Why did Carl Woese propose the three-domain classification system?

Carl Woese proposed the three-domain classification system to replace the traditional two-lineage view of life—which divided organisms into eukaryotes and prokaryotes—because his research revealed that prokaryotes actually consist of two distinct evolutionary groups.12

Working with Ralph S. Wolfe, Woese utilized ribosomal RNA (rRNA) sequencing to analyze the genetic relationships between organisms. This molecular approach demonstrated that certain microorganisms, which he named Archaea, were biochemically and genetically distinct from true Bacteria and were, in fact, more closely related to Eukarya than to bacteria.132

Woese’s system shifted biological classification from a focus on morphology—such as modes of nutrition or physical structure—to one based on phylogeny and evolutionary history. By identifying these three domains, Woese provided a more accurate reflection of the deep evolutionary divergence among living things, fundamentally changing how scientists understand the tree of life.31