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The names of the two major classes of cells—eukaryotes and prokaryotes—betray certain scientific assumptions about how the two are organized. Eukaryotes include all of the cells of plants and animals and are distinguished from the prokaryotic cells of bacteria by their structural complexity. Specifically, eukaryotic cells contain membrane-bounded compartments in which specific metabolic activities take place. Most important among these is the presence of a nucleus, the membrane-delimited compartment that houses the eukaryotic cell's DNA. It is this nucleus that gives the eukaryote—literally, true nucleus—its name. In contrast the prokaryote cell contains no membrane-delimited compartments and thus its name reflects its status as the proto-eukaryote. Most dangerous about these names is that they allow scientists to make assumptions about the way metabolism is carried out inside each cell type. In stark contrast to the eukaryote, the prokaryote has long been thought of as just a bag of enzymes in which reactions take place almost by random encounters. Our authors argue that this makes no sense. They discuss the way the prokaryote is organized into 'functional compartments' that lack membranous boundaries. Finally, they demonstrate how water itself can help define functional spaces.