Thursday, August 09, 2012

Still Digging: Part II

Bet you thought that this horse had been beaten to death when you read Still Digging: Part I.

Ha! You don't know why we call them IDiots!

Here's the latest contribution from lawyer non-scientist David Klinghoffer: Why We Call the Myth of Junk DNA a "Myth"
Jonathan M. does a fine job of putting University of Toronto's Larry Moran in his place on the "junk DNA" theme. I thought, though, that I would try to lift the dispute with Moran -- a biologist whose main contribution to the evolution debate has been introducing his trademark insult term "IDiot"® -- up from the specific to the more general.

It's very simple. Prominent biologists have equated non-protein-coding DNA with functionless "junk," even though we can be confident that if pressed they would admit that it's not all junk. In fact, new functions are being discovered all the time. It's indisputable.

The reason we call the "Myth of Junk DNA" a myth is this. When writing for the public, guys like Dawkins, Miller, Avise and Coyne imply or flatly state such an equation. But if you questioned them, they'd obviously know better than to stick by that. I say obviously because it's obvious to us but it wouldn't be to the general audience these men seek to persuade.

Hence the correct term, used in the title of Jonathan Wells's book: myth. It serves a propagandizing, mythologizing purpose to put it about that our genome is, but for the small portion that codes for proteins, nothing but a mass of functionless vestigial garbage. If true, that would seem to be a signature trace of an unguided evolutionary process.
You gotta give him credit for putting a different spin on the issue while still digging furiously. Now he says that all those prominent biologists equated junk DNA and noncoding DNA just like Jonathan Wells said ... but it runs out they were being deliberately deceptive. They actually new that some noncoding DNA had a function but they (Dawkins, Miller, Avise, and Coyne) wanted to persuade the public that all noncoding DNA is junk.

That's what scientists do, right? Lie to the public about their area of expertise. Aren't we lucky to have leading intellectuals like David Klinghoffer around to set things right?

For the record, I was a graduate student in 1970 working on, among other things, origins of replication (functional noncoding DNA). I followed closely the discussion about junk DNA and was at many of the meetings. Jonathan McLatchie wasn't born yet and I don't think Klinghoffer was either David Klinghoffer was only five years old. Jonathan Wells was studying geology and physics at Berkeley.


  1. The wonderful thing about the published literature from the 1970s and 1980s is that it still exists. Really. Seriously, you can go and read it yourself. And when you do, you'll find that function for non-coding DNA was the most common assumption.

    1. T. Ryan Gregory's blog has a marvelous list of quotes from the era in question, the 1970's and 1980's, showing what scientists REALLY said at the time. It's a marvelous resource. Go there now.

      That's how real history should be done.

      In contrast, the best evidence that Jonathan Wells and Casey Luskin can proffer for their lies are articles in newspapers or for general audiences, from the late 90's-00's, in which some journalist writes something like "Long dismissed as junk..."

      Which is hearsay, and inadmissible in a court of law. Those reporters never tell you WHO did the dismissing of junk! They never cite a peer-reviewed paper in which a scientist actually says non-coding DNA = junk. At best, it's hearsay.

      The kindest thing we can say about IDologues like lying Casey Luskin and Jonathan Wells is that some dumb reporters in newspapers wrote things just as stupid.

      However, those reporters, while ignorant, were not liars. Casey Luskin and Jonathan Wells, David Klinghoffer and Jonathan Maclatchie are pathological liars. It's important to note the difference.

      If you pointed out these mistakes to secular journalists, they would print a retraction.

      When you point out these mistakes to IDologues like Wells, Luskin, Klinghoffer, etc., they can't admit mistakes. They double down.

      So it's not ignorance. They're pathological liars.

  2. Now you can write a book called "The Myth of the Myth of Junk DNA", since the IDiots are clearly the mythmakers here.

  3. Hey that was easy, I just got a law degree from University of Larry Moran! (Larry calls me "lawyer David Klinghoffer.") Kindly, he also shaves 5+ years off my age. (Thinks I was not born yet in 1970.) This is my lucky day. Not only am I younger, but I'm going to make some money. Now I can advise Larry on the international trademarking of "IDiot" for use on t-shirts, coffee mugs, hats for sale at the county fair, etc. Down side is I can't take a cut of the business in exchange for the advice (ethics violation). I'll have to settle for an hourly rate. Upside is I plan to bill $800/hr.

    1. Thanks. I made the corrections.

      Is there anything else you'd like to say?

      You're more than welcome to defend yourself against the charge that you don't know what you're talking about.

    2. He knows what he's talking about. He's not that dumb. Klinghoffer was hired by the DI to tell lies about scientists and smear them. It's not easy to find someone that totally lacking in conscience.

      Klinghoffer has the time to correct Larry on his lack of a law degree. Hooray! But he can't correct Jonathan Wells or Casey Luskin when they say molecular biologists taught that non-coding DNA = junk DNA. No, he doesn't have time to correct them on that, even though their desks are probably next to his.

      I'd like to hear their conversations around the water cooler.

      Here's a conversation between Klinghoffer and Jonathan Wells around the water cooler.

      "Well, it's not technically true."

      "Not totally true."

      "Not remotely true in any way and never was."

      "But we can get away with it."

      "Right on. Our audience will love it. They'll believe anything that makes scientists look stupid. We must, we have to assuage their feelings of inadequacy."

  4. David,

    DI is lawyer heavy, so forgive him for the slip-up. To help him out, I've put together this handy fact sheet of DI all stars and their professions:

    Philip Johnson: law prof.
    Casey Luskin: lawyer
    Barry Arrington: lawyer
    David Klinghoffer: journalist
    David Berlinski: ??????
    William Dembski: theology school prof. who had to walk back an acceptance of modern physics
    Jonathan Wells: author of fiction

    1. Ann Coulter is a lawyer too, and Andy Schlafly. They're hemorrhoids on the anus of science.

    2. David Berlinski has a PhD in philosophy from Princeton. In the past, he has deceptively passed himself off as a mathematician because he taught freshman math courses at several universities as an non-tenure track lecturer.

  5. Klinghoffer
    produce evidence that any molecular biologist equated noncoding DNA = nonfunctional DNA.
    If you can't, you are a lying sociopath as we proved in the previous post. The scientific community will never forgive you for your scurrilous lies.

  6. Klinghoffer
    name 10 nucleotides of noncoding DNA with a novel function discovered by any ID proponent/ creationist. Oh hell I'll make it easy, just 1 bp noncoding out of 3 billion in human genome. If not, go fornicate yourself.

    1. These ID proponents aren't scientists, so you can't fault them for not doing science.

      Rather keep it simple and (since he seems to have forgotten) remind Klinghoffer what the discussion is about: Wells's fraudulent claim that "the dominant view [among biologists in 1970] was that non-protein-coding regions had no function".

      His attempt to provide a rationale for the title of Wells's book does not address Wells's lie. David: please stop avoiding the issue and admit that Wells lied to his readership.

    2. Yes. We demand that David stop dancing around the issue and admit Wells lied to his readers.

    3. I doubt that Klinghoffer will admit that Wells lied since he (Klinghoffer) repeated the lie twice in his Why We Call the Myth of Junk DNA a "Myth". Even after reading, supposedly, Jonathan M's post (ironically the comment starts by complimenting Jonathan M's "good job"), where Jonathan said that IDiots know that evil evolutionists know about promoters and tRNAs and rRNAs and et cetera. They can't read their own friends' comments carefully and thus happily contradict each other. That's because they don't care about truth. After all, Klinghoffer's comment is but a red-herring, a distraction from the main issue.

  7. try to lift the dispute with Moran...up from the specific to the more general.

    In scientific dispute, movement from specific to general is *not* "up" most often. Specifics often define a nice clean argument. Generalities give "wiggle room" that can be used by the unscrupulous for purposes of trying to obfuscate with BS.

    As Drs. Moran and Gregory mention, not only are there plenty of specific instances contradicting Klinghoffer's general statement that evolutionary biologists thought all non-protein-coding DNA was junk; the published proof that Klinghoffer's statement is wrong is available to anyone who desires to look it up.

    (Cue quote-mining fest to "prove" Klinghoffer's statement in 3...2...1....)

  8. I haven't read Wells's book, but does he address the origins of the term and concept of 'junk', Ohno's mutational load argument?

    It is instructive to read Ohno's original paper (or back further, to Kimura and Ohta and work from there). (Forgive me; this is a link to Pellionisz's site! Just read the paper)

    In it, he makes a persuasive argument that the 3 million genes implied by our genome size relative to a bacterium's cannot possibly be sustained due to mutational load. I have not seen that argument adequately refuted by anyone, and it has received much support with characterisation of the nature of the putative junk.

    It all seems to boil down to nit-picking over the word 'gene'. Anything that was not a 'gene' was junk, in Ohno's terms. But Ohno's audience did not need a lesson on genetics. They knew that he wasn't just talking about the part of sequence that corresponds to amino acids. Transcription/translation initiation and termination, control sequences, editing, and all the parts of sequence that contribute to those functions all contribute to the 'gene' that ultimately becomes manifest as phenotype. tRNA, rRNA, ssRNA etc, are all produced by 'genes', but they aren't protein-coding.

    The challenge for ID remains to explain why Ohno was wrong - how a large genome rich in sequence-dependent function avoids mutational load. Bits and pieces of 'extra' function are being discovered all the time. But there is a theoretical barrier to suppositions that, when all the results are in, we will get to some point at which functional sequence outweighs nonfunctional.

    And no amount of who-said-what bullshit addresses that question. Lawyers, contrarians and engineers both hard and soft: learn some bloody genetics! Biologists - surely you know better?

    1. Anyone know how often the phrase "mutational load" is used in Jonathan Wells' book, and as a subset of that number (if greater than zero), how often the concept is actually discussed?

    2. I don't think he ever discusses the genetic load argument for junk DNA.

      But in looking through the back of the book I found this in the glossary.

      JUNK DNA: ... People who assume that the only essential function of DNA is to code for proteins regard non-protein-coding DNA (about 98% of the human genome) as junk.

      The question is whether there are actually any people in this category or is it a null set?

      For future editions I suggest adding ...

      "People who assume that the only essential function of DNA is to specify origins of replication regard all non-origin DNA as junk."

      "People who assume that the only essential function of DNA is to specify genes that produce functional RNAs (e.g. rRNA, tRNA etc.) regard all the rest of the DNA as junk."

      "People who assume that the only essential function of DNA is to specify functional telomeres regard all non-telomeric DNA as junk."

      "People who assume that the only essential function of DNA is to identify regulatory sequences regard all non-regulatory DNA as junk."

      These are all equally true statements.

    3. I imagine they will invoke non-sequence-specific functions that could tolerate a bunch of mutations. Spacers etc. (Remember, their "answer" doesn't have to make sense, it just has to have the illusion of sense for those who want to believe.)

    4. "People who assume that the only essential function of DNA is to specify origins of replication regard all non-origin DNA as junk."

      "People who assume that the only essential function of DNA is to specify genes that produce functional RNAs (e.g. rRNA, tRNA etc.) regard all the rest of the DNA as junk."


      How about, "People who assume that all DNA for which functions have not yet been found, has no function, regard that DNA as junk."?

    5. I imagine they will invoke non-sequence-specific functions that could tolerate a bunch of mutations. Spacers etc.

      Yes - and Ohno would have been there ahead of them. He discussed possibilities for this fraction, and a lot more have been proposed since. His load argument was that, whatever the function of this "junk" (his quotes), it could not be sequence-dependent.

      The more this fraction has been characterised, the less likely it appears that any 'functional' explanation explains the sheer volume of this DNA. Yet the weekly trumpeting of another 'junk' function on UD ("another bad day for Darwinism!") almost invariably involves sequence (a few hundred base pairs of sequence, yet!).

      There is a theoretical limit to the functional sequence we are likely to discover - even if we weren't approaching it at about the speed Japan is approaching the US!

  9. And people who assume that the only essential function of DNA is to show off God's designing skills by exhibiting an appearance of optimality ("good design") regard all evidently non-optimal DNA as junk.

    There's a lot of junk out there.