Junk RNA: Cause Junk DNA was getting lonely

The worlds most famous living biologist, Casey Luskin, is either an IDiot, or the biggest IDiot in the known universe.

Being an expert in molecular biology, Casey has previously discussed Junk DNA, ie ERVs, at his blog ‘Evolution News and Views’. Now hes written a blog post on this paper about Junk RNA:

Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals.

Larry covers all the bases nicely. Now I know, as a fact, Casey does not understand this paper. I know he didnt even read the paper. Larry cites a relevant portion at his blag, but the paper, quite clearly, states that there is a LOT of RNA in your cells that is just being transcribed by accident. Its just noise. Yet Casey made a conscious decision to disrespect these authors and the scientific community by misrepresenting their work to the general public: “DIRP! JUNK RNA CAN HAS FUNKSHUN! I PREDICTED DIS IN 1998!!! I ALSO INVENTEDED POGS!”

Of course, Casey is an IDiot. You cant really expect him to tie his own shoes, much less be literate. However, his IDiocy is once again your gain! Cause this paper is super cool, and I want to explain the details of what this group did for everyone :)

Guttman et al knew they had a lot of crap RNA to deal with, but they figured some of the transcripts might have a function we dont know about. So, they stacked the deck in their favor by using epigenetics! Yay!

No, not the happy hippy ‘birds singing is epigenetics, man’ epigenetics, I mean histone modifications that alter gene expression. Modify a histone one way, and the DNA wrapped around it snuggles up even tighter, preventing any transcription machinery from getting in. Modify that histone a different way, and it loosens up its grip on its DNA, letting the genes be transcribed. Guttmans group knew that if Histone 3 has a trimethyl on its lysine 4, then the genes around that histone are probably going to be transcribed.

So they used chromatin immunoprecipitation to purify all the histones with that specific trimethyl marker to find DNA thats being transcribed ‘on purpose’. They then whacked the DNA out of those histones hands and sequenced it. What DNA is associated with this kind of ‘active’ transcription? Well, once they eliminated all of the genes we know code for proteins and regulatory RNA, they were left with ~1,675 putative ‘JUNK DNA WIT FUNCSHUN OMG!’

Next, they took this DNA and created a microarray– When they dumped cell lyases on this array, if that cell made RNA that matches the chunks of DNA on the array, the DNA lights up and a computer can quantify it. 70% of their putative “JUNK DNA WIT FUNKSHUN! BLAAAAAK!” makes putative “JUNK RNA WIT FUNKSHUN! SHHNIG!”.

So they focused on figuring out what those RNAs were– they totally werent protein coding genes we just hadnt discovered yet, but they really looked like lincRNAs (large intervention non-coding RNA).

Most of the JUNK RNA weve found in other studies isnt conserved evolutionarily at all. Like, at all, implying there is no evolutionary pressure to keep this junk around cause its not functional. So to see if the remaining RNAs in their study might be functional, they compared their sequences (from mice) to 21 other mammals. While their RNAs werent as conserved as some proteins, RNA is slightly more forgiving than aminoacids, so they were happy with the level of conservation– these RNAs might have a function!

Using extraordinarily clever means, they figured out that some of their RNAs might play a role in ‘cell proliferation’ or ‘immune surveillance’ or ‘muscle development’, etc. When they screwed around with cells, they could alter the transcription of their maybe-functional-RNA, implying they might really be functional! WIN!!

In the end, they found 150 lincRNAs that are probably functional, and provided experimental support-of-functionality for 85.

This paper is really friggen clever, but to quote Larry:

Casey Luskin ain’t gonna disprove junk DNA using this paper.

Comments

  1. #1 carlsonjok
    March 17, 2009

    Keep it up and Casey is going to have to add another slide to the “I iz opressed” section of his travelling roadshow.

  2. #2 Brian H
    March 17, 2009

    Well he needs some source of fluff in there, it’s not like he has anything original or content heavy…

    Also, pogs were awesome.

  3. #3 The Curmudgeon
    March 17, 2009

    Abbie, in this Discoveroid blog article from May of last year, Casey made a “scientific” prediction about junk DNA: “[I]ntelligent agents design objects for a purpose, and therefore intelligent design predicts that biological structures will have function.”

  4. #4 Paul Lundgren
    March 17, 2009

    I wonder how often Luskin is going to keep making a fool of himself by stepping on the same rake and having the handle hit him in the mouth over and over again? It’s endlessly entertaining, I admit, but it’s a shame such a towering intellect doesn’t know enough not to look for it by now…

  5. #5 ERV
    March 17, 2009

    “[I]ntelligent agents design objects for a purpose, and therefore intelligent design predicts that biological structures will have function.”

    Also, you will die a horrible, horrible death! wwooooOOOOOOoooooOOOOOoooo!!!

    Wait… isnt fortune telling forbidden by the Bible?

  6. #6 Joshua Zelinsky
    March 17, 2009

    Ok, so the bottom line is that a) Casey never predicted any function for this RNA and b) that only a small fraction of the junk RNA is turning out to have functions? Casey really needs to find some something productive to do with his time.

  7. #7 MikeMa
    March 17, 2009

    Casey has been foisting his IDiocy on the world in many forms for many years. This is just one more effort to climb the ladder of scientific respectability while promoting his brand of snake oil. He’s still wallowing in the failure of the Wedge and the drubbing he got in Dover. He cannot even recognize his defeat let alone accept it.

  8. #8 Paul Jones
    March 17, 2009

    I’ve been linked to this website by a few creationists, http://www.reasons.org/junk-dna-evidence-biological-evolution
    http://www.reasons.org/yet-another-use-“junk”-dna , could any relevantly qualified person here tell me if there is anything to this stuff?

  9. #9 Aaron
    March 17, 2009

    Isn’t there some way we can sue these bozos for disseminating false information? Some statute?

    Can you call him a liar outright? Technically it’s not libel if it’s true, right?

  10. #10 Who Cares
    March 17, 2009

    Paul:
    There is not. For some reason these [censored] think that scientists denied that unknown DNA (AKA junk DNA) could have a function.
    They mangle things. Like claiming that the similarity of this (unknown use) DNA between species was one of the pointers why it was classed as useless. The opposite is true, only if it has a use will it be preserved across species.

    Then past the babble about the amazing discovery of the a specific LTR having a function is the claim that it has to have happened multiple times. Wrong, it only has to have happened once. In the common ancestor of the species mentioned.

  11. #11 Joshua Zelinsky
    March 17, 2009

    Aaron, those links are more or less wrong from start to finish. The most serious problem is that it was biologists (not creationists) who a) discovered junk DNA and b) conjectured that some of it had a purpose. They were able to identify strings as likely having purpose when those segments were conserved more than one would expect than if the selection pressure on the strings was neutral. This is a prediction made using basic evolutionary theory. And it turned out to be strongly confirmed when biologists then through careful investigation found specific uses of various types of junk DNA.

  12. #12 Brian
    March 18, 2009

    70% of their putative “JUNK DNA WIT FUNKSHUN! BLAAAAAK!” makes putative “JUNK RNA WIT FUNKSHUN! SHHNIG!”.

    Uh, what exactly is the distinction between BLAAAAAK and SHHNIG? I do appreciate that you’re trying to explain things in lay terminology, really I do, but the more obscure onomatopoeic expressions just left me confused. Is the former bad and the latter good? Again, sorry.

  13. #13 Confused
    March 18, 2009

    One thing about the Junk DNA story that will never cease to amaze me is how creationists cite papers which rely on evolution being true to argue that evolution didn’t happen.

  14. #14 J-Dog
    March 18, 2009

    Abbie – I have to take issue with your word choice. Your second sentence refers to Evolution News & Views as Casey’s blog… not true. A blog encourages open responses and allows for interaction with the reader – Casey & the DI does neither. EN & V and anything Casey puts out should ONLY be referenced as “Press Release”, “Propaganda” or “Typical DI / Luskin Goebbles Goody”.

    My $.02 and worth every penny – maybe.

    HTH :)

  15. #15 Prometheus
    March 18, 2009

    “I ALSO INVENTEDED POGS!”

    I have been giggling for ten minutes.

    That is going in tiny tiny type on the bottom of my curriculum vitae.

  16. #16 Murray
    March 18, 2009

    I just started reading this blog. You are one funny writer, in a geeky kind of way. I love it.

  17. #17 James F
    March 18, 2009

    OT: Michael Behe must be so happy. Steve #1076 is Stefan Maas from…Lehigh University.

    BWAAAAAAAAAA HA HA HA HA HA HA!!!!!

  18. #18 Dustin
    March 19, 2009

    OT: Michael Behe must be so happy. Steve #1076 is Stefan Maas from…Lehigh University.

    BWAAAAAAAAAA HA HA HA HA HA HA!!!!!

    I think that, after having his own department put a disclaimer about him up on their website, having one of his colleagues on that list is a tiny little drop in that ocean of humiliation he’s drawn for himself.

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