There is much more about these chemical transactions and their proofs. First is that transactions are partially independent on the molecules. The blockchain may be useful only for having a distributed database of transactions and proofs, available for further use. But there’s more.
Think about this database as one of valid computations, which can then be reused in any combination or degree of parallelism. Then, that’s the field of several competitions.
The same transaction can have several proofs, shorter or longer. It can have big left pattern therefore costly to use it in another computation. Maybe a transaction goes too long and therefore it is not useful to use in combination with others.
When there is a molecule to reduce, the application of a transaction means:
– identify a subgraph isomorphic with the left pattern and pick one such subgraph
– apply the transaction to this particular subgraph (which is equivalent with: reduce only that subgraph of the molecule, and freeze the rest of the molecule, but do it in one step because the sequence of reductions is already pre-computed)
Now, which is more convenient, to reduce the molecule by using the random algorithm and the available graph rewrites, or to use some transactions which fit, which is fast (as concerns step 2) but costly (as concerns step 1), moreover it may be that there is a transaction with shorter proof for that particular molecule, which mixes parts of several available precomputed transactions.
Therefore the addition of transactions and their proofs (needed to be able to validate them) into the database should be made in such a way which profit from this competition.
If I see the reduction of a molecule (which may be itself distributed) as a service then besides the competition for making available the most useful transactions with the shortest proofs, there is another competition between brute force reducing it and using the available transactions, with all the time costs they need.
If well designed, these competitions should lead to the emergence of clusters of useful transactions (call such a cluster a “chemlisp”) and also to the emergence of better strategies for reducing molecules.
This will lead to more and more complex computations which are feasible with this system and probably fast enough they will become very hard to understand by a human mind, or even by using IT tools on a limited part of the users of the system.