>If I publish something claiming bacteria has a gene X that produces phenotype Y, then a subsequent study that transfers gene X into a different bacteria must also observe Y.

There is no guarantee (and it often isn't the case) that the phenotype observed in the first organism is purely the result of gene X; its effects may be context-dependent.

To take this a little further, I think it's plausible that a soft scientific question differs from a hard one specifically in terms of how easy it is to separate the phenomenon in question from its context.