I would be much more interested in tearing down much of our exiting house of cards w.r.t. "artifical" substances, resources and means of interaction and replacing them with more "natural" mechanims. What does that mean? Well, things like shell and poision and body are just stuff we made up to provide bots a means to interact and compete in the artifical environment in which bot phenotypes inhabit. Their "artifical" in my sense of the term in that they have little to do with the underlying ditigal genetype and more importantly, little to do with what IMHO should (evenutally) be a "more native" digital phenotype divorced from any noption of an artificaly imposed physics/graphics environment (the sole purpose of which is to provide humans something to look at which our brains are good at recognizing, because our brains evolved in a non-digital 3D world). Things like having a body, colliding, friction, gravity, movement in a 2D or 3D space, etc. are intuitive to us, but they are artifical in the most "native" digitial environment one might imagine digital organimsms inhabiting. An enzyme system as described above would IMHO just be more of the same.
I strongly disagree on three points here.
1. An enzyme system is actually a step towards removing "artifical" features. It does not take a huge stretch of imagination to imagine the interactions between substances and enzymes as forming the basis for things like motion. The system I suggest only takes in to account differences in free nrg as the "core" principle. Other properties are tacked on. But if you expand the system to create a rule set that described overall shape as an intrinsic property of the substances, you could build motors
in the chemistry. Machinations that take one type of substance and convert it in to another of a different shape. If those substances were connected in a chain, suddenly you have a linear actuator, without explicitly programming a linear actuator.
It would still be a far cry from actual biochemistry, but it's certainly a movement in that direction. So I definately think this would make a good basis for an alife program. But the program would need to be built from the ground up based on that principle to work properly.
2. Darwinbots follows a different geneology of Alife programs, one that I think is more promising. What you're suggesting sounds like something following along the lines of Core Wars, Avida, etc. Raw processes native to the computer as a whole. Basically trying to construct life native not to a software mediator, but to the actual hardware computers are made of.
But I strongly believe this line is a dead end. For all sorts of reasons I won't elaborate on too much, but in a nutshell raw hardware is way too hostile to anything like life. It's like trying to evolve life in the cold, irradiated nether regions of outer space. You need a medium for life to evolve in, wether that medium is a software environment or a tidal pool of thick, radiation absorbing water. From there it could theoretically be possible for some sort of existing and clever life to "escape" from its medium, maybe by packaging its medium to itself (like a space ship), but I strongly doubt any life will truly be able to exist outside of its protective medium without some Intelligent Creator.
3. Even assuming for a moment that alife can exist outside of its protective medium, you're still programing new features. To make a printer, for example, someone still needs to craft a way to convert electrical impulses in to printed paper. Or to implement multithreading, someone still needs to program a software interface. All you'd be doing is moving the responsibility from the alife creator to the hardware manufacturers.
The fact is that something needs to craft the base ruleset within which life is to exist. Laws of physics on the terrestrial level do not suddenly get new addendums. Chemical relationships are just nearly infinite, so to our finite mind it seems like life is coming up with new things over the eons. In reality chemical relationships stem from a few, finite and simple rules. Those rules could just as easily be crafted by a person as arise naturally over the evolution of the universe.
The trick, you see, is to arrive at a ruleset that creates a huge solution space based on simple rules. Raw hardware is such a ruleset, certainly. One has only to look at the crazy assortment of programs available. And things can run very fast. Many tasks can be done much faster than any biological equivelant. But it's not the most amenable to trial and error. Another ruleset is biochemistry. It's very robust to trial and error, but it's very hard to simulate on a computer. I think it's in a middle ground between the two that rich alife could be born.