This chapter will try to show that the formal issues that were discussed in the last chapter pale into insignificance – or, at least, into scientific and philosophical disinterest – in comparison with the substantive issues about reduction that arise once scientific explanations are considered in their full complexity. These issues are clustered around two questions:

1. (i) how is the system that is being studied [and the behavior of which is potentially being explained (or reduced)] represented?; and

2. (ii) what, exactly, has to be assumed about objects and their interactions for the explanation to work?

These questions have been posed generally enough to be applicable to all (natural) scientific contexts, including the physical sciences. Similarly, the analysis of reduction that is developed here is intended to be applicable to these other contexts. Nevertheless, given the limited scope of this book, the examples analyzed here will all be from genetics and molecular biology. Similarly, the general philosophical implications of this analysis that are drawn at the end of this chapter (§ 3.7–§ 3.12) will also be geared towards molecular biology and genetics though they are intended to be more generally applicable.

The basic strategy of this analysis will be to develop and use three substantive criteria to distinguish five different types of reduction. Three of these types of reduction are more important than others, and the rest of the book will proceed to use them to analyze the various types of explanation that are encountered in genetics.