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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).

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Would it be appropriate for me to completely rework the question based on my assumption?

No!

That's something the OP is responsible for, not an editor.

You may edit a question to improve its grammar, or formatting. But a complete rework is to put words in mouth of an OP that never were there.

... then there are some interesting general answers (binding specificity, Levinthal's paradox, etc).

If you think a question could be a good direction for writing a canonical, write a self answered canonical question, and flag/vote to close that other question as a duplicate.

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