The classification and grouping of organisms, the science called taxonomy, regards organisms as similar based on their visible characteristics. Thus, from the Greeks until recently, plants and animals were regarded as the two main kingdoms of life. Later, cell biologists divided organisms into prokaryotes and eukaryotes, that is, organisms without and with a nucleus. Most recently, a new taxonomy has been developed, largely by Carl Woese and associates, based on the information in the ribosomal RNA sequences. Ribosomal RNA, used as an evolution clock, is essential to life, easy to identify, and full of surprises.
Remarkably, the most information‐rich classifications of life shows three main divisions, sometimes called domains, which are more fundamental than the distinction between plants and animals, or prokaryotes and eukaryotes. These domains are:
- Eukarya: The most familiar domain, eukarya includes organisms with a nucleus. This division includes plants, animals, and a large number of what are sometimes called protists, or organisms that can be seen only under a microscope, such as yeasts or paramecia.
- Bacteria: The second domain includes microorganisms without a nucleus, including many that are familiar, like Escherichia coli.
- Archaea: The third group, on the molecular/biochemical level, is as different from bacteria as they are from eukarya. These remarkable microorganisms inhabit niches often thought of as inhospitable to life — for example, locations with high temperature, low oxygen, or high salt. Their biochemistry is unique and largely unexplored. Fully half of the known genes of these organisms are apparently unique, with no counterparts in bacterial or eukaryotic genomes.