Home » 'Junk DNA', News » Vid:The Debate That Never Was: Craig vs Dawkins – “junk DNA” does show up though

Vid:The Debate That Never Was: Craig vs Dawkins – “junk DNA” does show up though

We’re told that the panel’s biologist claimed that all the DNA besides the 2% protein-coding regions is redundant junk.

 

See also: What advice, on junk DNA, would Jonathan Wells give Francis Collins or Richard Dawkins?

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16 Responses to Vid:The Debate That Never Was: Craig vs Dawkins – “junk DNA” does show up though

  1. Cool, Thanks for the link,,, just in time to get a cup of coffee and watch! :)

  2. “the panel’s biologist claimed that all the DNA besides the 2% protein-coding regions is redundant junk”

    Boy, I hope not. Hard to think of a more clueless statement.

    If all this “junk DNA” was evidence for Darwinian evolution, as strongly stated over the years by Dawkins, Miller and others, then finding function for this junk DNA thus acts as evidence against Darwinian evolution.

    Unless, of course, they want to admit that junk DNA was never evidence for Darwinian evolution in the first place.

    The feet need to be held to the fire regarding junk DNA.

  3. I hate to be so dogmatic, but I only see two possibilities available after watching this debate.

    1. You understood Craig’s arguments and you agree that Dawkins’ arguments are totally flawed.
    2. You don’t understand Craig’s arguments and you accept Dawkins’ arguments as substantive.

    Note: this is not an argument about whether God exists or not, it is only about the quality of Dawkins’ arguments. If you are smart enough to understand Craig’s line of argumentation – you must accept that Richard Dawkins is basically ignorant about theology and puts forward a load of specious arguments.

    To still support Dawkins’ book as an intelligent defense of atheism – is to declare yourself unable to follow the straight forward arguments put forward here, and to affirm your own ignorance.

    Sorry, but I can’t help see it that way.

  4. Oops. Last line should have been. Sorry, but I can’t help see it any other way. ( Wish there was a way to edit obvious mistakes )

  5. If all this “junk DNA” was evidence for Darwinian evolution, as strongly stated over the years by Dawkins, Miller and others, then finding function for this junk DNA thus acts as evidence against Darwinian evolution.

    Yikes! If something stops being evidence for, that does not automatically make it evidence against! But your premise is shaky, let alone your conclusion.

    There seems to be a general opinion hereabouts that “Darwinian evolution” somehow ‘needs’ junk DNA. That’s not the case. Darwin himself never uttered a word on DNA, dying some 70 years before we knew much about it. And as a keen proponent of Natural Selection, Darwin might have been pretty surprised to find so much apparently costly vestigial stuff lying around. Finding function for another x% of DNA would not trouble an evolutionist one iota – what caricature are you carrying around in your head? We can deal with 10% or 25.778%, but if it turns out to be 100% we’d scurry round like headless chickens? Gimme a break.

    The presence of junk DNA is not evidence for evolution. Prokaryotes have barely any, but no-one supposes them not to have evolved. But the content of DNA – both junk and non-junk – is regarded as displaying excellent evidence for evolution, due to conservation of recognisable motifs. Junkiness doesn’t much come into that argument, except as it impinges on rate of change and degree of conservation.

    Unless, of course, they want to admit that junk DNA was never evidence for Darwinian evolution in the first place.

    If you can find a primary source where that opinion is expressed (that junk’s presence, as junk rather than functional sequence, is evidence for evolution) I’d be interested to see it.

    The feet need to be held to the fire regarding junk DNA.

    Yeah, of course they do.

  6. “We’re told that the panel’s biologist claimed that all the DNA besides the 2% protein-coding regions is redundant junk.”

    –He said that 2-3% code for protein and that up to “90%” are junk. At least, I think that’s what he said. It was a bit difficult to understand him. Everyone but Craig was speaking some funny language.

  7. DI KWEENZ INGLISH

  8. “If you can find a primary source where that opinion is expressed (that junk’s presence, as junk rather than functional sequence, is evidence for evolution) I’d be interested to see it.”

    Are you kidding? This is an extremely common line of argument (used even on this blog by our friend Nick Matzke). Just a few prominent evolutionary apologists who have made this argument:

    Kenneth Miller in Life’s Grand Design, 1994
    Richard Dawkins in A Devil’s Chaplain, 2004
    Douglas Futuyma in Evolutiion, 2005
    Michael Shermer, Skeptic Magazine, 2006
    Francis Collins in The Language of God, 2006
    Philip Kitcher, Columbia University, in Living With Darwin, 2007
    Kenneth Miller in Only a Theory, 2008
    Jerry Coyne, University of Chicago, in Why Evolution is True, 2009
    Richard Dawkins in The Greatest Show on Earth, 2009

    and on and on . . .

    Check out Jonathan Wells’ book “The Myth of Junk DNA”. Whether or not you agree with his argument about DNA supporting design, it will at least help get up to speed on the fact that junk DNA has been, and continues to be, a key piece of evidence used by evolutionists to argue for the veracity of evolution and to argue against design.

    So when the tide of evidence starts to turn, as it has over the past decade, we are left with two alternatives: either the evolutionary expectation is being falsified, or it wasn’t really evidence for evolution in the first place and was just rhetorical bluster.

    Evolution’s long track record of arguing for non-function in biology is abysmal, with a nearly universal failure rate.

  9. Sorry, all you’ve given me is a list of books. You’re making the claim that such a position has been advanced, and you expect me to do the leg-work to verify it?

    The theory of evolution was 110 years old when the first suspicions about junk DNA arose. How on earth can it be “a key piece of evidence used by evolutionists to argue for the veracity of evolution”? If it is, could you supply me just one quote to support that claim?

    Here’s what Wells says:

    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

    I don’t think both parts of that claim are true. Yes, they argue it is junk. No, I don’t agree they have argued that DNA being junk provides evidence for Darwinian evolution. I am prepared to be wrong, because I have not read everything they ever wrote, but I would like to see a relevant quote rather than 3rd-hand reportage.

    I have read pretty widely on the subject of evolution, including several of those books, and have never come across the claim that non-functional DNA per se is evidence for evolution. That is, its nonfunctional status, rather than the story it tells about history, matters to the evolutionary argument. Some genomes have barely any junk. Do you seriously think they are a problem for evolutionary theory?

    The relatedness between ‘live’ genes and pseudogenes is evidence for evolution, as is that between the various transposon families and their inactive members that litter our genomes, or the various means by which satellite DNAs accumulate.

    But nowhere have I seen any claim that those comparisons rest upon one or other of the compared sequences lacking function. We certainly need to take account of function, because it affects selection and hence rate-of-change. Indeed, one way to uncover function is to detect this rate-of-change signal, by comparison across the genome. But evolution would not be torpedoed by the ‘junkists’ being proven wrong, so I’d like to know whence comes the idea it would.

  10. The argument that junk DNA provides evidence supporting Darwinian evolution is quite common from well-known evolutionary proponents, as a Google search would quickly tell you. I’m willing to take time to provide you “just one quote,” in fact more than just one quote, from the books/articles I cited above, but before I waste my and your time, let me make sure I am understanding your position.

    Are you claiming that prominent evolutionary proponents have not argued that junk DNA provides evidence for evolution?

  11. Are you claiming that prominent evolutionary proponents have not argued that junk DNA provides evidence for evolution?

    Provides or contains? Most DNA contains it; junk only ‘provides’ it in response to a particular kind of denialism – an insistence that similarities in functional sequence can be explained away by common design. If we then point to nonfunctional similarities, we are not just talking of ‘junk’, but of silent substitutions, chemically conservative substitutions, those that have no impact upon enzyme activity, etc, in coding DNA. Nonfunctional DNA just happens to have a lot more scope for that kind of thing – it is no better as evidence for evolution; it is simply harder to explain away as ID. If some or all turns out to be functional, this causes no problem for the evolutionist, who is perfectly happy with Common Descent for functional sequences.

    Nonetheless, when I Google “junk DNA evolution evidence”, I get mostly creationist sites trying to refute the notion, and getting it wrong.

    Here is one version of the canard:

    Bill Pratt: One of the most common arguments you will hear that Darwinian evolution must be true is the “Junk DNA” argument. It goes like this:

    There are significant stretches of the human genome that appear not to code for any biological function. This is what you would expect if millions of years of random genetic mutations occurred in the genome.

    That messy genomes demonstrate “Darwinism”, I have never heard any ‘evolutionist’ claim – and particularly not a “Darwinist”. There are two principal ideas in Darwinism: 1) Common Descent and 2) the primacy of Natural Selection. All evolutionists are Darwinists sense 1; not so many are Darwinists sense 2 these days – and particularly in the matter of genome construction. Junk in the genome actually runs counter to Darwinism sense 2. It must be costly, and adaptationists are resistant to the idea that it nonfunctional. You would find many allies among “Darwinists” against the nonfunctional nature of junk!

    On the matter of Common Descent, the argument is a little different. It is not a matter of expecting the evolutionary process to make junk, but that, given that a sequence appears nonfunctional, common design ceases to be a tenable explanation for common sequence (not that I think it is in the first place!).

    To return to your original comment:

    If all this “junk DNA” was evidence for Darwinian evolution, as strongly stated over the years by Dawkins, Miller and others, then finding function for this junk DNA thus acts as evidence against Darwinian evolution.

    I’m not clear if you are saying that those authors invoke junk to support Natural Selection (Darwinism Sense 2) or Common Descent (Darwinism Sense 1). I might concede the second – but your conclusion still does not follow.

  12. The evidence for evolution that junk DNA provides is not based on it being junk, but rather based on the evidence that changes have accumulated in a nested hierarchy.

    There is some presumption that nested changes in non-functional code are stronger evidence than changes in functional code, because functional code could be attributed to common design.

    I think this last argument is the key to the ID proponent’s opposition to junk.

  13. Chas D:

    “Nonfunctional DNA just happens to have a lot more scope for that kind of thing – it is no better as evidence for evolution; it is simply harder to explain away as ID. If some or all turns out to be functional, this causes no problem for the evolutionist . . .”

    OK, so in your viewpoint, whether junk DNA is functional or non-functional is irrelevant as evidence for evolution. That is probably the safer position to take, but unfortunately it is not the position taken by several prominent evolutionary proponents. Just to quote a couple:

    Dawkins from the 2004 book I cited above:
    “Genomes are littered with nonfunctional pseudogenes, faulty duplicates of functional genes . . . And there’s lots more DNA that doesn’t even deserve the name pseudogene. . . . It consists of multiple copies of junk, ‘tandem repeats’, and other nonsense which may be useful for forensic detectives but which doesn’t seem to be used in the body itself. Once again, creationists might spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA.”

    Futuyma, from the book I cited above, argued that only Darwinian evolution ” can explain why the genome is full of ‘fossil’ genes: psedogenes that have lost their function.” He also argued that these features of DNA are “hard to reconcile with beneficient intelligent design.”

    Francis Collins argued that “ancient repetitive elements” in DNA provide support for Darwinian evolution, “unless one is willing to take the position that God has placed these decapitated AREs in these precise positions to confuse and mislead us.”

    Jerry Coyne: “Imperfect design is the mark of evolution; in fact, it’s precisely what we expect from evolution.” He went on to argue that, under evolution, we should expect to find non-functional pseudogenes.

    John Avise: Several features of DNA “defy notions of ID by a caring cognitive agent [but are] consistent with the notion of nonsentient contrivance by evolutionary forces.” He argued as an example that “the vast majority of human DNA exists not as functional gene regions of any sort but, instead, consists of various classes of repetitive DNA sequences, including the decomposing corpses of deceased structural genes.”

    ———-

    Each of these individuals clearly viewed the existence of DNA that was thought to be “junk” as evidence for evolution (and often also viewed it as evidence against ID). I agree with you that you are better off not taking that position.

  14. Eric Anderson,

    OK, I see more clearly where you are coming from. The problem is perhaps the catch-all use of the term “Darwinism” to cover what we might call ‘naturalistic evolution’. Darwin thought many things, some of which are still thought, others of which are not, and others form only part of a much broader picture of causes.

    But as regards the safety of various positions, I think that the ‘feet-to-the-fire’ angle is a little premature. There is a fraction of the genome that is nonfunctional, and it is greater than 0%. This can be demonstrated by within-species variation, where the natural ‘experiment’ of recombinational excision can be shown to have had no effect. And on present evidence, it is still a lot greater than 0% – the newly discovered functions have added only a couple of percent to the minuscule ‘functional’ pile.

    More speculatively, I’d be willing to bet that we could replace every intergenic Alu and LINE1, say, with randomly generated nonsense without any impact on fitness. That, of course, is deniable. You just have to say ‘prove it’, and I scuttle back into my corner with my tail between my legs. But to me (with no particular desire for any particular result) that would be an over-extended application of denial. It is not that we don’t want to give ground on junk, because it supports some mythic worldview, but that there is no good reason to suppose that these elements serve a function where they are. These intergenic sequences are inoperable as far as their transpositional abilities are concerned – transposons often ‘break on landing’. And they don’t appear to actually do anything dependent upon their sequence. So the fact that Wells can point to relatives of these sequences that have landed on genes and become functional – even beneficial – does not make the 20-odd% of the genome that these intergenic sequences occupy non-junk by association.

    And – to kind of contradict myself – transposons do provide excellent evidence of evolution (specifically: common descent). But this has nothing to do with their being ‘junk’ – they might be there for a reason, they might not. But what they do, by landing in a particular mappable place in the genome, is provide a clear binary signal. That place may either possess the transposon, or it may not; there is no ambiguity. Trying to find a plausible functional reason for the pattern that emerges on interspecies analysis requires one to explain how and why xxxTRANSPOSONyyy is functional in one group of organisms, while xxxyyy alone is functional in another – multiplied up tens of thousands of times, for the sundry instances of these insertions. One could say ‘common design’, but the organisms grouped by this binary signal are often very different.

  15. Thanks, Chas D.

    I am primarily talking about, as you say, naturalistic evolution (which is of course how the major defenders of evolution believe it to function). Except for the possibility of some kind of guided evolution, whenever evolution is discussed by the major proponents it is understood to mean a fully naturalistic and materialistic process, so I’m using it in that sense. You are right that whether descent happened is a different question from how the descent happened.

    Just a couple of thoughts to round out the discussion before the thread gets too buried.

    You say: “There is a fraction of the genome that is nonfunctional, and it is greater than 0%. This can be demonstrated by within-species variation, where the natural ‘experiment’ of recombinational excision can be shown to have had no effect. And on present evidence, it is still a lot greater than 0% – the newly discovered functions have added only a couple of percent to the minuscule ‘functional’ pile.”

    I don’t dispute that a non-zero portion of current DNA is non-functional. I do have to disagree, however, that “it is still a lot greater than 0%.” That stated formulation assumes, without basis, that we should assume non-function until function is proven. That is precisely the mindset that gave rise to the point we are discussing in the first place: namely, whether much or most of DNA is “junk DNA.”

    For some reason the Dawkins and the Millers of the world have shown a great deal of interest in the idea of junk DNA supporting evolution, and just as importantly for their worldviews, contradicting the concept of intelligent design. Junk DNA is, in essence, just another example of the invalid “bad design” line of arguments. The reason I say their feet need to be held to the fire is because they have clearly gone on record saying that a large amount of non-functioning DNA is evidence for evolution and against design. Now that the evidence is starting to lean the other direction I am not at all interested in letting them off the hook easily with any backpedaling (although, astoundingly, some of the folks I cited haven’t even started backpedaling, as they seem to be oblivious about recent research). It is absolutely reasonable to point out that their expectation, arising from their viewpoint in favor of evolution and against design, is starting to be falsified and to insist that they admit as much.

    You also state: “More speculatively, I’d be willing to bet that we could replace every intergenic Alu and LINE1, say, with randomly generated nonsense without any impact on fitness. That, of course, is deniable. You just have to say ‘prove it’, and I scuttle back into my corner with my tail between my legs. But to me (with no particular desire for any particular result) that would be an over-extended application of denial. It is not that we don’t want to give ground on junk, because it supports some mythic worldview, but that there is no good reason to suppose that these elements serve a function where they are.”

    Again, you are starting from an assumption of non-function, which is not an assumption based in science, but in something else. In fact there is no good reason to suppose that these elements don’t serve a function. Indeed, functions have been found for LINEs, including embryo development, repairing DNA breaks, mobilizing RNAs, silencing a gene needed at the fetal stage but not needed at the adult stage, and so on. You also mentioned transposons, several of which are now known to have function.

    The bottom line on so-called “junk DNA” is this.

    1. There is very little logical reason to assume that there is a lot of junk DNA. The possible exception being some excision experiments, but we have to be extremely careful to not misinterpret those results. Specifically, we cannot say that a particular part of DNA has no function based on an excision experiment. At most, we can say that, given the short amount of time the observation was conducted, it appears that removal of a particular part of DNA did not have an adverse impact on the organism in its current state. The reason we have to limit this inference is that we know (i) some processes occur only at specific stages of an organism’s life, and (ii) there is some redundancy built in. Think of it this way: If I am launching a Saturn V rocket to put an Apollo spacecraft in orbit and one of the five engines cuts out shortly after launch, the fact that they were still able to attain orbit does *not* mean that the cut engine did not have function, and I cannot validly claim that it didn’t have an important function just because that function wasn’t realized.

    Looking at DNA and proclaiming that we don’t know what most of it does, and therefore, it probably doesn’t have function, is intellectually equivalent to someone opening up a supercomputer and proclaiming that most of the parts must not have function because they don’t know what the parts do. It just doesn’t follow, and there is no reason to take that position.

    2. In contrast, there are very good reasons to think that the great majority, though perhaps not all, of junk DNA in fact has function. I will give just three off the top of my head.

    A. First of all, the non-functioning DNA argument (just like vestigal organs) has an abysmal track record, so we should be very cautious about jumping on that bandwagon. Introns are now known to be critical to alternative splicing. Pseudogenes help regulate DNA. LINEs and SINEs have known functions, as do certain transposons. And on and on. Adopting non-function as an initial assumption puts us on the wrong side of history.

    B. More importantly, there are numerous known biological functions, the programming for which has not yet been discovered or fully elucidated. Just looking at any basic biology text and drilling down to the details reveals numerous functions that must be in place for almost any meaningful biological activity. If we spent a day, we could come up with a list of thousands of known functions, every single one of which must, by definition, have some kind of instantiation in DNA or elsewhere in the cell. As a result, we know, by definition, that many thousands of functional programming elements remain to be discovered; indeed vastly more functional elements remain to be discovered than the number that have been discovered to date.

    C. From a basic engineering standpoint the idea of large amounts of useless DNA is problematic. Regardless of whether one thinks our current DNA came about by design or by random chemical processes, everyone understands that DNA, and the related cellular mechanisms, carry out an absolutely stunning symphony of carefully-orchestrated processes. It is also known that most DNA, including so-called “junk DNA” is transcribed at one level or another. So here is what the junk DNA proponents would have us believe: a sophisticated storage, retrieval, transcription, translation, error-checking, sheparding, building, functioning orchestra of thousands of concurrent processes just happens to take place with incredible fidelity from hour-to-hour, day-to-day, indeed generation-to-generation, while being almost completely overwhelmed in terms of volume by processes of storage, retrieval, transcription and translation of complete nonsense, which, at the very least uses precious resources, and at worst, has the ability to completely muck up the chemical orchestra and bring the whole system to a grinding halt.

    Think of it this way: Although our modern computer operating systems can occasionally handle a minor error here or there without crashing, in most cases a significant error will bring the system to its knees and require a reboot, despite huge efforts expended to get the operating system right in the first place and to prevent viruses and the like. Yet we are expected to believe that the human operating system, which is vastly more complicated and which operates much more robustly than any computer operating system, can swim in a literal sea of nonsense and garbage. It would be like having a computer filled to the brim with viruses, malware, nonsense strings and the like that are regularly being accessed and run, without being any worse off for it, indeed, without any noticeable or identifiable delays or hiccups. Such an idea is simply absurd, and might be best described as the “stupid man’s view of engineering.” I doubt you hold to this view, but it certainly applies to Dawkins and similar folks who would have us believe that the “good” DNA just by happenstance works fine, thank you very much, while swimming in a sea of “junk.”

    ——-

    There may be some DNA that has no function. Certainly even the most carefully designed machine can degrade or break down over time. But outside of materialistic philosophy there is no reason to think that much or most DNA is junk, while there is every reason to think that much or most DNA is functional. I don’t know whether we can put a precise number on it, but I would venture that more than 90% of DNA will eventually be shown to have function.

    Best,

  16. Tomorrow (23rd Feb 2012) will be a new event with Dawkins in the Sheldonian, and we must ask:

    http://www.youtube.com/watch?v=OO_wywhZBEc

    …will the Archbishop of Canterbury leave him an empty chair?

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