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Here is the latest I have found. link

This is the basic idea: Evolution does not look ahead and make plans. It would not create a system of mRNA with giant ribosomes to create proteins, until proteins were already useful. There must have been a simpler way to create useful proteins before, that got complexified after it was already useful.

Since enzymes can be made of RNA, presumably early life made just RNA enzymes and no proteins. It didn't matter whether RNA enzymes were as efficient as modern ones because protein competition hadn't evolved yet.

And since we now make peptides off an RNA template, probably early proteins were also made off an RNA template. It is hypothesized that particular amino acids would be attracted to particular RNA pairs, and they would be put in just the position that would help them link to neighboring amino acids. This could be slow and inefficient compared to modern protein production because again the competition was not stiff back then.

Between two pairs of coding bases, the RNA needed a noncoding base for spacing. Possibly the noncoding base might be particularly good for catalyzing the joining of amino acids.

The system did not have to use the same amino acids we use today. It could use amino acids that were good at attaching to RNA, and later after the system got changed around the modern list of 22 amino acids could have developed.

There are various ways this is a satisfying idea. For example, the machinery to make proteins is largely made of RNA. The mRNA carries the message. tRNAs decode the message. Ribosomes are giant machines which transcribe proteins efficiently, and they are largely made of RNA with a lot of little proteins that help them hold their shape etc. Presumably the first protein-building machinery was itself built entirely from RNA -- because that's what was there to build with -- and over time evolution found ways to improve that machine with protein scaffolding.

This 2005 paper link describes a reasonably plausible way it could have been once. They imagine a few alternate amino acids which might have once been part of the genetic code -- ornithine. Homoserine. 2,4-diaminobutyrate. They imagine ways that the crevices between pairs of bases could be like the binding sites of enzymes. They fit the ideas together.

Have there been advances since 2005?

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    $\begingroup$ I doubt it, and I doubt whether you'll find anyone here who is even familiar with the idea. However I suggest you try to answer your own question yourself by looking for papers that cite the 2005 paper. The online PNAS site may have this, otherwise I am sure that there are tools for doing so. $\endgroup$
    – David
    Jun 9, 2018 at 21:17
  • $\begingroup$ @David I don't think your comments are fair or constructive. They don't help improve this valid and interesting question. The paper has been cited 75 times so it seems like research continued after 2005. The question seems like it was written after J Thomas put effort into getting an answer. $\endgroup$
    – Michael_A
    Jun 10, 2018 at 8:40
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    $\begingroup$ @Michael_A — On the contrary, my remarks were absolutely constructive. I told the poster how to get an answer to his question, assuming that my subjective view of the likelihood of his getting an answer here was correct. (A view based on my experience of responses to questions on protein synthesis.) You confirm that this approach will bear fruit. The poster may well have tried to get an answer, but had been adopting wrong approaches. As an educationalist on this list I try to help people to learn how to learn, rather than spoon-feeding them. (In this case I have no spoon.) $\endgroup$
    – David
    Jun 10, 2018 at 9:12
  • $\begingroup$ I don't find this advice insulting, and it is of course a valid approach. I wanted to ask the question first because if someone is following the topic, they may point to great research that many of us would like to know about. While I would like to eventually study all of the literature since 2005, there is no harm in getting tips about important links. And second, I thought that some people who are unfamiliar with the topic might like to hear about it. $\endgroup$
    – J Thomas
    Jun 10, 2018 at 14:14

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