Friday, April 01, 2011

Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?

This is the second in a series of postings about a new book by Jonathan Wells: The Myth of Junk DNA. The book is published by Discovery Institute Press and it should go on sale on May 31 2011. I'm responding to an interview with Jonathan Wells on Uncommon Descent [Jonathan Wells on his book, The Myth of Junk DNA – yes, it is a Darwinist myth and he nails it as such].

Denyse O'Leary asks, "Interestingly, in the “nail dump is Ming vase” story, no one insists that nobody ever thought it was just another piece of junk. They almost always say, “Yes, we thought so but had no idea …” So what’s behind the failure to admit an error in this case?" It's hard to figure out what she means but I think she's wondering why biologists don't just admit they were wrong about junk DNA. Jonathan Wells interprets the question differently.
Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”

This claim is easily disproved: Francis Crick and Leslie Orgel published an article in Nature in 1980 (284: 604-607) arguing that such DNA “is little better than junk,” and “it would be folly in such cases to hunt obsessively” for functions in it. Since then, Brown University biologist Kenneth R. Miller, Oxford University biologist Richard Dawkins, University of Chicago biologist Jerry A. Coyne, and University of California–Irvine biologist John C. Avise have all argued that most of our DNA is junk, and that this provides evidence for Darwinian evolution and against intelligent design. National Institutes of Health director Francis Collins argued similarly in his widely read 2006 book The Language of God.

It is true that some biologists (such as Thomas Cavalier-Smith and Gabriel Dover) have long been skeptical of “junk DNA” claims, but probably a majority of biologists since 1980 have gone along with the myth. The revisionists are misinformed (or misinforming).
It's in the best interests of the IDiots to promote the idea that all "Darwinists" believed in the "myth" of junk DNA and that it wasn't until the predictions of the IDiots were confirmed (not) that the biologists changed their minds.

The truth is somewhat different. Wells says, "Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”" The truth is that the mainstream biologist community never, ever claimed that all non-coding DNA was junk. Most of them didn't even believe that a majority of our genome was junk.

The issue has come up many times over the past few years on blogs and newsgroups. The last time I took a poll was a few years ago and here are the results.


As you can see, there's a wide range of opinion among people who read Sandwalk. I think this is a pretty good reflection of the opinions of most biologists.

In responding to the question, Wells makes one serious error when he claims that biologists promoted junk DNA because it "provides evidence for Darwinian evolution." It does nothing of the sort. In fact, it goes against any prediction of Darwinian evolution by natural selection. The reason why the concept of (huge amounts of) junk DNA was resisted by so many biologists was because of this conflict.

Wells also says that junk DNA was promoted by some biologists because it "provides evidence ... against intelligent design." This is partly true, especially when the arguments center on conserved pseudogenes. That part of junk DNA (pseudogenes) is accepted by almost all biologists but it's only a tiny part of our genome. There is no evidence to suggest that pseudogenes are anything but junk and all the evidence indicates that we have thousands of them in our genome. (If they have a function then they aren't pseudogenes.)

Many mainstream biologists have supported the idea that a majority of our genome is junk. There's no denying that. I agree with them. None of them are changing their minds in spite of what Jonathan Wells is telling you. What Wells is doing is picking sides in a genuine scientific dispute. He could have done this 30 years ago and the result would have been the same. The genuine scientific controversy is not about to be resolved and there's no new evidence that seals the case one way or the other.

In my opinion, our genome is almost 90% junk DNA and that's the view that's going to win in the end.


61 comments :

  1. Questions spring to mind:

    1. Historical: If bacteria have no junk, and mammals have a lot, is it a straight line (more or less) towards greater junkiness of genomes as we read the genetic evidence forward over the last 2.5 billion years? Do we know the point at which genomes became primarily junky (quantitatively)? If life has been getting increasingly junky, isn't that primary evidence for junkiness itself?: life has not tended toward either greater or less fitness over time.

    2. Ideological: Are the Dawkins/Dennett crowd so uncomfortable with junkDNA's apparent prevalence because they see evolution acting on the genome specifically, while the Mayr/Gould crowd have less trouble with it because they see evolution as acting on "populations"?

    ReplyDelete
  2. 1. Humans didn't evolve from today's bacteria.

    2. Dawkins and Dennett have a nonstandard definition of evolution.

    ReplyDelete
  3. If bacteria have no junk, and mammals have a lot, is it a straight line (more or less) towards greater junkiness of genomes as we read the genetic evidence forward over the last 2.5 billion years?

    While I don't know the subject well enough to make any real statements, I can think of two potential issues with this question. On the one hand, it could well be the exact opposite (genomes tend to become less junky, not more). Because bacteria have such short generation times compared to mammals, they've effectively had more scope for junky DNA to be weeded out by selection. Contrariwise, there may not necessarily even be a relationship between junkiness and phylogeny. For instance, Mycobacterium leprae has an extremely junky genome (despite being a bacterium) but the closely related M. tuberculosis does not.

    Also, it occurs to me that, in terms of questioning how much of our genome could be potentially deleted without effect, you've not only got to ask how much of our genome is non-functional, you need to ask how much of it is redundant. How much of the genome is taken up by multiple copies of the same gene, with the loss of one potentially compensated by the continued function of another?

    ReplyDelete
  4. Dr. Moran you posted:
    "In responding to the question, Wells makes one serious error when he claims that biologists promoted junk DNA because it "provides evidence for Darwinian evolution."

    From what you posted about what Wells said, he did not claims that biologists promoted junk DNA because it "provides evidence for Darwinian evolution."

    He said:
    "Since then, Brown University biologist Kenneth R. Miller, Oxford University biologist Richard Dawkins, University of Chicago biologist Jerry A. Coyne, and University of California–Irvine biologist John C. Avise have all argued that most of our DNA is junk, and that this provides evidence for Darwinian evolution and against intelligent design."


    Moran why do you always distort what people say? And try to slip it past us?

    ReplyDelete
  5. In the earlier post I commented:
    "If a DNA sequence has been changed could the previous DNA sequence be kept as a pseudogene? As stored history?"

    If pseudogenes are stored history of changes to the DNA, then they could be quite numerous (a large percentage) but have value and make sense.

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  6. Hello Prof. Moran,

    I would like to thank you for doing this series and I hope you will continue when the book comes out. I think it is very important to counterbalance the distortion of science and its history, and the fairy tale and myth creation by the dishonesty institute.

    Keep up the work!

    ReplyDelete
  7. anonymous asks,

    Historical: If bacteria have no junk, and mammals have a lot, is it a straight line (more or less) towards greater junkiness of genomes as we read the genetic evidence forward over the last 2.5 billion years? Do we know the point at which genomes became primarily junky (quantitatively)? If life has been getting increasingly junky, isn't that primary evidence for junkiness itself?: life has not tended toward either greater or less fitness over time.

    As a general rule, modern bacterial species have very little junk DNA in their genomes (less than 5%). I don't know if there are many exceptions to this general observation.

    Eukaryotes are all over the map in terms of the amount of junk DNA n their genomes. Some modern single-cell eukaryotes have huge genomes full of junk DNA and others have relatively compact genomes. Many multicellular eukaryotes have large genomes with lots of junk. There aren't any that I know of that have junk-free genomes but the range is enormous.

    Since we don't know how much junk was present in our ancestors from three billion years ago, we can't really tell if the trend in bacteria has been to lose junk DNA over time or whether the trend has been to gain junk in eukaryotes.

    I suspect it's a bit of both.

    ReplyDelete
  8. anonymous asks,

    Ideological: Are the Dawkins/Dennett crowd so uncomfortable with junkDNA's apparent prevalence because they see evolution acting on the genome specifically, while the Mayr/Gould crowd have less trouble with it because they see evolution as acting on "populations"?

    No, both sides of the junk DNA debate are mostly concerned with the power of natural selection acting on individuals within a population.

    If junk DNA really is junk then why hasn't it been eliminated from the genome since it almost certainly has a cost (making all that extra DNA takes energy)? Those who see natural selection as a powerful force in evolution will think junk DNA needs to have a function in order to keep it.

    Some of us don't believe that natural selection is all that powerful so we have much less trouble accepting the idea that much of the genome could be useless junk. It isn't eliminated because it's not enough of a disadvantage to be subjected to selection.

    ReplyDelete
  9. anonymous says,

    Moran why do you always distort what people say? And try to slip it past us?

    I do it just to keep the IDiots on their toes. It seems to be working.

    I can always count on people like you to come up with ways of defending your heroes by parsing every word instead of looking at the big picture.

    It's an amusing tactic that seems to only apply to your enemies. But that doesn't matter. It provides a certain amount of comic relief in those threads that tend to become quite technical.

    Thanks.

    BTW, which "anonymous" are you? You should sign your comments so we can distinguish between the various IDiots. Why don't you become "anonymous1" and put that at the bottom of each comment.

    ReplyDelete
  10. When Moran is caught in a falsehood he has a number of tactics he draws on.

    One is to distract.

    Another is to pretend that he is making some hugely important point and that it is quibbling on our part to point out his falsehoods.

    And of course there is always the personal attack.

    ReplyDelete
  11. Dr. Moran posted:

    "The truth is somewhat different. Wells says, "Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”" The truth is that the mainstream biologist community never, ever claimed that all non-coding DNA was junk. Most of them didn't even believe that a majority of our genome was junk."

    We notice that Moran has added the word "all".
    This is a distortion of what Wells said. He did not say "all".

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  12. As Dr. Moran has said:
    "In fact, it [junk DNA] goes against any prediction of Darwinian evolution by natural selection."

    Good to know.

    ReplyDelete
  13. In responding to the question, Wells makes one serious error when he claims that biologists promoted junk DNA because it "provides evidence for Darwinian evolution." It does nothing of the sort. In fact, it goes against any prediction of Darwinian evolution by natural selection.

    "Darwinian evolution" is an ID synonym for "evolution", rather than just the part presided over by Natural Selection. The "junkome" is of course stuffed full of evidence for evolution, by whatever mechanisms one might be disposed to feel predominate (ie, all of them!).

    I think it unfair to invoke Darwin anyway, in the "neo-Darwinians think it has a role" manner. Darwin's Natural Selection was applied to characters that did vary and produced a differential in offspring numbers. He did not insist that any and every character must be subject to this law.

    It is, I think, possible to be both an unashamed adaptationist and simultaneously to consider it probable that the vast majority of the genome really is junk. It seems unlikely that the cost of the extra DNA and protein is sufficiently high that selection must act to reduce it. The kind of cheese-paring that is permitted to reduce a bloated genome without harm is unlikely to provide much adaptive advantage - particularly in organisms that bear the 'cost' of many trillions of cells without apparent strain. Likewise, an organism that adds a few hundred thousand base pairs is not much worse off, if at all, than its more economical cousins - certainly not on a par with the 'cost' of being a couple of inches taller, for example.

    But a particular range of c-values in a species becomes part of the developmental parameters of the growing organism. I would suspect that you can't remove a significant fraction without dire developmental consequences - which is a long way from saying that this is its 'function'. But it can accumulate by ratchet.

    ReplyDelete
  14. In another thread we see Moran acknowledging his anti-religion prejudice:
    Anonymous:
    "Your anti-religion prejudice is showing. That is what is driving you and it is plain for the rest of us to see."
    Moran:
    "You are very perceptive. I bet you were educated at a private school—or a Roman Catholic one."


    We should be concerned that Moran is distorting what Wells has said, because Moran is prejudiced against religion.
    He think in terms of IDiots and enemies. And unfortunately this taints his thinking about "evolution".
    And this may well be true of many other "evolutionists".

    ReplyDelete
  15. It is so cute to see that Jon Wells has his protection-brigade scouring the net for instances of exposure.

    These people are like cockroaches - they thrive on shit and attempt to spread their filth to those that are not interested.

    AnonymousX

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  16. AnonymousX is moving the discussion into the gutter.
    Just one more attempt at distraction from the fact that Dr. Moran has distorted what Wells said.

    The sad fact is that "evolutionists" distort the truth because they feel they are fighting the good fight against the "creationists", so they feel they are not bound by the regular rules of honesty and objectivity.

    ReplyDelete
  17. Anonymous Prime is simply doing what creationists of all stripes do - distract, divert, annoy.

    Best to just ignore.

    AnonymousX

    ReplyDelete
  18. Anonymous writes:

    We should be concerned that Moran is distorting what Wells has said...

    I wouldn't be concerned. Wells' arguments are perfectly capable of falling on their own.

    ...Moran is prejudiced against religion.

    I do not think the word "prejudiced" means what you think it means. Dr. Moran makes no secret of the fact that he finds religious explanations of the world wanting. He's put forward the bases for his judgment. There is no pre-judging (the root and meaning of pre-judice) - that is, judging prior to evaluation of evidence - taking place.

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  19. anonymous writes:

    The sad fact is that "evolutionists" distort the truth because they feel they are fighting the good fight against the "creationists", so they feel they are not bound by the regular rules of honesty and objectivity.

    Yes, it's been an absolutely perfect conspiracy for the past 150 years among virtually all the world's leading biological researchers, and science teachers, and conservative Republican-appointed federal trial judges, and several iterations of the United States Supreme Court. Perfect. 150-year. Conspiracy.

    Or, instead of a perfect worldwide conspiracy 150 years old and still running strong, the alternative explanation is that the "evolutionists" are factually correct. Hmm, let's consider which of these alternatives is more likely....

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  20. Jud is "not concerned" that Moran is distorting what Wells has said.

    So be it.
    But by distorting what Wells has said and then refuting the distortion, it does not really refute what Wells actually said.

    In fact after all this, nothing that Wells actually said has been refuted.

    And that seemed to be the idea of this thread.

    ReplyDelete
  21. Wells:
    "It is true that some biologists (such as Thomas Cavalier-Smith and Gabriel Dover) have long been skeptical of “junk DNA” claims, but probably a majority of biologists since 1980 have gone along with the myth."

    Moran:
    "Many mainstream biologists have supported the idea that a majority of our genome is junk".

    Sounds like agreement.

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  22. In the earlier post you said:

    "Those scientists who oppose the concept of plentiful junk DNA may have taken comfort from the transcription data but their minds weren't changed either."

    I don't understand what you are getting at.
    Since the evidence of transcription data supports their thinking, why would those scientists who oppose the concept of plentiful junk DNA even think of changing their minds?

    ReplyDelete
  23. Anon Prime claims Moran is distorting Well's position. I think most people can see that he is not.
    Or does anyone read Well's statement as NOT saying that biologists promoted the 'junkiness' of junk DNA because they thought it was pro-evolution and contra-ID? Regardless of because/and? So what is anon saying, that biologists did NOT promote junk DNA because it supported darwininsm? Why is Wells even bringing it up, he's just mentioning it as an aside?

    ReplyDelete
  24. Anonymous writes (again):

    Moran is distorting what Wells has said.

    Your entire argument comes down to Dr. Moran using the word "all" in describing non-coding DNA when Wells didn't. This in no way weakens the case against what Wells says.

    Wells didn't say "all" non-coding DNA, but he did speak of non-coding DNA without qualification. Are you trying to say Wells is just talking about a tiny fraction of non-coding DNA? Unless that's your contention (or Wells'), and I seriously doubt that it is, then the argument against Wells' position is exactly the same, whether he is saying 98% of the genome isn't junk or "only" 90%. Whether you're talking about all or slightly less than all, that's a distinction without a difference.

    You don't discuss the second problem with Wells' statements, his incorrect characterization of what "Darwinists" thought. As Dr. Moran says, many biologists were quite uncomfortable with the idea of such a lot of junk DNA, feeling selection ought to have culled the waste. But unlike the IDers, whose forte seems to be holding onto the idea of some vastly intelligent and powerful Designer despite all evidence to the contrary, the "Darwinists" actually faced facts and searched for explanations.

    ReplyDelete
  25. Moran has already undercut your arguments guys.
    He said:

    "Many mainstream biologists have supported the idea that a majority of our genome is junk".

    And that is what Wells said also.

    ReplyDelete
  26. Anonymous writes:

    Moran has already undercut your arguments guys.

    He said:

    "Many mainstream biologists have supported the idea that a majority of our genome is junk".

    And that is what Wells said also.

    Honing your mad quote-mining skillz, I see. Yep, that's what Dr. Moran said, right after he said:

    The truth is that the mainstream biologist community never, ever claimed that all non-coding DNA was junk. Most of them didn't even believe that a majority of our genome was junk.

    So Dr. Moran presented a true, balanced picture of the disagreements within the scientific community - many believed a majority of the genome was junk, most didn't - then went on to note, as you yourself point out, Wells' inaccurate characterization of scientists as having a uniform, monolithic position on the subject.

    C'mon, Anonymous, you're better than that. Don't take the lazy way out. If you're going to quote-mine, at least go outside the thread to do it.

    ReplyDelete
  27. Anonymous Prime writes:

    "Moran has already undercut your arguments guys.
    He said:

    "Many mainstream biologists have supported the idea that a majority of our genome is junk".

    And that is what Wells said also."


    So, is that relaly wells' point?

    Some 'Darwinists' believed that yes, some DNA is junk?
    And this is acondemnation of evolution someow?

    OK...

    Does that work both ways*?

    It is a fact that many ID advocates are young earth creationists (e.g., Paul Nelson, most of the people that post on UD).
    Therefore, ID is in 'crisis' because some ID advocates want to claim thet ID is not religious?

    Whatever. Wells does have a documented history of using edited quotes to prop up his assertions. I'm betting his latest foray into the gutter of his own making will be more of the same.

    AnonymousX

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  28. Jud:
    "Wells' inaccurate characterization of scientists as having a uniform, monolithic position on the subject."

    Since Wells did not say that, we can see that Jud is taking his cue from Dr. Moran and distorting what Wells actually said.

    It looks like people cannot deal with what Wells actually said and need to distort it.

    So be it.

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  29. So it looks like the folks here basically agree with what Wells actually said.

    For some reason Dr. Moran wanted to pretend that he did not agree.

    But that is okay.
    Dr. Moran is curmudgeonly.

    ReplyDelete
  30. Anonymous said...

    Jud:

    "Wells' inaccurate characterization of scientists as having a uniform, monolithic position on the subject."

    Since Wells did not say that

    You are absolutely right, I misspoke.

    What Wells actually did was utilize a strawman:

    Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”

    ReplyDelete
  31. Anonymous (one of, anyway) said:

    As Dr. Moran has said:
    "In fact, it [junk DNA] goes against any prediction of Darwinian evolution by natural selection."

    Good to know.


    It is? Why? Okay, let's parse this.

    If the evidence goes against Darwin's conclusions, then supposedly evolution itself falls (because we all know, either Darwin was 100% right or 100% wrong; nothing in-between), and if evolution falls, therefore, since it couldn't be some other explanation, that proves there's a god, and therefore the Christian God, too (because the other ones are just made up, after all)...

    And what is the evidence? Why, that the wisest, smartest, all-powerful, infinitely-(insert every conceivable superlative here) Designer of the Universe stuffed the genome of his central focus of creation, humankind, with DNA that by and large does nothing, codes for nothing, and contributes nothing -- the floor-sweepings of biology, part and parcel of His image. And that was the best He could do.

    Eeeeeeyuup, that's "good to know", alright.

    ReplyDelete
  32. I am glad that Jud acknowledged that he "misspoke".
    I have caught Jud in a number of these falsehoods.

    ReplyDelete
  33. Anonymous writes:

    So it looks like the folks here basically agree with what Wells actually said.

    I'm a bit confused as to what you're saying. What, in your estimation, is Wells saying about the following:

    (1) Whether there is "junk" DNA, and how large a proportion of the genome it comprises;

    (2) The implications of this for mainstream evolutionary theory; and

    (3) The implications of this for Intelligent Design?

    ReplyDelete
  34. Jud, if you want to know what Wells is saying, read what he is saying.

    Your posts to this point have been full of falsehoods including distorting what Wells has said.

    ReplyDelete
  35. Dr. Moran, in the earlier post you said:

    "Those scientists who oppose the concept of plentiful junk DNA may have taken comfort from the transcription data but their minds weren't changed either."

    I don't understand what you are getting at.
    Since the evidence of transcription data supports their thinking, why would those scientists who oppose the concept of plentiful junk DNA even think of changing their minds?

    ReplyDelete
  36. anonymous says,

    I don't understand what you are getting at.
    Since the evidence of transcription data supports their thinking, why would those scientists who oppose the concept of plentiful junk DNA even think of changing their minds?


    I was trying to be as accurate as possible in responding to the myths being created by the IDiots.

    Denyse asks, "What caused the change of view about junk DNA? Can you suggest a couple of key findings?" And Wells replies,

    Wells replies: In a word, evidence. The first to emerge was the fact that almost all of an organism’s DNA is transcribed into RNA.


    They are implying that scientist have recently changed their minds about junk DNA and one of the factors was "evidence" that most of the genome was transcribed.

    I pointed out that there always were two groups of scientists. The proponents of (lots of) junk DNA didn't change their minds. The opponents of junk DNA didn't change their minds either.

    In other words, no significant number of scientists have changed their minds in the last decade in spite of papers claiming that most of the genome is transcribed.

    Denyse and Jonathan are mistaken. (Surprise!)

    I realize that pointing out the obvious—that the large number of opponents of junk DNA didn't change their minds—seems unnecessary to intelligent people but when dealing with IDiots it's often necessary to point out the obvious. Several times.

    ReplyDelete
  37. Wells said:
    "Since the 1980s, however, and especially after completion of the Human Genome Project in 2003, biologists have discovered many functions for non-protein-coding DNA."

    Dr. Moran, are you saying that this is not true?

    ReplyDelete
  38. anonymous asks,

    Dr. Moran, are you saying that this is not true?

    It depends on how you interpret what Wells said.

    If he means that scientists have discovered many new classes of function that were unknown before 1985 then this is certainly incorrect. I can only think of one possibility (some small RNAs). Regulatory sequences, centromeres, telomeres, origins, SARs, introns, recombination sites, ribosomal RNA genes, tRNA genes, and most genes for small RNAs were all known before 1985.

    If he means that considerably more DNA is now known to be non-junk than we thought before the mid-1980s then he's also wrong.

    If he means that there are many unique examples of function in parts of the genome that we thought were junk then he is correct. If you add up all the examples of functional defective transposons and former pseudogenes from all species then I bet there are about 20-30 all together. That counts as "many."

    Of course, in the genome of any one species those discoveries would account for less that 0.01% of the genome but that won't stop the IDiots from promoting it as a major event.

    ReplyDelete
  39. Dr. Moran:
    "If he means that scientists have discovered many new classes of function that were unknown before 1985 then this is certainly incorrect. I can only think of one possibility (some small RNAs). Regulatory sequences, centromeres, telomeres, origins, SARs, introns, recombination sites, ribosomal RNA genes, tRNA genes, and most genes for small RNAs were all known before 1985."

    You are referring specifically to 1985.
    But Wells is referring to the 1980s. The decade of the 1980s.
    You seem to confirming that prior to the 1980s much less was known about the functions of "junk DNA".

    ReplyDelete
  40. Larry Moran said:

    If you add up all the examples of functional defective transposons...

    Funny how it goes, huh? Not long ago the big G-meister was parting seas, flooding the entire world, and his son was yer actual Sea of Galilee pedestrian. Now he's reduced to demonstrating his existence by jury-rigging SOME kind of output for defective transposons. Wow, God sure is lucky we've reached this level of technology just as he's really feeling his age, or else we'd NEVER believe in the guy, huh? :)

    ReplyDelete
  41. anonymous says,

    You are referring specifically to 1985. But Wells is referring to the 1980s. The decade of the 1980s. You seem to confirming that prior to the 1980s much less was known about the functions of "junk DNA".

    I don't know what game you're playing but it's getting to be very annoying.

    Many of us have kept up with the literature in this field. Some of us even remember the 60s, 70s, and 80s. (I was a graduate student in 1968.)

    Many scientists firmly believe, in 2011, that most of the DNA in our genome is junk. That's what the evidence suggested in the 1970s and that's what the evidence suggested in the 1980s, 1990s, and the first decade of the 21st century.

    If that what Wells meant then I agree with him.

    But you know damn well that's not what he means.

    ReplyDelete
  42. Dr. Moran you posted:

    "If he means that scientists have discovered many new classes of function that were unknown before 1985 then this is certainly incorrect. I can only think of one possibility (some small RNAs). Regulatory sequences, centromeres, telomeres, origins, SARs, introns, recombination sites, ribosomal RNA genes, tRNA genes, and most genes for small RNAs were all known before 1985."

    Why have you included in your list:
    ribosomal RNA genes and tRNA genes?
    Are they considered "junk DNA"?
    Were they ever considered "junk DNA"?
    It seems you have listed items that are not relevant to the topic.

    ReplyDelete
  43. Wells has made statements that are quite reasonable and you are pretending they are not.
    Each time people ask you about any specific point, you actually confirm what Wells has said.
    But this annoys you.
    Expressing your unjustified annoyance is just another distraction from the topic being discussed.

    ReplyDelete
  44. If I understand it, there is:
    protein coding DNA,
    non-protein coding DNA,
    and junk DNA.

    Is that correct?
    If so, what is the current thinking about the percentages of each?

    ReplyDelete
  45. Someone asked,

    If I understand it, there is:
    protein coding DNA,
    non-protein coding DNA,
    and junk DNA.

    Is that correct?
    If so, what is the current thinking about the percentages of each?


    The genome can be divided into coding regions (less than 2% of the genome) and non-coding regions (all the rest).

    Within the non-coding regions there is a lot of junk DNA. The exact amount is being debated by scientists. Almost all scientists agree that a few percent of our genome is junk. Some think that as much as 90% of our genome is junk.

    These numbers depend on the species. In some species there is very little junk DNA and almost all of the genome is coding seuence.

    ReplyDelete
  46. Moran:
    "The genome can be divided into coding regions (less than 2% of the genome) and non-coding regions (all the rest).
    Within the non-coding regions there is a lot of junk DNA. The exact amount is being debated by scientists. Almost all scientists agree that a few percent of our genome is junk. Some think that as much as 90% of our genome is junk."

    What is the defining characteristic that distinguishes junk DNA from the rest of the non-coding DNA?

    ReplyDelete
  47. Moran:
    "The genome can be divided into coding regions (less than 2% of the genome) and non-coding regions (all the rest).
    Within the non-coding regions there is a lot of junk DNA. The exact amount is being debated by scientists. Almost all scientists agree that a few percent of our genome is junk. Some think that as much as 90% of our genome is junk."

    What is the defining characteristic that distinguishes junk DNA from the rest of the non-coding DNA?


    The answer to this question might clear up a lot of misunderstanding around the words "junk DNA".

    ReplyDelete
  48. anonymous asks,

    What is the defining characteristic that distinguishes junk DNA from the rest of the non-coding DNA?

    Lots of non-coding DNA has a well-defined and well-understood function.

    Junk DNA is the part that has no known function and could be safely deleted without affecting the survival of the individual or its offspring. In other words, junk DNA provides no selective advantage: it is either neutral or slightly deleterious.

    ReplyDelete
  49. It looks like quite a few pseudogenes have a defined and understood function. So they would not be considered "junk". Right?

    http://en.wikipedia.org/wiki/Pseudogene
    "It has been established that quite a few pseudogenes can go through the process of transcription, either if their own promoter is still intact or in some cases using the promoter of a nearby gene; this expression of pseudogenes also appears to be tissue-specific.[4] In 2003, Hirotsune et al. identified a retrotransposed pseudogene whose transcript purportedly plays a trans-regulatory role in the expression of its homologous gene, Makorin1 (MKRN1) (see also RING finger domain and ubiquitin ligases), and suggested this as a general model under which pseudogenes may play an important biological role.[19] Other researchers have since hypothesized similar roles for other pseudogenes.[20] A bioinformatics analysis has shown that processed pseudogenes can be inserted into introns of annotated genes and be incorporated into alternatively spliced transcripts.[10]"

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  50. ...and a lot of pseudogenes are know to do nothing but take up genomic space. Some things have function does not equal all things have function.

    One examples over at another discussion within Sandwalk, we are talking about fragments of the mitochondrial DNA inserted into the nuclear DNA.

    http://en.wikipedia.org/wiki/Numt

    A freely available review...
    http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1000834

    The other comment line...

    http://sandwalk.blogspot.com/2011/04/idiots-vs-francis-collins.html?showComment=1302573458119#comment-c4419125312027693310

    (I hope this is a different Anonymous).

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  51. I am trying to get a handle on what is meant by "junk DNA".

    Concerning mitochondrial DNA:
    "the mitochondrial DNA inserted into the nuclear DNA" code for mitochondrial-related proteins.

    http://www.sens.org/sens-research/research-themes/mitosens
    "Mitochondria are very complex; they contain about a thousand different kinds of protein, each encoded by a different gene. But nearly all of those genes are not in the mitochondrial DNA at all – they are in the nucleus!"

    So they are not junk, since they have a well-defined and well- understood function. Right?

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  52. So they are not junk, since they have a well-defined and well- understood function. Right?

    Nope. You are mis-understanding the statement.

    In human mitochondria there are 13 protein genes, 22 tRNAs and 2 rRNAs. These "mitochondrially encoded" genes are transcribed and the protein ones translated within the mitochondria.

    Then in the nucleus, there are ~1500 different proteins. Not the 13+22+2 in the mitochondria. Totally separate genes.

    But, quite frequently, chunks of "broken" mitochondrial DNA ends up in the nucleus's DNA. So you get copies of the "mitochondrially encoded" 13+22+2 genes in the nucleus's DNA (called numts). These quite literally just take up space. They are not used to make any products, and even if the product was made into an RNA, they do translate properly into the protein within the nucleas's translation system. Some of these are very old (a cytb pseudogene shared by many of the great apes, for instance).

    Read the links.

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  53. Some mitochondrial DNA is transposed to the nucleus.
    Some of this is considered "junk".
    However it may not be junk, but rather minisatellite sequences that actually have a function.
    The function is to stimulate recombination.

    http://www.ncbi.nlm.nih.gov/pubmed/7932781
    "We report here a recent remarkable transposition of 7.9 kb of a typically 17.0-kb mitochondrial genome to a specific nuclear chromosomal position in the domestic cat. The intergrated segment has subsequently become amplified 38-76 times and now occurs as a tandem repeat macrosatellite with multiple-length alleles resolved by pulse-field gel electrophoresis (PFGE) segregating in cat populations."

    http://www.cell.com/retrieve/pii/009286749090719U
    Hypervariable minisatellite DNA sequences are short tandemly repeated sequences that are present throughout the human genome and are implicated to enhance recombination. We have constructed a consensus hypervariable minisatellite sequence and analyzed its effect on homologous recombination in human cells in culture. The consensus sequence d(AGAGGTGGGCAGGTGG)6.5 is shown to stimulate homologous recombination up to 13.5-fold.

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  54. http://en.wikipedia.org/wiki/Retrovirus
    When retroviruses have integrated their own genome into the germ line, their genome is passed on to a following generation. These endogenous retroviruses (ERVs), contrasted with exogenous ones, now make up 5-8% of the human genome.[3] Most insertions have no known function [yet] and are often referred to as "junk DNA". However, many endogenous retroviruses play important roles in host biology, such as control of gene transcription, cell fusion during placental development in the course of the germination of an embryo, and resistance to exogenous retroviral infection.

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  55. Anonymous Wednesday, April 13, 2011 11:21:00 AM,

    Hmmm... you were 2 sentences short of the punchline.

    From the same abstract.
    "Numt genes do not function in cats; rather, the locus combines properties of nuclear minisatellites and pseudogenes."

    "Some other site recombines, so therefore this one must too" is not precisely hard evidence, is it?

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  56. Benjamin L. (belgian student)Wednesday, April 13, 2011 5:46:00 PM

    If "Junk" DNA has not been lost during the evolution of eukaryotes, maybe it is because it has not been significantly detrimental yet (I mean in terms of metabolic cost) and/or that this "Junk" DNA actually serves a function. Indeed, there are numerous compelling facts for the role of most of what we call "Junk" DNA in the evolution of eukaryotes. For the most part of it, Junk DNA seems to be the result of transposable elements (TEs) activity. Junk DNA = autonomous and non-autonomous elements or scattered products of transpositions, repeated DNA sequences, retropseudogenes... By the way, in plants of the genus Lilium, TEs can account for 99% of the total DNA. Is it really "Junk" DNA ? Evidences for different roles of TEs and scattered products of transposition in the evolution of eukaryotic genomes have accumulated for years: Chromosomes organisation, ectopic recombination, chromosomal inversion, segmental deletion, exon/gene shuffling, rewiring of genes regulatory networks, blocking gene conversion and so promoting neofunctionalization, horizontal gene transfer, gene duplication... It has also been proposed that keeping a large amount of "Junk" DNA helps the cell to keep a constant cytonuclear ratio which could be necessary for an optimal cellular function (skeletal DNA hypothesis). It could also reduce the burden of mutations (mutations happening randomly around genome are more likely to occur in non-coding sequences, thereby protecting gene integrity).

    How do Junk DNA persist? There are several defense mechanisms against parasitic or repetitive DNA but if these mechanisms aren't able to delete all these sequences, some of them will be transferred to the next generation. TEs have predominantly deleterious effects on their host but can occasionally provide some positive effects, so they represent a threat for short-term evolution of the host, but at the same time an indisputable potential source of advantages for long-term evolution and adaptation of their host. Cases of complete elimination of "Junk" DNA among eukaryotes exist but are rare and one could argue it doesn't seem to be advantageous. "Junk" DNA could be seen as a "reservoir" where new structures are constantly emerging from mutations and TEs activity. Sometimes they are deleterious for the host and sometimes they provide advantages and so are exapted at the molecular level and the individual is positively selected in the population. But TEs can't be retained by natural selection for their potential advantageous to the host genome because Natural Selection acts in the present time and has no considerations about possible future advantages TEs could provide for the host (By the way Natural selection is not an entity, nor a God, only a mechanism). And here is the key: TEs are retained because of their own parasitic features and selfish "behaviour" and this allow them to represent an enormous fraction of the genome without serving its short-term interrests. Moreover, TEs are able to mobilize and amplify other "Junk" sequences, allowing them to persist without serving any purpose to the cell. I think we must stop thinking about a genome as a "unique entity". Genomes are filled with "selfish" DNA if I may say (I don't really like this term because it is anthropomorphic, a DNA sequence has no goal, no intentions) and some scientists are now thinking about studying the genome like a complete ecosystem, studying relations between TEs and host genome towards a community ecology of the genome. The genome is dynamic and even unstable at some point. What matters is the result of the hole system. If the hole system (the genome) is working, then the individual will survive, if he is able to reproduce, he will be selected and will positively influence the population. Genome is more complex than a simple "blueprint", which it is definitely not, and we can't say "because it is non-coding, it is junk".

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  57. http://www.ncbi.nlm.nih.gov/pubmed/7932781
    "We report here a recent remarkable transposition of 7.9 kb of a typically 17.0-kb mitochondrial genome to a specific nuclear chromosomal position in the domestic cat. The intergrated segment has subsequently become amplified 38-76 times and now occurs as a tandem repeat macrosatellite with multiple-length alleles resolved by pulse-field gel electrophoresis (PFGE) segregating in cat populations."

    What was the evolution value of this "remarkable transposition" to
    "a specific nuclear chromosomal position ".

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  58. Benjamin L. writes:

    some scientists are now thinking about studying the genome like a complete ecosystem

    World's molecular biologists to themselves:

    [Forehead slap] "Damn! Studying the genome as a complete system! Why didn't I think of that?!"

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  59. anonymous asks,

    What was the evolution value of this "remarkable transposition" to
    "a specific nuclear chromosomal position ".


    There was no "evolution value" in any meaningful sense of that term. It was a unique accident.

    Your question makes it seem like you are missing the whole point of the discussion.

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  60. http://www.ncbi.nlm.nih.gov/pubmed/7932781

    Dr. Moran has called this finding by Lopez et al, a unique accident.
    Is anyone familiar with any other instances of this?
    I would like to know how "unique" this is.

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  61. Jud said...
    [i]World's molecular biologists to themselves:

    [Forehead slap] "Damn! Studying the genome as a complete system! Why didn't I think of that?!"[/i]


    I’m sorry if my English is sometimes not very clear and my previous comment was already too long, I couldn’t add any other explanation. I mean developing ecological models specific to the genome in order to model the dynamics of TEs within the genome and understand how selection influences the evolution of the TE community and its impact on genome evolution, which is something new. Because TEs have an influence on “Junk” DNA, it is a way to understand how Junk DNA can be maintained in the genome. So… Why didn't they think of that before? ... Yes, you can continue to consider “Junk” DNA alone and wonder how, given that it is (alone) neutral or slightly deleterious, it can be “retained by selection” or try to understand its “evolution value”, but in this case you will do mistakes because you forget to consider that “Junk” DNA is integrated in a dynamic and complex system… Even if it doesn’t serve any purpose to the cell it can be maintained in the genome by TEs activity, so where’s the problem? Now, the goal is to study in what extend “Junk” DNA can be maintained by TEs (is there a kind of organisation in there or just stochastic processes?) and what are the consequences for the host fitness.

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