Wednesday, May 15, 2013

Michael Denton on Junk DNA

I was reading the latest spiel from Sal Cordova (scordova) when I noticed a reference to Michael Denton. Cordova was ranting about how Taxonomic nested hierarchies don’t support Darwinism and he began with ...
Taxonomic nested hierarchies don’t support Darwinism or common descent, actually the opposite. Michael Denton convincingly argued that nested hierarchies can be used to argue against macro evolution. If the fish are always fish, then they will never be birds, reptiles, apes, or humans.
I knew that this was a misrepresentation of Denton's views since he (Denton) supports the idea that nested hierarchies represent the true history of common descent.

Michael Denton thinks that evolution was directed and that explains why fish and mammals are so different even though they contain a common ancestor. He accepts common descent but rejects spontaneous mutation and mechanistic fixation of alleles as the explanation. I checked his latest book Nature's Destiny (1998) to confirm that I was right.

Denton supports a teleological view where God created conditions (first cause) that would lead to humans (final cause) but that the process included evolution from common ancestors. In Denton's case the "design" was inherent in the laws of physics and chemistry and the rules of mutation and gene expression.

While refreshing my memory, I came across this paragraph that I had highlighted in his book fifteen years ago.
If it is true that a vast amount of the DNA in higher organisms is in fact junk, then this would indeed pose a very serious challenge to the idea of directed evolution or any teleological model of evolution. Junk DNA and directed evolution are in the end incompatible concepts. Only if the junk DNA contained information specifying for future evolutionary events, when it would not in a strict sense be junk in any case, could the finding be reconciled with a teleological model of evolution. Indeed, if it were true that the genomes of higher organisms contained vast quantities of junk, then the whole argument of this book would collapse. Teleology would be entirely discredited. On any teleological model of evolution, most, perhaps all, the DNA in a genome of higher organisms should have some function. (pp. 289-290
I wonder what Intelligent Design Creationists think of this argument?


  1. How does Cordova explain something like this?:

  2. Maybe Cordova is making reference to Denton's old argument in his 1985 book "Evolution: A Theory in Crisis". This was that molecular evidence showed humans and frogs to be about equally different from fish, and how could this be if amphibians were ancestral to mammals? Shouldn't they then be closer to fish than mammals were?

    This was a wrong argument, of course. I believe Denton has since withdrawn it. That wouldn't stop creationists from continuing to cite the argument, of course.

    1. Yes, that's it. In his first book, Denton rejected common descent, but he changed his views in his second book (without acknowledging his previous ones, by the way...). So this is cherry picking, as usual.

    2. Where's Larry? Because I'm pretty sure he disagrees with you on Denton. He thinks that Denton didn't change his beliefs at all between his first and second books, and that "Evolution: A Theory in Crisis" doesn't reject common descent. I would love to see a discussion of that between two people who actually have access to the book.

    3. I don't think Denton changed his view very much at all. I think that most of us jumped to an incorrect conclusion when we first read Evolution in Crisis. This was mostly because Denton did a very bad job of explaining himself.

      If you take the time to understand his current point of view in Nature's Destiny then go back a read his first book, you'll see the similarities. Denton is arguing against the common misconception that modern mammals descend from modern amphibians (or fish).

      He then argues that the correct trees show evidence of design. According to Denton, they can't be explained by fixation of neutral alleles by random genetic drift at a constant rate. He thinks this correlation between mutation rate and rate of evolution must be due to built-in design.

      In the end it doesn't matter whether Denton changed his mind or not. We mustn't misrepresent his current view by invoking statements from the past. The IDiots mustn't do this either but at least they have an excuse—they're IDiots and we don't expect them to act rationally.

    4. I read the books a long time ago, but I'm sure in his first book he didn't acknowledge common descent but in the second one he does? Directed, of course.

      "In the end it doesn't matter whether Denton changed his mind or not. We mustn't misrepresent his current view by invoking statements from the past."

      That's what I meant by cherry picking (on the IDiots side).

    5. Hey Larry,

      aren't you in charge of the TalkOrigins server? I was under the impression you were in charge of that server. Anyway, it's down.

    6. "That wouldn't stop creationists from continuing to cite the argument, of course."

      Of course not. I still see references to Denton's first (and sillier) book from IDiots and YECs. It is as if time stops for these people.

  3. In Denton's case the "design" was inherent in the laws of physics and chemistry and the rules of mutation and gene expression.

    It just occurred to me that this view is really indistinguishable from the "we are living in a simulation" idea. Difference is, the later is typically called "mainstream science" while the former is viewed as a pile of BS.

  4. Good points, Larry.

    And just as an aside, here is a link to an article that discussed junk DNA that gets it right:

  5. "if the junk DNA contained information specifying for future evolutionary events"

    That was Timothy Leary's theory :-) Leary believed in intelligent design by a cosmic quantum force. He was very excited about histones as the agents of evolution, suppressing the appearance of future phenotypes until the time was right.

  6. Larry,

    I guess somebody told you that TalkOrigins is down?

  7. I'm perplexed by just how horrible philosophers of science these non-junk, IDiots and teleology-proponents are.

    No, junk would actually not falsify a teleological theory of evolution, since one can still imagine a directed process that yields waste and noise of various sorts. There isn't a complete dichotomy here.

    The problem with teleological models is that you have to have some a priori knowledge of the intent of the process. You can't simply look at the results of the process and then declare that they were the intended goals all along. This hypothesis needs to be predicted "from the outside", you need to have external reasons to think what you see is the result of intent. Only then can you then distinguish what you see (observationally testing your hypothesis) from non-teleological hypotheses.

    This is in some respects related to the problem with "bare ID" hypotheses. That's ID hypotheses that don't offer explanatory ID mechanisms or a priori reasoning for thinking what the designer wanted to achieve. They're postulating "design" on no grounds and then interpret everything they find as "this could have been what the designer wanted" in an ad-hoc manner. They're caught in this judicially and logically untenable position of simultaneously trying to circumvent the establishment clause(cannot openly state religious reasons for making specific design mechanisms), shield their design-hypothesis from falsification(the designer works in mysterious ways, "we musn't anthropomorphize the designer") while also trying to claim ID is a real scientific hypothesis with explanatory and predictive power. This simply can't be done, they can't have their cake and eat it too.

    Fuck, if only these people would stop and THINK for a few moments.

  8. Just took a quick peek at the UD article and comments. The stupid there is unfathomable. They seriously have problems comprehending how phylogenies work, or how it could be that humans, birds and frogs could nest within "fish".
    In response to the lucid explanation by "wd400" of how this can be, somebody responds with a reference to ENCODE "refuting neo-Darwinism". As if the ENCODE debacle has any fucking bearing on taxonomy.

    You can't make this stuff up. They're so incredibly stupid I literally laughed out loud and smacked my forehead when I read the thread.

    When I read a thread like that, I have to try to tell myself that it's because they're not *really* stupid, but simply misinformed. That's very hard to do, given the evidence before me.

    1. I follow Larry's links to UD every once in awhile (when the horror has worn off from the last visit) and wd400 is a real trooper, I don't know how s/he persists in the face of such smug and self satisfied ignorance.

    2. It's always horrifying to read that mountain of ignorance at denialism at UD.

      They banned me, so I can't comment at all, but it's hilarious that that idiot Sal Cordova says nested hierarchies are evidence AGAINST evolution, and that intelligent agents usually created nested hierarchies [he uses the example of classical music!].

      And Joe "Security Clearance" Gallien says a phylogenetic tree is not a nested hierarchy, and nobody corrects him. Not one of the IDiots at UD correct him on that. He's like their Einstein, their Stephen Hawking. He could says shit is shinola and no one would correct him.

    3. Hahahaha... nested hierarchies are evidence against evolution.


    4. How the fuck can classical music be arranged in a nested hierarchy? [per Sal Cordova]

      I want this stupid fuck Cordova to come and organize my CD music collection into a nested hierarchy. Where, oh where to put The Pogues? Punk, or Irish? etc. etc. etc.

    5. I suppose it just might be possible if composers routinely plagiarize their predecessors. Perhaps Cordova had in mind Stravinsky's quip that "Good composers borrow, great composers steal."

    6. In any case, Cordova has missed the boat. The argument isn't that designers can't design nested hierarchies, of course they can, it's that designers can design any imaginable pattern. It can not be observationally falsified.

      A violation of the nested hierarchy would falsify evolution, but it would still be compatible with bare design. It's what the designer wanted they reason ad-hoc, all the while insisting we mustn't anthropomorphize the designer(so he can keep working in mysterious ways, staying infinitely compatible with the observed while simultaneously giving us no grounds to think it's reminiscent of design).

    7. Maybe there's a classical music nerd here who can explain why Cordova's "classical music" argument is bullshit?

      Here's Cordova's idiotic comment about classical music.

      Further, intelligent agents create nested hierarchies, not only out of necessity but out of their sense of aesthetics. In the world of classical music there are somewhat well defined music forms: sonatas, minuets, concertos, symphonies, operas, variations, nocturnes, preludes, etudes, rhapsodies, etc. These forms create nested hierarchies and have little to do with Markov chains.

      How the fuck does that form a nested hierarchy? What is "opera" a subset of? What is "minuet" a subset of?

      Is "concerto" a subset of symphony, or vice versa? As I understand it, a concerto is similar to a symphony (with one movement, IIRC) PLUS some guy doing solos once in a while. Right? So does that make "concerto" a subset of symphony, or vice versa?

    8. I am a classical music nerd and Sal Cordova is talking absolute bullshit.

      A sonata in its broadest terms is a solo piano work or a work for solo instrument and piano (e.g. a violin sonata is a work for solo violin with a piano accompaniment). There is such a thing as the "sonata form" which can appear in different types of instrumental music (usually in the opening movement) outside of sonatas, but that doesn't make sonatas group inside, say, symphonies. Ditto minuets, which can be stand-alone pieces or movements within a symphony, concerto, sonata, etc.

      Concertos are usually multi-movement pieces, often with three or four movements. They do feature a single soloist or sometimes groups of soloists (two, three, even four or more featured performers are not unheard of) backed up by an orchestra. Although there are some single-movement concertos these are comparatively rare. Usually when composers write single-movement concerti, they call them fantasies, romances, poems, rhapsodies, etc.

      Symphonies are large-scale, multi-movement works for orchestra. Like a concerto, they usually have three or four movements. Any featured performer is usually featured only for a short time.

      Operas are combination of stage works, singing, and orchestras. There are featured singers, also often choruses, and the featured singers sing in various combinations. There's a classic moment in the second act of The Marriage of Figaro by Mozart where one person is on stage, then more and more people enter over a period of about twenty minutes until the stage is filled. They really don't derive from any other musical form; they were originally created in the late Renaissance (Jacopo Peri's 1597 work Dafne is credited as being the first true opera) to mimic what they thought classical Greek theater was like.

      Variations can either be full pieces or movements within a larger piece. One of my favorite piano trios (Youtube link) by the 19th century French composer Louise Farrenc has a beautiful second movement set of variations. Variations can also be performed by a soloist (like Farrenc's Air Russe Varie for piano), chamber ensemble (the above piano trio), soloist backed by an orchestra (like Rachmaninoff's famous Rhapsody on a Theme of Paganini), or symphony orchestra (Hindemith's Symphonic Metamorphoses on a Theme of Carl Maria von Weber).

    9. Nocturnes, preludes, and etudes are terms commonly associated with Chopin's piano works, although he didn't invent any of them. The first composer of nocturnes was John Field. Preludes began during the Renaissance (as the name implies) as lead-ins to larger works. During the Romantic era, they came to denote stand-alone pieces, although Wagner gave them back their original meaning by writing "Vorspiels" to his operas. And etudes are study pieces for a soloist to drill her or him on technique, though the challenge is to write etudes that are aesthetically pleasing (and to perform them in an aesthetically pleasing way!) while emphasizing one particular aspect of technique. While Chopin is most associated with this type of work, I also have to give a shout-out to Farrenc for her etudes.

      Finally, rhapsodies are free-flowing musical works, usually of only one movement, that can be written for soloist (Lizst's Hungarian Rhapsodies for solo piano), soloist and orchestra (Gershwin's Rhapsody in Blue and Rachmaninoff's which I mentioned above), or orchestra (like Ravel's Rapsodie espagnole or Enesco's Romanian Rhapsodies).

      tl;dr - There's no way to nest any of these within a hierarchy. If rhapsodies nest within symphonies, for example, then what do you do about the rhapsodies that are for soloist or a few performers or soloist and orchestra? Where do preludes fit in the hierarchy, and does it matter if we're talking about the preludes composed for solo piano by John Field or the ones composed by Wagner for the orchestra to play before his operas? Where can operas possibly fit in? There are no concertos for singers, and they can't be symphonies given that singing and acting are such an integral part of the work (some symphonies may feature singing, like Beethoven's 9th, but not acting).

      You could come up with objections all day. The idea of a nested hierarchy for classical music forms just simply doesn't work at any level. It's just Cordova trying to sound cultured and failing, while the other denizens of the echo chamber at UD just lap that garbage up.

  9. Take this goldnugget from "Joe" in the UD comments: "A phylogenetic tree is not a nested hierarcy".

    Against that level of stupid, even the gods toil in vain.

    1. "Against that level of stupid, even the gods toil in vain"

      That's one of the most beautiful pieces of poetry I've ever read.

    2. Good, isn't it? The original is in German, by Friedrich Schiller, and the usual translation is:

      "Against stupidity the gods themselves contend in vain".

    3. Thanks for the info. I prefer "toil" instead of "contend", though.

    4. This comment has been removed by the author.

    5. That reminds me of the stupidest thing a creationist ever said to me: "Adaptation still isn't evolution. At least not the evolution that Darwin was talking about."

      I adore this quote. I want to do it in needlepoint with a country-style border of crocoducks and hang it in the bathroom.

      (I really have to learn to hit "preview" and not "publish"!)

  10. Here's something Michael Denton DID say about nested hierarchies. Let's analzye:

    "In the final analysis the hierarchic pattern is nothing like the straightforward witness for organic evolution that is commonly assumed. There are facets of the hierarchy which do not flow naturally from any sort of random undirected evolutionary process. If the hierarchy suggests any model of nature it is typology[4] and not evolution. How much easier it would be to argue the case for evolution if all nature’s divisions were blurred and indistinct, if the systema naturalae was largely made up of overlapping classes indicative of sequence and continuity." [Michael Denton, "Evolution: A Theory in Crisis", p. 136-137]

    Well, idiot, the whole point of evolution is that it predicts no overlapping classes (barring HGT). This idiot is saying that that which evolutionary theory predicts is that which evolutionary theory forbids [barring HGT].

    However, if it's "sequence and continuity" you want, THAT we have a lot of, in the fossil record.

    If you want some classifications that are "blurry and indistinct", I'll point out that for decades creationists believed that hyenas were canids not felids. They can't even tell dogs from cats. (Of course I'm not suggesting the common ancestor of dogs and cats would look like a hyena; a better living model of the common ancestor of dogs and cats would be the palm civet.)

    By "typology", Denton is here resurrecting dead German philosophies about the Gestalt and Humboldtian naturphilosophie, the sort of shit philosophy that was promoted by German philosophers like Houston Stewart Chamberlain and a bunch of early 20th century vitalist crackpots, now forgotten.

    All of Intelligent Design is just a resurrected version of early 20th century German shit philosophy of vitalism and "Gestalt" that's been "modernized" by adding jargon from information theory, which the IDiots use incorrectly because they don't know what it means. The IDiots replaced "vital force" with "information" and never knew what either one meant, then called it cuttin' edge science.

  11. Professor Moran wrote on his blog:

    "I wonder what Intelligent Design Creationists think of this argument?"

    If all but one of the creationists capable of arguing this issue had not been banned, maybe someone would have made a comment or two.

    1. OMG! What are you saying? Are you implying that there are only four Intelligent Design Creationists and three of them have a potty mouth that gets them banned from multiple blogs?


    2. Sal Cordova, Casey Luskin, Niwrad, Klinghitler and the other IDiots over at UD and ENV have not been banned here nor at Panda's Thumb, but they never defend their asinine blurts in any forum where counter-arguments are permitted.

      They know they can only maintain respectability if they make their counter-factual assertions in forums like ENV which permit no comments, or UD where almost all anti-creationists have been banned, including me.

      The only UDite banned here was Atheistoclast, and he's banned at UD too, I believe.

    3. This comment has been removed by the author.

    4. I meant creationist visiting your blog and commenting regularly, such as Pepe and Dominic, who I believe were banned without sufficient cause.

      And you can go on thinking that, but at the end of the day it isn't your blog.

    5. Milosh: Do you believe that people from UD, such as the ones listed by Diogenes really visit this blog except andyjones? I personally don't think so, but I might be wrong.

      At UD and ENV they frequently post attacks on Larry Moran based on his recent posts here. Thus, they clearly read Larry's blog.

      For example, when Larry said, regarding students who don't believe in evolution, "Flunk the IDiots", this was widely quoted by IDiots as if Larry were the most prominent "Darwinist" in the world.

      While they all read Larry's blog, they don't dare comment here. They only emit their counter-factual blurts at forums like ENV, which permit no comments, or UD where almost all anti-creationists are banned, including me. They know they cannot stand up to questioning.

    6. This comment has been removed by the author.

    7. I have never banned anyone because they are a creationist. Dominic was banned for insulting my mother. PePe was banned for using foul language and consistently insulting me for no good reason. Others were banned for writing nasty letters to my Chair, Dean, or President of the university. That's cause for instant banning.

      I would ban Jerry Coyne if he ever complained to my Chair about Sandwalk.

    8. I guess using foul language by non-creationists doesn't bother the host that much? Well, there is nothing else to say is there?

    9. Diogenes

      You got banned at UD for using foul language as you should have been here long time ago, if the same rules applied to all not only creationist. Well, I'm done here, so it doesn't matter anymore.

    10. Since plenty of ID-creationist foul-language users still persist on this blog, your hypothesis is falsified. There must be something else going on.

    11. @Milosh,

      Using foul language is not sufficient to get you banned on Sandwalk. I think I've explained that several times already.

      I'm thinking of adding stupidity and lack of reading comprehension to the criteria for banning but that really would preferentially target creationists.

    12. Milosh, Larry Moran's tolerance of alternative viewpoints, as well as criticism, is beyond fair. It is in fact quite exemplary.

    13. Milosh,

      Words are just sounds coming out of ones mouth and of themselves can be neither foul nor fair.

      It's the ideas behind them and the consequent translation into actions that have those qualities.

      Yours are pretty foul.

      And for once I actually agree with Andy Boerger.

    14. Milosh, you lying fuck, you say: Diogenes

      You got banned at UD for using foul language

      You're lying, but why would you think that? No reason was ever given for my banning at UD, and in fact I NEVER used foul language at UD. But how would you know what I do not?

      Who are you, "Milosh", and where did you get this information? Did you get your insider information from the administrators at UD? Do you personally know the administrators at UD, and did you get your information about me from them?

      The IDiots at UD do use foul language [Joe G, ya see]-- I never did. Prove me wrong by linking to an example of me using foul language at UD.

      Everyone including me who visits UD knows it exists for the sake of a double standard: ID creationists get to insult evolutionists, be uncivil, use ad hominems and foul language, but evolutionists are held to a far stricter standard. Even evolutionists who are NEVER uncivil, are always polite and do not insult people still get banned anyway-- and then after they're gone, the IDiots make up a story about how the banned evolutionists was "uncivil" and immoral, and they cluck about how this fairy tale they just invented is "typical of Darwinists."

      Milosh, you said I used foul language at UD. I say you're lying. It's easy for you to prove me wrong by linking to a comment of mine at UD-- go ahead, deliver the link, since you're so familiar with UD and you know its administrators. Since you know its administrators, go ask them why I was banned, you lying fuck.

    15. @Diogenes,

      I'd appreciate it if you could cut down on your use of "fuck" and other swear words on Sandwalk. These words can be effective at times but when you use it to demean other people who comment, it tends to cheapen my blog.

      I'm not going to ban you but I might consider deleting some of your comments.

    16. Milosh,
      I cannot think that you believe UD to be a fair and balanced blog - no creationist-run site is. Most do not allow comments at all - yet the bloggers will often whine that their own comments were deleted at some non-YEC forum (self-awareness is a trait not very common among the ID/YEC crowd). People are banned at UD for the crime of merely disagreeing with certain prominent IDcreationists. I was banned years ago, for example, for pointing out several errors in former UD boss Dave Scott's claims. The IDcreationist crowd works by stifling dissent. If they allowed more than a token presence of rational thought (e.g., wd400), their facade would crumble.

  12. I would say that sticking to your guns about your DNA being major Junk is ... a little strange, being 1. we don't know that, 2. what exact science is saying so sternly in results that it is appropriate to take away this possibility? When do we do that, I mean guys, I know there is an army that wants to cover it up, but the research clearly is there .... there is activity and function in "Junk DNA" there is.... watch this

    1. Gibberish. Nothing "strange" about this, the reasoning for thinking it's largely junk comes from evidence. It has nothing to do with "sticking to guns". Why would anyone even care whether it's junk or not, outside of religious fanatics who can't get over the idea that some part of their life isn't the direct result of purpose, planning and foresight by a divine and invisible wizard?

      The facts are what the facts are. To someone like myself, I couldn't actually care less whether all my DNA has a function or not. Whatever the case, it's the job of science to find out how/why. The work that has been done so far all seems to suggest that yep, it's mostly junk. Tough shit, time to accept it and move on.

    2. ... enter the Bladderwort genome. Transposible elements are lacking, and the genome has ~29,000 genes (more than us or most other plants) in 60Mb (much, much smaller than ours, or most other plants). It regulates itself quite well, and is arguably more complex than other plants (it is carnivorous, and has a complex trapping mechanism to catch prey).

      The genome's main difference - the lack of selfish genetic elements (Transposible elements) that make up the bulk of what is called junk DNA in our genome. Other bladderworts have substantially more DNA (1500Mb). Sequencing them will let us confirm whether the trend really hold up.

      As stated by many who had long worked on the DNA content problem, the ENCODE main paper over-interpreted it's results, and ignored what we actually know in an attempt for a sexy sound bite of their project. Junks DNA is real. Our genome is not computer code, despite that over-stretched metaphor.

    3. JS sez: I know there is an army that wants to cover it [Junk DNA] up

      How the fuck would you know that? Have you ever set foot in a science lab? Have you ever read an article in the peer-reviewed scientific literature? You didn't cite any; you cited a YouTube video.

      So you learned science from YouTube, and thus you know what really goes on inside the science labs you've never entered?

      ...the research clearly is there...

      O RLY? Then why didn't you cite "the reasearch" that's "clearly there"?

      If the evidence is "clearly there", why is it that the majority of scientists who worked for the ENCODE consortium, and who made statements about junk DNA, admitted that Junk DNA is still viable, that ENCODE did no functional assays and could not in principle have disproven the Junk DNA hypothesis?

      Here is Ewan Birney, lead author on the ENCODE paper, he who cooked up the "80% activity" figure, interviewed by the BBC, and agreeing that in fact, 80 to 90% of the human genome is still JUNK.

      Chris Ponting: So I think we can probably agree between us that between 10% and say 20% [of the human genome] is vital for life.

      Ewan Birney: ...I think we would agree with that.

      [Transcript of Interview with Ewan Birney]

      Would you like to see some recent, post-ENCODE evidence that's "clearly there"?

      The ENCODE project: Missteps overshadowing a success. Eddy, Sean R. (2013). Current Biology 23: R259–R261.

      The C-value paradox, junk DNA and ENCODE. Sean Eddy. Current Biology, Volume 22, Issue 21, 6 November 2012.

      On the immortality of television sets: “function” in the human genome according to the evolution-free gospel of ENCODE. Dan Graur, Yichen Zheng, Nicholas Price, Ricardo B. R. Azevedo, Rebecca A. Zufall and Eran Elhaik. Genome Biology and Evolution Advance Access. February 20, 2013.

      Can ENCODE tell us how much junk DNA we carry in our genome? Niu DK, Jiang L. Biochem Biophys Res Commun. 2013 Jan 25; 430(4): 1340-3.

      Is junk DNA bunk? A critique of ENCODE. Doolittle, W.F. (2013) Proc. Natl. Acad. Sci. (USA) published online March 11, 2013.

      there is activity and function in "Junk DNA"

      Interesting how you try to equivocate between "activity" and "function"! Wow, we're not going to catch that one! What makes you think "activity" disproves that a stretch of DNA is incapable of suffering a deleterious mutation?

      I also like how specific you are: "there is"! Really!? How specific of you to say "there is"!

      The human genome has 3.2 billion base pairs. How many of those, in billions, are involved in regulating genes?

      Which gene in the human genome (out of 25,000) has the most nucleotides regulating it, as shown by experiment, and how many nucleotides, in millions, are there regulating that gene?

    4. The evidence that most of the so called ‘junk DNA’ (jDNA) is not implicated in gene regulation is overwhelming. The recent sequencing of the bladderwort’s genome is an additional piece of evidence. However, as recently stated by Ford Doolittle in his recent paper “Is junk DNA bunk? A critique of ENCODE” (, by using a “larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon …much that we now call junk could then become functional.”

  13. @ Claudiu Bandea,

    Absolutely! Surplus, non-fuctional DNA can quite easily serve (like any other "mutation") as the raw material of evolution and the source of new functions. Given the amount of in-group variation, this group of bladderworts will be an interesting group to dissect all of these processes out.

    1. This comment has been removed by the author.

    2. I was once camping in Northern Ontario and when I was setting up camp I realized I had forgotten the mallet to hammer my tent pegs into the ground. Fortunately, there was a rock nearby that was just the right size to fit my hand and served the purpose perfectly. I'm no geologist, but the rock appeared quite different from any of those surrounding, and was likely an "erratic": A rock that was transported by glaciers from hundreds of miles away, hundreds of thousands of years ago.

      Would it be correct to say that the "function" of this rock and the process that brought it to be there was to provide me with a tool to put up my tent?

    3. @lutesuite,

      I am not implying purpose. The fact that junk DNA may, at some rare rate, develop into something interesting is a real possibility. But that is not why it is there. The same with more common mutations. They happen, but their purpose is not to supply genetic diversity. But the can and do supply variation that evolution then sorts out.

    4. OK, I guess I was misreading your intent because you agreed with Claudiu. He's not a creationist (at least, I don't think he is.) But if you look thru his posts here and elsewhere, you'll see he's quite stuck on his own personal hypothesis about junk DNA, a hypothesis that is only marginally more credible than creationsm.

    5. @lutesuite: Would it be correct to say that the "function" of this rock and the process that brought it to be there was to provide me with a tool to put up my tent?

      Obviously not, but if you use the rock as tool to put up your tent, then the ‘function’ of the rock in your hands if that of tool. And, if the rock does a good job, you might keep it, if not you might discard it.(BTW, your rock example is right on the money in the context of jDNA discussion!)

      When it comes to my model on the evolution of genome size, C-value paradox, and the biological function of the so called junk DNA (jDNA), you might not fully understand it. However, my evolutionary model attributing a biological role to jDNA is not the only one. There are other theories, including the he ‘nucleo-skeletal hypothesis’ proposed by Thomas Cavalier-Smith (2), and the ‘nucleotypic hypothesis’ proposed by Michael Bennett and Ryan Gregory, which have been discussed in dozen of papers and books. Are they “only marginally more credible than creationism”?

      And, what about Ford Doolittle’s take, that by developing a “larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon …much that we now call junk could then become functional.”. Is he flirting with creationism or he has deeper understanding of the evolutionary process?

  14. @ lutesuite

    Claudiu and I have had our share of disagreements. I thought I would be nice and point out that we agree on that point.

    But I suspect you are correct that we differ in how important it is. I think bladderworts seem to be doing fine without this source of excess DNA that may do something later. The paper did not discuss ophan genes, as far as I can tell, it is unclear what the difference between them and other plants is with regard to this form of "novel innovation".

    1. Jim,
      In my response to lutesuite’s comment above,I asked a few questions regarding the ‘nucleo-skeletal hypothesis’ proposed by Thomas Cavalier-Smith (2), and the ‘nucleotypic hypothesis’ proposed by Michael Bennett and Ryan Gregory, as well as Ford Doolittle’s take on jDNA. I asked some of these questions several times here at Sandwalk, but everyone, including our host Larry, is keeping very quiet on these well-developed scientific perspectives and theories on the potential biological role of jDNA. Even Ryan is mute on this issue, which is puzzling. What do you think?

    2. They are not "well-developed scientific perspectives" and they don't make sense. They don't for example, pass the Onion Test.

      That's why nobody but you is paying attention.

    3. Larry: “That's why nobody but you is paying attention.”

      That’s true, here at Sandwalk and the blogosphere nobody seems to pay attention to these perspectives. But that’s not the case with the scientific literature. For example, Ryan Gregory, who according to Ford Doolittle is “now the principal C-value theorist”, has written extensively about the ‘nucleotypic hypothesis”, which was first proposed and developed by Michael Bennett. And, that’s also the case with Thomas Cavalier-Smith, who developed the ‘nucleo-skeletal hypothesis.’

      Similarly, Ford Doolittle concludes his PNAS paper on ENCODE/junk DNA story that: by developing a “larger theoretical framework, embracing informational and structural roles for DNA, neutral as well as adaptive causes of complexity, and selection as a multilevel phenomenon …much that we now call junk could then become functional.”.

      I think these are highly knowledgeable and reputable scientists, so it would make sense to consider their views and perspective. Don’t you?

    4. Sorry I overlooked your straightforward answer that: the ‘nucleo-skeletal hypothesis’ proposed by Thomas Cavalier-Smith, and the ‘nucleotypic hypothesis’ proposed by Michael Bennett and Ryan Gregory, as well as Ford Doolittle’s take on jDNA, “do not make sense”.

      The reason you say is that: “They don't for example, pass the Onion Test”. This is interesting, because the author of the ‘Onion Test’ is Ryan Gregory who has been promoting the ‘nucleotypic hypothesis’ most of his scientific career. What do you make of this rather ironic situation?

      Also, maybe these theories *do* explain the ‘C-value enigma’, but the ‘Onion Test’ metaphor is ill conceived?

      Or, possibly, you are saying that these theories “do not make sense” because you don’t fully understand them?

    5. @Claudiu,

      My 2 second reply - within plants and metazoa, there is a lot of variation in cell size within a single individual. Given the identical genome content, how can excess DNA required?

      And generally, I'm usually not impressed with observational correlations. When someone deletes the junk from an amoeba and shrinks the cell size, I'd become more interested.

      (I missed the thread line - sorry for the deleted comment at the end)

    6. Cladiu Bandea says,

      Or, possibly, you are saying that these theories “do not make sense” because you don’t fully understand them?

      That's certainly a possibility that you might want to cling to if it makes you happy.

      Meanwhile, I getting tired of seeing you bring this up again and again on my blog (and in email messages to me). I've given you ample opportunity to promote your favorite theory to explain junk DNA and to advertise your twenty-year-old paper.

      Give it a rest.

    7. TheOtherJim says: "within plants and metazoa, there is a lot of variation in cell size within a single individual. Given the identical genome content, how can excess DNA required?”

      That’s a sensible question that should be answered, if it has not been yet!

      @Larry: In this post, I specifically discussed the mainstream scientific theories and perspectives on the putative biological roles of the so called junk DNA (jDNA), namely the ‘nucleo-skeletal hypothesis’ proposed by Thomas Cavalier-Smith, and the ‘nucleotypic hypothesis’ proposed by Michael Bennett and Ryan Gregory. And, I would also think that any discussion about jDNA should include the thinking and ideas put forth by the current leading experts in the field, such as Ford Doolittle.

  15. Cordova is not all that bright, in my experience. I recall that he once claimed that because in an "experiment', he had used a 10 base "DNA sequence" and after changing one base per 'generation', that after only 10 generations the original sequence was totally different, thus, he concluded, evolution cannot happen. When it was explained to him that genomes are generally larger than 10 bases, he would not budge. And, of course, there was his multi-forum boast thatID and he had been mentioned in the "prestigious journal Nature" - but he failed to mention that ID was rebuffed and he was portrayed as a stooge for the cause.

    He's an IDiot.