that the proposal these folks are after is that higher order levels influence the future higher order levels by influencing lower order levels. That of course is strong downward causation. I don't see any room for a 'medium' causation that somehow doesn't allow a higher level to influence a lower level but still allows higher levels to have some kind of influence. The higher level is made up of lower level constituents, so if there's no change in the lower level constituents caused by the higher level, there's no change.
I think this is a good lead in to strong emergence and strong downward causation which, in one way or another, is necessary for mental causation and free will. The question really is, can the higher physical levels somehow subordinate the local interactions of neurons? And if so, how?