The biological world is hierarchically organised – larger wholes are composed of smaller parts. One take on the different levels might look like this: genes, cells, organs, multicellular organisms, social groups of animals, species, and ecological communities. What processes formed this hierarchy? For the hierarchical structure has a history – many parts and wholes that we now take for granted simply did not exist before. In some cases parts aggregated to form a larger whole: once free-living ants formed the first eusocial colonies. In other cases, the parts were formed within an already aggregated whole: kidneys, hearts, and the like came after multicellular creatures were formed. What can we say in general about these repeated transitions in biological organisation? Can we explain the production of each new level by appealing to the same, or similar, processes? The thesis addresses some of these questions, and how we might go about answering them.