One fundamental project of biology is to determine which groups of organisms are “the same” and which are different, for taxonomic purposes but more fundamentally so that one can make general, meaningful claims about specific groups. Traditional bifurcating taxonomies have been and remain useful. However, what was designed to name unchanging “natural kinds” of relatively large organisms with distinct morphologies is not adequate for grouping and dividing very small organisms, reticulated histories, endosymbiosis, horizontal gene transfer, asexual reproduction, or ecosystems. Biological explanations need to be flexible enough to account for hierarchically embedded processes and structures at vastly different scales, from the molecular to the global. Modern biology has moved beyond naming things, and biological explanations now require more sophisticated ontologies.