How Self-Replicating RNA Got Made - Naturally

A hydrothermal vent on the Niua underwater volcano in the Lau Basin, southwest Pacific Ocean. The sort of place abiogenesis could have happened.

Chemical evolution in a tiny Gulf Stream - LMU Munich

I hate to say, "I told you so!", but... I told you so!

Readers of my books and blog-posts may remember how I elaborated on the ten-step process, proposed by Nick Lane and Michael Le Page in New Scientist in 2009, to explain how abiogenesis could have come about, in my blog-post Perfectly Plausible Abiogenesis, and in my popular book What Makes You So Special? From the Big Bang to You, in which I wrote:

We do not know if it was a single line of development or two or more that later got together. However, laboratory experiments have come up with a very plausible series of steps, as outlined in a New Scientist article by Nick Lane and Michael Le Page (Lane & Le Page, 2009). They assumed that the most likely location for it to have happened was in porous rocks in alkaline waters around geothermal vents and outlined ten steps:

1. Water filtering down into newly–formed rocks around geothermal vents reacted with minerals to produce an alkaline, hydrogen and sulphide rich fluid that welled up in the vents.
2. This fluid reacted with acidic sea water which was then rich in iron to form deposits of highly porous carbonate rock and a foam of iron–sulphur bubbles.
3. Hydrogen and carbon dioxide trapped in these bubbles reacted to make simple organic molecules such as methane, formates and acetates; reactions that would have been catalysed by iron–sulphur compounds.
4. The electrochemical gradient between the alkaline fluid in the pores and the acidic seawater would have provided energy to drive the spontaneous formation of acetyl phosphate and pyrophosphate. These behave like ATP (adenosine triphosphate) which powers modern cells. This power supply would in turn power the formation of amino acids and nucleotides.
5. Currents produced by thermal gradients and diffusion within the porous carbonate rock would have concentrated the larger molecules creating the conditions for building RNA, DNA and proteins and creating the conditions for an evolutionary process where molecules that could catalyse the formation of copies of themselves would quickly dominate and win the struggle for resources.
6. Fatty molecules would have coated the surface of the pores in the rock, enclosing the self–replicating molecules in a primitive cell membrane.
7. Eventually, the formation of the protein catalyst, pyrophosphatase enabled the protocell to extract more energy from the acid–alkaline gradient. This enzyme is still found in some bacteria and archaea.
8. Some protocells would have started using ATP as their primary energy source, especially with the formation of the enzyme ATP synthase. This enzyme is common to all life today.
9. Protocells in locations where the electrochemical gradient was weak could have generated their own gradient by pumping protons across their membrane using the energy released by the reaction between hydrogen and carbon dioxide, so producing a sufficient gradient to power the formation of ATP.
10. The ability to generate their own chemical gradient freed these protocells from dependence on the pores in the rock, so they were now free to become free–living cells. This could have happened at least twice with slightly different cells, one type giving rise to bacteria; the other to archaea.

The above ten–step process is of course speculative and probably impossible to test and verify in a laboratory because the conditions around these geothermal vents deep below the ocean would be impossible to replicate in a laboratory, as would the time it might have taken. No–one is claiming it all happened in a day or two, or even weeks or years; not even the lifetime of a working scientist. It could have taken tens or hundreds of millions of years. No–one was in any hurry and there was no objective. Things happened when they happened.

Now further support for that proposition has been provided by a team of researchers led by biophysicist Dieter Braun, from the Ludwig Maximilian University of Munich, Germany who, according to the university news, have shown the circulation of warm water (provided by a microscopic version of the Gulf Stream) through pores in volcanic rock can stimulate the replication of RNA strands.

RNA, unlike DNA can form complex and functionally versatile molecules that can act as catalytic enzymes (known as ribozymes) to make other RNA strands. The team showed that a Darwinian selection process can produce ribozymes that can produce RNA polymerase which can make more strands of RNA. The news release went on to explain:

In order to simulate conditions under which the process could have become established, Braun and his colleagues set up an experiment in which a 5-mm cylindrical chamber serves as the equivalent of a pore in a volcanic rock. On the early Earth, porous rocks would have been exposed to natural temperature gradients. Hot fluids percolating through rocks below the seafloor would have encountered cooler waters at the sea-bottom, for instance. This explains why submarine hydrothermal vents are the environmental setting for the origin of life most favored by many researchers. In tiny pores, temperature fluctuations can be very considerable, and give rise to heat transfer and convection currents. These conditions can be readily reproduced in the laboratory. In the new study, the LMU team verified that such gradients can greatly stimulate the replication of RNA sequences.

One major problem with ribozyme-driven scenario for replication of RNA is that the initial result of the process is a double-stranded RNA. To achieve cyclic replication, the strands must be separated (‘melted’), and this requires higher temperatures, which are likely to unfold – and inactivate – the ribozyme. Braun and colleagues have now demonstrated how this can be avoided. “In our experiment, local heating of the reaction chamber creates a steep temperature gradient, which sets up a combination of convection, thermophoresis and Brownian motion”, says Braun. Convection stirs the system, while thermophoresis transports molecules along the gradient in a size-dependent manner. The result is a microscopic version of an ocean current like the Gulf Stream. This is essential, as it transports short RNA molecules into warmer regions, while the larger, heat-sensitive ribozyme accumulates in the cooler regions, and is protected from melting. Indeed, the researchers were astonished to discover that the ribozyme molecules aggregated to form larger complexes, which further enhances their concentration in the colder region. In this way, the lifetimes of the labile ribozymes could be significantly extended, in spite of the relatively high temperatures.

The munich team published their findings a couple of weeks ago in Physical Review Letters, regrettably behind a paywall.

Although the hydrothermal vent origin of living organisms is not the only contender, and this research mentions volcanic rocks particularly, this piece of research brings it to the fore and makes it look increasingly likely that Nick Lane and Michael Le Page were substantially right in their summary of the plausible chain of events. Of course, if it happened in volcanic rocks as they met ocean water, then this increases the number of available site where this could have happened.

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