Dear Erik,
Thanks for taking the discussion forward.
It appears, your claim of misunderstanding is indeed true. For example, you state, "A non-deterministic system will still have strictly fixed supervening levels. The state of the cell supervenes (is determined by) the constellation of elementary particles below it."
I suppose, for a non-deterministic system, a given microstate description may still allow more than one possible description at supervening level. Is not that the very definition of non-determinism? Then, we cannot assert, "A non-deterministic system will still have strictly fixed supervening levels." There must be something more than strictly determined description of the microstate to give rise to a given supervening state description. I am sure, somewhere our definitions do not coincide.
Misunderstanding goes deeper. In a specific context I stated, "If the elements of transition matrix are probabilities, that means it is not a fully described system, as per the presumption of determinism, or the determinism does not hold, or determinism is limited", it was meant to show the Smicro is also a 'multiply realized' description (not an ultimate description of unique reality). Here, the idea was to show that logic that applies to Smicro to Smacro, must be true even for Snano to Smicro, as well as to remind that you are not building a case here from a deterministic micro world to supervening Smacro, but rather a case for one indeterminate system to another.
"It's a metaphysical assumption on your part that all systems are deterministic."
Ah! This response goes deeper than simple misunderstanding, since if I responded to your statement, "In this reductionist view, a biologist studying a cell is really referring to some astronomically complex constellation of quarks", with, "The function at the cellular level may not be entirely determined by the quarks", I am also questioning the very presumption of determinism itself. I am implying here that 'a cell' is not just mere 'constellation of quarks'. So, I am not sure, how you happened to miss this argument to infer I am for determinism? By the way, I assert here, even greater indeterminism by saying, "one does not require a cosmic rays, or anything external to disturb a system exhibiting indeterminism, all systems at all levels inherently possess limited determinism." That is, even at microscopic level, even a quantum system exhibits indeterminism within limits. Therefore, 'determinism' could not be my metaphysical assumption.
I suppose, there is enough misunderstanding already, therefore, I will hold my further queries at the moment.
Rajiv