Tuesday, May 03, 2011

Junk & Jonathan: Part 3—The Preface


Here's the preface to The Myth of Junk DNA by the IDiot, Jonathan Wells. After each paragraph I've inserted a short version of the truth just so you don't get misled by all the untruths and distortions that are found in creationist books.

See:

Junk & Jonathan: Part I—Getting the History Correct

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

Jonathan, Moonies, and Junk DNA

The discovery in the 1970s that only a tiny percentage of our DNA codes for proteins prompted some prominent biologists at the time to suggest that most of our DNA is functionless junk. Although other biologists predicted that non-protein-coding DNA would turn out to be functional, the idea that most of our DNA is junk became the dominant view among biologists.
  • It's true that in the 1970s the experts in the study of genomes proposed that most of our genome is junk.
  • It's not true that they thought non-coding DNA had no function. Functions of non-coding DNA were well-established by 1970.
  • The idea that most of our genome is junk was never the "dominant" view among biologists even though it's correct.
That view has turned out to be spectacularly wrong. Since 1990--and especially after completion of the Human Genome Project in 2003--many hundreds of articles have appeared in the scientific literature documenting the various functions of non-protein coding DNA, and more are being published every week.
  • It's not true that the idea of a large amount of junk DNA has turned out to be "spectacularly wrong."
  • It's true that there have been lots of examples of of novel functions for small pieces of the genome that were previously lumped into the junk DNA category. These dozens of functional parts of the genome may amount to as much as 1-2% of the genome (probably less).
Ironically, even after evidence for the functionality of non-protein coding DNA began flooding into the scientific literature, some leading apologists for Darwinian evolution ratcheted up claims that "junk DNA" provides evidence for their theory and evidence against intelligent design. Since 2004, biologists Richard Dawkins, Douglas Futuyma, Kenneth Miller, Jerry Coyne and John Avise have published books using this argument. So have philosopher of science Philip Kitcher and historian of science Michael Shermer. So has Francis Collins, former head of the Human Genome Project and present director of the National Institutes of Health, despite the fact that he co-authored some of the scientific articles providing evidence against "junk DNA."
  • It's true that well-established bits of junk DNA—like known pseudogenes—have been effectively used to challenge the idea that our genome appears designed. Those examples remain powerful, and true, examples of evolution that cannot be explained by Intelligent Design Creationism. They have not been refuted and they have not been explained by the IDiots.
These authors claim to speak for "science," but they have actually been promoting an anti-scientific myth that ignores the evidence and relies on theological speculations instead. For the sake of science, it's time to expose the myth for what it is.
  • The truth is that those authors still speak for science and truth and their evidence is sound.
  • Wells, on the other hand, speaks for the other side.
Theme

Genomes
& Junk DNA
Far from consisting mainly of junk that provides evidence against intelligent design, our genome is increasingly revealing itself to be a multidimensional, integrated system in which non-protein-coding DNA performs a wide variety of functions. If anything, it provides evidence for intelligent design. Even apart from possible implications for intelligent design, however, the demise of the myth of junk DNA promises to stimulate more research into the mysteries of the genome. These are exciting times for scientists willing to follow the evidence wherever it leads.
  • It's certainly true that non-coding DNA performs a wide variety of functions. Some of them are listed in various postings under Genomes & Junk DNA
  • It's certainly not true that the organization of our genome—the majority of which is junk—provides evidence of intelligent design.
  • It's certainly not true that the idea of junk DNA is a myth.
  • It's true that these are exciting times and that smart people must follow the evidence wherever it leads even if it refutes cherished religious beliefs.

[Hat Tip: Preface to The Myth of Junk DNA by Jonathan Wells]

35 comments:

  1. The idea that most of our genome is junk was never the "dominant" view among biologists even though it's correct
    Did you "mis-speak" here? In my experience (hardly quantitative) as well as according to my old undergrad text (circa mid-1990's), the idea most of our genome is junk is the dominant view (if not sole view) of biologists*. The only people I've ever heard argue to the contrary are creationists.

    *although I have seen many arguments as to potential functions played by the bulk of the junk DNA.

    To say a lot of us (myself included) don't concern ourselves much with the junk portion would be true (if it isn't a cDNA, I simply don't give a damn), but that doesn't mean I think the genome comprises solely of cDNA...

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  2. @Bryan,

    Follow the link in my posting to What Did Biologists Really Say About Junk DNA?.

    Most biologists understand that there's junk DNA in our genome but many of them are not prepared to admit that MOST of our genome is junk. That's why you see so many papers being published that question the prevalence of junk DNA.

    It's related to The Deflated Ego Problem.

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  3. I have noticed that you refer to proponents of ID as IDiots. This is an attempt at insulting humor.
    Would it be acceptable to call you Dr. Moron?

    ReplyDelete
  4. Most biologists understand that there's junk DNA in our genome but many of them are not prepared to admit that MOST of our genome is junk. That's why you see so many papers being published that question the prevalence of junk DNA.

    It's related to The Deflated Ego Problem.


    For actual practicing biologists, this has nothing to do with the Deflated Ego Problem and everything to do with "absence of evidence does not equal evidence of absence". The many biologists that suspend judgement about the "junkiness" of the genome while additional data on the topic are collected suspend this judgement equivalently for all genomes, not just the human one.

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  5. I still don't see this as supporting your original statement - i.e. that the conclusion most of our genome is junk DNA is not the dominant view among biologists.

    Even taking into account the attempts to "expand" the role of coding DNA (modification, splicing, etc) and the attempts to find roles for the non-coding stuff, the majority is still junk and I don't think that many biologists would disagree with that statement.

    I'd also point out that trying to find potential roles for junk DNA hardly qualifies as denial it is junk. We, as scientists, would be negligent in our duties if we didn't challenge our conclusions - including the conclusion that junk DNA is non-functional DNA.

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  6. Bryan,

    When I was working for my PhD i was introduced for the first time to the concept of junk DNA. The professor teaching that class, who is both an atheist and a molecular biologist, said:

    "We should call it DNA whose function we haven't found."

    You might not have noticed, but there is a kinda school of thought, where everything has to be the result of natural selection. To them, long time ago, it was a shock to realize that most of the variability we see in homologous proteins was neutral to semi-neutral. Later the idea that most DNA would be selfish or, shudder, junk!

    This you can only notice if your faculty and students tend to debate issues a lot. Otherwise you might not truly know what people around you think. Of course. I am talking just about one place in the world. But the same was true at some conferences. Meaning it was not just a local thing to have some division on these issues.

    N.E.

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  7. "Anonymous":

    If Larry was actually a moron, sure.

    Here's why the label "IDiot" is applicable to ID proponents (if a bit snarky): there exists NO evidence for ID and there exists no gap in the understanding of evolution that supports or even suggests ID. Evidence supporting evolution is such that to deny it means you either don't understand it (which can just mean you're ignorant - but it isn't honest to criticise something of which you are ignorant) or that you do understand it but don't want to accept it (which means you're putting your personal opinion or belief before objective evidence, which makes you a denialist, which frankly makes you an idiot - after all, what would you call a flat-earther, given the evidence we have for the Earth's shape?).

    BTW: why can't you people use a name? It smacks of cowardice & troll tactics, plus it's hard to keep up with the IDiots that keep showing up in force to present their 'arguments'.

    Hank (my real name)

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  8. Anonymous,

    I don't know about Larry, but I resisted a lot calling the IDiots "IDiots." That until I exchanged a bit with a few of them. Their display of dishonesty, rhetorical contortions, obvious disguising of creationist propaganda, their lying, distorting, and quote-mining of scientific articles, while denying their true intentions, and their obviously imbecilic arguments, left me with no choice but to call them for what they are: IDiots.

    Take Larry's post here. Why does Jonathan present his "case" by lying so much about everything, such as the position of biologists in general, ignore the true meaning of those published articles, as if he could not have figured out that they don't give functions but to a tiny portion of DNA, misrepresent the meaning of both junk and selfish DNA. Long et cetera. Why?

    They leave little to no space to give them the benefit of the doubt. Thus ...

    Let me tell you something else. It is not a matter of agreement or lack thereof. Larry has corrected several of my misunderstandings about one thing or another (just look at his style, he has to hit the top of the nail on some of us and without the slightest compassion). I have just taken my lesson, licked my wounds, and that's that. Recently, we exchanged a few comments, and we did not reach an agreement. Neither I nor he got convinced by the other. So, we left it, and that's that. It would never occur to me to call Larry names for disagreeing. It is not a matter of whether we can all agree on something or not. To me, it is a matter of principles. A thing that the IDiots lack. Of course, again, this is why I call the IDiots "IDiots." I can't speak for Larry.

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  9. Anonymous: it's not an attempt, it's successful. Another evocative epithet is "IDolators" (which I first read at Thoughts from Kansas), although that may not be quite as accurate.

    Etymologically, IDiot is an appropriate term for ID propagandists, as it originally derives from the Greek word for a person lacking in professional skills (according to Wikipedia), which correctly describes at least one of their deficiencies. "Moron", on the other hand, just means a person a person with mental retardation, which obviously cannot be accurately applied to Dr. Moran.

    tl;dr: No, that would be incorrect.

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  10. ^
    How would that make any sense at all?

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  11. anonymous asks,

    I have noticed that you refer to proponents of ID as IDiots. This is an attempt at insulting humor.

    Would it be acceptable to call you Dr. Moron?


    If you can demonstrate that I don't understand science or evolution and that I consistently make misleading statements about evolution, and even lie about it, then you would have every right to refer to me as a "moron."

    ReplyDelete
  12. Nice try. It is not:
    "If you can demonstrate that I don't understand science or evolution and that I consistently make misleading statements about evolution, and even lie about it, then you would have every right to refer to me as a "moron."

    The issue is that you consistently make misleading statements about ID, and even lie about it.

    On that basis you are a moron.

    What you claim about proponents of ID applies to you. You just do not see that.
    But it is always hard to see one's own projection.

    ReplyDelete
  13. anonymous says,

    For actual practicing biologists, this has nothing to do with the Deflated Ego Problem and everything to do with "absence of evidence does not equal evidence of absence".

    I don't understand what you're referring to. There's plenty of positive evidence that most of the DNA in our genome is junk.

    The problem is that most biologists don't know—or don't care—about this evidence. They've never heard of genetic load and they have no idea how significant it is that most of our DNA shows no evidence of sequence conservation. They haven't thought about the C-value "paradox" and they certainly haven't come to grips with The Onion Test.

    Most Biologists are unaware of the experiments where large regions of DNA have been deleted. They don't understand why we know that the vast majority of transposons are defective. They don't appreciate the significance of studies on intron size and sequence conservation. They don't know that we have 20,000 pseudogenes.

    On the other hand, they get all excited whenever a paper is published that suggests we should ignore all this evidence for junk DNA. That's why those papers get published in Nature and Science and that's why those papers always fail to even mention the positive evidence for junk DNA that their paper supposedly "refutes."

    The standard view is that the only reason to beleive in junk DNA is "the absence of evidence." This is a completley false, but widespread, viewpoint. I think the reason for this is because: (a) most biologists are adaptationists, and (b) most biologists are looking for some magical function in junk DNA that will make humans much more special than friut flies and nematodes. (I list the possibilities in The Deflated Ego Problem.) We know for a fact that most biologists will look at a dog ass plot and see nothing wrong with it. In fact, they take it as "evidence" that "noncoding DNA" must have some significance.

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  14. Re calling ID proponents 'IDiots', I have to agree it's inappropriate...

    ... as I've always figured it's roughly as likely they're being deliberately deceptive, really. 'IDiots' seems to me too much to let them off the hook, there.

    ... But it'll do, I guess. It's short, anyway.

    Now, as to the anonymous cowards' earlier complaints re Dr. Moran being 'prejudiced' against religion, this, too, I have to contest.

    I mean, really, to me, that just seems a bit of a misnomer. A bit like saying someone's 'prejudiced' against polio because he doesn't want people to catch it. Doesn't so much scan, really...

    (You bastard. What have you got against it, after all? Just cripples people, after all. Leave an honest enterovirus alone!)

    Oh, and yeah, I think religions are mind-eating bollocks, too, by and large. But it's not 'prejudice' there, at all, at least, if y'ask me.

    See, 'prejudice' generally denotes an ill-considered opinion, possibly something you just assume, for want of experience...

    And, quite the contrary, my antipathy toward religion is rather more a considered opinion, supported by long and painful experience. Yea, I have thought long and hard on this, and have very definitely concluded religions are bollocks, damn straight. Lo, over many decades, I have watched the rot they do work in human minds and concluded: there may be worse things in the world, but most of those, the UN cordons off the area when we find them...

    (/Like I said: an opinion built of experience. And, might I add, with every comment from DI-supporting loons, my sheaf of evidence on said score doth verily grow thicker.)

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  15. anonymous,

    The issue is that you consistently make misleading statements about ID, and even lie about it.

    I can assure you that any misleading statements are entirely unintentional. I'd be happy to correct any of them that you'd care to point out.

    I have never lied about Intelligent Design Creationism. I challenge you to either prove that claim or retract it.

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  16. That's why those papers get published in Nature and Science and that's why those papers always fail to even mention the positive evidence for junk

    Could you point out an article which claims that most/all junk is not junk? A brief look through nature found papers about junk that has a function, but none of them claimed that their evidence proved that most of our DNA is not junk.

    We know for a fact that most biologists will look at a dog ass plot and see nothing wrong with it
    Everything is wrong with it...but what do you expect, its in SciAm; science's answer to the Daily Enquirer...

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  17. "We should call it DNA whose function we haven't found."
    One could make the argument that "junk" is just as prejudicial - and just as wrong. I rarely teach anything to do with genetics, but if the topic comes up I usually refer to it as "non-coding DNA", which is about as accurate a description as we have.

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  18. Thank your for your posts on this topic - as an evolutionist and Christian who's "out" at a conservative church, I fully expect to get an earful of conversation about junk DNA over the coming months as a result of this book and the ammunition is greatly appreciated. Can you recommend any books or papers on the subject, written at a level a humanities grad can grasp?

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  19. Re: the idea that if all "junk DNA" were shown to have an integrated function, then that would lend credence to ID -- just the opposite!

    In software development (and other types of engineering), there is a term called "coupling", and it is a bad thing. When you design a system, any system, you've got a number of modules that perform different functions. When the modules talk to each other, ideally they should only care about the other modules' functions ("loose coupling"), not about the details of how they work ("tight coupling"). That way, you can swap in a different module that performs the same function, and you are good to go, with no or minimal modifications to modules that depend on it.

    Even ignoring junk DNA, everything we know about how the genome functions could well be characterized as "tight coupling". Everything depends on everything else in a messy, interwoven way.

    Now, how do software systems end up with tight coupling? Well, loosely coupled systems are typically ones that were well designed up front, with an overarching plan of what modules would exist and what their functions would be. Tightly coupled systems tend to be the result of a poor or inadequate design, where changes to the system layout are made on an ad hoc basis as the need is encountered. They grow organically, without the necessary intelligent foresight to avoid the tight coupling issues.

    So yeah... if every piece of DNA depends on every single other piece of DNA in some intimate and interconnected way, that sounds like a system that was somehow built with no plan and no design whatsoever.

    That's even if there were no junk DNA. Which there is, of course. But if there weren't, that would be an even stronger argument against ID than if there were.

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  20. Anonymous (abbrev. "Anus."),

    I don't think Larry needs any help, let alone from me. So, instead I will just comment on the problems of your attempt at a Tu quoque fallacy.

    The issue is that you consistently make misleading statements about ID, and even lie about it.

    There are a few problems here beyond the fallacy itself. For instance, "consistently" means "every time." I do not see any misleading statement in the current post about ID, nor any lies. Nor have I seen any before.

    On that basis you are a moron.

    On that basis you don't even know what the words "misleading" and "lie" mean.

    What you claim about proponents of ID applies to you. You just do not see that.

    No, it does not apply. You just don't like it when the "talents" of the IDiots are presented to you so clearly that you can't even deny them, to the point that you had to fall back into this attempt at a Tu quoque fallacy.

    But it is always hard to see one's own projection.

    You make a very good example of this.

    As I have told you before, Anus., I truly tried not to use the word IDiots when referring to those creationists. Believe me. I tried hard not to call them that, I tried decent exchange, and got back only rhetoric, lies, red-herrings, misrepresentations, and overall bullshit from them. They work hard to win the epithet. They deserve it. So don't come and try to take away what they worked so hard to earn.

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  21. Bryan,

    But the point was that a majority of it being junk DNA was not the prevalent view among biologists.

    As of "but if the topic comes up I usually refer to it as "non-coding DNA""

    Well, first, you are being an example yourself that it being mostly junk is not that much of a prevalent position among biologists; second, you are then misleading your students, because "non-coding DNA" is a lot of stuff. Non-coding DNA includes genes that produce rRNA, tRNA, siRNA, et cetera. Non-coding DNA includes regulatory regions too. Then you have the selfish and the junk, which might overlap depending on your definition of junk.

    Best,
    N.E.

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  22. Bryan says,

    ... if the topic comes up I usually refer to it as "non-coding DNA", which is about as accurate a description as we have.

    That's a very inaccurate statement as "Negative Entropy" has already pointed out. It suggests that you aren't very familiar with the subject.

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  23. Bryan asks,

    Could you point out an article which claims that most/all junk is not junk? A brief look through nature found papers about junk that has a function, but none of them claimed that their evidence proved that most of our DNA is not junk.

    I was thinking of the original ENCODE paper (Nature 447:799-816, 2007) where the conclusion was, "The human genome is pervasively transcribed, such that the majority of its bases are associated with at least one primary transcript ...."

    This paper is widely interpreted as evidence that most of the genome has a function because it's transcribed. A recent Nature review says,

    "Just one decade of post-genome biology has exploded that view [simple lac operon regulation]. Biology's new glimpse at a universe of non-coding DNA—what used to be called "junk" DNA—has been fascinating and befuddling. Researchers from an international collaborative project called the Encyclopedia of DNA Elements (ENCODE) showed that in a selected portion of the genome containing just a few per cent of protein-coding sequence, between 74% and 93% of DNA was transcribed into RNA." Hayden, E. (2010) Nature 464:664-67.

    These kind of statements are common in the scientific literature. They imply that there's still a great deal of mystery in our genome and that referring to most of it as "junk" is naive. Unfortunately, none of these papers ever mentions the massive amount of evidence supporting the idea of junk. They never bother to point out that the latest data conflicts with earlier data. I think this is because most of these authors are completely unaware of the earlier data.

    We know that 50% of our genome consists of defective transposons. Even if a lot of that DNA is transcribed, what kind of function could it have? We know that a lot of intron sequence is non-functional even though it is transcribed. What this measn is that we already have good evidence that the mere fact of transcription isn't evidence of function. Those arguments are never addressed. Why?

    (The correct conclusion, by the way (IMHO), is that most of the the transcripts are Junk RNA or Imaginary RNA.

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  24. I've mixed-and-matched replies here...chalk it upto lazyness

    That's a very inaccurate statement as "Negative Entropy" has already pointed out. It suggests that you aren't very familiar with the subject
    I thought I was clear before that I was not an expert, nor claimed any expertise in the area. If this comes up in future lectures I'll obviously have to rephrase my answer*

    *In my defense, the only times I can recall the topic coming up was during lectures of V(D)J recombination; and non-coding would be an accurate description of the DNA being discussed.

    We know that 50% of our genome consists of defective transposons. Even if a lot of that DNA is transcribed, what kind of function could it have?
    You're being anthropocentric. From the "broken" transposons point of view, its done a pretty good job of parasitizing us and propagating. From ours, its either junk or a parasite.

    Well, first, you are being an example yourself that it being mostly junk is not that much of a prevalent position among biologists
    How do you figure - I said before that I'm certain most of it is junk. But belief is not fact, hence why I also think it would be stupid of us to stop looking for potential functions.

    I was thinking of the original ENCODE paper (Nature 447:799-816, 2007)...This paper is widely interpreted as evidence that most of the genome has a function because it's transcribed
    Fair enough, I had not seen the commentary. But its the commentary, not the paper, which matches your complaint. The commentary is where "function" is assigned to the junk. the actual paper showed transcription of most of the genome, and their conclusion reflected that. Accurately describing your results is hardly a scientific 'sin'. Not critically thinking about them and insufficient controls (both of which may have happened here), are.

    Lets assume for a second they are correct (although even my minimal experience with working with RNA makes me hesitant to accept their conclusion). Does is refute the junk hypothesis - I think not. Lots of pseudogenes are transcribed into RNA; some are even spliced into mRNA. But they code for nothing, and deleting them has no apparent effect. Ergo, they're still junk. I'd expect the vast majority of the RNA detected in that paper would fit the same category (it its actually being transcribed at all) - transcribed, perhaps processed in some form, but otherwise functionless. Junk, in every sense of the word.

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  25. Bryan says,

    Lets assume for a second they are correct (although even my minimal experience with working with RNA makes me hesitant to accept their conclusion). Does is refute the junk hypothesis - I think not.

    I agree with you but that's not the point.

    The point is that most biologists disagree with us—especially biochemists and molecular biologists. They think that most of our genome has a function and the fact that it is transcribed is evidence of function.

    The commentaries in Science and Nature reflect that perspective. They often include interviews with the authors of the papers.

    Here's an example from the December issue of Science. It contains the "insights of the decade" and one of them is Shining a Light on Genome's 'Dark Matter' by Elizabeth Pennisi. The focus of the article is on questioning junk DNA and the mysteries of "non-functional" DNA (dark matter). It's obvious to some of us why her analysis is wrong but the very fact that Science would publish this as an "insight of the decade" reveals that many scientists are skeptical of junk DNA.

    Pennisi's article has the obligatory mention of the deflated ego problem and I honestly believe she's reflecting the beliefs of many scientists.

    The scope of this "dark genome" became apparent in 2001, when the human genome was first published. Scientists expected to find as many as 100,000 genes packed into the 3 billion bases of human DNA; they were startled to learn that there were fewer that 35,000. (The current count is 21,000.) Protein-coding regions accounted for just 1.5% of the genome, Could the rest of our genome really just be junk?

    All knowledgable scientists who had studied genome organization expected there to be 30,000 genes or less [False History and the Number of Genes] [Facts and Myths Concerning the Historical Estimates of the Number of Genes in the Human Genome].

    The amateurs who were "startled" are the very ones who continue to look for excuses in order to explain why a human is so much more complex than a fruit fly or a mouse. Elizabeth Pennisi's article is a nice summary of all the current excuses.

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  26. Most Biologists are unaware of the experiments where large regions of DNA have been deleted. They don't understand why we know that the vast majority of transposons are defective. They don't appreciate the significance of studies on intron size and sequence conservation. They don't know that we have 20,000 pseudogenes.

    I have to disagree. You can know all these things and still suspend judgement about whether most of the genome (human, mouse, fly, onion, whatever you like) has no functional significance whatsoever.

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  27. The point is that most biologists disagree with us—especially biochemists and molecular biologists

    FWIW, I am a molecular biologist and biochemist/biophysicist, masquerading as an immunologist...but I "believe" in junk.

    I think we could go around in circles, ad infinitum and never reach an agreement. A couple final comments on my part, and the you can have the last word if you choose.

    As much as we may wish otherwise, part of he "job" of science journals is to promote themselves and the work in them. Like with conventional media, this usually means exaggeration and simplification. I pay little attention to commentaries for that very reason, as do most of the people I work with. In the case of your own example, the commentary was written by natures staffer Erika Check Hayden, whose own bioptic states she has a B.Sc but no formal science experience, and instead has been a reporter for her whole career. We can hardly use her viewpoint as evidence of scientists opinions in general.

    As I said before, in my limited experience most biologists (or maybe I should say "working biologists") have no issue with the concept of most our genome being junk. The paper you cited did not make the contrary claim, and even was quite muted in their claims surrounding their data which points to the opposite conclusion ("...suggests that we take a more 'neutral' view of many of the functions conferred by the genome"). Contrary to refuting the junk hypothesis, this paper simply proposed nothing more radical than neutrality on the role of non-coding sequences.

    You seem to be implying that studies like these mean people reject the hypothesis that most of our genome is junk. I disagree - challenging our past conclusions is an important part of science, and in terms of junk, there very well may be functional elements we don't know of still hidden within the junk. We would be remiss in our work to not challenge our past conclusions, or to look for functional elements we have missed.


    I guess a short sum-up would be where you see evidence of people rejecting junk DNA I see evidence of scientists doing their job. Genomics is a rapidly growing field; mis-steps are to be expected. But its better we make those missteps than mis something important because we are married to one hypothesis or another.

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  28. anonymous says,

    I have to disagree.

    The question is whether most biologists know those things. Do you really think they do?

    How many of your biologist friends know about genetic load and why it predicted only 30,000 genes back in 1969?

    How many of them could describe the Cot and Rot curve experiments of the 1970s and why they suggested strongly that most of our DNA was junk?

    How many know the difference between SINES and LINES and why most of those sequences are non-functional?

    You must hang out with a very special group of biologists.

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  29. Anonymous ID advoicate:

    The issue is that you consistently make misleading statements about ID, and even lie about it.


    Examples?

    AnonymousX

    ReplyDelete
  30. You must hang out with a very special group of biologists.

    No, they're not that special. They are generally aware of all of those things, commonly taught at the undergraduate level (or used to be anyway), with the takehome message that if there is a function to non-coding regions generally, it is not going to be dependent on the primary sequence of those regions, in the manner in which conserved-sequence regions of the genome usually are. Mostly they also understand the importance of keeping an open mind, and dispassionately assessing the validity of new data as it comes in.

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  31. Larry, I don't think we're as much of a minority as you make it out to be. Most biologists I hang out with both offline and on the internet accept the proliferation of junk DNA as common sense, even the die-hard adaptationists (maybe I set the bar a little low for that one...).

    Ok, I guess then again, for some reason I tend to attract the type of biologists that drool over The Origins of Genome Architecture for some reason... speaking which, I think it's heavy enough to knock out the junkless folk, we should try that... ;-)

    But yeah, junk DNA, particularly in large eukaryotes, is no longer a minority view. Those who disagree are the fringe minority.

    The general public may be a whole other question though...

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  32. Psi Wavefunction says,

    Larry, I don't think we're as much of a minority as you make it out to be. Most biologists I hang out with both offline and on the internet accept the proliferation of junk DNA as common sense, even the die-hard adaptationists (maybe I set the bar a little low for that one...).

    We need to distinguish between those scientists who admit the existence of (some) junk DNA in our genome and those who think that MOST of our genome is junk.

    The first group is like the adaptationists who insist that they know about neutral mutations and random genetic drift. It's one thing to admit that junk DNA exists but it's quite another to accept that MOST of our genome is junk.

    In my experience, the majority of biologists are very skeptical about the idea that a huge percentage of our genome could have no function whatsoever. That's why the scientific literature is so friendly to papers that question this idea.

    In my department only 1/3 of the scientists (PI's, graduate students, post-docs) raised their hand when I asked them to agree with the statement that most of our genome was junk. About half disagreed with the statement.

    When I took a poll on Sandwalk a few years ago, about 40% said that more than half of our genome was junk and 60% said less than half.

    Have you asked your colleagues whether they believe that MOST of our genome is junk?

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  33. the majority of biologists are very skeptical about the idea that a huge percentage of our genome could have no function whatsoever. That's why the scientific literature is so friendly to papers that question this idea.

    Do not underestimate the power of the selective effect of the literature in not publishing negative results as an explanation for the apparent enthusiasm for these papers.

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  34. I completely agree with Wells.

    Moran is wrong.

    His argument is essentially an argument from personal incredulity and poor analysis.

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  35. It's so fascinating watching materialists like Larry Moran rewrite history! It's like 30-40 years of clear, uncompromising statements about "junk" DNA just didn't happen.

    Larry Moran's blog is a truly fascinating study in human psychology and sociology!

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