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Some empirical and sociological data on how scientists use the term 'gene' in different subfields with some discussion can be found in publications stemming from a project done by Paul Griffiths and Karola Stolz called "Representing Genes".

Other relevant papers:

The 'you can't put a square peg in a round hole' problem from Putnam has often been discussed in relationship to the idea of 'multiple realizability'. This is used by Fodor as an argument against reductionism, but Sober argues it is not a good argument.