Shortly before New Year's Day, we lost Carl Woese, one of the 20th Century's greatest scientists. It is fitting to use the first blog of 2013 to pay homage to this creative and determined pioneer of molecular phylogenomics.
Carl put our picture of living organisms on a solid empirical basis using the tools of molecular biology. In the course of his work:
•He established precise molecular methods for determining phylogenetic relationships.
•He discovered a whole new kind of cell.
•He made it possible to understand the relationships between prokaryotes (bacteria and archaea) and eukaryotes.
Any one of these accomplishments would be extraordinary. Altogether, they make Carl the most outstanding figure in understanding the diversity of life in well over a century. The detailed story is told in Jan Sapp's 2009 book, The New Foundations of Evolution: On the Tree of Life.
The basics of Carl's approach to taxonomy derived from his interest in the process of decoding the messenger RNA intermediate between DNA sequences in the genome and amino acid sequences in proteins. In all living cells, this decoding occurs on an organelle called the "ribosome." The organelle was so named because it is about 50 percent RNA, or ribonucleic acid.
Increasingly turning his attention to evolutionary issues in the 1970s, Carl realized that the ribosome would be a good basis for establishing phylogenies. All organisms have them, they perform a central task essential for cell reproduction (and so are constrained in how much they can change structure), and there are clear similarities between the ribosomes of the smallest and largest organisms.
Small organisms without a defined nucleus are called "prokaryotes." They have ribosomes of size 70S with two subunits of size 30S and 50S (all in S or "Svedberg" units, named after a Swedish biophysicist). Large organisms with a defined nucleus are called "eukaryotes," and they have 80S ribosome with corresponding subunits of size 40S and 60S.
One particular feature made ribosomes especially attractive for molecular studies 40 years ago. Since the ribosome is where amino acids are joined to make proteins, they are abundant in all cells (in some cases half the total cell mass). Thus, it is easy to obtain ribosomal RNA molecules from all biological material.
Accordingly, Woese and his colleagues chose the RNA of the small ribosomal subunit as the molecule to use as a phylogenetic marker. They developed methods for identifying differences in RNA sequence.
When they did their initial analysis of small ribosomal subunits RNA, they had a big surprise. Remember, surprises are what you want in science because they mean you have discovered something new.
The surprise was that there were not just two groups of sequences, distinguishing the 16S RNA of the prokaryotes from the 18S RNA of the eukaryotes. There was a second class of 16S RNA from a group of prokaryotes that produce methane during anaerobic growth. Woese had obtained these methane producers from his University of Illinois colleage, Ralph Wolfe.
Were the methane producers just fluke outliers, or did they represent a larger group of evolutionarily distinct organisms? When ribosomal RNAs from more prokaryotes were analyzed, there emerged a group of prokaryotes similar to the methane producers. Often, these were isolated from extreme environments (highly salty waters, hot springs). The ribosomal RNA of this group was clearly distinct from that of bacteria and also eukaryotes.
RNA phylogenies indicated that there were three kinds of cells, not two as previously believed. The ribosomal RNA evidence was quickly bolstered by finding that these exceptional prokaryotes had different lipids in their membranes from bacteria and eukaryotes and different cell walls from bacteria. They were clearly a new and different type of cell.
Because they seemed to live mostly in extreme environments, these unexpected prokaryotic organisms were originally thought to resemble cells from the earliest stages of earth history and were named "archaebacteria" (old bacteria). We now know that related organisms are found in virtually all environments, but the name stuck. So they are now called Archaea, even though we have no evidence they are older than Bacteria and Eukarya, the other two cell groups.
Discovering a new kind of cell, a new form of life, was not a trivial matter in the 1970s, when some people believed virtually all the secrets of molecular biology had been revealed. Woese's discovery was initially accepted more readily by German scientists than by Americans. The Germans did critical work characterizing Archaeal cell biochemistry and solidifying their position as a third type of cell.
The evolutionary implications of Woese's discoveries were revolutionary.
The use of ribosomal RNA as a phyologenetic marker made it possible to confirm the status of mitochondria and chloroplasts in eukaryotic cells as descendants of free living bacteria. This result confirmed the endosymbiotic hypothesis for the origin of these organelles and established symbiogenesis as a major force in evolution.
The unexpected discovery of a new cell type as recently as the 1970s, meant that all our assumptions about the nature of early life were open to question. It was now possible to hypothesize that additional cell types had once existed but gone extinct without leaving fossil evidence of their presence. Perhaps they had played a role in the evolution of existing cell types.
The establishment of ribosomal RNA as a central molecular character in the identification of species has made it possible to analyze DNA and RNA sequences directly from nature and ask how many species are present. This kind of analysis is known as "metagenomics" and has taught us that we have only isolated a small fraction of existing life forms in the laboratory.
In sum, Carl Woese represented the best kind of scientist. He let the empirical data lead him (and the rest of us) to places no one had ever expected to go. That is truly the result of major discoveries.