Carl Woese, a microbiologist at the University of Illinois, challenged long-held biological classifications in the 1970s. His work was not initially accepted because it contradicted the established understanding of life’s divisions. Through molecular analysis, he revealed a more complex picture of evolutionary relationships, leading to a complete redrawing of the universal tree of life.
The Five-Kingdom Model of Life
For much of the 20th century, the dominant system for classifying life was the five-kingdom model, proposed by Robert Whittaker in 1969. This system was based on observable characteristics, such as an organism’s appearance, mode of nutrition, and its basic cell structure. Life was sorted into the kingdoms Plantae, Animalia, Fungi, Protista, and Monera.
The kingdom Monera served as a catch-all category for every organism that lacked a true nucleus, known as a prokaryote. These organisms were all grouped together under the assumption that they shared a close evolutionary history. This classification implied that visible differences between a plant and an animal were more profound than any differences among the unseen world of microscopic bacteria.
This framework presented a simplified view of the microbial world because the tools to look deeper did not yet exist. The classification relied on what could be seen under a microscope or cultured in a lab. The assumption was that all prokaryotes were a single, cohesive group, representing the simplest form of life.
A New Tool for Classification
Woese sought to classify organisms based on their genetic code rather than physical traits. He needed to find a piece of genetic machinery present in all life that changed very slowly over evolutionary time, acting as a molecular clock. He found this in ribosomal RNA (rRNA), a molecule that is a core component of the ribosome, the cellular machinery responsible for building proteins.
He focused on a segment of rRNA known as the 16S subunit in prokaryotes. The gene that codes for 16S rRNA is ideal for this purpose because its function is the same across all known life, meaning its overall structure is highly conserved. This universal presence and functional constancy make it a valid chronometer for comparing all organisms.
The 16S rRNA gene contains both highly conserved and hypervariable regions. The conserved regions change very little over billions of years, allowing scientists to compare deeply divergent life forms. The hypervariable regions, in contrast, change more quickly, providing a way to distinguish between more closely related species.
The Three-Domain System
In 1977, Woese and his colleague George Fox published their findings. The 16S rRNA data showed that the organisms within the Monera kingdom were not one group, but two different kinds of life. The genetic gulf between these two prokaryotic groups was as vast as the gulf between either of them and all eukaryotes. This discovery effectively shattered the five-kingdom model.
Based on this evidence, Woese proposed a new level of classification above kingdoms: the domain. He organized all life into three domains: Bacteria, Eukarya, and a newly identified group he named Archaea. The Bacteria domain contains the familiar prokaryotes, such as E. coli and the bacteria that cause strep throat, and their cell walls contain a substance called peptidoglycan.
The Archaea are also single-celled prokaryotes, but they are genetically and biochemically as different from bacteria as they are from us. Their cell membranes are made of different lipids, and their cell walls lack peptidoglycan. Initially, Archaea were thought to be exclusively “extremophiles,” organisms thriving in harsh environments.
While many do inhabit these niches, like volcanic hot springs and deep-sea vents, they are now known to be widespread in all environments, including soil and oceans.
The third domain, Eukarya, includes all organisms whose cells have a nucleus: protists, fungi, plants, and animals. An insight from Woese’s new tree was that Archaea and Eukarya are more closely related to each other than either is to the Bacteria. This finding reshaped our understanding of our own evolutionary origins.
Redefining Our Understanding of Evolution
The discovery of the three domains transformed biology. It revealed that the microbial world held a level of diversity previously unimaginable, with the Archaea representing an entirely new branch of life that had gone unnoticed. This new map of life forced scientists to reconsider the nature of the Last Universal Common Ancestor (LUCA), the organism from which all three domains descended.
Woese proposed that LUCA was not a single, discrete organism but a “communal” state of primitive cells he called progenotes. In this early stage of life, genetic information was not just passed down from parent to offspring (vertical gene transfer) but was shared between unrelated cells in a process called horizontal gene transfer. This sharing of genes would mean that early life evolved collectively.
This concept suggests the base of the tree of life is less like a single trunk and more like an interwoven thicket or web. Genes for innovations could move between different lineages, creating “evolutionary chimeras” that combined traits from different ancestors. This view complicates the simple branching pattern of a traditional evolutionary tree but provides a more realistic picture of how the complex cellular systems of modern life may have emerged.