In this matter of extreme complexity and nonlinearity, how can you ever tell the point where being paranoid is the right thing to do? E.g. how can you know tha

In this matter of extreme complexity and nonlinearity, how can you ever tell the point where being paranoid is the right thing to do? E.g. how can you know that transferring a gene from maize to petunias is still "sufficiently close" to the level of variation seen in ancient natural processes and evolution? (Genuine question but also genuine worry about this.)