  Much confusion concerning the classical way to think about genes is due to the fact that geneticists have sometimes talked as if classically conceived genes are for gross phenotypic characters (phenotypes) or as if individual genes produce phenotypes. This talk was very misleading on the part of classical geneticists and continues to be misleading in the context of contemporary genetics. The production of a gross phenotypic character, such as purple eye-color, involves all sorts of genetic and extra-genetic factors including various cellular enzymes and structures, tissue arrangements, and environmental factors. In addition, it is not clear what, if any, gross phenotypic level functions can be attributed to individual genes. For example, it is no clearer today than it was in Morgan's day that the function of the purple gene discussed in section 2.1 is to contribute to the production of eye color. Mutations in this gene affect a number of gross phenotypic level traits. Legitimate explanatory reasoning invoking the classical gene concept does not depend on any baggage concerning what genes are for or what function a gene might have in development. What the explanatory reasoning depends on is the difference principle, that is, the principle that some difference in the gene causes certain phenotypic differences in particular genetic and environmental contexts (section 2.1). Many gene-based explanations in contemporary biology are best understood in terms of the classical gene concept and the difference principle.