Why did Carl Woese propose separating Archaea from Bacteria?

In the late 1970s, American microbiologist Carl R. Woese proposed separating Archaea from Bacteria after discovering that what were previously grouped together as "prokaryotes" actually comprised two distinct evolutionary lineages.12

Woese’s classification system was revolutionary because it shifted the focus from morphological traits—such as cell shape or mode of nutrition—to molecular characteristics, specifically the analysis of ribosomal RNA (rRNA) sequences. His research revealed that the rRNA of Archaea and Bacteria are as different from each other as they are from eukaryotic rRNA, suggesting that these two groups diverged from a common precursor long before the development of eukaryotic cells.1354

Beyond genetic sequences, this separation is supported by radical differences in their biological makeup, including:

• Biochemistry: Differences in lipids and cell wall composition.54
• Metabolism: The utilization of distinct metabolic pathways, enzymes, and enzyme cofactors.54

This work led to the three-domain system of life, which replaced the older, morphology-based five-kingdom model.3