Taxonomists have been naming and classifying organisms for hundreds of years, but still not all organisms in our planet have been identified or classified. Each year, new species are discovered. And as we try to discover and learn more about life on Earth, the need for good organization and an effective classifying scheme is inevitable.

Usually, classification of organisms are done based on their complex morphological features. However, organisms with very simple structures, such as bacteria and other microbes, cannot be classified based on morphology alone. That is why in 1990, Carl Woese, Otto Kandler, and Mark Wheelis proposed an alternate way to classify organisms. They called it the three-domain classification system.

The three-domain classification presents a more accurate way of showing the evolutionary relationships between organisms. Instead of the usual classification using morphology, it proposes the use of genetic analysis to categorize organisms. Its basis is the differences in the patterns of the nucleotide sequences in the cell’s ribosomal RNA (rRNA).

rRNA was the chosen point of comparison in classification because it has a fixed function in all organisms: translation. Its molecular structure also changes little over time and the patterns in its nucleotide sequences show indications of how related and unrelated organisms are.

Woese and company introduced domain as a taxonomical level higher than kingdom. Based on their observation of rRNA patterns, they divided the organisms into three domains: Archaea, Bacteria, and Eukarya.

Archaea are prokaryotes with membranes that are composed of branched hydrocarbon chains attached to glycerol by ether linkages. Their cell walls do not have peptidoglycan. Because of their stable ether linkages, Archaea can withstand extreme environments like strong acidity and high temperatures.

Bacteria are also prokaryotes but their cell membranes are composed of unbranched fatty acid chains attached to glycerol by ester linkages. Their cells walls have peptidoglycan. This group includes the gram positive and gram negative bacteria, the mycoplasma, and the cyanobacteria.

Eukarya are eukaryotes with cell membranes like those of bacteria’s. Their cell walls, if any, do not have peptidoglycan. Eukarya is divided into four kingdoms: Protista, Fungi, Plantae, and Animalia.

Further studies following the three-domain system showed that Archaea are more related to Eukarya than to Bacteria, even though Archaea and Bacteria are prokaryotes. Studies also revealed that Archaea and Bacteria overwhelm Eukarya in terms of number.

However, the three-domain classification system received a lot of criticism. Well-known scientists like Salvador Luria and Enrst Mayr contested the system’s overemphasis on domain Archaea and ignoring its similarities with domain Bacteria. Some scientists still prefer to use the precedent Two-empire System (prokaryotes and eukaryotes). There are also studies concerning rRNA that showed that some organisms tend to have fast-evolving rRNA, causing them to be misplaced in the phylogenetic tree.

At present, the three-domain classification system is the most organized, updated, and promising system. However, as further studies are done and discoveries are made, the system is bound to change. There is also a need to further discuss the refinement of the overall structure and subcategories of the three domains.