Metaphysical presuppositions are important for guiding scientific practices and research. The success of twentieth-century biology, for instance, is largely attributable to presupposing that complex biological processes are reducible to elementary components. However, some biologists have challenged the sufficiency of reductionism for investigating complex biological phenomena and have proposed alternative presuppositions like organicism. In this article, contemporary cancer research is used as a case study to explore the importance of metaphysical presuppositions for guiding research. The predominant paradigm directing cancer research is (...) the somatic mutation theory, in which mutated genes are presumed to be ultimately responsible for explaining carcinogenesis. This reductionistic approach to cancer has been criticised recently, and an organistic approach has been proposed. The article concludes with a discussion of the reciprocal interaction of metaphysical presuppositions and scientific practices for investigating cancer's complex nature. (shrink)