This series of posts is intended as a basic introduction to the science of evolution for non-specialists. You can see the introduction to this series here. In this post we explore the “RNA world” – a proposed stage in the origin of life that predates modern DNA and protein-based biochemistry.
Weizsäcker’s book The World View of Physics is still keeping me very busy. It has again brought home to me quite clearly how wrong it is to use God as a stop-gap for the incompleteness of our knowledge. If in fact the frontiers of knowledge are being pushed back (and that is bound to be the case), then God is being pushed back with them, and is therefore continually in retreat. We are to find God in what we know, not in what we don’t know; God wants us to realize his presence, not in unsolved problems but in those that are solved.
Dietrich Bonhoeffer, Letters and Papers from Prison
In the last post in this series, we introduced the “RNA world” hypothesis – the idea that life was RNA based prior to DNA-based biochemistry. As we noted, this hypothesis received a great boost in the early 2000s, when it was determined that the ribosome – the enzyme responsible for making proteins from information coded in DNA and RNA – was in fact a ribozyme: an enzyme constructed out of RNA.
We can better appreciate ribozymes for the marvels that they are with a brief review of some basic cell biology we covered earlier in the series (and those requiring a more thorough refresher can use the links provided). You might recall that DNA is a polymer formed from monomers, and that the information in DNA is transferred to proteins, which have a three-dimensional shape that can perform structural and enzymatic functions. In this way, DNA functions as a hereditary molecule and proteins do the day-to-day work in the cell. “Messenger RNA”, as we discussed, is the intermediate between DNA and protein. As a “working copy” of a gene, messenger RNA is used as a template for directing the order of monomers in the resulting protein. What we did not discuss, however, is the key role that a different type of RNA plays in this process – the RNA that makes up the enzymatic core of the ribosome, the enzyme that connects protein monomers together as directed by the messenger RNA.
These RNA molecules, called “rRNA” for “ribosomal RNA” are strings of monomers similar to DNA monomers. Yet these molecules also have an enzymatic function that depends on their three-dimensional shape – their sequences direct them to fold up into a structure that can perform an enzymatic function. In this way, they are similar to proteins, which also fold up into functional shapes to do their jobs. Despite this shape, they remain a polymer that in principle can be used as a template for replicating themselves, much like DNA. While it is not possible to show a complete structure of rRNA here (since it is such a large molecule), a smaller ribozyme can be used to illustrate its features: a string of nucleotide monomers that folds up to form an active enzyme based on its three-dimensional shape:
Given that RNA can have both DNA-like and protein-like attributes, it’s not surprising that researchers have proposed that RNA in fact precedes both. From the beginning of this hypothesis, one of the key goals of researchers investigating the RNA world has been to identify a self-replicating RNA ribozyme. Such a molecule would have the essential ingredients for evolution: a genome subject to mutation, thereby producing genetically different “offspring” that would be subject to natural selection.
Challenges and difficulties
One of the main problems with the RNA world hypothesis, among many (after all, this is a frontier area), is that as far as we can tell, a self-replicating RNA ribozyme needs to be quite complex. To date, scientists have not succeeded in identifying an RNA sequence that is capable of being a general RNA replicator, and RNA molecules that do have at least some ability to replicate RNA tend to be quite long (i.e. comprised of many building blocks). The probability that such a molecule would arise spontaneously from a pre-biotic mixture of chemicals is vanishingly slim, even if one grants an environment where the required chemicals are common (a problem in itself that we will discuss further below).
One conjecture that addresses this issue is the idea that the original self-replicating RNA ribozyme was not a single molecule, but rather a collection of molecules – a sort of molecular ecosystem where a number of smaller RNA molecules contribute to the replication of the entire set. Such a system might be easier to hit upon by chance (since each individual molecule is less complex), or, conversely, such a system might be easier to develop from some as-yet-unknown precursor system.
While seemingly farfetched, this idea recently received some empirical support. In this paper, a research group reports their findings that self-sustaining catalytic networks of small RNA molecules can spontaneously arise from mixed populations of RNA precursors, and that such networks can evolve increased complexity over time. While far from solving all of the problems with the RNA world hypothesis, these results indicate that the first RNA-dependent RNA replicating enzyme was in fact a population of small, simpler RNA molecules rather than one large and complex one.
Further challenges and difficulties
Despite these recent advances, one of the longstanding challenges to the RNA world hypothesis remains: the difficulty of the required precursors arising directly through pre-biotic chemistry. RNA ribozymes, while simpler than cellular life, are themselves quite complex, and formed from relatively complex precursors. While the evidence we have is suggestive that life went through an RNA world stage, recent work has not demonstrated an easy path by which such a world could form directly from nonliving components. Accordingly, some researchers have begun to search for other “worlds” – simpler ones that predate the RNA world, and might have served as an intermediate stepping-stone on the gradient between non-living chemistry and RNA-based life. While this work is by its nature quite speculative (it is, after all, the frontier of a frontier) recent work has supported the hypothesis that RNA could have been preceded by simpler chemistry more amenable to spontaneous assembly in a pre-biotic chemical mixture. In the coming years it will be interesting to see if any of these hypotheses gain additional support. After all, for a research scientist, the frontiers are the exciting areas – and few areas in evolution are more at the frontier than work on abiogenesis.
So, will science ever solve the problem of abiogenesis? Perhaps not – though when I reflect on the fact that we are only 400 years removed from the time of Galileo, I am reminded that many seemingly unsolvable scientific problems have indeed been solved. And along with Bonhoeffer, I delight in these scientific advances that give us an ever-larger picture of God and his faithfulness to his creation.
In the next post in this series, we’ll move on to another frontier area of evolutionary biology – the ongoing debate between those who view evolution as a primarily convergent process, and those who see evolution as primarily driven by chance events (i.e. as a contingent process).