I liked the individual words, but putting them together left me seriously questioning the underlying premise. This may simply be that I don't understand the underlying argument. You're suggesting that some prebiotic molecules will perform a configurational search? How? You cite Grover's algorithm but this is a highly designed process in a quantum computer - it requires extremely fine dynamical control that wouldn't occur in natural conditions. Given we can assume that is not what's happening (why build quantum computers if the ocean can run a quantum algorithm), I'm left with a few questions.
First, assuming that there are local environments which have some protection from decoherence, what process is first putting those already decohered molecules in a coherent superposition? Furthermore, how is such a superposition actually helping you? Surely the issue here isn't the state, but the effective Hamiltonian describing the joint system?
What I mean is that if we have initial reactants whose dynamics are described by Hamiltonians H_A and H_B, the product molecule will be described by H_A +H_B +H_int. The combinatorial problem here is searching for the form of H_int which leads to the thermal state with the lowest expected energy. The point here is that different product molecules don't correspond to different states, they correspond to different Hamiltonians. Putting a state in a coherent superposition of eigenstates still requires you to specify which basis that is with respect to. The problem you're targeting is really a meta-problem of possible interactions between two systems. You've correctly identified this as a combinatorial issue, but quantum properties of states do not help us at all here.
Consider that a single molecular state, will have a different energy with respect to two different Hamiltonians, H_1 and H_2. It simply doesn't matter whether that state is thermal or in a coherent superposition, the meaning of that state is defined only with respect to the Hamiltonian. Therefore, a "superposition of configurations" is physically meaningless without specifying the Hamiltonian it is a superposition with respect to. The ultimate problem being targeted is how that Hamiltonian is selected. Fundamentally while this combinatorial can be formulated as a variational search problem, it is emphatically not a search over states, so notions of coherence do not enter. Much as I hate to say it, I suspect the essay's idea of searching for 'the best' state is simply a category error.
