Simmer Down: Viruses Not ‘Fourth Domain’ of Life

This article was originally posted on RealClearScience.

Biologists have categorized life into three large domains: Bacteria, Archaea (weird, bacteria-like microbes), and Eukarya (unicellular and multicellular organisms such as fungi, plants, and animals that possess nucleated cells). Under this classification system, viruses are left out in the cold. They certainly are not “alive” in the classical sense because they are not capable of metabolizing or replicating on their own. But it does not feel quite right to classify them as “inanimate,” either, because they are built of biological molecules and contain genetic information. Thus, for the most part, viruses languish in the no man’s land between the living and the dead.

The debate about how to classify viruses received a jolt with the discovery of extremely large viruses (such as Pandoravirus) that are so gigantic they can be seen with a light microscope and contain more genetic information than some bacteria. It has been proposed, due to some intriguing similarities in DNA sequences — specifically, in the gene that encodes for an enzyme called RNA polymerase — that such large viruses actually constitute a “fourth domain” of life. If that is the case, then perhaps all viruses should be awarded this new status.

“Sacrebleu!” say French scientists in a recent issue of Trends in Microbiology. Considering viruses to be a fourth domain would unnecessarily complicate evolutionary biology. For instance, the authors indicate that using RNA polymerase to redraw the tree of life presents a gigantic challenge. Large viruses do not all cluster into a single new domain. Instead, classifying life based on RNA polymerase would likely demand the creation of several new domains. (See figure.)

Such a phylogenetic tree is unwieldy, or as evolutionary biologists call it, “non-parsimonious.” A foundation of building evolutionary trees is that they ought to be as simple as possible. This is referred to by scientists as the principle of parsimony but is more colloquially known as Occam’s Razor. Essentially, a model that requires fewer assumptions (in this case, evolutionary changes) is superior to a model that requires more.

This is not the only problem with a viral fourth domain. The biggest difference between cells and viruses is their method of replication. All three domains of life replicate by cell division, which implies that this trait was derived from the Last Universal Common Ancestor (LUCA). (In other words, LUCA is the theoretical ancestor of Bacteria, Arcahea, and Eukarya.)

Viruses, which do not replicate by cell division, probably evolved independently multiple times, “here, there, and everywhere,” as the authors conclude. Some probably evolved before LUCA, and others well after LUCA. Many have likely exchanged genetic material via horizontal gene transfer. Lumping them all into a fourth domain, therefore, makes little sense.

Though the debate over the classification of viruses may at first seem to be purely academic, it touches upon underlying questions that are of much greater significance: What exactly is life, and how did it evolve? The answer to those questions may be partially found within the enigmatic world of the viruses.

Source: Patrick Forterre, Mart Krupovic, and David Prangishvili. “Cellular domains and viral lineages.”Trends in Microbiology, 22 (10): 554-558. October 2014.