It is widely presumed that the world exhibits hierarchical structure: that the objects of science can be arranged into levels and that some of those levels are higher than others. Organisms, on this view, are at a higher level than cells, which are at a higher level than molecules, which are at a higher level than atoms.

Although it is popular, this "layered worldview" faces notable challenges. Some critics contend that it is hopelessly idealized or even ultimately incoherent. Others contend that it makes no difference to our explanatory practices and has no metaphysical or epistemic significance.

I argue that these critics are mistaken. By undertaking a comprehensive analysis of the logical and metaphysical nature of hierarchical structures and their application within contemporary philosophy and ecology, I argue for three claims: that hierarchies exist (insofar as the objects of scientific discourse exist); that the domain of ecological interests is hierarchically structured in a way that is incompatible with ontological reductionism - the idea that everything in the scientific domain is, in fact, contained within the "fundamental level of reality"; and that the hierarchical structure of the world often (but not always) justifies the practice of describing, explaining, and analyzing things using hierarchical terms.

My analysis begins with a review of the existing accounts of hierarchies in ecology, biology, sociology, and economics. Arguing that these accounts are inadequate, I then develop an improved account called Core Hierarchy Theory (CHT). CHT, I argue, is an improvement over its predecessors in two respects: generality and simplicity. Other accounts are either too narrow (e.g., failing to count branching hierarchies as genuine hierarchies) or make unnecessary theoretical commitments. Using a formalized version of CHT, I then prove four theorems that are relevant to well-known philosophical debates that involve hierarchies. For example, I show that two of the core metaphysical commitments of the ontological reductionist - that the higher level sciences reduce to fundamental science and that all of reality is, in fact, contained within the fundamental level - are in fact inconsistent with the most basic and unrestricted conception of hierarchical structures provided by CHT.