A Challenge to ericB, gpuccio, UprightBiped, et al

The origin of the genetic code seems to be a hot issue in the ID community. Take a look at this and tell us what you think.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0072225

The genetic code shapes the genetic repository. Its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with tRNA.

A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the ‘operational’ RNA code and the late implementation of the standard genetic code. The emergence of codon specificities and amino acid charging involved tight coevolution of aminoacyl-tRNA synthetases and tRNA structures as well as episodes of structural recruitment.

Remarkably, amino acid and dipeptide compositions of single-domain proteins appearing before the standard code suggest archaic synthetases with structures homologous to catalytic domains of tyrosyl-tRNA and seryl-tRNA synthetases were capable of peptide bond formation and aminoacylation.

Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins. These enhancements of phenotypic robustness were likely internalized into the emerging genetic system with the early rise of modern protein structure.

I realize their conclusions are speculative. So feel free to point out where they are wrong.

35 thoughts on “A Challenge to ericB, gpuccio, UprightBiped, et al

  1. I have long argued a parallel sentiment: The value of an idea is in the amount and quality of research it spawns.

    I cannot predict where this conjecture is going, but it sure looks like it could inspire some research.

  2. A related paper, unfortunately behind a paywall.

    http://rsif.royalsocietypublishing.org/content/10/88/20130614.abstract

    This paper describes a novel application of information-asymmetric (signalling) games to molecular biology in which utility is determined by the message complexity (rate) in addition to the error in information transfer (distortion). We show using a computational model how it is possible for the agents in one such game to evolve a signalling convention (separating equilibrium) that is suboptimal in terms of information transfer, but is nonetheless stable. In the context of an RNA world merging with a nascent amino acid one, such a game’s equilibrium is alluded to by the genetic code, which is nearly optimal in terms of information transfer, but is also near-universal and nearly immutable. Such a framework suggests that cellularity may have emerged to encourage coordination between RNA species and sheds light on other aspects of RNA world biochemistry yet to be fully understood.

  3. A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the ‘operational’ RNA code and the late implementation of the standard genetic code.

    (emphasis mine)

    Hah. That’s where the big-D Designer interfered, doncha know. We just don’t know who it was, or exactly what it did to the proto-genetic chemical molecules in that early form of life, nor how it did it whatever it did (supernatural fingers? pure will of mind?) – but by gourd, we know that big-S Step between ‘operational’ RNA code and standard genetic code was WAY TOO BIG A STEP to have been possible without intelligence/intention/guidance. Not god of the gaps, no, not at all, because. Reasons.

    And anyone who denies Reasons is just being an atheo-materialist poopyhead. So there!

  4. hotshoe: (emphasis mine)

    And anyone who denies Reasons is just being an atheo-materialist poopyhead.So there!

    Yes, it’s amazing really. Despite knowing nothing about the first self-replicator they know that it was designed.

  5. “congruence should be considered the most powerful statement of evolutionary biology.”

    Indeed.

  6. One thing the alert critic of the mainstream may pick up on is that the peptidyl transfer centre (and other ribosomal units) arrives on the timeline somewhat after the origin of the proteins they are using to date other events – most notably aaRSs. The modern proteins they are using to do this analysis are synthesised in modern ribosomes, but to possess any phylogenetic signal that predates the ribosome, there must be some mechanism of sequence or structure conservation across the ‘ribosome boundary’.

    This issue is discussed here, section ‘Proteins first’, in relation to an earlier Caetano-Anolles paper.

    Two possibilities suggest themselves: one is that RNA and protein sequences evolve at different rates, and recalibration according to this might place the ribosome ‘where it belongs’, at the head of protein sequence/structure phylogenies. The RNA dataset (just containing rRNA and tRNA) is poorer than the protein one (a cast of thousands), and more subject to saturation, rendering it much more susceptible to artifacts and the vagaries of evolutionary history.

    Another possibility is that the ribosome took over some now extinct version of protein synthesis that nonetheless used the same fundamental link between mRNA and amino acid. Since aaRSs appear very early in the picture, this is possible, since they are the real heart of the code. The first protein aaRSs, on this view, were not made in ribosomes, but in something functionally equivalent: a system with the capability to read mRNA and attach charged tRNAs (charged, obviously, by something other than protein). These replaced (but retained the assignments of) the ancestral charging chickens, making the first protein eggs. When the ribosome arrived, it took over the ancestral mRNA-tRNA linking function, possibly incorporating elements of it in a larger, localised structure. Or analiendidit.

  7. Or analiendidit.

    It’s Zeno’s Gaps. Every time biology finds a transitional form, it creates two new gaps. Therefore — even though the OOL train has left the station — it will never reach its destination.

  8. Wow. All these males together in the same tub scratching each others backs. Am I invited? All the skepticism around here, but no skepticism of the OP.

    You all leave your brains at the door when entering “The Skeptical Zone”?

    Here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-tRNA synthetase enzymes and their interactions with tRNA.

    It should be otherwise? If what utility is a code without a context?

  9. Hi Mung. Sounds like you have some revelations on how the designer did it. Finally! Do share!

  10. Richardthughes:
    Hi Mung. Sounds like you have some revelations on how the designer did it. Finally! Do share!

    Samuel Morse. Designer. There’s even a code named for him.

    Arthur Scherbius. Designer. Enigma.

    ASCII

    Do you have any idea how many different codes and how many different designers there are?

    Shall I continue?

    Wikipedia:

    A code is a rule for converting a piece of information (for example, a letter, word, phrase, or gesture) into another – usually shortened or covert – form or representation (one sign into another sign), not necessarily of the same type.

    But the genetic code is no code because there is no rule and no conversion of information from one form to another. Right?

  11. OMagain:

    Yes, it’s amazing really. Despite knowing nothing about the first self-replicator they know that it was designed.

    Please share with all of us your knowledge about the first replicator.

  12. Blas:

    One question about organic chemistry how do you get polypeptides without ribosomes?

    So you know now, based upon the non-responses you got?

  13. Mung: Samuel Morse. Designer. There’s even a code named for him.

    Arthur Scherbius. Designer. Enigma.

    ASCII

    Do you have any idea how many different codes and how many different designers there are?

    Shall I continue?

    Wikipedia:

    But the genetic code is no code because there is norule and no conversion of information from one form to another. Right?

    So we can can tell if something is a code because it is named after its designer. Thank you, you’ve been very helpful. You might want to tend that bullet hole in your foot…

  14. Richardthughes:

    So we can can tell if something is a code because it is named after its designer.

    Yup!

    The ASCII code is named after it’s inventor. ASCII no questions and I’ll TELLU no lies. Mr. Enigma is on the phone ASCII ing for you.

  15. What would be really funny is if ASCII was actually an acronym and the first letter told us about the designer(s). OMG Mung, your other foot!

    I thought we were going to get some ID insights, Mung. You never fail to disappoint. But it sure wasn’t evolution, that’s for sure !

  16. So, Mung comes a long and makes a couple of posts, none of them offer any criticism of the paper in the op. How come?

  17. Mung: Please share with all of us your knowledge about the first replicator.

    I know the same as the ID proponents who make strong claims about it, i.e. nothing. Yet they make those claims and I don’t.

    I’m perfectly prepared to accept it was designed, should you offer evidence of such. However I would note that “complex things exist” is not “evidence of design” as much as you’d like it to be.

    In the meanwhile progress continues on a non-ID version of OOL. And the ID version, well, you can’t really progress “it was designed” can you? Nowhere to go with that really.

  18. He’s actually one of the more engaged ID supporters. Most don’t venture out of the echo-chamber so the few pearls of wisdom Mung drops are gratefully received, even if it’s just a post’n’run.

    Or something like that anyway….

  19. OMagain:

    I know the same as the ID proponents who make strong claims about it, i.e. nothing.

    If you know nothing about it, how do you know that ID proponents know nothing about it? You have some algorithm that matches your ignorance to theirs?

    So your lack of knowledge permits you to criticize what, exactly?

  20. Mung:
    OMagain:

    If you know nothing about it, how do you know that ID proponents know nothing about it? You have some algorithm that matches your ignorance to theirs?

    So your lack of knowledge permits you to criticize what, exactly?

    Feel free to bring us up to the current state of ID theorizing. Get all mechanistical and stuff.

  21. Mung:
    OMagain:

    If you know nothing about it, how do you know that ID proponents know nothing about it? You have some algorithm that matches your ignorance to theirs?

    It’s simple really. They’ve provided no details and yet make strong claims. Of course, prove me wrong and show where those details are provided?

    So your lack of knowledge permits you to criticize what, exactly?

    Their unsupported claims.

    Too easy, any more?

  22. Mung:
    So your lack of knowledge permits you to criticize what, exactly?

    Feel free to tell me all about how the designer did it, rather then how evolution did not, in the thread you just started Mung….

    And also I would note that lack of knowledge about evolution never stopped any ID supporter from criticizing it. So double standards much? Go back to UD and sort them out first before trying it on here would be my advice, it’s a much bigger problem over there…

  23. You didn’t notice my skepticism in the post I wrote above, or that in the Berhardt paper I linked regarding Caetano-Anolles’s interpretation of his own findings? I don’t accept the timelines uncritically.

  24. Seriously? There was nothing in that Google to answer the question, so someone must laboriously explain the detail? You could always enlighten him yourself, since you actually do know about NRPS.

  25. You’re right, he’s just taking a wild stab based on their total silence on the matter.

  26. So, Mung comes a long and makes a couple of posts, none of them offer any criticism of the paper in the op. How come?

    Because I, unlike so many others here at TSZ, do not doubt the existence of a code.

    A timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the ‘operational’ RNA code and the late implementation of the standard genetic code.

    Results reveal that genetics arose through coevolutionary interactions between polypeptides and nucleic acid cofactors as an exacting mechanism that favored flexibility and folding of the emergent proteins.

    Haven’t you heard? A polypeptide is a protein and a protein is a polypeptide. What, exactly, did proteins emerge from?

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