Realities depending on intentions are always of a conceptual nature, they are the synthesis of percept and concept, of matter and mind, of phenomenon and idea. The three different gene concepts outlined, require different prerequisites or complementation by three different 'worlds'. The gene that is manipulated is dependent on living organisms that are competent to integrate it into their own genome. Life itself is a prerequisite for genetic manipulation and, as such, cannot be explained in molecular terms, it transcends molecular reductionism. Genes are not causes, but conditions for life processes.
Genes provide the information for the primary structure of proteins.
And finally, the functions of gene products need to be integrated into the entirety of an organism, by the organism itself. Proteins allow for the expression of phenotypic characters, they are not their causes. It is the mouse that specifies the meaning of a given function, it is the fly that interprets mouse genes in its own context. We are therefore left with a situation that urgently requires some rethinking as well as a methodological enlargement of science. It is a situation which has resulted from molecular biology itself.