Simon -
An excellent, imaginative and impressively well-written essay, thank you! There aren't many here that compare with it, and I only wish mine were as clear and readable.
Your discussion of the "origin gaps" is very good... though I think there's something a little one-sided about taking the notion of "self-reference" as the key element in the major transitions from fundamental to macroscopic physics, from molecular physics to biology and from the sociality of primates to that of humans.
I can easily see why, from a computational perspective, you focus on memory and self-reference. These are surely important aspects of the naturally emerging technologies through which "systems gain new powers" that lead to new and unpredictable phenomena. But there are others equally important, e.g. anticipation, or communication between systems. So I'm not convinced that self-reference is the key to explaining these "gaps". Likewise it seems to me that the possibility of "coarse-graining" information arises from the emergence of new kinds of systems, not the other way round.
The "self-reference" at the basis of biology, for example, is specifically self-replication, the ability to create new copies that create more copies. Then of course there are many levels of looping self-reference involved in maintaining homeostasis in all the molecular networks in and between cells. Which is all very different from the kind of self-reference we humans discover as kids, as we first learn to talk with other people, and then later gradually being talking with ourselves. And none of these is like the kinds of self-reference we might see in physics. (From your abstract, I was hoping you'd say something illuminating about the self-interaction of particles in their fields, since you mentioned renormalization... but no such luck!)
In my own essay I tried to describe what's special about the "gaps" in our history in terms of emerging technologies that recursively regenerate the conditions for their own success... becoming subject to natural selection when they fail. Each such process is unique, involving its own ways of doing self-reference along with much else. Since you and your colleagues in the Santa Fe research project have been thinking through these issues for a long time, I'd very much appreciate your feedback.
Thanks again for renewing my faith in this contest -
Conrad