Life Was Chemically Inevitable
Offline - 21 April 2010 by Catherine Brahic
Black smokers, hotbeds for life (Image: Charles Fisher/NSF Ridge 2000 programme)
IN THE beginning there were Ida and Luca. The initial Darwinian ancestor - Ida - and the last universal common ancestor - Luca - assembled themselves from the spare parts sloshing around on the early Earth. Once all the ingredients were in place, it looks like life was all but inevitable.
The finding comes from recent discoveries about the behaviour of chemicals thought to have been present on the primordial Earth, relating to two key stages in the evolution of life. Ida was the first molecule that was able to self-replicate. Once it was around, busy making copies of itself, it somehow evolved the ability to store information in the form of the genetic code. That led to the life form from which we all descended: Luca
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Luca probably popped up about 4 billion years ago - some 500 million years after a spinning galactic cloud coalesced into planet Earth and a few hundred million years before complex life evolved and began to leave fossil traces. We can deduce Luca must have existed because all life forms that we know of - from bacteria and viruses to T. rex, bananas and humans - share the same genetic code, with a few small exceptions.
Luca is thought to have been based on RNA, the close cousin to DNA, because strands of RNA can act as enzymes. This means metabolism could operate before proteins evolved to take over.
The genetic code consists of triplets of genetic building blocks, or nucleotides, with each triplet coding for a particular amino acid or acting as an on/off switch for amino acid production. Amino acids are the building blocks of proteins and hence of organic life forms.
According to Michael Yarus of the University of Colorado at Boulder, Luca evolved the code as a result of natural chemical affinities between nucleotides and amino acids. Chemical bonding, he says, means that different amino acids naturally like to sit next to some triplets and not others.
The genetic code is the consequence of chemical affinities between RNA and amino acids
In other words, the genetic code is the inevitable consequence of affinities between the molecular building blocks of RNA and those of the proteins they code for. If he's right, it will explain why individual triplets always code for the same amino acids, whether in a virus or a human.
Natural attraction
Yarus works with artificial RNA and has shown that these chemical affinities do exist. Mix strands of RNA with amino acids and the amino acids will more or less spontaneously nestle up to their corresponding triplets. "Yarus found that anticodons [a type of triplet found in some RNAs] were particularly good in this regard and bind the 'correct' amino acid with up to a millionfold greater affinity than other amino acids," says Nick Lane of University College London.
Now David Johnson and Lei Wang of the Salk Institute for Biological Sciences in La Jolla, California, have shown for the first time that these natural affinities occur in real organisms.
Johnson and Wang decided to look for evidence in ribosomes - key components of the cellular machinery that assemble proteins from amino acids. Ribosomes are made of a tangle of RNA and amino acid chains, so if there was natural attraction going on, it should be found there, they reasoned.
Sure enough, when the pair looked at where amino acids sat in the ribosome, they found that 11 of 20 standard amino acids were far more likely than not to be positioned next to the "right" triplet according to the genetic code (Proceedings of the National Academy of Sciences, DOI: 10.1073/pnas.1000704107).
"Not only is there a chemical reason for these affinities between amino acids and their triplets but you can see them in a natural, biological system," says Yarus. What's more, he adds, the ribosome is an evolutionarily ancient structure, supporting the idea that these affinities go way back. All this, he says, backs his theory that relatively simple chemical interactions allowed Luca to evolve the universal genetic code.
It also allows him to speculate about Ida. While the genetic code is central to life as we know it, there is no reason to think that other self-replicating life forms have to use it. However, since Ida gave rise to the RNA-based Luca, it is logical to assume Ida was also made of RNA or something very similar. But that creates a problem: how did RNA - made from a long chain of nucleotides - assemble itself?
Nucleotides don't tend to form chains without catalysts to help them. In living cells, those catalysts are always proteins, yet the first proteins were made by Luca; they did not exist in the time of Ida. Something is needed that is like RNA but simple enough to replicate itself without a catalyst.
Yarus says that the answer lies in small-molecule enzymes called cofactors that help RNA and DNA do their jobs. "They're absolutely universal in biology today and therefore very old," he says. Because they are made of nucleotides, the cofactors could have started RNA chains (Cold Spring Harbor Perspectives in Biology, DOI: 10.1101/cshperspect.a003590).
The catalyst that allowed the first RNA chains to form is a missing link in the evolution of early life, says Lane. "There is kind of an assumption that it was there somehow, but no one has ever found it." While Lane agrees that cofactors might have been involved in the early stages of life, he thinks there could be an even simpler way to explain how the first chains of RNA appeared.
That comes from a team led by Ernesto Di Mauro at Sapienza University of Rome, Italy. In their experiments, they have shown that cyclic nucleotides, which are a chemical variation of the nucleotides that make up RNA (see diagram), will spontaneously link to each other and form viable RNA chains (The Journal of Biological Chemistry, DOI: 10.1074/jbc.M109.041905).
This suggests that if there were cyclic nucleotides in the primordial soup, there was no need for a catalyst, says Lane. Given the right ingredients, the first self-replicating life forms would have essentially booted themselves up. "Cyclic nucleotides are just as likely to occur in these primordial environments as any other nucleotides," he says.
With the right ingredients, the first self-replicating life forms would have booted themselves up
For Lane, these reactions in all probability happened around the piping hot black smokers of the oceanic abyss, where the Earth's crust is wrenched apart by immense geological forces. "In environments like hydrothermal vents it is likely, but as yet experimentally unproven, that a range of amino acids and nucleotides would be formed by the laws of chemistry," he says. Local currents, he adds, would probably draw the molecules together, making it more likely that self-replicating chains of RNA could form and associate with amino acids.
http://www.newscientist.com/article/mg20627573.900-selfstarter-life-got-going-all-on-its-own.html
"Experiments are the only means of knowledge at our disposal. The rest is poetry, imagination." Max Planck
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Another interesting article. Here I don't see the authors locking themselves out of possible lines of inquiry or at least not to the same level as the guy behind the other article. Still, I suppose that scientist need to block out some possibly interesting ideas, if for no better reason than retaining a focus is better than getting lost in the noise of possible speculations.
One point that they seem to be going with is that proteins could not form without RNA but then RNA does not seem to form spontaneously either. Then they appeal to the cyclic nucleotides. To my lay person's mind, that really does not work out all that well.
OK, we know from the Miller Urey experiments that the basic chemicals of life appear to form spontaneously (amino acids, nucleotides, sugars, lipids and so on). I posit a pre-Ida world, which for convenience I will call the Miller Urey World (MUW).
As the MUW begins to form, we now have a much more complicated chemistry to deal with. One thing that must have happened at this point is that simple molecules became more complicated as dimers, trimers and so on. Whatever the arbitrary division that we then call polymers, the first ones would have been more or less random.
So here we have the first cyclic RNA forming, probably in shorter loops more often than longer ones. And any run of three nucleotides is a potential codon. There are, of course 4^3 possible codons which is not that large of a number. However, for them to code for any meaningful peptides, you need to consider longer runs. Here I am getting into the probabilities of long chain molecules forming in meaningful ways.
OK, so we can consider pre-biotic cyclic RNA. It will form more or less at random. However, it needs to form unbroken runs of longer chains in order to catalyze meaningful polypeptides. Let me consider some possible numbers here.
4^3 possible codons.
22^3 possible tripeptides (don't forget tetrapeptides and so on but for convenience I will keep this simple).
The number space for a codon is clearly much smaller than the number space for random tripeptides. However, that is not good enough. If RNA is a necessary precursor to a tripeptide, then we need unbroken runs of nine nucleotides. Or fifteen nucleotides if we consider codons that do not have the chemical affinity as start/stop markers.
Well, 4^15 nucleotides being a requirement for tripeptides to form...I am sure that we can all see a possible problem here. Don't get me wrong, even 4^15 is nothing compared to Avogadro's number but still, might it be rather more likely that tripeptides formed quite early and then catalyzed the formation of the far less probable RNA runs?
Then too, many tripeptides are quite biologically active apart from that. If even some of the early ones to form helped to facilitate the formation of larger molecules, well, then what will become life is well started.
Past that, if the simpler peptide molecules help to catalyze primitive RNA string that then fall away, might those float around and link up with other strings to form cyclic RNA that really does code for ever more interesting peptide molecules?
If you want a name for this speculation, call if the peptide first world (PFW).
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I guess I need to start hitting that site on my daily surfing routine, lots of great stuff seems to show up.
Everything makes more sense now that I've stopped believing.
new scientist
makes me think of think of this video:
great post btw, very cool stuff
nice article
you've done it again extremeatheist