I really like your recipe analogy, I think it would be very useful for teaching molecular biology.

I think our discussion mirrors the tension between traditional biology and bioengineering. As a bioengineer I'm primarily concerned with what is possible to build given the biology we already know.

While I agree that a "blueprint" isn't a good analogy for naturally evolved living organisms, this doesn't prevent us from engineering new molecular systems that are built from a blueprint. As I mentioned, we already have turing complete molecular computers- and software compilers that can turn any code into a set of molecules that will perform the computation. It's currently too slow and expensive to be useful, but it shows that programmable molecular systems are possible.