THE THIRD DOMAIN OF LIFE

The Music of Science: by paying attention, Carl Woese spotted archaea. Oliver Morton thinks he deserved the Nobel

From INTELLIGENT LIFE magazine, March/April 2013

In a graphic novel by the great Alan Moore, "The Ballad of Halo Jones", Halo shares a cabin on a starship with two companions, Toy and the Glyph. But Halo and Toy think they are just a twosome. The Glyph has so little personality that no one, even in cramped quarters, notices heror possibly himwithout the closest attention. Even then, any memory of the Glyph soon fades.

As on the starship Clara Pandy, so on Earth. Life seems to come in two forms: things with big complicated cells, and things with small simple cells. Amoebae, aardvarks, aspergilli, aspidistras and apes like us fall into the first category, known as eukaryotes. Bacteria fall into the second. Pay attention, though, and a third category appears: the archaea.

The person who first paid the requisite attention was an American researcher, Carl Woese, who died at the end of last year without ever receiving the Nobel prize he richly deserved. In the 1960s he realised that molecular biology offered a way to see how different types of bacteria were related to each other. All living things have ribosomes, nanomachines which make proteins. By determining the sequence of the nucleic acids in the ribosomes of various different creatures, Woese thought, he would be able to tell which were more closely related to each other and which more distantly, and thus put together a family tree.

In a world where sequencing machines of ever greater speed and sophistication analyse a billion fragments of DNA every day, this seems obvious. In a world where sequencing was a new idea and had to be done by hand, it seeemed a lot of work for a benefit that could not be known and might well be small—no one was very interested in the family tree of the bacteria, partly because they thought it would never be known with any accuracy. But Woese undertook the task anyway. He found, as he had expected, that the sequences from bacterial and eukaryotic ribosomes were quite different, and that all eukaryotes looked much more similar to all other eukaryotes than to any bacteria. But he also found that some of what had been taken to be bacteria were as far removed from bacteria on his family tree as bacteria were from eukaryotes. This is the group now known as the archaea.

Woese’s work was not warmly received—in fact it was mostly rejected, ignored or belittled. But it stood the test of time. Evolutionary relationships established through the analysis of nucleic-acid sequences—these days those of whole genomes, not just of a scrap of a ribosome—are now fundamental to the study of life’s history. And the archaea discovered by that approach have turned out to be quite unlike both bacteria and eukaryotes in a number of fundamental biochemical ways, standing separate but equal in those family trees as a third domain of life.

When they were first discovered, it appeared that the archaea lived primarily in extreme environments—hot springs, salty brines and the like. This gave them a certain interest, but also made them rather marginal. Now it has been found that they are in fact widespread in all sorts of more mundane environments. They were simply overlooked before, because the techniques used to look at bacteria—essentially, giving them food and watching them grow—don’t work for archaea.

But though they are now accepted as commonplace, the archaea still, it seems to me, get less attention than they deserve. There is a pragmatic reason for that: they don’t, it appears, cause diseases (though in concert with bacteria they may exacerbate a few). But though this makes them a lower research priority than the minority of bacteria that make people sick, it also raises a rather fascinating question—why not? Is this difference linked to the fact that archaea use different vitamins in their metabolism? Is it because they like low-energy environments, and can’t take the pace involved in actively infecting something? Is it because they have different sorts of viruses (bacteria get their disposition to virulence from genes passed around by viruses)? Or because they have different chemicals in their outer membranes—a difference which, itself, suggests that the differences between bacteria and archaea were set down before life had invented cells?

One reason for searching for life elsewhere in the universe is that when you have only one example of something to study, you can’t tell what is fundamental and what is just an accident. Life on Earth is just one example: it all shares the same origin and the same basic mechanisms when it comes to genes and cellular energy systems. But it does come in three different forms, and the differences between them, if thought about deeply rather than simply accepted, might provide new insights into deep mysteries of ecology, pathology and even the origin of life. Woese’s industry and insights provided the wherewithal to start asking such questions. It would be a fitting tribute if more people were to look harder for the answers. If only because it is basic good manners to pay attention to everyone in your cabin—even the fellow passengers you can only see when you concentrate.

Oliver Morton is briefings editor of The Economist and author of "Eating the Sun"

Illustration Pete Gamlen