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Monday, August 20, 2012

Pseudogenes Are Pseudogenes and They Are Almost Always Junk

The IDiots have found a paper by Wen et al. (2012) with a very provocative title, "Pseudogenes are not pseudo any more."

Naturally, lawyer Casey Luskin is all over this: Paper Rebuffs Assumption that Pseudogenes Are Genetic "Junk," Claims Function Is "Widespread". And just as naturally, the folks at Uncommon Descent (probably lawyer Barry Arrington) jump on the bandwagon: Junk DNA: Yes, paper admits, it WAS thought to be junk.

The authors of the paper, including Templeton Prize winner Francisco J Ayala, claim that pseduogenes exhibit two puzzling properties: (a) similar processed pseudogenes occur in mouse and humans suggesting that they are conserved, and (b) many pseudogenes are transcribed.

Processed pseudogenes arise when mRNA transcripts are reverse transcribed and inserted back into the genome. They usually come from genes that are highly expressed in germ line cells. Such genes tend to be highly conserved in related species. Mammals are closely related on the scale that were talking about. It's not surprising that a few new pseudogenes in such lineages are very similar in sequence. They're still pseudogenes. The vast majority of known pseudogenes are evolving at a rate that approximates the rate of mutation indicating that they are not constrained by negative selection.

Many pseudogenes are derived from gene duplications followed by mutations in one of the copies that make them incapable of producing a functional product. There's no reason to suspect that the first of these debilitating mutations will prevent transcription; therefore, one expects that many pseudogenes will be transcribed.

Some pseudogenes have been co-opted to provide a different function. There aren't very many examples but that doesn't stop the IDiots from making the fantastic leap from 0.0001% to 100%. (Pseudogenes represent about 1% of the genome [What's in Your Genome? ] so even if we assume that every single pseudogene is not a pseudogene, it hardly makes a dint in the amount of junk DNA.)

I discussed all this when I reviewed Jonathan Well's book The Myth of Junk DNA. The relevant chapter is Chapter 5 [Junk & Jonathan: Part 8—Chapter 5]. That review was posted in May 2011. It seems clear that the lawyers on the IDiot websites haven't read it.

Here's what one of them says on Uncommon Descent.
Darwin’s followers considered junk DNA powerful evidence for their theory, which is really a philosophy (often a cult), and that they often expressed that view, often triumphantly. Others insist it is true anyway.

The problem they hope to suppress is that if lots of junk in our DNA is such powerful evidence for their theory, then little junk throws it into doubt. That is, if it is such a good theory, why was it wrong on a point that was announced so triumphantly?

So it is a good thing that the science-minded public is reminded of the historical fact that Darwinism was supported by junk DNA. And it will be fun when the squirming editorials come out in science mags, warning people not to read too much into this, Darwin is still right.
I'm not even going to bother pointing out how stupid that is. If you're reading Sandwalk, chances are high that you could detect the lies1 with your eyes closed.

1. Yes, "lies." At this point there's no other explanation.

Wen, Y-Z., Zheng, L-L., Qu, L-H., Ayala, F.J., and Lun, Z-R. (2012) Pseudogenes are not pseudo any more. RNA Biology 9: 27 - 32. [doi: 10.4161/rna.9.1.18277]


  1. What is the evidence presented by Wen et al. for widespread function in pseudogenes? Is it the usual "they're transcribed" shit we've seen before?

    The article's behind a paywall, I can only read the first page. That page goes on about transcription.

    If that's their best argument, then it's begging the question. How do you know DNA is always functional? Because (they assume) transcription is always functional! Duh.

    If you know the mind of God like Casey Luskin, who knows that God only makes functional things, then it follows that anything transcribed must be functional. But then, if like Luskin, you know that God only makes functional things, then you also know all NON-transcribed DNA must be functional too.

    But if you're free to just assume transcription is always functional, why not just skip it and assume DNA is always functional?

    So how does transcription improve such a circular argument? They know DNA is functional because they assume transcription is always functional, because they know the mind of God.

    Casey Luskin and Jonathan Wells don't need no stinkin' transcription-- they're hierophants who know what God is thinking. But using jargon does make them sound scientific, though.

  2. Ah - a squirming editorial!

    This and many other UD op-pieces and comments, are evidence of a more disturbing trend: the campaign of misinformation is working. Repeatedly, people pop up and insist that "Darwinists' feet be 'held to the fire" over junk - because they trumpeted it as evidence for evolution (wrong); because they are blind to the 'masses' of function that is being discovered (hardly - they are the ones discovering it); because they have never considered any fraction functional until ID started gathering the facts 'They' don't want made public (tripe).

    It's perhaps unfortunate that the authors of the paper appear to equate pseudogenes directly with junk DNA (pseudogenes [...] sometimes called “garbage genes” or “junk DNA").

    If pseudogenes never gained function we would never get new genes by gene duplication, of course, which would harm the 'Darwinist' cause more than the ID one. And of course, the fraction of junk that isn't pseudogene massively outweighs that which is.

  3. Geez. Even the ENCODE group - who is gaining a reputation for being a little, shall we say, "unconsevative" in applying function to things - recognizes what most psueodgenes are.

    You've been at this game longer than I, Larry. Is this apparent trend to over-stating you work based on little evidence actually getting worse, or have we just forgotten about the bad papers in the earlier days?

    -The Other Jim

  4. I am actually working on a functional pseudogene at the moment (it's under review, unfortunately, so I can't say the name.) Even so I think Larry is correct in saying "They Are Almost Always Junk " since the proportion of pseudogenes that actually do something is likely to be a tiny fraction of the total pseudogene population.

  5. Based on what is posted at Jerry Coyne's blog er website, it appears that "Dave Johnson" above is Dennis Markuze.

  6. Based on what is posted at Jerry Coyne's blog er website, it appears that "Dave Johnson" above is Dennis Markuze.

    Yep - he's out of supervision. Spotted at Panda's Thumb also.

  7. Who's Dennis Markuze and why should I care?

    I don't recall seeing either at PT.

    1. Dennis Markuze has threatened to murder or maim several atheist bloggers, including me. He has also threatened many nonbelievers who post comments on various blogs, including Sandwalk.

      He is bipolar and he has a drug problem.

      It's up to you to decide whether to care.

      Montreal Police: Take "Mabus" death threats seriously

    2. Oh. That Dennis Markuze.

      Is he a Muslim now or what? His comment (since deleted) was "5000 whining atheists vs. the Great Prophet."

    3. The 'Great Prophet' is Nostradamus.

    4. Perfectly sane, perfectly normal. Don't kill me.

      Only if materialism is true should you ASSUME that medieval psychedelics can't predict the future by staring into a fishbowl.

  8. Nagel says ID claims should be taken seriously
    Maybe Nagel wasn't paying attention when ID claims were taken seriously, examined, and dismantled. Maybe he slept through the entire Dover trial.