It is well known that most organisms are composed of smaller subunits, including not only cells and semi-independent organelles but often also a whole suite of parasites, commensal organisms, and other symbionts (Buss 1987; Margulis 1970; Bouchard and Huneman 2013). The process of association of these subunits has been recognized as contributing to many of the major transitions that have occurred in the course of evolution (Maynard Smith and Szathmary 1995; Michod 1999). As a result, the selective forces that have led to the subunits foregoing their evolutionary sovereignty are being better appreciated (van Baalen and Jansen 2001), but little is known yet about the mechanisms that maintain the dynamic coherence of the associations. In this respect there are many parallels with classical ecological questions. In spite of the fact that the processes that dynamically generate and maintain biodiversity in ecosystems (competition, herbivory, predation, parasitism, and so forth) are quite well known, we still have difficulty in understanding and predicting the outcome. This parallel is obvious if one considers the history of the disciplines. Biologists and philosophers of biology have long been concerned with the status of associations of entities that are not stricto sensu organisms, but look like organisms at least as much as they look like collectives: ant colonies, wasp colonies (Seeley 1995; Holldobler and Wilson 2008), termite mounds (Turner 2000), Portuguese men-of-war, slime molds (Bonner 1959), etc. The insight that organisms can be composed of other organisms is quite old, and dates back to the concept of ‘‘superorganism’’ already developed by the geologist Hutton in the 18th century. Since then, the idea has resurfaced multiple times, for instance, from the ecologist Clements (1916), following Forbes (1887) who suggested that lakes are microcosms, and more recently in Lovelock’s Gaia hypothesis. Sober and Wilson (1998) reinitiated a discussion on precisely what superorganisms are (Bouchard 2010). This includes questions such as whether they are really targets of selection just like organisms (Gardner and Grafen 2009), and how they come into being (Reeve and Holldobler 2007). Some evolutionary biologists argue, however, that the very concept of superorganism is unnecessary and can be replaced by a more general understanding of organism (Queller and Strassmann 2009). Ecologists such as Clements were concerned by the fact that ecosystems (or at least some of them) seem to behave in a functionally unified and coherent way, with feedback loops, division of labor, regulations, and other features supposed to be characteristic of metazoan organisms. The notion of a ‘‘superorganism’’ thus carries at least implicitly a link with ecology. However, history proved to be on the other side–with those who, with Gleason (1926) and against Clements, argued that nothing special makes an ecosystem cohesive, and that the assemblage of species in a community does not reflect any kind of organicity. Ecological theory as it further unfolded in the 1950s and ’60s (e.g., Hutchinson, MacArthur and Wilson, etc.) was built upon the notions of population, community, and ecosystem without using the concept of superorganism. M. van Baalen (&) Eco-Evolutionary Mathematics, Institut Biologie de l’Ecole Normale Superieure (UMR 8197), CNRS, Paris, France e-mail: minus.van.baalen@ens.fr