Dear Erik,
You have already received so many comments that I am not sure, if this will add much to that. Yet ...
In many statements in the essay, there is one point reverberates as a non-violative presumption that the nature is deterministic in the absolute sense at the most fundamental scale (level). For example,"In this reductionist view, a biologist studying a cell is really referring to some astronomically complex constellation of quarks." The function at the cellular level may not be entirely determined by the quarks, if there is a certain degree of indeterminism in the processes at any scale.
In statements like, "Recent research has argued exactly this [14, 15] by demonstrating the possibility of causal emergence: when a macroscale contains more information and does more causal work than its underlying microscale.", it is not clear what is referred to as more vs less information. I suppose, you just showed all along that complete description of microstates carry more information than any abstraction of the same at a macrostate. As you also mentioned Shannon's quantification principle, the detail in microstate can distinguish a state among much larger set of states, therefore contains more information. But the quoted statement seems to violate that.
Though, as I have shown that ignoring certain detail gives rise to emergence of abstraction that is not present in any one the components. This is a process of generalization that applies to all objects, say states, relations, functions, and processes. But in Shannon's view, it corresponds to loss of information.
With respect to transition matrix, Smicro and Smacro, I am not claiming that I understand it completely, but this is what appears to me. Imagine the micro states are designated as (a,b,c,q), and after ignoring the distinction between a, b and c, we call the resultant macrostate as p. So, if the elements of the transition matrix are probabilities of transitions, then the following points can be noted, 1) 'a' may transition into a, or b, or c, with equal probability of 1/3. The same is true for b and c. Whereas, with Smacro, p remains p, and q remains q for all times. So, I conclude that Smicro certainly has more information distinguishing among finer transitions than Smacro. Keeping the same logic as proposed by you, if we ignore all internal state details and transitions of elements in universe U, then U remains U in perpetuity, a very definitive statement, no degeneracy, absolutely deterministic, but that hardly tells anything worth distinguishing. 2) 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. That is, Smicro is also already an abstraction of even more fundamental description. Talking the language of quantification of information, I can represent the Smacro with mere 4 bits, but Smicro would take many more. But in my view Smacro is an abstraction of Smicro, where certain details are of no importance.
Given your definition of teleology, are we to understand that bacterium also possesses a sense of goal and purpose, acts accordingly to discover resource?
Rajiv