Thanks so much for reading Rajiv, I appreciate it.
I'll try to address some of these objections, which are rooted in misunderstandings or misconceptions.
"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."
This is a misunderstanding between determinism and supervenience (where the lower levels determine, or fix, the higher levels). 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.
"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"
This is the opposite of what is shown in my essay (and the associated papers). The definition of more or less information is pretty clear in the essay itself (given in the equation for effective information), and in the associated papers there are numerous examples demonstrating how to calculate this information and showing it done on model systems.
"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's a metaphysical assumption on your part that all systems are deterministic. And it's simple not true - any open system will experience noise (for instance, a cell being bombarded by cosmic rays). Even in the deterministic universe the only way to get rid of any notion of noise is to avoid partitioning the universe into notionally separate systems (like a cell, by itself). If you can't do this, it leads to very serious problems (discussed in Appendix D). And besides, as said in the essay, the point is moot anyways, because causal emergence can occur even in deterministic systems.
"Given your definition of teleology, are we to understand that bacterium also possesses a sense of goal and purpose, acts accordingly to discover resource?"
Great question. It may be possible to design even simple systems with the kind of teleology I propose. I would view it as a matter of degree, not a binary answer, where humans might have orders of magnitude more "teleology" than a bacterium.
Thanks again,
Erik P Hoel