An Approach to Reasoning in an Artificial Chemistry

Artificial chemistries are usually used to study what phenomena occur in a given setup, and simulators are the primary tools. This paper attempts to address a reverse question, that is, what setup is required to produce given molecules, using reasoning as the tool. We give a procedure to answer whether specified molecules can be produced in a given system described in our artificial chemistry, which is based on string pattern matching and recombination with no spatial structure. The process of reasoning is similar to backward reasoning in logic: it starts with setting the specified molecules as the goal, and gradually constructs a possible reaction path in the reverse order of recombinations. The process is illustrated using simple example systems, including one that produces imaginary protein from imaginary DNA.