Artificial life and the RNA world

August 5, 2010 • 3:14 pm

by Matthew Cobb

Two things come together from earlier this year. First, there was a lot of argument here, in the Times Literary Supplement and elsewhere over Stephen C. Meyer’s Signature in the Cell. One of the many issues in question was the ancient “RNA world”, which Meyer has argued is implausible. Then, in May, there was Craig Venter’s amazing creation of an artificial organism (but not an artificial cell), which Jerry rightly said was indeed “playing God”.

Now there’s an excellent 30-minute BBC Radio 4 programme “Acts of Creation” which puts the two stories together, and looks at attempts round the world to push the field of “artificial biology” even further. The “RNA world” refers to the suggestion that before life used DNA as the universal genetic code, its simpler, more fragile sister, RNA, was the molecule of life – around 4 billion years ago.

One of the problems with this idea is that precisely because RNA is so fragile, it is very difficult to imagine molecules of it sloshing around in Darwin’s “warm little pond” without simply degrading. Venter’s competitors – including my Manchester colleague John Sutherland – are trying to see under what conditions life might have originated. And one of the answers – or rather, one of the leading hypotheses – is remarkably cool. Literally.

You should be able to listen to the programme from anywhere in the world by going here. If it won’t play outside the UK, my sincere apologies, but you can still follow the links to the various labs that are working on this fascinating area.

14 thoughts on “Artificial life and the RNA world

  1. I cannot really see why Craig Ventner creating life in a laboratory is ‘playing God’. Even if we follow Genesis, God rested on the seventh day. Maybe now he’s retired and passed the job of creating life on to us. In any case, creating life is what women do when they have babies. In a sense, we all create life every minute of the day when we replace worn out tissue in the chemical laboratories within our cells. I see nothing fundamentally God-like about creating life. Some people worry that life made by human beings must be soulless but I disagree. Even by Christian standards this is heresy. God may incarnate a soul into whatever he so wishes, be it life created in a laboratory or a supercomputer. There is real potential for evolution to become teleological at last in that having produced intelligent life, for the first time there is the possibility that evolution will be directed and God will manifest not just as a metaphor, or a myth but as reality. Perhaps this is what she planned all along?

  2. Neat. Very neat, and a good supplement to Luisi’s The Emergence of Life: From Chemical Origins to Synthetic Biology which I am reading at the moment.

  3. Cool post – thanks for the link!

    I thought Bernard Strauss’ (another wonderful U of C professor) comments on the matter of whether putting DNA into a cell really constitutes synthetic life were particularly well conceived. After all, little intellectual distinction exists between what Venter’s group did (an incredible technical accomplishment) and what one does every day in plasmid transformation.

  4. Thanks. It was very interesting.
    However, there was no mention of the “alkali vent” or “lost city” which is a hypothetical place where biochemistry may have started.
    Another point not touched upon: the bacteria and archaea have the same genetic code but they use different chemistries to synthetize their membranes. This likely means the common ancester of the two shared the code, but it may have used inorganic matter as its “membrane”.
    Any thoughts?

    1. I’m just a layman here, but I don’t see how that is feasible.

      The archaeabacteria seems to be a young group, since you can take single genes like rRNA and get pretty stable phylogenetic trees; high resolution, little depth. Despite their extreme adaptations, they are a mere subset of bacteria (~ 20 % in biomass, IIRC), again pointing to youngness.

      In fact, while better methods are needed, I believe at least two full-genome papers finds that archaeabacteria are likely sisters to eukaryotes, or nearly so. They shar a lot of hereditary and protein transport machinery, I think. And eukaryotes should be young, seeing that they are archaebacteria/bacteria endosymbiosis results.

      If you want a mechanistic/ evolutionary pathway explanation, Cavalieri-Smith gives one. The overhead of his complete theory is massive, but that part at least is simple and predictive: bacteria may loose walls and membranes. (See for example Mycobacteria.)

      Starting from the most robust and likely ancestral membrane/cell wall/membrane structure you could loose away to something akin to the eukaryote state, which likely then is the archaeabacteria-eukaryote ancestral state. Not as robust, and in the then frenzied reconstruction among surviving attempts a metabolic switch may have been an early contingent happenstance inaugurating a sturdier membrane.

      [In that perspective, eukaryotes choose a more precarious but ultimately successful pathway. Not as successful in biomass, but in surviving extinction!]

  5. I still insist that Venter is not playing God. He’s playing human.

    This is what we do. We take things apart and see how they work; then we try to put them back together again and improve on the original.

    Nothing godlike about that at all.

  6. I’m watching the PNAS site weekly for Szostak’s work, that I heard about at a meeting last month (from someone who had spoken with him after his Lindau lecture), & which is supposedly coming out in PNAS soon. It should explain the details of the work described in general terms in his Lasker lecture (The Lindau and Lasker lectures are much the same, but the Lasker video pays better attention to showing the slides. NB: part 1 of 5):

    1. Thanks for the video recommendation — that lecture is fascinating. It really sounds like we’re getting pretty damned close to producing simple replicating and metabolizing cells in the lab from scratch.

      1. Replicating cells, anyway, I guess. They start with something other than RNA, which is partly why I can’t wait for the details. Glad you appreciated the recommendation!

  7. I have had a disagreement with Jerry over this – I suspect something like the cell came first, if only because of the RNA problem outlined above. Jerry was strongly opposed to this. How on earth we could prove it either way is hard to see…

  8. Thanks all for the various references! Shostak’s work is hot/cool.

    Prompted by Matthew Cobb’s question on cell/non-cell first pathways: I’m not a biologist, but I would attempt testing. In fact, I’ve seen biology paper do this, and in proto-biology systems too.

    An example is the Zn world (non-cell first pathway), which tests well against its many predictions.

    [The problem being more that the tests themselves fail. For example, it was believed that ribozymes may have had metal ion close to active centers, and the Zn world predicted the specific metal preference. But at least two classes of ribozymes, including the ribosome core, is actually geometrically fitted water molecule machines AFAIU. The near metal ions function is perhaps more of a mystery.]

    I would presume Shostak’s pathway would test extremely well too: it self-assembles, et cetera. Since none can be excluded, the result would be somewhat like bayesian methods on phylogenetic trees, as I understand them. Passing tests would increase likelihood of the contingencies studied.

    So it would be not a phylogenetic tree, but a pathway tree, working on the same type of fact (pathway/phylogenetic pathway, as predicted by evolution). It would point to the most interesting pathways and at the same time their outstanding problems.

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