Reductionism is one of the oldest and most controversially debated issues in the philosophy of biology. Many arguments have been proposed for and against it, and many attempts have been made to spell out what exactly reductionism entails. The traditional opponent to reductionism is holism, a general approach to the study of complex systems that grants the whole a special ontological or epistemological significance that the parts of the system allegedly lack. Reductionists, by contrast, believe that once the parts of a system and their interactions are understood, there is nothing left for science to explain. The debate between holists on the one side and reductionists on the other side has accompanied biology's maturation as a scientific specialty since the nineteenth century (Weber and Esfeld 2003).

In modern philosophy of biology, the debate over reductionism has taken a somewhat narrow direction, in spite of the broad range of epistemological and ontological issues that are connected to reductionism. In the tradition that emanated from the logical positivism of the Vienna circle, the main issue has been the problem of theory reduction. Since the influential book by Ernest Nagel (1961), this term has designated the derivation of the laws of some higher-level theory from the laws of some more fundamental theory with the help of so-called bridge principles. Such principles relate the terms of the theory to be reduced to the terms of the reducing theory, which – presumably – is necessary in order to effect the derivation.