Dear George
(As a courtesy to Professor Ellis, and to keep discussions focused I hope other posters will not respond to this on his page unless he does.)
You make a convincing case for being wary of simplistic down-up causation. Your arguments make sense but only in the context of present-day physics which is far from being a harmonious conceptual whole where one theory applies both to the very large and the very small - please see my present fqxi essay Fix Physics! about that. I am conviced that if such a simple theory of everything were to be found, causation would be always local and linear at the smallest scales and the effects of large systems will be the resultant of effects transmitted locally and causally down to the local level and vice-versa simultaneously in a balanced way:
Think of a ripple tank where one 'simple local' point sends out waves to a 'complex system' consisting of points on a surrounding perimeter. Anywhere in the space between the 'local or down point' and those of a larger 'higher complex perimeter' system the resulting interference pattern will be caused by both systems simultaneously. Here is my tentative approach to such a ToE Beautiful Universe Theory .
With best wishes from Vladimir