Monday, October 24, 2011

The Myth of Junk DNA by Jonathan Wells

This is the final installment of my review of The Myth of Junk DNA by Jonathan Wells (Discovery Institute Press, 2011). The other posts are listed at the bottom of this summary and in the theme posting "Genomes & Junk DNA."

Most of the IDiots at the Discovery Institute feel threatened by the existence of large amounts of junk DNA in some eukaryotic genomes, including our own. That's why they are determined to refute this idea by showing that most putative junk DNA actually has a function. Jonathan Wells feels confident enough about his reading of the scientific literature to announce that junk DNA is a "myth" and he's written a book to promote this idea.

Wells never defines "junk DNA" correctly. The correct definition of "junk" is DNA that has no known function. Wells pretends that the original definition of junk DNA was "noncoding" DNA. Thus, all those bits of noncoding DNA that have a function are evidence that refutes the notion of junk DNA.

The truth is that no knowledgeable scientist ever suggested that regulatory regions, origins of replication, centromeres, telomeres, genes that produce functional RNA molecules, and chromatin organizing regions were ever classified as junk DNA. They all knew that there was lots of noncoding DNA that had a well-defined function. Right from the beginning of his book, Wells is attacking a strawman and misleading his readers.

That's not the only example of deception. Wells also claims that the existence of large amounts of junk DNA was a prediction of Darwinism and is promoted as proof of Darwinian evolution. This is a lie. Junk DNA actually represents a serious problem for Darwinism (evolution by natural selection) and it certainly was never "predicted" by adaptationists. Having set up this second strawman he proceeds to knock it down (in his mind) thus challenging the very idea of evolution.

I believe that 90% of the human genome consists of junk DNA (DNA with no known function) [What's in Your Genome]. There is excellent scientific evidence to support this claim but you won't find very much of that evidence in The Myth of Junk DNA.1 Instead, you'll find after page of page of evidence that tiny bits of DNA here and there in various species have a function that we may not have known about twenty years ago. If you add up all the little bits, it doesn't amount to more than a few percent of the genome.

Theme

Genomes
& Junk DNA
Almost 50% of our genome consists of defective transposons and viruses (junk) but Wells never tells his readers why that huge amount of DNA has a function.

There are many scientists who don't believe that most of our genome is junk. I think it's fair to say that the consensus is swinging against them. More and more scientists are starting to accept the idea that junk DNA is supported by evidence and, more importantly, consistent with modern evolutionary theory. Wells gives the opposite impression in his book and he goes out of his way to discredit the reputations of scientists who disagree with him.

The really sad thing about this book is that it could have discussed a real scientific controversy and presented both sides of the scientific case, for and against junk DNA. It's the same problem that we saw in Wells' first book, Icons of Evolution: Science or Myth?. Instead of discussing genuine scientific controversies, Wells chooses to misrepresent science in order to discredit evolution and impugn the reputations of "Darwinists."


1. The genetic load argument is never mentioned. The significance of the C-value "paradox" is never explained. Evidence for the defective nature of pseudogenes isn't presented. Variation in deletions and insertions within a species isn't discussed. No interpretation of gene replacement and knockout experiments in mice is given. The nature of modern evolutionary theory is ignored.

38 comments:

  1. When there is work going on as subtle and exciting as, e.g., Joe Thornton's re the evolutionary history of our biochemistry, and the roles played by adaptation, contingency, drift, etc., working together over time to produce what we see in our cells today, Wells' brand of ham-fisted deliberate misunderstanding and ignorance is just plain boring by comparison.

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  2. "The correct definition of "junk" is DNA that has no known function."

    That's kind of a negative definition for what appears to be a positive statement: "junk". I would add something like "and the presence of the DNA is plausibly or probably attributable to non-functional explanations."

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  3. 1. The genetic load argument is never mentioned.

    Color me shocked.

    Who says ID doesn't allow us to make any predictions?

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  4. The original definition of "junk DNA" was gene duplicates that had lost coding function (later named "pseudogenes"). Junk, as in something previously functional but now broken.

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  5. Maybe someone here can explain this to me:

    Why are IDists so keen on pointing out bits of junk DNA that have a function? If e.g. a (modified) repetitive element is found to have some function in one organism but not in others and not in other places in the genome of the same organism, isn't that a clear-cut example of a gain of function, something that mustn't exist according to ID?

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  6. isn't that a clear-cut example of a gain of function, something that mustn't exist according to ID?

    Heck, you're way into the sophisticated stuff here. Wake me up when Wells, Behe, et al., get together and decide whether or not they agree on something fundamental like common descent.

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  7. Ryan Gregory says,

    The original definition of "junk DNA" was gene duplicates that had lost coding function (later named "pseudogenes"). Junk, as in something previously functional but now broken.

    There may have been a few people who used such a restrictive definition but by the time the term "junk DNA" was in widespread use the definition was more like "nonfunctional DNA."

    That's the definition I first encountered at scientific meetings and courses in 1974.

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  8. I dunno. There's a fair amount of DNA that has no known function but still is clearly not junk, i.e. we have good reason to suppose it has a function but we have no current idea what it is. Those hyper-conserved short RNAs, for example. How about "DNA that is not conserved and therefore has no function associated with sequence"?

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  9. John Harshman says,

    There's a fair amount of DNA that has no known function but still is clearly not junk, i.e. we have good reason to suppose it has a function but we have no current idea what it is.

    When you say "fair amount" what kind of numbers are we talking about? Is it 2%, 20%, 80%? I've tried to take that DNA into account in my calculations. I figure it can't be more than a few percent of the genome. Therefore, it has no significant effect on the debate.

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  10. Sorry, I was too brief. I was taken issue with your definition of "junk", not with your estimate of its prevalence. Junk isn't DNA with no known function; it's DNA we have good reason to think has no function, which is quite a different thing.

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  11. Wait, why is junk DNA a problem for darwinism? And how is that problem addressed?

    Tim Martin

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  12. Larry Said:
    Wells also claims that the existence of large amounts of junk DNA was a prediction of Darwinism and is promoted as proof of Darwinian evolution.

    Umm Wells referenced the scientists who said that Larry- that means those evos are the liars, not Wells.

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  13. Joe G says,

    Larry Said:
    Wells also claims that the existence of large amounts of junk DNA was a prediction of Darwinism and is promoted as proof of Darwinian evolution.

    Umm Wells referenced the scientists who said that Larry- that means those evos are the liars, not Wells.


    Let me make it clear what Wells said by paraphrasing ....

    Darwin's Theory of Natural Selection predicts that the genomes of complex organisms will be chock full of non-functional junk DNA. Furthermore, the existence of large amounts of junk DNA is proof of evolution by natural selection.

    That's an outrageously ridiculous claim that could only be accepted by IDiots.

    Proponents of natural selection (Darwinists) expected exactly the opposite and that's why they rejected—or were highly skeptical of—junk DNA. Present-day Darwinists are still skeptical.

    How could Wells have possibly screwed up things so badly? His claim is the exact opposite of the truth.

    Let's give him the benefit of the doubt and attribute his error to ignorance. Maybe he's confused about what some evolutionary biologists have said.

    There are some, like Richard Dawkins, who point out that "selfish DNA" (e.g. transposons) are consistent with evolution by natural selection. He is correct. but transposons aren't junk. They encode perfectly functional reverse transcriptases and enzymes for excision and integration.

    There are many evolutionary biologists who point to the existence of pseudogenes as a problem for both advocates of strong natural selection (Darwinists) and Intelligent Design Creationists.

    Pseudogenes are true examples of junk DNA. They make the point that the persistence of pseudogenes in some genomes can be explained by non-Darwinian mechanisms (e.g. they are invisible to purifying selection).

    Evolutionary biologists do NOT claim that the existence of huge amounts of junk DNA is evidence for evolution by natural selection. It's mostly evidence for non-Darwinian evolution.

    Evolutionary biologists never "predicted" that natural selection, or any other mechanisn of evolution, would lead to genomes with huge amounts of junk DNA. That's why bacterial genomes with practically no junk DNA were not a big shock.

    There are only two possible explanations for the mistake that Wells makes. Either he doesn't understand evolution and junk DNA, or he is lying.

    Which one do you choose, Joe G?

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  14. Re your comment:
    'The correct definition of "junk" is DNA that has no known function.'

    I would recommend that we drop the use of the word "junk" in favor of "unknown" as this is more accurate and conveys the correct sense to the reader.

    Reason:
    Doesn't the work "junk" carry the connotation that we are sure there is "no function at all?" What value is there in using a word that needs to be redefined?

    I read the following article from PubMed Central that would support my recommendation:
    "It is now known that a large fraction of the transcriptome is constituted of long and short ncRNAs (up to 93% of the genome is transcribed), with disparate functions, many still unknown. These include transcriptional regulation by sense–antisense, activation or inactivation of transcription through regulatory regions, and numerous other functions that have been reviewed elsewhere."

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853385/

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  15. anonymous asks,

    Doesn't the work "junk" carry the connotation that we are sure there is "no function at all?"

    Perhaps that's the connotation. If so, it's correct. We are very sure that most of the genome has no function because it's made up of obviously defective transposons.

    We know a lot more about genes and genomes than you think. We know what functional genes and transposons look like because we've been studying them for fifty years. Because of this knowledge, we know what broken and defective genes and transposons look like and that's why we are confident that they are junk.

    I read the following article from PubMed Central that would support my recommendation:
    "It is now known that a large fraction of the transcriptome is constituted of long and short ncRNAs (up to 93% of the genome is transcribed), with disparate functions, many still unknown. These include transcriptional regulation by sense–antisense, activation or inactivation of transcription through regulatory regions, and numerous other functions that have been reviewed elsewhere."

    http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2853385/


    This is a paper published by Piero Carninci in the journal DNA Research last year. When you read these papers you should look for certain clues to check whether the author is presenting a rigorous scientific argument.

    In this case we see four obvious indicators that this is not a serious paper.

    1. The author thinks that the number of genes in the human genome was a surprise.

    2. The author doesn't understand the Central Dogma of Molecular Biology.

    3. The author never mentions the actual percentage of the genome that he claims is functional.

    4. The author attacks a strawman definition of "gene" in order to make his argument look revolutionary.

    Science is characterized by openness and skepticism. That's why there are so many conflicts and disagreements in the scientific literature. It's a fundamenatlly important part of the process.

    This is confusing to most outsiders because they think that every scientific paper is an accurate representation of scientific facts. That's not true. The real answers in science come from consensus developed over many years of debate and discussion.

    You have to look at the big picture and not just select quotations from a few papers. This is especially true when dealing with an ongoing controversy like the amount of junk iin our genome.

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  16. First of all, your approach as a scientist is pretty agressive. Never help in a controversial debate to start by saying that people who don't share you're idea are IDiots even if you're right.

    That said, the main problem with junk DNA is that it is difficult to prove that something don't have any functions. So it is not because we didn't find any function yet that "junk DNA" is not functionally important. The best we can do is try to devonvolute our genome and reduce as possible what we refer as "let's called that junk DNA because we have no idea why it's there !" .

    What is sure is that 10-15 years ago, people were thinking that 99% of the genome was kind of junk and the now it's more like 90%. Similarity with people that say that we use only 10% of our brain because we have no idea what is going on.

    I work in research (bioinformatics and functional genomics) and I think that majority of "junk DNA" is functional (coding, non-coding, open, structure, close-structure, kinetic relevant, etc...).

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  17. @ anonymous

    Do we have to bring up the megabase deletion mouse again? The tiny mite genome? Fugu versus other vertebrates? Mitochondrial inserts into the nuclear genome?

    Your "thinking" about function is not supported by comparative genomics or direct knockout studies...

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  18. anonymous says,

    What is sure is that 10-15 years ago, people were thinking that 99% of the genome was kind of junk and the now it's more like 90%.

    Really? Can you name a reputable scientist who claimed in 1995 or 2000 that 99% of our genome was junk?

    Bet you can't.

    I work in research (bioinformatics and functional genomics) and I think that majority of "junk DNA" is functional (coding, non-coding, open, structure, close-structure, kinetic relevant, etc...).

    I work in biochemistry and evolution and I say you're wrong.

    Nyah! Nyah!

    About half of our genome consists of defective transposons. Those are formerly active (functional) transposons that have acquired mutations rendering them inactive. If your claim is accurate then you must believe that a substantial percentage of those sequences have a function. What is that function?

    Does it pass the Onion Test?

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  19. Do we have to bring up the megabase deletion mouse again?

    No. I can cut one of your finger and you will probably be able to do whatever you do... Does that mean that your finger is "junk"

    For the onion... I don't get it... (well I get the example but I don't find it relevant) Someone can have a one tool to perform a task and another one have five tools te perform a similar task... That doesn't mean that 4 of is tools are useless... You have to do thing with what you have...

    Otherwise, It's all about your definition of functional. functional doesn't mean perfection... when thing works, they work and if something is completely useless, selective pressure will take care of it... I mean we have 2 meters of DNA so it is not like we can expand our genome as we wish...

    For my though about the function, I keep it for myself for right now !

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    1. Your analogy is broken. Your finger does have a function. The megabase deletion did more than study lethality.

      And you did not comment on the comparative genomics issue I mentioned. Which leads to the onions...

      http://sandwalk.blogspot.com/2011/10/twofer.html#comment-form_8920249522236242480

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  20. By the way, you don't have to post that but I just wnat to mention that I appreciate the fact that you didn't focus on my "poor" English which is obviously not my first language... Too often people just reply about my writing more then my idea.

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  21. I don't think that my analogy is broken. My point is your finger have a function but if I cut it... You will still be viable, I don't think that your fitness will be affected whatsoever and so on... Same thing for the gene desert... The authors themselves claim that may be the deletion part can have a function non identified in the screen they performed... I agree that it is an evidence that point for no function DNA but it is far from proving that this DNA have no function. Your logic is broken.

    I respect the fact that you believe that there is "no function DNA" but you can't use this megabase, comparative and Onion test as a proof of that... The Onion test use a human logic not an evolutionary/dawarnism logic...

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    1. Stop the hand waving.

      The onion test is...

      http://www.genomicron.evolverzone.com/2007/04/onion-test/

      "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?"
      &
      "...if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?"

      Please enlighten us.

      Delete
  22. I don't know how I'm supposed to say that because I think I was pretty clear... Onion test is irrelevant.

    The Onion test is so bad that I don't know where to start but in two points :

    1. Onion doesn't NEED five time more DNA... Onion have five time more DNA.

    2. More is not necessarily better... It's not because you have more "junk" that it's better. So the WHY question is kind of useless... In a sense of even if you have a reason that doesn't mean that you can't do without.

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    1. Sorry, but I am completely failing to understand your point. First you start by saying "... I think that majority of "junk DNA" is functional (coding, non-coding, open, structure, close-structure, kinetic relevant, etc...).

      Then above, you agree with my point by saying "Onion doesn't NEED five time more DNA... Onion have five time more DNA."

      I am discussing why you think junk DNA has a function. The onion test, especially the onion versus onion part, is a great exercise, as it forces one to think of why in two closely related species, one has an extreme excess of DNA with no obvious physiological difference. My perspective is that since there is no observable function, and no reproductive advantage to (ie. no selection for or against) having less or more of the stuff, it in unnecessary. And since most of it is defective retro-transposons, psuedogenes, nucmts, repetitive elements, etc. a good hypothesis is that it is junk in a real sense - broken stuff that is just laying around.

      So please clarify your point.

      Delete
  23. I know it is confusing...

    It's the definition of NEED....

    Let give a example : James has a TV. He bought a new one and install the old one in is bedroom. So now he have 2 TVs. Someone can say he don't NEED 2 tv... he can move is TV from one room to the other one or he can watch tv from the livingroom only. So he don't NEED two tv but he has 2 TVs. So Onions don't NEED five times more, Onions have five times more...

    Now let's say that the old TV was not working but he decided to keep it anyway. May be he will never use the TV again so it will be considered as waste but he can also at some point re-use some pieces.

    I think that the way we use our "junk DNA" is more efficient and allow more complex regulation. Also the example of TV is not perfect because my hypothesis about the funtion of junk DNA is not really transposable on this analogy... It was more to clarify the ambiguity with the use of the word NEED.

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    1. You are hung up on the word "need", which is irrelevant to the discussion. People who collect decorative wall plates may be passionate about their hobby, but the do not need these things.

      About half of our genome is made up of transposable elements. They originated as "DNA parasites". Most of them are now inactivated by mutation, so even from the perspective of the elements, these are junk DNA - ie used to work but now do not. The ones that do anything for us have been co-opted by our system long after the fact. What efficiency was gained by allowing parasites into our DNA, then allowing them to litter our genome with their dead? Extending your analogy would require that James' house be filled up with something the mice brought in.

      And finally, thinking by analogy is dangerous. The way we have taught our undergraduates to understand molecular phenomenon has an impact, and allows for incorrect assumptions. The teaching of PCR as two little primer arrows that copy all the way to the end, without considering Taq's poor processivity and other molecular factors has led to a number of papers that claim to observe in vivo recombination, where it was in vitro template switching during the PCR steps. The analogy used to teach PCR gave an imperfect understanding of the actual process, and led to peer-reviewed publication of errors.

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  24. I suggest a paper by Makalowski published in Science in 2003 (if you consider Science as a decent journal) which explore some avenue for "junk DNA".

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  25. I also suggest reading this paper :

    Waves of Retrotransposon Expansion Remodel Genome Organization and CTCF Binding in Multiple Mammalian Lineages from Odom...

    Basically it suggest a possible mechanism on how cell can modulate transposon integration and if you can modulate and control, you can eventually use it... Right ?

    I start giving hint here...

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  26. Junk DNA is anything but that. It is required as proven by recent developments

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  27. "Junk DNA actually represents a serious problem for Darwinism (evolution by natural selection) and it certainly was never "predicted" by adaptationists."

    I saw this bit and knew right away that this guy was a liar. It just goes to show that evolutionists are willing to bend to any bit of evidence and claim it fits their theory.

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    1. Temi, you just called me a liar.

      Feel free to post evidence that significant numbers of Darwinists (those who believe that evolution is caused by natural selection) promoted junk DNA back in the 1970's. While you're at it, please give us a brief summary of the reasons why junk DNA is favored by natural selection. You don't have to believe it, I just want you to prove that Darwinists had such an explanation.

      If you can't back up your accusation then I suggest you withdraw it. Otherwise, your comment just becomes more evidence that you are an IDiot.

      Delete
    2. This is conjecture of my own, but I've thought for some time inactive genes might be kept because it might become active and useful again in later or serve as useful material for future beneficial mutations.

      The cost or difficulty of successfully removing useless genes may be more than the cost of replicating them.

      Delete
  28. Will this be updated to reflect the ENCODE findings?

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  29. Thank you for this clarification! So "junk DNA" = "DNA with no known function". One question then arises for me: why call it "junk" DNA? I ask because the word 'junk' already expresses a certain judgment about it, namely that it is useless, and has no function. That is exactly what we mean in everyday life when we use the word 'junk'. So why not call it "Mystery DNA", or something like that? The phrase 'junk DNA' is seriously misleading if what we mean by it is 'DNA with no known function'.
    Also, this definition implies that as research unfolds, we may find out what the function is for all those bits of DNA currently labelled 'junk'. So in some sense, 'junk DNA' may well disappear as research progresses. This seems a bit of an awkward consequence of this definition, but scientists can define their terms as they see fit.
    One last question: what are the chances, in your view, that all those bits of DNA currently labelled 'junk' actually do have functions we are unaware of.

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  30. you may be interested in this podcast - an ID proponent puts forward that their view made sense because they " knew" junk DNA had a function
    Steven Meyer - Darwins Doubt
    http://media.premier.org.uk/unbelievable/22d8050f-6511-467b-9128-013c51e6221b.mp3

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