Why can’t we figure out what a polyamide does? is a poorly worded question which I assume is trying to ask about why it's hard to determine biological function from chemistry/primary structure. Would it be appropriate for me to completely rework the question based on my assumption?
If the question was something more general like "Why can't the biological function of a molecule be easily determined from it's chemical structure?", then there are some interesting general answers (binding specificity, Levinthal's paradox, etc).