The state of the art in the RNA world

As an employee of the National Center for Science Education, Nick Matzke was involved with everything from situations that never made the press to coaching the lawyers in the Dover trial, which gained international attention. One thing that apparently became clear is that, due to the highly technical material and a flood of misinformation on the topic, the public (and even many scientists) simply don't know what the current state of knowledge is when it comes from evolution. As part of an effort to rectify that, the NCSE and the AAAS's Dialog on Science, Ethics, and Religion organized a session on the state of the art in our understanding of evolution, which Matzke moderated.

Four speakers took on topics that appear to be the frequently misunderstood by the public. One of these—the origin of life—isn't directly part of evolutionary theory, but is frequently associated with it by the public. The remaining topics covered major events in the evolutionary history that produced humans, including the origin of bilateral animals during the Cambrian explosion, the origin of tetrapods, and the evolution of human ancestors. Throughout the talks, there were two recurrent themes: we can identify major environmental changes that might have sparked new selective pressures, and many of the major adaptations we view as designed for a specific lifestyle actually originated as an adaptation for something else entirely.

The origin of life

Evolutionary theory, both as proposed by Darwin and elaborated since, deals with the diversification of modern living organisms from a limited number of ancestral living organisms. But the lack of a strong theory for the origin of life is actually treated as an argument against evolution by many of the opponents of teaching the theory. Many of the principles of evolution, including heritable variations and selective pressures, are also applied by origin of life researchers. As such, the two topics appear inextricably linked.

The discussion of life's origins was handled by Andy Ellington of the University of Texas - Austin. He started by noting that simply defining life is as much of a philosophical question as a biological one. He settled on the following: "a self replicating system capable of Darwinian evolution," and focused on getting from naturally forming chemicals to that point. To do so, Ellington developed three different themes.

Chemicals in living organisms can form without life





An RNA ligase ribozyme

The basic idea has been recognized for over a century, but the work of Stanley Miller was cited for triggering the modern era of scientific work on the topic. Since the classic Miller-Urey experiments, science has steadily expanded the range of essential molecules that can be produced under conditions that might reasonably expected to have been present on the early earth.

Ellington emphasized that progress has been slow—we knew how cyanide could react to form the DNA component adenine in the 1960s, but it took over three decades to recognize that a few more reactions converted it to its relative, guanine. And the roadblocks continue to fall. After all attempts to produce sugars created a tar-like sludge, someone eventually found that a small amount of borate could help ethanol form large amounts of ribose, another component of RNA.

The first molecules that could replicate led directly to modern life

With the components of nucleic acids in place, Ellington traced a path through the RNA world to a molecule that could self-replicate. Past attempts to jump to a complex, self-replicating RNA molecule seem to have been on the wrong track. Short palindromic RNA sequences can apparently help catalyze the formation of complementary sequences, meaning what's needed is actually an RNA that can link these short sequences into longer, more complex ones. A number of such sequences, termed RNA ligases, have been identified. Several labs have shown that these ligases can then be improved by an essentially Darwinian process of random mutation followed by selection for increased efficiency.

Modern RNA activities tell us about the RNA world

Ellington's final point was that we can still see remnants of the RNA world in aspects of biology that are common to all life. He noted that many of the cofactors used by modern proteins, including ATP itself, are derivatives of the chemical components of RNA. Researchers have also been able to evolve RNAs that successfully bind these cofactors, which suggests that proteins would only need to have gradually replaced these RNAs. That replacement, Ellington suggested, has never actually been completed: the central core of the ribosome, a complex essential for protein production in all organisms, turns out to be formed from RNA. During questions, he also emphasized that basic cellular metabolism uses some amino acids as intermediates, and suggested that proteins resulted from early RNA "life" simply using what it had lying around, tying in nicely with the theme of preadaptation.

Ars spoke to Dr. Ellington after the talk and asked him about the separate thread of origin of life research that focuses on identifying the energy-harvesting reactions required for the first life. He was very excited about the potential for user-generated genomes to help unify the two fields. The ability to customize a genome would not only help scientists identify the very minimal metabolism necessary for life, but would eventually allow researchers to start replacing proteins with their catalytic RNA equivalents. Ellington suggested that the result—a cell with a hybrid RNA/protein world—would eventually allow us to explore the transition to the first cells.

Ellington's summary of the state of the art is that "we'll never know exactly what happened, but we're getting a really good idea of what is possible."