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Tuesday, December 30, 2014

Simulated meteorite impact produces RNA bases. So what?

A group of Czech scientists have fired a big laser at a solution of formamide and found traces of adenine, guanine, cytosine, and uracil (Ferus et al., 2014). The result is reported in an article in Science [From hell on Earth, life's building blocks]. The image is from the Science article.

Here's the abstract of the PNAS article ...
The coincidence of the Late Heavy Bombardment (LHB) period and the emergence of terrestrial life about 4 billion years ago suggest that extraterrestrial impacts could contribute to the synthesis of the building blocks of the first life-giving molecules. We simulated the high-energy synthesis of nucleobases from formamide during the impact of an extraterrestrial body. A high-power laser has been used to induce the dielectric breakdown of the plasma produced by the impact. The results demonstrate that the initial dissociation of the formamide molecule could produce a large amount of highly reactive CN and NH radicals, which could further react with formamide to produce adenine, guanine, cytosine, and uracil. Based on GC-MS, high-resolution FTIR spectroscopic results, as well as theoretical calculations, we present a comprehensive mechanistic model, which accounts for all steps taking place in the studied impact chemistry. Our findings thus demonstrate that extraterrestrial impacts, which were one order of magnitude more abundant during the LHB period than before and after, could not only destroy the existing ancient life forms, but could also contribute to the creation of biogenic molecules.
In case you don't appreciate the significance of this research, PNAS provides you with a brief summary ...
This paper addresses one of the central problems of the origin of life research, i.e., the scenario suggesting extraterrestrial impact as the source of biogenic molecules. Likewise, the results might be relevant in the search of biogenic molecules in the universe. The work is therefore highly actual and interdisciplinary. It could be interesting for a very broad readership, from physical and organic chemists to synthetic biologists and specialists in astrobiology.
The problem with all these studies is that they don't answer the most important question; what happens next?

Let's assume that the four bases were created in the atmosphere as meteorites crashed into Earth four billion years ago. Let's assume there was water in the form of early oceans or big lakes. Then what happens? Do these researchers imagine that the concentrations of these bases built up gradually over thousands of years until there were spontaneous reactions with five-carbon sugars and phosphate to form nucleotides? Then did these nucleotides assemble into short RNA molecules?

It's a very large step from demonstrating that RNA bases can be made from formamide under extreme conditions to showing that their concentrations could have been high enough to make RNA spontaneously.

We need to demand more of these researchers. If they are going to postulate that life arose in a primordial soup then it's no longer sufficient to publish one more paper on how you can make organic molecules from inorganic precursors. Enough already. That's the easy part of the hypothesis. Let's see some evidence for the hard part.

Ferus, M., Nesvorný, D., Šponer, J., Kubelík, P., Michalčíková, R., Shestivská, V., Šponer, J.E., and Civiš, S. (2014) "High-energy chemistry of formamide: A unified mechanism of nucleobase formation." Proceedings of the National Academy of Sciences Published online before print December 8, 2014. [doi: 10.1073/pnas.1412072111]


  1. I don't think we can ever have "enough" evidence for a given phenomenon. Of course, there are still lots of unknowns, but that doesn't mean we should not welcome more evidence of what's already known, because the more the evidence the more robust that hypothesis gets. The RNA world hypothesis is getting stronger with these new reports. But now Larry is demanding evidence for something which this particular paper did not mean to address in the first place.

    1. We already have enough evidence showing that it's possible to make the four bases under certain conditions. Nobody disputes that part of the hypothesis.

      The authors of this paper just assume that's sufficient to explain the origin of life so they don't even address the important steps that follow. What sort of concentrations could be achieved by this mechanism? How stable are the bases? How do you get nuleosides from a mixture of nitrogenous bases? What about the phosphate?

      We've known for sixty years that complex organic molecules can arise spontaneously and we've known for forty years that they can be found in space and in meteorites. We don't need any more evidence of that. What we need is evidence that these molecules can come together in a primordial soup to produce macromolecues and life.

      There are an awful lot of people out there who think the problem is solved once you've shown that the molecules can be made. That's because most of them aren't biochemists and they haven't thought about the problem very seriously.

    2. ///We've known for sixty years that complex organic molecules can arise spontaneously and we've known for forty years that they can be found in space and in meteorites...///

      But nobody had demonstrated before that meteorite impacts could actually produce RNA bases. That's what this work does. We've long suspected that the Late Heavy Bombardment on nascent earth is connected to the origin of life because we've known that those two events overlap. Now this work lends some experimental support to that hypothesis.
      Demonstrating how RNA bases can polymerise to form RNA and lead to life is another story for another day. That was never intended to be addressed by this particular paper. I don't think it is right to belittle the relevance of this work solely because of that reason.

    3. I belittle the work because it's no longer sufficient to just demonstrate another way of making complex molecules under certain extreme conditions that may or may not have been present four billion years ago.

      The weakest link in the primordial soup speculation is the step where there are sufficient concentrations of these molecules in an environment that could lead to polymerization. We've known for years that this is the main weakness of the speculation.

      About 20 years ago scientists began to develop an alternative speculation that overcomes this limitation. It's called Metabolism First. The problem with this paper is that it assumes that primordial soup is the only game in town and that it's only necessary to demonstrate that complex organic molecules can be made in order to led support to this scenario. Stanley, Miller, and Oparin already did that sixty years ago.

      I would have more respect for the authors if they had acknowledged that getting sufficient concentrations of these molecules in the ocean is a serious problem and they had made reference to alternative possibilities that don't require spontaneous generation of the bases.

      That's what good scientists do.

    4. The concentration problem can be solved if RNA can be compartmentalized in protocells. There's some progress in this regard, for example, from Jack Szostak's lab, although many hurdles remain.

  2. I find it hard to believe that meteorites would produce enough organic material to be sufficient. Although sadly I cannot seem to find the article again, I once read about self-sustaining reducing chemical reactions in marine rock-cracks (using a certain type of rock as a catalyst). To me at least the author argued convincingly that such an environment would be ideal for abiogenesis: This process would go on for extremely long times, in many places, and in a nice closed environment giving it some protection, and it produces a great diversity of organic molecules...

  3. Larry left out an interesting point: the reaction can make uracil but not thymine. Constituents of RNA but not DNA. Coincidence?

    1. Not really, as the paper focuses on RNA. This is obviously based on the RNA life hypothesis, which is a valid theory.

    2. I can't find the full text, so unsure of the full range of products. But what would be a coincidence is if the reaction only produced those bases that have an antiparallel complement when 3'-5' bonded in a homochiral polymer. One would expect a broad mixture of bases, of which the familiar ones are but 4 (or 5).

  4. I think to be fair, there is a lot of evidence suggesting the more important self replicating aspects of these types of reactions occur. There is even a publication (Angewandte Chemie I believe) showing how this self replication can be enhanced by a lipid structure and that the size of these structures has an influence on replication.

    However, regardless, this is not a small paper as creationists are always ready to point out that this is perhaps not the exact conditions. However, with more and more work demonstrating these bases can form they run under a variety of conditions. Creationists are running out of the "this is not realistic possible conditions excuse."

  5. Why not take the results for what they are? They demonstrate ease of production and production sources of key metabolic molecules, and contribute to knowing the constraints during abiogenesis.

    "What happens next" is a basic topic in astrobiology books, where "soup" theories look at diverse means of concentrations (minding all the time that gradients help their theories). Clay surfaces are popular, so are wet-dry cycles, hydrothermal systems with or without ponds, and, yes, protocells. Astrobiologists claim they can get the concentrations up to necessary levels as far as I understand it, toy models seem to agree, so they are good. I can't fault astrobiologists for not going over the basics in a press release. (But if it isn't in the paper, we can fault them.)

  6. @Vimal Ramachandran: ". We've long suspected that the Late Heavy Bombardment on nascent earth is connected to the origin of life because we've known that those two events overlap."

    We don't know that (the overlap). We know that the rock record makes it difficult to observe earlier life, and we know from model work that any earlier life should easily survive the LHB.

    For both these cases zircons are complicating your claim. It is possible that zircon birth conditions can be used to observe a biosphere; research is ongoing. And the zircons lack the otherwise observed record of a late cataclysm (a hundreds of millions of years spike in the impactor flow rate), if that is taken as some sort of time stamp. Where is it? The cataclysm hypothesis is attacked from several sides at the moment, and is not as certain as it has been usually assumed. More likely the late bombardment was simply the tail of the early bombardment, plateaued by the new, improved Nice 2 planet system model much milder contribution of impact flow.