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Thursday, November 29, 2007

More Misconceptions About Junk DNA

iayork of Mystery Rays from Outer Space is upset about an article on retroviruses that appeared in The New Yorker [ “Darwin’s Surprise” in the New Yorker]. Here's what iayork says,
The whole “junk DNA” has been thrashed out a dozen times (see Genomicron for a good start). The bottom line? If you search Pubmed for the phrase “junk DNA” you will find a total of 80 articles (compare to, say, 985 articles for “endogenous retrovirus”); and a large fraction of those 80 articles only use the phrase to explain what a poor term it is. Scientists don’t use the term “junk DNA’. Lazy journalists use it so they can sneer at scientists (who don’t use it) for using it.
Wrong! Lots of scientists use the term "junk DNA." Properly, understood, it's a very useful term and has been for several decades [Noncoding DNA and Junk DNA].

Yes, it's true that journalists often don't understand junk DNA and they are easily tricked into thinking that junk DNA is a discredited concept. The journalists are wrong, not the scientists who use the term.

It's also true that there are many scientists who feel uneasy about junk DNA because it doesn't fit with their adaptationist leanings. Just because there's controversy doesn't mean that the term isn't still used by it's proponents (I am one).

I'm sorry, iayork, but statements like that don't help in educating people about science. Junk DNA is that fraction of a genome that has no known function and based on everything we know about biology is unlikely to have some unknown function. Junk DNA happens to represent more than 90% of our genome and that's significant by my standards.


  1. I think you use the term "junk DNA" to be deliberately provocative because you have an anti-adaptionist axe to grind, rather than out of any scientifically valid reason. Calling it "junk" is a form of scientific arrogance along the lines of, "If I don't understand what it's good for, then it can't be good for anything". If nothing else, this DNA takes up space in the genome. Unless you've done the actual experiment of deleting the "junk DNA" and thereafter assessing fitness relative to the wild-type situation, you don't know what the utility (if any) of the "junk" is (or is not) so it's better to simply not comment on this DNA's relative value at all.

  2. As a layman (with respect to biology) I'm not sure I really understand exactly what you guys (you, PZ, etc) mean by "adaptationism" and its sins, or particularly why it would imply that most or all DNA should have a function. The (short) description of adaptationism on Wikipedia helps but doesn't delve into the question of genetics.

    Perhaps an example would help. My layman's understanding is that there's a gene that codes for a protein for producing vitamin C in humans that's broken by a random mutation that became fixed in the population because there was little selective pressure to eliminate that mutation in the fruit-rich region of the world we apparently evolved in (or at least that would be the non-adaptationist explanation, I assume). At least, that's the story I've heard. I would imagine this gene would continue to accumulate random mutations because there's no selection acting on it now that's its lost its function, and it would eventually turn into unrecognizable gibberish (i.e. junk). Is that wrong?

    What would an adaptationist expect? That it would be "repaired" when the right mutation happened in the right place? Gain a new function through additional mutations? Or eliminated altogether? Would an adaptationist assume that gene had some different function precisely because it *did* survive?

  3. Zombie, I too am curious, and hope our host will shed some light on the matter for interested laypersons.

  4. zombie,

    You're right, Pseudogenes are examples of junk DNA.

    The problem arises when we face up to the fact that a huge percentage of our genome seems to be composed of pseudogenes and other junk. Those who promote the power of adaptation to explain (almost) everything (i.e., adaptationists) tend to be uncomfortable with this amount of junk in our genomes.

    Most of them feel that it has to serve some (unknown) purpose otherwise it would have been eliminated by natural selection.

    Thus, adaptationists resist the term "junk DNA" because they think its probably not true.

    However, in addition to the evidence that's accumulated over three decades, we now have some actual experiments where large amounts of junk DNA have been deleted from the mouse genome and it seems to have no effect.

    The adapatationists are having a hard time defending their case for function. Junk DNA is real.

  5. Zombie raised the point already, but I will elaborate. The debates over how much of it is really "junk" aside, junk DNA is fully congruent with an adaptationist perspective. It's just not adaptive for the organism or the genomic collective; rather, it's adaptive for the DNA sequences to be passively replicated even if it confers no benefit for higher level entity.

    Trivers, Matt Ridley, Dawkins are all in the adaptationist camp and have no problem with junk DNA as it fits in perfectly well with the concept of selfish genetic elements.

    Whether derived from endogenous viruses or defectors of original host genes, junk and deleterious selfish DNA fits in perfectly well with adaptationism at a gene-level analysis.

    Modern (post-Hamilton) adaptationism is not synonymous with organism-level functionalism (or in the case of DS Wilson, group level functionalism). It's about the fitness of entities.


  6. it's adaptive for the DNA sequences to be passively replicated even if it confers no benefit for higher level entity.

    The problem is that the majority of the junk is incapable of being replicated. They are either pseudogenes, dead transposons, or dead viruses. Some are remnants of selfish elements, but there's a boatload of junk that's just not deleterious enough to be purged by natural selection

  7. What I mean by "passive" is that it is replicated through host generations rather than independently or through new hosts.

  8. Thanks, Larry. It sounds like these mouse experiments are basically what the first anonymous was asking for experimentally.

    Tupaia, I don't really understand what you mean by it being adaptive for certain junk DNA to be copied along with the rest of the genome. A mutation in a junk sequence wouldn't increase or decrease the likelihood of it being copied or transferred anywhere, or increase or decrease the organism's chances of survival. It seems entirely neutral. Doesn't that sort of define adaptationism into nothing?

    If there was some mutation that resulted in certain sequences being copied and duplicated within the genome so that it was very likely to be conserved even if a given copy is damaged, and I have vague memories of there being such things, then I would understand how a specific not-functional-to-the-organism gene could be regarded as adapted or fit for survival, but that wouldn't seem to apply to most "junk" genes.

    Finally, if "junk" DNA isn't incompatible with adaptationism, then why the debate over the term "junk" in the first place? Are there different camps of adaptationists?

    Apologies for my foggy comprehension...

  9. Richard Dawkins, 1998

    "... most of the capacity of the genome of any animal is not used to store useful information. There are many nonfunctional pseudogenes ... and lots of repetitive nonsense, useful for forensic detectives but not translated into protein in the living cells. ... Why the Creator should have played fast and loose with the genome sizes of newts in such a capricious way is a problem that creationists might like to ponder. From an evolutionary point of view the explanation is simple ..."

    Dawkins, The Selfish Gene, 1976:

    "Biologists are wracking their brains trying to think what useful tasks this apparently surplus DNA in the genome is doing. But from the point of view of the selfish genes there is no paradox. The true ‘purpose’ of the DNA is to survive, no more no less. The simplest way to explain it is to suppose that it is a parasite, or at best a harmless but useless passenger hitching a ride in the survival machines created by other DNA."


  10. The mouse experiments sound interesting. Could you provide a reference for the paper(s)?

  11. Re: junk (truly junk) DNA:

  12. Do a search on:

    Peter Borger variation inducing genetic elements