"I introduced the quote from the Science paper, because this important quote cannot be found in your essay." There are numerous important quotes I could not include because of the length limits on the essay. I have no obligation to include any particular one that you prefer.
"*All* the examples that you believe show that bottom-up causation "is wrong" are compatible with ordinary bottom-up causation and invalidate your hypothesis." I deny this claim of yours. In particular it does not apply for example to the way that abstract algorithms control computerised robots. There is no way you can derive those algorithms from the underlying physics in a bottom up way. The relevant variables are not coarse grained versions of lower level variables, or derivable from them in any other way. It also does not apply to the physiology of the heart, as explained by Denis Noble in his writings on physiology, or to epigenetics, as explained by Gilbert and Epel.
"The macroscopic arrow of time can be obtained from the microscopic description. The cosmological description is a coarse-grained approximation to the microscopic description. This is all well-known and explained in many excellent textbooks although ignored by some cosmologists." Of course the cosmological description is a coarse grained approximation to the microscopic description; see my GR10 lectures from 1984 for a clear description of how this works. This feature is incapable of explaining the arrow of time, as there is no arrow of time in the micro level physical laws. This was known already to Loschmidt and Boltzmann (the key point is that Boltzmann's derivation of the H-theorem works equally well for both directions of time). It is for this reason that authors such as Roger Penrose and Sean Carroll relate the arrow of time to a global low entropy state in the early universe. That is a macro state that has to be described at a macro level of description.
"The "counter term" in the Caldeira-Leggett model is an ordinary renormalization term. In the same textbook that you use as reference, the Caldeira-Leggett model is introduced in the section on quantum Brownian motion. As everyone knows quantum Brownian motion is compatible with ordinary bottom-up causation." I will reconsider this when I have the chance, the issue being whether renormalisation can be regarded as representing a purely bottom up effect or not. It is conceivable this review could lead me to change my opinion in this particular case. But your claims of a purely bottom up explanation won't work for example in the case of superfluidity, as is carefully explained by Robert Laughlin in his Nobel lecture.