That discovery, and the molecular biology tools that made it possible, have revolutionized our view of evolutionary history. That man is Carl Woese of the University of Illinois, who this year received the Crafoord Prize. The Crafoord Prize is a sort of “floating Nobel,” presented annually by the King of Sweden to a scientist who deserves a Nobel but whose work does not fit into one of the categories of the more famous prize. Woese is a member of the National Academy of Sciences, and he had previously received a Macarthur “genius” award and the National Medal of Science, among many other honors.
More than perhaps any other scientist, Carl Woese has focused our attention on the invisible but pervasive microbial world, a realm that extends far beyond the pathogenic bacteria that are studied in medical science. Understandably, most of biology has dealt with the larger creatures, which are organized into the three “kingdoms” of plants, animals, and fungi. By the 1970s, it was common to think in terms of two additional microbial kingdoms, the prokaryotes (or bacteria), simple cells without internal structure, and the eukaryotes (including the familiar protists such as amoeba, paramecia, and foraminifera) that did have a nucleus and other internal cell components. As a practical matter, the prokaryotes and eukaryotes could usually be distinguished by laboratory staining techniques, since their cell walls have a different chemical structure.
The emerging technology of molecular biology (which has led us into the genomics of today) allows a different look at the fundamentals of life. All life on Earth, in each of these 5 kingdoms, is based on the same biochemistry. All life uses the same genetic code stored on long strands of the nucleic acids DNA and RNA. The great variety of life represents differences in the base-pair sequences in the DNA and RNA. From this perspective, scientists wanted to find a classification of life based on genetic sequences rather than on external appearances -- hence a molecular taxonomy.
After a great deal of experimentation, Woese settled on one particular set of genetic information, found in the so-called 16s mitochondral RNA. This sequence of genetic code appears in the genomes of all living things. It is a highly conserved sequence, meaning that it has evolved slowly and can be used to track evolutionary changes over very long times. And perhaps most important, it is a sequence that could be measured in the lab.
The most useful way to display the differences in 16s mRNA among different organisms is to show them graphically on the “molecular phylogenetic tree of life” or “universal tree of life,” as it is sometimes called. In this depiction, the distance between any two species, traced along the lines connecting them, is proportional to the difference in their mitochondral RNA. Species with nearly identical sequences are presumably related and are plotted close together. Those that are widely separated are more distant relatives, and when a great deal of data is combined it is possible to infer lineages -- to estimate relationships among species and to determine when one line diverged from another. When applied to the familiar plants and animals, these “tree of life” plots are very similar to the evolutionary trees that had been deduced from structural anatomy. But the big surprises came when the technique was applied to the microbial world.
In a 1977 publication with colleague Ralph Wolff, Woese showed that a previously little-known group of microbes called the archaebacteria were actually more closely related to the eucarya than to the other, true bacteria. Plotted on the tree of life, these obscure microbes occupy a large space, distinct from that of both the eukarya and the bacteria. Based on these discoveries, Woese in 1990 proposed the now-accepted division of life in a paper entitled “Towards a natural system of organisms: Proposals for the domains of Archeae, Bacteria, and Eucarya.” In spite of their name, the archaea are not older than the bacteria. But they are an ancient lineage, many of whose members avoid oxygen (they are anaerobes) and seek high temperatures (they are thermophiles).
The tree of life developed by Woese and his collaborators deserves careful study by astrobiologists. It tells us some surprising things. The wide spread in the various microbial species, which is roughly proportional to the passage of time, shows us the tremendous range of evolutionary change that has taken place within the microbial world. Contrary to the ideas of conventional biology, life did not lie quiescent on Earth for the three billion years that preceded the burst of evolution that constitutes the “Cambrian explosion” 600 million years ago. The great physiological diversity we associate with plants and animals represents a rather small change as measured by these RNA sequences. In fact, the three kingdoms of plants, animals, and fungi are confined to a few outlying twigs in the much greater tree of microbial life.
A look at the new tree of life should also caution us against calling any of these microbes “primitive.” All of the species alive today have followed a long evolutionary trajectory from their early common ancestors.
While the tree of life can provide rich insights into evolution, it is important to remember that it shows only the genetic relationships among species extant today. There are no extinct species on this tree of life, since we cannot extract 16s mRNA from fossils. Thus in spite of similarity in presentation, this is not an evolutionary tree in the traditional sense of showing our descent from previous species. We can learn who our relatives are from this tree, but not necessarily how we got to be where we are today. This tree is complementary to the traditional tree that shows evolutionary lineages derived from fossils.
The pioneering work done by Woese and his collaborators is today being supplemented by other ways of comparing the genomes of different species. The revolution in genomic technology now allows numerous other sections of both DNA and RNA to be sequenced and compared. Each of these techniques is yielding its own tree of life, generally similar to that based on 16s mRNA, but not identical. In fact, we have reached the stage where entire genomes can be compared.
Woese continues his work in the microbiology labs at the University of Illinois in Champaign-Urbana. In 1996 he was part of team that sequenced the first archaeon, and much of his current work is related to efforts to define the “last common ancestor”, if there really was such a thing. He calls himself today an evolutionary biologist. The ultimate objective of taxonomy, the classification of organisms and their relationships, is to better understand the evolutionary process through which life has expanded over the past 4 billion years to create our living world.