Professor Ellis,
Thank you for your comments. Since we seem to be dealing with two different conversation threads with different points raised in both, I will try and keep my answers separate to avoid confusion as much as possible.
"Second, you say Agency is the capacity of a system/entity/agent/ organism to act on it's environment. Is is the Moon an agent n that respect? (after all it causes tides on the Earth)."
--> Correct me if I am wrong, but you seem to prescribe to a definition of agency rooted in psychology? The agency I am talking of (takes the definition from philosophy and it) is simply the capacity to act. To act involuntarily, unconsciously or consciously with a purpose will all fall under it. The moon with the ability to act on earths waters makes it an agent, but doesn't have to fall under the category of making it a purposeful one for the moon. It is very possible to think of physical systems that have no agency, can change their state based on the influence of external systems but do not have the ability to 'act' and affect its environment. It is also possible to have systems that have 'agency' as I define but not have a purpose or intent for that agency. I limit purpose and intent only to a small set of systems that fall under my hypothesis. And a sense of agency as defined in the essay, need not be present in all agents. I have it there to show that a minimal dissipative system with an hierarchical structure can have something like that because of the physics of the structure alone.
"So there has to be a structure that underlies the existence of this function, and the kay issue is where this structure came from. That cannot be via non-equlibrium thermodynamics alone."
--> For the emergence of the structures themselves, I used England's dissipation driven adaptation to explain that. Your statement on structures not coming from non-equilibrium thermodynamics alone is an assumption I would argue. While the biological explanation of selection mechanisms are more explanatory and necessary, it is possible these selection mechanisms themselves are manifestations of deeper thermodynamic principles, which is what England argue for in his papers. While some aspects of his hypothesis seems to have been misunderstood and his results are specialized, I used it to clarify anyone who immediately dismisses the essay that minimal dissipation and dissipation driven are obviously contradicting (something that I struggled with for a while and some of my colleagues pointed out). Section 4 was dedicated to better clarify the assumptions in England's hypothesis and how it complements my derivations (Two sides of the same coin).
Thanks for a delightful exchange. I am enjoying myself!!
Natesh