Good point regarding machine code, I wasn't thinking at that level of detail. But at this point the similarity is metaphorical at best.

The metaphor fails to go far enough, I think, because the non-DNA context and the DNA are working at the same level. Both are objects with shapes that interact. Yes, software is always embodied in matter, and yes processing happens in matter rather than some kind of abstract logical space, but part of the point of most computers is that the same matter can carry all kinds of different patterns. In biology the DNA builds the context and the context builds the DNA, and both of them alter each other when they interact. The interations also produce effects that tend to much more closely resemble physics-model-type actions - of he sort that can be modeled via differential equations when you are at a large enough scale that the single-molecule variances average out - rather than really embodying particular operations or logics.

I get the feeling there is an inferential gap happening here...