On BioScience and Life and Such

More crap from the junkies

In Uncategorized on May 22, 2010 at 12:09 am

post to news.thinkgene.com

My three favourite junkies (junk-DNA supporters) out there are Professors Dr. Moran, Dr. Gregory and post doc. fellow Dr. White. This week they received a strong argument for their junk-DNA cause, which was this paper on how there appears to have been a lot of noise in some of the larger RNA-studies over recent years. This was covered elegantly in this Sandwalk post by professor Moran.

Now if only the Adaptive Complexity blog written by White would have just jumped on the same solid bandwagon all would have been fine, but no. Instead he attacks a lead author behind some of the above mentioned RNA-papers. Again, this would have been fine had it not been for the argument he uses, an argument which has the quality of third grade primary school science:

Second, John Mattick is clueless, and he should not be quoted. So junk DNA holds the secret to human complexity? Then I supposed it also holds the secret to the incredible complexity of an onion, which has five times more non-coding DNA than humans.

He goes on to give us professor Ryans definition of “The onion test”

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA1. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

This “test” I hope everyone sees is utter crap. If you don’t I’ll explain: the assumption is “more DNA = more biological complexity/functions” – which of course is wrong since organisms who apparently have very few functions can have more coding genetic material than more complex organisms (try google the number og genes corals have vs. humans). The assumption is wrong also because the onion may need to meet it’s changing environment with an entirely different genetic arsenal than primates, – the comparison is just way off unless you specify more.

I think the first comment to this Adaptive complexity post is brilliant:

Just out of curiosity tho, what’s the standard explanation for junk DNA? Is it just structural or something? – kerr jac

That question emphasizes what has been my main point all along: Dismissing something as junk is contrary to my idea of science being driven out of curiosity and the need to explore. If you label this DNA as “junk”, how do you answer this question with any confidence ?

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  1. “Junk DNA” is that part of the genome that has no function. It could be deleted without any effect on the individual or the species.

    Back in the 1960s, people were curious about the reason for all this excess DNA in eukaryotic genomes. They developed and tested a number of hypotheses to explain it. The one that has stood the test of time is that the DNA is mostly junk. Please explain why this is contrary to your idea that science is driven by curiosity?

    Do you think that “believing” in pseudogenes is anti-scientific? Why? Do you think that the genetic load argument is a way of being uncurious?

    You probably think that we don’t know anything about genome organization and function so we just throw up our hands and say that it’s all junk. You probably think that the term “junk DNA” is merely a way of expressing our ignorance. That’s not correct. We know a great deal about genomes and their organization and we know a great deal about the kind of functions that DNA carries out. That vast amount of knowledge is what leads us to the conclusion that a high percentage of our genome (90%?) is junk. It’s not from ignorance that we make that claim, it’s from knowledge.

  2. I know ! you keep saying that. And you may be right of course. But, if I may, I’d like to counter with the exact same arguments only opposite: You probably think that opposing the term “junk DNA” is merely based on adaptionist beliefs that everything needs to have a function. That’s not correct. We know a great deal about genomes and their organization and we know a great deal about the kind of functions that DNA carries out, but there’s still a lot to learn. That certainty that there’s still things to learn is what leads us to the current conclusion that a significant percentage of our genome is not junk. It’s not from belief or ignorance that we make that claim, it’s from the knowledge that we do not know everything, and that dismissal of anything as junk is scientifically counterproductive.

  3. We know for an absolute fact that more than 50% of our genome consists of defective transposons and pseudogenes. We know for an absolute fact that at least 10% (probably 20%) of our genome consists of intron sequences that are not required for function.

    We know from genetic load arguments that only a few percent of our genome is susceptible to mutations that affect viability. The rest may not be junk because it may have a purpose that doesn’t depend on sequence but that’s not a very likely possibility.

    We know for a fact that most of genome is not conserved and that the human population contains large numbers of insertions and deletions that have all the characteristics of junk DNA.

    We know that there are some mammals with less than half as much DNA as we have. It takes a lot of special pleading to imagine that we need twice as much DNA as bats, for example.

    You say that we still have a lot to learn. That’s a truism that nobody will disagree with. However, to use that as an excuse to deny the existence of junk DNA doesn’t make logical sense. How much more do you think we need to learn about defective transposons in order to declare that they are non-functional? How much more do we need to learn about pseudogenes in order to conclude that they are, indeed, pseudognes (= junk).

    If your logic applies then we can’t even say that a transposon is defective or a pseduogene is a pseudogene because we don’t know everything. Maybe they have some mystical function that nobody suspects. Does that really make sense to you?

  4. I am not denying the existence of “junk” DNA, I just do not like the term “junk” because what you coin as “defective” may have regulatory or structural functions (see my previous posts on this, specifically the references on the “junk-DNA coffin” post). Call it DNA “of unknown function” or something instead. I also do not believe in your estimation of how much of our DNA that is non-functional, but aknowledge that it is a guestimate, albeit way too high.

  5. I just do not like the term “junk” because what you coin as “defective” may have regulatory or structural functions …

    This is 2010. The onus is on you to show that a significant amount of our genome has regulatory or structural functions. Just “imagining” that possibility isn’t good enough because if you are correct it flies in the face of 40 years of evidence and knowledge.

    At some point we have to accept the most reasonable hypothesis and right now the most reasonable explanation that’s consistent with what we know about evolution, genetics, and biochemistry is that most of our DNA is junk.

    Why are you avoiding that reasonable explanation? What do you know about evolution, genetics, and biochemistry that leads you to believe that most of our genome contains functional sequence?

    How much “regulatory sequence” do you think is necessary to control expression of a single gene? Would it be 100 bp., 1000 bp., 10,000 bp. …? Even if 10,000 bp were required to regulate each gene that still represents less than 10% of the genome. You’re not being reasonable if you claim that mysterious, unknown, regulatory sequences could account for a significant fraction of what we now think of as junk DNA.

  6. I am being reasonable. I am not the one criticizing every single paper that comes out saying that they have found some function for a piece of DNA previously believed to have no function. You are. What is more unreasonable, ignoring the increasing number of these papers or take them as a sign that something is left to be found in these parts of DNA ?

  7. What is more unreasonable, ignoring the increasing number of these papers or take them as a sign that something is left to be found in these parts of DNA ?

    I take them as a sign that there are parts of our genome that have a function that we previously didn’t know about. That’s pretty cool.

    The unreasonable part is to claim that junk DNA is dead just because we’ve discovered a new gene or regulatory sequence in 0.1% of the genome. Your position seems to be that these papers are showing much more than they are. How much of our genome has been shown to have a previously unknown function over the past decade? Do you believe that most of our genome isn’t junk on the basis of those papers? That’s unreasonable.

  8. Does the 10% of our genome that is old retroviruses do anything?

  9. sciphu,

    I think your mistake, as evidenced by the final paragraph of your original post, is in thinking that the “junk” label is applied simply through ignorance. As Dr. Moran has pointed out, that’s not so. It’s supported by lots of evidence.

    It’s true that we’re finding more and more functional bits in non-protein-coding regions. But those only account for a tiny fraction of the putative junk. Those findings show that there’s probably more non-junk hidden in the junk, but they don’t suggest that there’s little or no junk at all.

  10. qetzal: No ! I do not think the “junk” label comes from ignorance. And, no ! I do not think there’s little or no “junk” at all. But, as long as we do not know what is junk and what isn’t within this DNA of unknown function, I feel that the term “junk” is misplaced. The term may also discourage further scientific inquiry.
    Devin: I believe more than 10% of our genome comes from retroviruses. Nevertheless, like all DNA with unknown function (parts of) it could potentially serve a function – see http://www.nature.com/news/2010/100221/full/news.2010.82.html and http://sciencelife.uchospitals.edu/2010/02/22/a-fishfinder-for-the-junk-dna-seas/

  11. sciphu,

    On the one hand, you state: “I do not think there’s little or no “junk” at all.” I interpret this to mean that you agree there is a significant amount of “junk DNA” in, e.g., mammalian genomes. Yes?

    But then you say you feel the term “junk” is misplaced. Would calling it “non-functional DNA” address your concern? Or is your concern that, even if we’re sure that big parts of our genome are “junk,” we can’t be sure whether any particular bit is really junk?

    In any case, I think we’re all in agreement that small bits of what we previously thought was junk is actually functional. My objection (and Dr. Moran’s, I think) is when people cite that data as an indication that most or all “junk” DNA is actually functional.

  12. Ah, so if we suddenly started calling the space between star systems “vacuum”, then no scientist would search for dark matter? That picture of our colleagues that you are drawing with your logic is unrecognizable to me…

  13. Mintman says “Ah, so if we suddenly started calling the space between star systems “vacuum”, then no scientist would search for dark matter?” – well yeah, something like that ! But, junk is not the same as vacuum is it, – vacuum is “nothing” while junk is “less than nothing” if you see what I mean. Who wants to search for something in a junkyard or a trashbin. But, thankfully !, you are right, some scientists are still looking for possible functional bits within this DNA.
    Qetzal says: “Or is your concern that, even if we’re sure that big parts of our genome are “junk,” we can’t be sure whether any particular bit is really junk?” – yes that is my concern, and in addition, I am unsure whether “big” is appropriate.

  14. “Who wants to search for something in a junkyard or a trashbin.”

    Um, scientists? Like the scientists who are currently doing research on junk DNA, despite (or possibly in spite) of it being called junk.

  15. Since we have reasons to divide DNA into discrete classes (functional/non-functional; coding/regulatory, etc), there is no sensible naming system that can anticipate a misappellation. It’s reminiscent of some of the problems of taxonomy. “Provisionally non-functional” would be cumbersome … and a synonym of the commonly-used ‘junk’. How big that set ‘really’ is is another matter. My own bet is >90%, but I’ve been wrong before.

  16. The explanation for most of the genome, BTW? The debris of infection. Many selfish genetic elements are STDs spreading through meiosis; retroviral insertions the equivalent of smallpox scars.

    Sex is a marvellous way to spread for parasites internal and external (see Burt & Trivers’ excellent Genes in Conflict). Baterial transposons exist, of course, by jumping ahead of the replication fork, but dead weight is more highly selected in their ecological world. It costs us a tiny fraction of our lifetime needs to replicate in our germ line. There is an eventual interplay with selection, but the ceiling is higher in the eukaryote.

  17. sciphu, On the one hand, you state: “I do not think there’s little or no “junk” at all.” I interpret this to mean that you agree there is a significant amount of “junk DNA” in, e.g., mammalian genomes. Yes? But then you say you feel the term “junk” is misplaced. Would calling it “non-functional DNA” address your concern? Or is your concern that, even if we’re sure that big parts of our genome are “junk,” we can’t be sure whether any particular bit is really junk? In any case, I think we’re all in agreement that small bits of what we previously thought was junk is actually functional. My objection (and Dr. Moran’s, I think) is when people cite that data as an indication that most or all “junk” DNA is actually functional.

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