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Shouldn't they have replaced them with a gene of the same length, filled with only stop codons?

Otherwise, it would be like cutting out instructions from an assembly language file, without knowing whether one of the instructions does something like adding a constant integer value to the program counter. You might think the code that was removed was critical to the operation of the program, but you could have instead replaced all the instructions with an equivalent number of no-ops, and it would still work as expected.



Stop codons aren't a noop either though, since genes can encode different functionality based on "intentional" frameshifts by various means.




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