Magic RNA editing!


One of those wacky Intelligent Design creationists (Jonathan McLatchie, an arrogant ignoramus I’ve actually met in Scotland) has a theory, which is his, to get around that obnoxious problem of pseudogenes. Pseudogenes are relics, broken copies of genes that litter the genome, and when you’ve got a gang of ideologues who are morally committed to the idea that every scrap of the genome is designed and functional, they put an obvious crimp in their claims.

So here’s this shattered gene littered with stop codons and with whole exons deleted and gone; how are you gonna call that “functional”, creationist? McLatchie’s solution: declare that it must still be functional, it’s just edited back into functionality. He uses the example of GULOP, a gene responsible for vitamin C synthesis, which is pretty much wrecked in us. Nonfunctional. Missing big bits. Scrambled. With missing regulatory elements, so it isn’t even transcribed. No problem: it’s just edited.

As I mentioned previously, the GULO gene in humans is rendered inactive by multiple stop codons and indel mutations. These prevent the mRNA transcript of the gene from being translated into a functional protein. If the GULO gene really is functional in utero, therefore, presumably it would require that the gene’s mRNA transcript undergo editing so that it can produce a functional protein. It’s not at all difficult to understand how this could occur.

Yes, RNA editing is a real thing. RNA does get processed before it’s translated into protein. McLatchie has a teeny-tiny bit of knowledge and is abusing it flagrantly.

I’ve hammered out dents in a car, and I’ve touched up rust spots with a little steel wool and a can of spray paint. My father was also an auto mechanic and could do wonders with a wrench. Auto repair exists, therefore…

old-wrecked-car-outback-australia-14466708

…patching up that vehicle should be no problem at all, right? I expect to see it cruisin’ down the highway any time now.

Maybe two cans of spray paint this time…?

Comments

  1. Akira MacKenzie says

    Of course it’s functional! It functions by giving the citrus fruit indusrty an excuse to exist.

    Checkmate atheists!

  2. Holms says

    If the GULO gene really is functional in utero…

    To borrow the original ‘laconic reply': if.

  3. arthurhunt says

    I may come to regret this, but McLatchie could have been more clever if he had invoked phenomena along the lines of the mechanism proposed by Lolle et al. (Nature 434, 505-509 (24 March 2005) | doi:10.1038/nature03380).

  4. naturalcynic says

    This is perfect for a Christianist meme: the fetus is in a perfect, glorified status. Fetal life is just about as perfect as it gets, except for the second fetal state beyond the Pearly Gates. It’s life ex utero here on earth that becomes a problem state, filled with imperfections and sins.

  5. robro says

    Pffft…just pray, PZ. God can fix it. It will just wave its magic finger and Poof! that car will be like new.

  6. Larry says

    Throw it into a hat with some cake mix and a stick of dynamite and I think you’ll be pleasantly surprised at the result.

  7. says

    Why not just declare that the GLUO gene was perfectly functional at the creation, but was rendered dysfunctional due to all the delicious citrus fruit in the garden of Eden + the super high mutation rate during the Flood?

  8. raven says

    McLatchie’s solution: declare that it must still be functional, it’s just edited back into functionality. He uses the example of GULOP, a gene responsible for vitamin C synthesis, which is pretty much wrecked in us. Nonfunctional. Missing big bits. Scrambled. With missing regulatory elements, so it isn’t even transcribed. No problem: it’s just edited.

    This kook’s model makes testable predictions.

    1. It should be transcribed.

    2. No one should get scurvey as mentioned in comment #1.

    3. It should produce a protein product that we can see.

    Three predictions. All wrong. And he is wrong. It’s the magic of toxic religion, once again.

  9. arthurhunt says

    Hi PZ,

    Don’t forget, we’re talking Intelligent Design here. Just because you think a silent 50 million year old mRNA cache is unlikely doesn’t mean a designer cannot go about things this way.

    Heck, we can even invoke a nearly-invisible sub-cellular compartment where the designers keep these mRNAs – the cache drawer.

    Yeah, that’s the ticket …

  10. says

    “2. No one should get scurvey as mentioned in comment #1.”

    To be fair, his hypothesis, if it can be called that, assumes that too much Vit. C is harmful to adults because it exacerbates the pathology of malaria. He cites some oldish papers to try to back that up, but needless to say it’s just speculation.

    More importantly, the GLUO pseudogene exists as it does in all primates (above a certain branch), most of which are not susceptible to any malarial parasite (the parasites are usually species-specific). And then there are lots of vertebrates that get malaria, like rats and birds, but have perfectly functional GLUO genes. And then there’s the classic problem with “design theory”, which is why the heck was malaria designed in the first place, thus necessitating screwing with another design to thwart it? It all makes no sense.

  11. Ray, rude-ass yankee says

    I’m sure that I could fix that up, how much time & money do you want to put into it?

    On the other hand, if you have to replace everything is it still the same car? Like my favorite axe, It was my Grandfathers, I still have it. My Father replaced the handle and I’ve replaced the head.

    More seriously, If we could fix that broken gene, should we? What effect would it have on human physiology? Apart from no more scurvy I mean.

  12. alwayscurious says

    The mystery he presents is in babies, not the general population–babies shouldn’t get scurvy according to Jonathan’s model because of endogenous Vitamin C production. The mystery presented in his linked research papers is: Why do babies appear to have high levels of Vitamin C (despite an apparent absence in their diet)? Why do babies with low Vitamin C not appear to show signs of scurvy (despite other obvious associations with malnourishment)? Hmmmm, must be endogenous Vitamin C production later turned off as children age! Yep, only possible answer!

    {60 years later, I’m guessing they have exactly resolved this apparent mystery; but I’m too lazy to look atm}

  13. Stephen Minhinnick says

    Here is a very unambiguous paper published in PLOS one that puts up a direct challenge to evolution deniers. Check out the abstract and the tail-end of the discussion at the bottom.

    Beyond Reasonable Doubt: Evolution from DNA Sequences
    W. Timothy J. White , Bojian Zhong , David Penny
    http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0069924

    It concludes, “Given our results, we suggest that researchers need to be more assertive that evolution has both occurred, and continues to occur. It is essential that any person who does not accept the continuity of evolution puts forward alternative testable models. As we tell our first year undergraduates, ‘belief is the curse of the thinking class’.”

  14. David Marjanović says

    Great paper!

    If the GULO gene really is functional in utero…

    To borrow the original ‘laconic reply’: if.

    Yup.

  15. Andy Groves says

    It’s the amateurishness of this that I find so offensive. McLatchie managed to find a number of references on how RNA editing could modify stop codons, but he doesn’t appear to actually know how the editing system works. If he did, he would realize in an instant that RNA editing would not be able to correct the large scale mutations in the coding regions, nor could it repair the regulatory elements in the locus.

    All he had to do was to read the Wikipedia entry on RNA editing or use The Google. Even that was beyond him. So now the question is: Is he ignorant or disingenuous?

    I know where I come down on that particular question.

  16. moarscienceplz says

    I don’t think an mRNA cache preserved in the cytoplasm for 50 million years is very likely.

    I’m pretty sure Doctor Who fought a monster like that.

  17. says

    “So now the question is: Is he ignorant or disingenuous?”

    He’s obviously just reaching. He needs to come up with a mechanism to get the pseudogene to work, so grabs RNA editing, the only thing that comes anywhere close. Then he makes all sorts of speculative assumptions in which RNA editing is vastly more powerful than current evidence suggests (so powerful it can replace missing exons, somehow “knowing” what their sequence should be).

    This is kind of par for the course, piling one wild speculation on top of another in order to get a bad hypothesis to work. The rest of us meanwhile go with the obvious hypothesis.

  18. alwayscurious says

    “So now the question is: Is he ignorant or disingenuous?”

    My vote is disingenuous. For example, Jonathan did manage to cite this article:

    http://biologos.org/blog/understanding-evolution-is-there-junk-in-your-genome-part-4

    The author explains in plain language how pseudogene inheritance supports the patterns we see in the inheritance of genes which both support evolution. Included are links to additional details of how certain kinds of pseudogenes may gain function, complete with mechanism, requirements and rarity. However, in the main text, the first paragraph mentioning GULOP places into a class of pseudogenes that CANNOT gain function. At the end of the post, the author complained about EXACTLY the tactic Jonathan turns to (months before Jonathan’s article I might add). I think Jonathan is practicing for Luskin’s job: hunting & pecking to find all those papers & websites from which to borrow so little; molding them carefully into a reasonable sounding article despite the glaring holes in the evidence; and this isn’t the first time he’s mangled this end of molecular biology & been corrected. Well, at least there is a testable hypothesis this time (which, while ridiculous, is at least falsifiable).

  19. sethmassine says

    One of my creationist friends has a very funny, kind of cute, little ‘argument’. It follows: “Seth, look at your hand. Now move it. Did you make your hand move?” Me: “Uhm, yeah….of course I did. Your point?” Him: “Your intelligent decision elicited an intelligent response.” Me: “Ooooh….right…”. I wish that I was joking….but alas, speaking as a former Fundamentalist, I can recall the formation process of those little ‘arguments. Requirement one: does it make since to me? Requirement two: Does it make sense to Gawd? If both points are satisfied, you have you razor.

  20. says

    That’s the Paul Nelson argument. I once spent an evening in a bar with him, in which that was his crowning argument: oooh, look at your hand, you can move it under your intelligent control. Checkmate, atheist!

  21. Holms says

    Is he ignorant or disingenuous?

    In the case of religious apologists, I would suggest that it is always dishonesty.

  22. Nerd of Redhead, Dances OM Trolls says

    That’s the Paul Nelson argument. I once spent an evening in a bar with him, in which that was his crowning argument: oooh, look at your hand, you can move it under your intelligent control. Checkmate, atheist!

    Ah, yes, the typical housecat can move their claws with exquisite precision, scratching you as little or as hard as they want. From barely dent the skin to the death grip….Oh, that’s right, the housecat is a mere animal, while humans are made in the delusional image they carry of their deity….

  23. sethmassine says

    Well PZ, we have both encountered that mountain of ignorance. Considering we both reside in small communities, surrounded by the hyper religious, it doesn’t surprise me! What is a reasonable person to do? Go to blogs like this and vent, I guess…

  24. Thumper; immorally inferior Atheist mate says

    What’s the genetic equivalent of duct tape? That’ll fix ‘er right up.

  25. rnilsson says

    I’m with Larry here: Just apply a can (maybe two) of Pray Paint.
    After applying some knee- and elbowgrease.
    Make a couple motorbikes.

  26. cheesynougats says

    Isn’t the Paul Nelson argument that you have a paper in the works that shows you’re right, And you will produce it any day now. ..