The latest computer technology has buttressed a revolutionary look at how life evolved, while offering new potential for medicines.
Carl Woese startled the scientific world in 1977 by positing that there are three essential domains, or types of life. Before, there were thought to be two, bacteria and everything else: eukaryotes, whose cells contain membrane-coated parts, such as the nucleus.
Woese's third domain, archaea, are neither bacteria nor eukaryotes, though they have some similarities with each of the others. Most of the archaea discovered lived in extreme conditions, deep in the sea, under intense heat or in a methane-rich environment.
"The life we know effectively arose three times. That is, the cells of the three domains look like the same kind of thing invented by three different inventors," Woese said.
The University of Illinois professor challenged the mainstream by basing his distinctions on genetic relationships rather than structural similarities, divided life into 23 main divisions, all incorporated within three domains: bacteria, archaea and eukaryotes.
Woese solved the riddle by painstakingly looking at a genetic information molecule, RNA, in the ribosomes, protein-builders found in every living cell.
Now, researchers working with Woese have published high-tech confirmation in the Proceedings of the National Academy of Science. They found that changes in ribosome structures are "molecular fossils" that track evolution.
UI Professor Zaida Luthey-Schulten and graduate student Elijah Roberts, the lead author, use techniques that were unthinkable in the 1970s, when Woese proposed the three domains of life.
"The ribosomal crystal structures and the many genomic and environmental ribosomal sequences did not begin to accumulate until starting around 2000," Luthey-Schulten said. "So we are really just now starting to get enough raw data to perform these sorts of comparative analyses."
Also, Roberts contributed to the UI's new software for the structural analysis and visualization of the genetic complexities, finding molecular sequences common to all members of a single domain of life, but not to another, Luthey-Schulten said.
Woese said Isaac Newton influenced scientists to see "the world as comprising material particles" like billiard ball atoms "with forces between them," including chemical bonds.
"All living things were looked at as little machines," he said. "The job of such a biology was to take the machines apart and come up with a 'parts list' from which the machine (in principle) could be assembled.
"Now it appears that just having a parts list is insufficient to give you an understanding of the 'machine.' You have to understand these molecular mechanisms in terms of the behavior of the whole."
The scientists want to understand more deeply the process of how ribosomes synthesize protein.
Luthey-Schulten said their work could eventually lead to new medicines, including new ways to attack the problem of antibiotic resistance by stopping production of specific proteins.