Monday, May 16, 2011

See the IDiots Gloat over Jonathan Wells


This is part of my discussion about The Myth of Junk DNA by Jonathan Wells. I still haven't read the book—it won't be released in Canada until May 31st.

Over on Evolution News & Views (sic) David Klinghoffer is already counting his chickens [Junk DNA and the Darwinist Response so Far].
Over the weekend, Jonathan Wells's The Myth of Junk DNA broke into the top five on Amazon's list of books dealing with genetics -- a list normally dominated at its pinnacle by various editions of Richard Dawkins' The Selfish Gene. Not bad, Jonathan.
Not bad indeed, except I can't tell if it's true. When I check the top selling recently published books I don't see The Myth of Junk DNA in the top five. Never mind, I'm sure there will be many skeptics like me who will buy the book just for a good laugh.

UPDATE: The latest information shows that Wells' book is ranked 23rd under "Genetics." I'm sure the IDiots just made a simple arithmetic error when they said it had broken into the top five.
The juxtaposition with Dawkins' Selfish Gene is appropriate, notwithstanding the demurrals of biochemist Larry Moran et al. Dawkins and other Darwinists, such as Jerry Coyne, have indeed posited that neo-Darwinian theory predicts that swaths of the genome will turn out to be functionless junk. The Junk DNA argument has been a pillar of the Darwin Lobby's efforts to seduce public opinion and influence public policy. Professor Moran wants to imagine that Dawkins never held that neo-Darwinism predicts junk DNA. But that's not how other Darwinists see it. (Compare, for example, Dennett's Darwin's Dangerous Idea, page 316.)
The IDiots have a bit of a problem. In order to make this book look important they have to first establish that the concept of abundant junk DNA in our genome was a "pillar" of support for evolution. That's hard to do when their understanding of evolution is so flawed that they don't see the difference between "Darwinism" and evolution by random genetic drift.

Their claim that evolutionary theory PREDICTED the presence of huge amounts of junk DNA in our genome is just plain false. They been told this but they keep repeating their error. There's a word for that kind of behavior.

It's easy to see how they got confused. It's because they're IDiots. It's partly because they don't understand that an argument for inheritance of a few pseudogenes is not the same as an argument that more than 50% of our genome is junk. There are plenty of scientists who will use the pseudogene argument to challenge Intelligent Design Creationism but who don't believe that MOST of our genome is junk.

It's also partly because the IDiots don't know the difference between selfish DNA and junk. Here's what Daniel Dennett says on page 316 of Darwin's Dangerous Idea.
The presence of functionless DNA in the genome is no longer regarded as a puzzle. Dawkins (1976) selfish-gene theory predicts it, and elaborations on the idea of "selfish DNA" were simultaneously developed by Doolittle and Sapeinza (1980) and Orgel and Crick (1980) (see Dawkins 1982, ch. 9, for the details).
Selfish DNA is not junk DNA. The classic examples of selfish DNA are active transposons and integrated viruses. These bits of DNA have a function—even if it's only to propagate themselves. As you can see from my summary [What's in Your Genome?]. I don't count them as junk.

It's remarkable that Klinghoffer quotes Chapter 9 of The Extended Phenotype (1982) since Dawkins take pains to point out that much of the junk DNA in our genome could have a function. This is exactly the sort of skepticism one would expect from a Darwinist.
This does not mean, however, that the so-called junk DNA is not subject to natural selection. Various 'functions' for it have been proposed, where 'function' means adaptive benefit to the organism.
He goes on to describe several of the proposals that are common arguments against junk DNA. If the DNA has a function and it's adaptive, then it is not junk. Selfish DNA is not junk.

Let's be very clear about one thing. The scientific dispute is not over the existence of junk DNA. That's well established. The dispute is over how much of our genome is junk (DNA with no function). In order to refute the idea that MOST of our genome is junk, you have to show that most of it has a function of some sort. I'm looking forward to Jonathan Wells' book where he is going to prove to us that >50% of our genome has a function. (Not holding my breath!)
So far, with none of them having actually read the book (though P.Z. Myers threatens to do so), the Darwin apologists' response to The Myth of Junk DNA has followed along four lines of defense.

1) The usual insults. In his blog Larry Moran of the Department of Biochemistry at the University of Toronto, a grown man and from the looks of him not a young one either, repetitively derides Jonathan as an "IDiot." (How embarrassing for this mature gentleman, you might think. Can you imagine Jonathan Wells or anyone else prominent in the ID community replying in kind, designating Professor Moran as "Larry Moron" or similar? The question is self-answering and tells you a lot about how desperation kindles anger among these people.)
You know, there's one sure way to prove you're not an idiot. The IDiots have been trying for over twenty years to show that they understand science. I'll gladly stop calling them idiots as soon as they deserve it.

Speaking of insults. There's one sure way to ensure that you aren't going to be insulted and that's to stop calling evolutionary biologists "Darwinists" and stop saying that they don't understand their own discipline. I find that extremely insulting and I'm not going to refrain from responding in kind.

I don't know what Jonathan Wells is going to say in his latest book but here's a few examples of insults in Icons of Evolution.
There is a pattern here, and it demands an explanation. Instead of continually testing their theory against the evidence, as scientists are supposed to do, some Darwinists consistently ignore, explain away, or misrepresent the biological facts in order to promote their theory. One isolate example of such behavior might be due simply to overzealousness. Maybe even two. But ten? Year after year? (p. 230)

Fraud is a dirty word, and it should not be used lightly. In the cases described in this book, dogmatic promoters of Darwinism did not see themselves as deceivers. Yet they seriously distorted the evidence—often knowingly. If this is fraud when a stock promoter does it, what is it when a scientist does it? (p. 234)

If dogmatic promoters of Darwinian evolution were merely distorting the truth, that would be bad enough. But they haven't stopped there. They now dominate the biological sciences in the English-speaking world, and use their position of dominance to censor dissenting viewpoints. (p. 235)

The truth is that a surprising number of biologists quietly doubt or reject some of the grander claims of Darwinian evolution. But—at least in America—the must keep their mouths shut or risk condemnation, marginalization, and eventual expulsion from the scientific community. This happens infrequently, but often enough to remind everyone that the risk is real. (p. 239)
Klinghoffer continues with his four lines of defense that we "Darwinists" apparently use to defend the existence of abundant junk DNA (>50%) in our genome.
2) Denying that junk DNA ever figured preeminently in the Darwinist's quiver of arguments against design. Moran, for example, asserts, "There was never a time when knowledgeable molecular biologists equated 'junk' DNA and 'noncoding' DNA." Huh, that's strange. I'm not aware of anyone who has scientifically polled the community of professional biologists on the subject. But I do know that in the struggle for public opinion over the question of Darwin versus Design, junk DNA has again and again been employed, by all the most eminent protagonists on the Darwinian side, as a bludgeoning weapon against intelligent design. Never mind The Selfish Gene, in his most recent book, The Greatest Show on Earth (2009), Dawkins observed that "the greater part...of the genome might as well not be there, for all the difference it makes," and that this fact is "useful for...embarrassing creationists."

Similarly, in Why Evolution Is True (2009), Jerry Coyne offers it, again, as a "prediction" of neo-Darwinian theory that we'll find the genome littered with useless "vestigial genes."
I said that knowledgeable scientists never said that all non-coding DNA is junk. Klinghoffer says, blah, blah, blah, not even addressing my statement.

You can't make this stuff up. At every single opportunity the IDiots demonstrate that they deserve the title.
3) When not denying that junk DNA is a prime, staple argument for Darwin apologists, Professor Moran wants to have it the opposite way. In the same series of blog posts attacking "the IDiot" Jonathan Wells, Moran maintains his own belief that the genome is indeed overwhelmingly useless junk. "Some (I am one)," he writes, "still think that as much as 90 percent could be junk." He insists that "it's not sufficient to show that a few bits of repetitive DNA have gained a function in some species."

Dr. Moran's problem is that he has neither read Jonathan's book nor, it seems, followed the cascade of evidence from the scientific publications. It's a heck of a lot more than just "a few bits of repetitive DNA" that have been shown to be functional. In a brief (and enviably readable and accessible) 115-page book, Jonathan Wells offers over 600 references to recent peer-reviewed literature.

Twenty-five thousand studies further down the road from where we are now, no one knows how much of the genome will turn out to be truly functionless and therefore genuinely worthy of the appellation "junk." But for Darwinists, the speedily mounting evidence against junk DNA is an ominous portent. As Casey Luskin and others have put it, it's the trend that stands out prominently here, on which the likes of Larry Moran have so far been in denial.
Theme

Genomes
& Junk DNA
I've tried and tried to get the IDiots to have a serious, scientific, discussion about the evidence for and against abundant junk DNA in our genome. Some of them have tried but their arguments soon degenerate into insults about my lack of knowledge of the scientific literature. This is in spite of the fact that I have dozens of postings on the subject over the past few years and nobody has ever shown that I've been ignorant of the science behind the controversy. We may disagree about the interpretation but that's not what I'm being accused of here.

As soon as I read the book I'll post a bunch of articles pointing out why it's wrong. That will give the IDiots, like Jonathan Wells, a chance to debate the points I make and show that he is right and I am wrong. I'm looking forward to it.
4) Finally, in my own small contribution to this debate, I made a facetious comment here about how the identification of Osama bin Laden's corpse by DNA fingerprinting, using his "junk DNA" as the media habitually referred to it, provided a welcome news hook for the publication of Jonathan's book. This provoked braying responses from the Darwin Lobby. For example, our journalist friend Lauri Lebo, challenged as ever in her reading-comprehension skills, somehow understood that I was saying the usefulness of non-coding DNA for this forensic purpose proved it isn't junk.

P.Z. Myers tried to show that the usefulness of non-coding DNA for genetic fingerprinting is another demonstration that the stuff really is junk, being "subject to random changes at a higher rate than coding DNA, because it is not subject to functional constraints."
Every now and them some IDiots get something right—even if it's just by accident. One example is when Klinghoffer describes his posting as "my own small contribution."
But whether "junk DNA" is functional is exactly the question at issue, isn't it? The fact that our DNA is pervasively transcribed, as Jonathan Wells points out in Chapter 3 of his book, itself suggests pervasive functionality. As has become clear, too, DNA may serve in various functions even if it does not code for functional RNA.
It will be fun to read how Wells deals with the issue of spurious transcription based on his understanding of how RNA polymerase and transcriptional activators bind to DNA. I'm certainly looking forward to learning about the reliability of those genome studies on transcription and I'm sure Wells is going to discuss conflicting data in the scientific literature. After all, Wells has a Ph.D. in molecular biology so he must know about the real scientific controversy, right?

As for functions that don't require transcription, I highly recommend my short summary of these in What's in Your Genome. We've known about them for decades but apparently the IDiots think this is a new discovery.
So far, the Darwinist response fails to appreciate that Jonathan is in the act of very seriously blunting a Darwinian icon. What, in this context, is an icon? It's a mainstay in the public debate about Darwinian evolution that turns out, on inspection, to be based not on solid science but on puffery, illusion or deception.

This is another icon that, as Jonathan shows, was in the process of being blunted by biologists who are not ID advocates, well before Dr. Wells gathered the evidence together so concisely and conveniently in these pages.
Whatever. Wells' first book, Icons of Evolution was full of lies and I suspect this one will be too. Only one of the ten so-called icons was "blunted" by Wells and that one was the Haeckel drawings. Even then, Wells seriously distorted the significance of those fake drawings by claiming that there was now no evidence of similarities in the development of all mammals.


111 comments :

  1. sigh.

    Take a look at this paper.

    Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates.

    http://www.ncbi.nlm.nih.gov/pubmed/19607716

    It starts by agreeing with Larry:

    About 45% of the human genome is comprised of mobile transposable elements or "junk DNA".

    Only to show him to be dead wrong:


    The exaptation or co-option of these elements to provide important cellular functions is hypothesized to have played a powerful force in evolution; however, proven examples are rare. An ancient primate-specific Alu short interspersed element (SINE) put the human CAMP gene under the regulation of the vitamin D pathway by providing a perfect vitamin D receptor binding element (VDRE) in its promoter . Subsequent studies demonstrated that the vitamin D-cathelicidin pathway may be a key component of a novel innate immune response of human to infection.



    Take a look at another paper:

    Ancient exaptation of a CORE-SINE retroposon into a highly conserved mammalian neuronal enhancer of the proopiomelanocortin gene.

    http://www.ncbi.nlm.nih.gov/pubmed/17922573

    The authors conclude.

    We found that this CORE-SINE family of retroposons is likely to still be active in American and Australian marsupial genomes and that several highly conserved exonic, intronic and intergenic sequences in the human genome originated from the exaptation of CORE-SINE retroposons. Together, our results provide clear evidence of the functional novelties that transposed elements contributed to their host genomes throughout evolution.

    ReplyDelete
  2. Yeesh! Were I transported to a planet populated by organisms whose every DNA base had a vital role, would I there find my evolutionary inclinations sorely tried? Nah. Conversely, on a planet populated by organisms where 'true' sequence-irrelevant junk was very much the rule, would this blunt my fervour? Nope again.

    As luck would have it, we don't need to go anywhere; this planet has plenty of examples of the former, and a very good case could be made for the latter state predominating among the Eukarya. Evolutionary theory can explain both circumstances with ease, and both kinds of genome are smeared with the grubby fingerprints of the evolutionary process in action.

    If unequivocal economy of genome function is the hallmark of the Designer, then look to the prokaryotes!

    ReplyDelete
  3. @Atheistoclast,,

    What's your point? We all know of examples like this where junk DNA sequences have acquired a function. That does not mean that the rest of those defective sequences aren't junk.

    Are you trying to make the argument that junk DNA is functional because it serves as a reservoir for future evolution? If so, why not state that explicitly so we can discuss it?

    Simply stating scientific facts that we all know about isn't very helpful. (But it's typical IDiot behavior.)

    ReplyDelete
  4. Atheistoclast cites two articles saying a SINE, and a CORE SINE retrotransposon, respectively, may serve functions in the human genome.

    That's great, Atheistoclast, keep at it! You've only got 1,499,999 more SINEs and 5,999,999 more retrotransposons to go, and you'll have shown their less-than-majority contributions to the human genome may not be mostly junk.

    Best of luck with your (long-term) project!

    ReplyDelete
  5. Wells' unpublished book is currently at #23 in Amazon's list under Science > Biological Sciences > Genetics.

    Dawkins' Selfish Gene 30th Anniversary Edition is #1; Meyer's Signature in the Cell leads ID literature at #10.

    This subject doesn't exactly seem to be a hotbed of book sales for Amazon. A couple of genetics textbooks are listed higher than the Wells book.

    ReplyDelete
  6. Larry says:

    Are you trying to make the argument that junk DNA is functional because it serves as a reservoir for future evolution?

    Exactly, professor.These SINE and LINE sequences have the potential to affect gene expression and variation through their insertions.
    What troubles you is that they may have no immediate benefit to the organism so you think of them as garbage.

    It may well be true that evolutionary degeneration has inactivated many retotransposons ,as it has with various pseudogenes. But both can also be reactivated by mutation.

    You continue to believe that selection has no future reach. But I will confidently *predict* that those individuals with the most preserved SINEs and LINEs are at an evolutionary advantage over those where degeneration is in fact prevalent.

    Also, I think this is only one of the ways in which they are not junk. I told you before of my contention that they protect exons from cases of illegitimate recombination and translocation that can be disastrous.

    You have to seriously ask youself how and why these SINES and LINEs happen to donate translational enhancers and transcriptional silencers - especially in plant genomes.

    I recommend you read this fascinating article

    LTR-retrotransposons and MITEs: important players in the evolution of plant genomes

    http://www.ncbi.nlm.nih.gov/pubmed/8745082

    It is an old paper but very insightful.

    ReplyDelete
  7. Someday, Mr. Klinghoffer, who purports to be an orthodox Jew, should be asked to justify his association with an organization like the Dishonesty Institute whose executive director, John West, is a Holocaust revisionist.

    ReplyDelete
  8. Atheistoclast writes:

    You have to seriously ask you[r]self how and why these SINES and LINEs happen to do[mi]nate translational enhancers and transcriptional silencers - especially in plant genomes.

    Why, it's because onions are the pinnacle of Creation. Everyone knows that.

    ReplyDelete
  9. "Yeesh! Were I transported to a planet populated by organisms whose every DNA base had a vital role, would I there find my evolutionary inclinations sorely tried? Nah. Conversely, on a planet populated by organisms where 'true' sequence-irrelevant junk was very much the rule, would this blunt my fervour? Nope again."

    Equal fervour no matter what the evidence.

    ReplyDelete
  10. Larry has to examine the following:


    1) Why is whole genome duplication and polyploidy a feature of plants?

    2)Why is it observed that retotransposons have played a critical role in plant evolution by modulating gene expression and increasing variation?

    There was a big event held in Edinburgh last month on the subject of mobile elements:

    Genetics conference

    Larry wasn't invited because all he wants to do is be the grinch that stole the transposon.

    ReplyDelete
  11. Atheistoclast writes:

    Larry has to examine the following:


    1) Why is whole genome duplication and polyploidy a feature of plants?

    2)Why is it observed that retotransposons have played a critical role in plant evolution by modulating gene expression and increasing variation?

    And what you have to examine is the necessary consequence of contending that there is little if any junk in genomes: Many plants have far larger genomes than humans. Onions, for example, have up to five times the amounts of various types of non-coding DNA that humans do. See http://www.genomicron.evolverzone.com/2007/04/onion-test/ .

    So please give us your explanation as to why life is so much more complicated for onions than humans, or why the Creator apparently equipped them to accomplish so much more in the world than we humble humans.

    It's good you're posting about plants, too, since it will avoid any wild speculation (speaking of junk) that all the non-coding DNA was being saved up by earlier animals to later evolve into humans. And oh, by the way, does that mean you accept the fact of common descent?

    Meanwhile, I, for one, humbly welcome our new onion-y overlords.

    ReplyDelete
  12. Atheistoclast writes:

    You have to seriously ask you[r]self how and why these SINES and LINEs happen to do[mi]nate translational enhancers and transcriptional silencers - especially in plant genomes.

    Could it be because they are so abundant?

    How does that prove that there is no junk DNA, or that most DNA is not junk? If something is very abundant, then some of their variants will eventually be used. It's an accident waiting to happen. Accidental use does not mean "no junk."

    ReplyDelete
  13. Atheistoclast asked:

    1) Why is whole genome duplication and polyploidy a feature of plants?

    Maybe because they can tolerate more of these accidents without some seriously deleterious morphological problems?

    2)Why is it observed that retotransposons have played a critical role in plant evolution by modulating gene expression and increasing variation?

    Because they are so abundant? Again, if something is very abundant, most accidents will involve such somethings. Should they not be there, some other accidents would have done.

    I think your problem is more philosophical than scientific. Sure we owe our evolutionary history and ourselves, to whatever the accidents/sources of variation/whatever that were around. Someone might claim that without the junk and the selfish DNA (no necessarily the same), we would not be here. But that's a finalist argument. That does not mean that any of it was there "in order to make humans." It just means that humans were the result of such historical intricacies. In the same vein, the abundance of junk DNA makes them the most probable item to be involved in any kind of accidents and thus variation. That does not mean they have the "purpose" or "function" of providing variation. That's just a side effect of abundance.

    Clear?

    ReplyDelete
  14. I strongly recommend everyone reads this review of retrotransposons and their impact on human evolution.

    Retrotransposons and human evolution

    I just hope Larry soaks it all in before he declares his critics IDiots.

    ReplyDelete
  15. This was interesting:

    "1) The usual insults. In his blog Larry Moran of the Department of Biochemistry at the University of Toronto, a grown man and from the looks of him not a young one either, repetitively derides Jonathan as an "IDiot." (How embarrassing for this mature gentleman, you might think. Can you imagine Jonathan Wells or anyone else prominent in the ID community replying in kind, designating Professor Moran as "Larry Moron" or similar? The question is self-answering and tells you a lot about how desperation kindles anger among these people.)"

    What is interesting is that attempts at RIDICULE have become a very common technique that people like Dr. Moran and others use. (Think of how often Obama uses it).
    In politics, this traces back to Saul Alinsky and his "Rules for Radicals". Rule number 5.

    ReplyDelete
  16. Can you imagine Jonathan Wells or anyone else prominent in the ID community replying in kind, designating Professor Moran as "Larry Moron" or similar?

    Right, because ID supporters, as we know, are morally flawless and would never resort to ridicule of any kind.

    link

    In politics, this traces back to Saul Alinsky and his "Rules for Radicals". Rule number 5.

    Right, because before Alinsky no politician would have ever thought of ridiculing his opponent.

    link

    ReplyDelete
  17. Perhaps because I am older than many of the people here, I can recognize the exceptional level of ridicule that has infected the public discourse in recent years (compared to earlier years).
    And in Obama's case we know that he studied, practiced and taught the Alinsky methods.
    (I am not saying that Dr. Moran has studied these methods. Just that he uses the ridicule method. That is a fact).

    ReplyDelete
  18. Jeffrey,

    Most intelligent design proponents wouldn't write a piece of diatribe and pass it off as scholarship - as Barbara Forrest did in the journal Synthese for its special anti-ID issue.

    It is interesting that the guest editor for this polemic, Jim Fetzer, believes in some of the most diabolical conspiracy theories and accuses the "religious right" of mass murder against the American people.

    And you have the gall to call IDers "crackpots".

    ReplyDelete
  19. Atheisttoclast,

    I just hope Larry soaks it all in before he declares his critics IDiots.

    The IDiots are not Larry's critics. They IDiots are nothing but buffoons trying to make it appear as if their creationism can be disguised as science.

    As for you, you keep insisting not only in showing examples where your interpretation is wrong (abundance-thus-accident does not mean "function", nor "not-junk"), but also where you mistake selfish DNA, such as transposons, with junk, despite the many times Larry has told you he does not equate them.

    ReplyDelete
  20. Most intelligent design proponents wouldn't write a piece of diatribe and pass it off as scholarship - as Barbara Forrest did in the journal Synthese for its special anti-ID issue.

    Actually, quite a lot of what ID proponents write are diatribes masquerading as scholarship, certainly most of what comes out of the Discovery Institute

    ReplyDelete
  21. Atheistoclast,

    OK, now I know what I suspected, that you are an IDiot yourself. Thanks for clarifying.

    Most intelligent design proponents wouldn't write a piece of diatribe and pass it off as scholarship - as Barbara Forrest did in the journal Synthese for its special anti-ID issue.

    I understand that you being an IDiot, you will call "diatribe" any exposure of your trickery and of your distortion of science and everything that might interfere with the disguising of creationism as if it were science. But I tell you what. You admit that ID is creationism, your hypocrisy pretending it not to be so, and we might start respecting you. In the meantime, don't act so surprised that we call you and your actions by their proper names.

    blah, blah, blah ... "conspiracy theories" ... blah, blah, blah

    I don't know anything about that guy you accuse. However, given your record, and your defence of the ID crack-pottery, I can't say that I am too inclined to believe your words. Seems more like an attempt at an ad hominem. Typical.

    ... And you have the gall to call IDers (sic) "crackpots".

    You surely meant "IDiots." Yes, they are crackpots. Willfully so.

    You have shown a complete disregard to any explanation. For instance, you have ignored many times that Larry does not equate selfish and junk DNA. That alone tells me that you are deserving of the IDiot title. Whether you officially are one or not.

    There is no point in talking to you any more. You are not looking for answers.

    Bye bye IDiot. Feel proud, you won the title all by yourself.

    ReplyDelete
  22. I can recognize the exceptional level of ridicule that has infected the public discourse in recent years.

    Come back when you have actually read the book in the link I gave - American Aurora - and try to say that with a straight face.

    Personally, I see nothing wrong with a bit of ridicule when the target is truly being ridiculous.

    ReplyDelete
  23. Anonymous writes:
    Equal fervour no matter what the evidence.

    So which of those architectures should blunt my confidence in evolutionary theory? The existence of genomes of such extreme economy that the same sequence can take part in different genes? Or the existence of bloated genomes stuffed full of irrelevant fluff?

    Neither has the slightest bearing on the validity of evolution. But Wells et al seem to be working hard to discredit the latter - a fact that is inconvenient to those who expect to see perfection of design in nature - it must be so, whatever the evidence!

    OK, say 99.99% of every genome were found to be functional. How would that discredit evolution?

    ReplyDelete
  24. My "equal fervor no matter what the evidence" seems to have hit a nerve.

    Everyone knows that what I have said is true.

    ReplyDelete
  25. Jeffrey Shallit (a professor no less) rationalizes ridicule.
    So be it.

    ReplyDelete
  26. Allen Miller says:

    OK, say 99.99% of every genome were found to be functional. How would that discredit evolution?

    I don't think ID proponents claim that the genome is entirely functional. It is certainly true that many creationists like John Sanford, the inventor of the gene gun, are adamant that the genome is deteriorating due to mutational degradation.

    Larry has repeatedly asserted that most retrotransposable elements are defective and inactive. He may be right to an extent - although I don't see why inactive bits cannot be reactivated in the future.

    What I have tirelessly tried to convince him of is the fact that these elements, when they do move around the genome, often have profoundly beneficial effects and keep gene expression and variation dynamic. Sure, they can also contribute to diseases but their benefits outweigh their costs.

    Larry, and Negative Entropy, would suppose that their identified uses are merely "accidental". But random bits of truly junk DNA do not donate cis-regulatory elements to promoters. There is a method in the madness of these repetitive sequences.

    ReplyDelete
  27. Atheistoclast writes:

    I strongly recommend everyone reads this review of retrotransposons and their impact on human evolution.

    Retrotransposons and human evolution

    I read the article. Did you? And do you feel you understood it?

    Here's an excerpt from that article:

    ...it has long been recognized that recombination
    between TEs
    [transposable elements] can trigger genomic deletions in humans
    (these deletions have caused several genetic disorders)....


    If you claim to understand the article, and still contend no TEs are junk but are evidence of intentional design, then please explain

    - How the genetic disorders caused by the action of TEs are examples of design perfection; and

    - If these genetic disorders are not accidents caused by "junk," but represent the carrying out of intended design functions, why the designer's intent was so malign.

    I just hope Larry soaks it all in before he declares his critics IDiots.

    I'll let that statement stand without commentary as I wait for your reply to my questions on the article you urged us all to read.

    ReplyDelete
  28. And you have the gall to call IDers "crackpots".

    What, no anti-semitic slurs this time? You're really slipping.

    ReplyDelete
  29. It seems to me that the problem with Atheistoclast's position is that if a perfect being designed us, then his work doesn't end with demonstrating a purpose for one item in the genome reputed to be useless... it's explaining away the existence of even ONE such instance.

    There may well be a god, and we may indeed be his/her/its handiwork. But if our genome is indicative of the quality of craftwork of which that god is capable, then he ain't the guy they keep claiming he is.

    ReplyDelete
  30. Atheistoclast says:

    I don't think ID proponents claim that the genome is entirely functional. It is certainly true that many creationists like John Sanford, the inventor of the gene gun, are adamant that the genome is deteriorating due to mutational degradation.

    Then I think people like you have a problem. If you're proposing, as you seem to be here, that some god created human beings as perfect, and that our genome's been degrading ever since then, you are faced with the problem of discovering what deficiencies humanity has been inflicted with due to the degradation and outright failure of gene after gene after formerly-perfectly-functioning gene. In other words, what features and functions did Adam and Eve enjoy that we've lost along the way? Did we once have eighteen arms, and could see in X-rays, and breathe underwater?

    But if we're essentially the same despite the apparently HUGE loss of function implied by DNA that really doesn't do much anymore, how do you account for that? This is certainly a problem for the ID crowd, but it isn't for science. Evolution predicts, and we observe, broken genes for things like vitamin C production or atrophied ones for external tails or scenting ability. But if we're still in the image of God, despite all that we've apparently lost along the way, your theory doesn't provide much wiggle room at all in terms of squaring observation with conjecture.

    ReplyDelete
  31. Jeffrey,

    I think you'll find your colleague, Dr. Jim Fetzer, believes that 911 was a Mossad job.

    911 was the work of the Israeli Mossad

    You may not like ID, but its proponents don't accuse Jews of killing thousands of Americans.

    Of course, many people would nevertheless agree with Fetzer.

    ReplyDelete
  32. Atheistoclast writes:

    ...these elements, when they do move around the genome, often have profoundly beneficial effects and keep gene expression and variation dynamic. Sure, they can also contribute to diseases but their benefits outweigh their costs.

    Not what the science says.

    The depletion of TEs in certain regions of the human genome that are enriched in regulatory sequences, such as Hox gene clusters and other transposon-free regions, attests to the deleterious nature of TE insertions in genomic environments that contain a high density of cis-regulatory elements. However, like any mutational event, it is conceivable that these disruptive insertions might be beneficial under some circumstances.

    ReplyDelete
  33. My "equal fervor no matter what the evidence" seems to have hit a nerve.

    Everyone knows that what I have said is true.


    Hitting nerves, and getting on them, are not quite the same thing. I remain unclear as to why anyone's position on evolution should be influenced by the degree of functionality found in sundry genomes. But, hey, if you've really checked with everyone, and they concur with your position, that just about seals it!

    ReplyDelete
  34. And LINEs play a role in DNA repair

    DNA repair mediated by endonuclease-independent LINE-1 retrotransposition.

    http://www.ncbi.nlm.nih.gov/pubmed/12006980

    Gee, I'm such an IDiot!

    ReplyDelete
  35. I really get a laugh out of people who cite Saul Alinsky as an influence on President Obama. In actual fact, the politicians most influenced by Alinskys' ideas are the Rethuglicans, like Karl Rove. Alinsky wrote that the way to progress was to rub raw the sores of discontent. That is exactly how the Rethuglican Party has been operating since the days of Lee Atwater (anyone remember the Willie Horton ads). Karl Rove perfected Atwaters' approach with the Swift Boat ads against Senator Kerry.

    ReplyDelete
  36. Atheistoclast said:

    "What I have tirelessly tried to convince him of is the fact that these elements, when they do move around the genome, often have profoundly beneficial effects and keep gene expression and variation dynamic. Sure, they can also contribute to diseases but their benefits outweigh their costs."

    A bit of knowledge about mutations (or DNA movement) will show quite the opposite. The vast majority of mutations/DNA alterations are either neutral or deleterious. Getting a beneficial mutation is as rare as winning the lottery.
    You would know that if you have taken a course about basic molecular evolution.

    ReplyDelete
  37. Jeffrey Shallit writes:

    What, no anti-semitic slurs this time? You're really slipping.

    Thanks, Jeffrey, the bit of Googling this inspired me to do has saved me from wasting any future time on a fool who apparently has never once admitted he might be wrong about anything (to the extent of blaming helpful hints from experts when his software programs don't run).

    Couple of other gems from his past posts around the Web just to give the flavor:

    I revel in the fact that I don't even have a high school qualification in biology.

    * * * * *

    As with holocaust revisionism, evolutionism revisionism is important in establishing the truth.

    ReplyDelete
  38. Atheistoclast is Joseph Esfandiar Hannon Bozorgmehr from Manchester, United Kingdom. He infected other postings on Sandwalk under the name "Reza" [Darwinism and Junk DNA].

    He's been banned from Pharyngula and was banned from RichardDawkins.net except that he created 95 new identities in order to get around the ban.

    He is a holocaust denier. He used to run a business "selling components - just nuts and bolts - to the Iranian nuclear and missile industries" but it was shut down because of sanctions. Now he rants against British conspiracies.

    I always willing to give someone a chance to make a scientific case but my patience with Atheistoclast has worn out.

    Please don't respond to him any more.

    ReplyDelete
  39. This comment has been removed by the author.

    ReplyDelete
  40. SLC wants to distract from the fact that Obama learned, practiced and taught the Alinsky ideas for years.
    And Obama continues to use them today.

    My point is that Dr. Moran uses ridicule (as do many of the people here). I am not implying that Dr. Moran and the others here have Obama's background and expertise in these ideas.

    ReplyDelete
  41. Atheistoclast: It is interesting that the guest editor for this polemic, Jim Fetzer, believes in some of the most diabolical conspiracy theories and accuses the "religious right" of mass murder against the American people.

    Perhaps it is interesting. But is it relevant?

    ReplyDelete
  42. Bayesian, is Atheistoclast's background and beliefs relevant? According to Dr. Moran they are.
    Are there two different standards?

    ReplyDelete
  43. Re anomymous

    SLC wants to distract from the fact that Obama learned, practiced and taught the Alinsky ideas for years.
    And Obama continues to use them today.


    Mr. anomymous uses the technique known as the big lie, perfected by Josef Goebbels, to obfuscate the fact that the most loyal followers of Saul Alinsky are Rethuglicans like Karl Rove and the late and unlamented Lee Atwater. They are the ones who rub raw the sores of discontent by attempting to make scapegoats of African descended Americans and American Muslims. In the aftermath of the Civil War, this was called waving the bloody shirt.

    ReplyDelete
  44. @Atheistoclast

    I was gonna argue with you but then I accidentally came across you pathetically slandering my very-potential advisor on a certain forum, and have no particular reason to maintain a civilised conversation with someone not only as ignorant about evolution as you appear to be (verifiable fact, not ad hom), but someone who goes around insulting reputable professional scientists who are far more experienced and accomplished in the area than you can ever dream to be.

    Little annoys me more than know-it-all laymen atheist/skeptic activists who go around thinking they understand science better than reputable professional scientists in their respective fields. You're worse than creationists as far as I'm concerned. Fuck off.

    ReplyDelete
  45. Bayesian, is Atheistoclast's background and beliefs relevant? According to Dr. Moran they are.
    Are there two different standards?


    They are relevant in this case because there's a pretty reasonable chance that all his activity on the internet, from holocaust denial to evolutionary biology and getting papers published, is one enormous and very elaborate troll. At the very least some of his activities are.

    It pays not to take seriously much of what he writes, even when he writes it and submits in to journals. His first paper to be published was basically him throwing together a bunch of his posts from Talk Rational (a messageboard which you may be familiar with as you sound an awful lot like "socrates") and then submitting it to a low impact factor journal. Given that he admitted to trolling at the time he was writing those posts, I'm not alone in suspecting that an enormous practial joke has been played on some overly credulous journal editors.

    ReplyDelete
  46. SLC:

    Not coincidentally, a couple of weeks after bin Laden's death, Anonymous wants us all to concentrate on ancient history. (There was an even more risible comment posted on a very old thread here saying IIRC that the fact Obama insisted on bin Laden being given a religiously respectful burial is proof Obama is a Muslim terrorist.)

    I'd say we resist the temptation, especially in a thread about a junk book on junk DNA.

    ReplyDelete
  47. It is hard for SLC to admit that Obama learned, practiced and even taught the Alinsky ideas and methods for years. And is still using those methods.

    But I am not claiming that Dr. Moran and others here have learned and taught these ideas. Just that they follow Rule #5 which is ridicule.

    Ridicule is what children do. It is childish and immature. It strikes me as odd that people here who are University professors operate at that childish level. And like children, they are quite proud of themselves about it.

    ReplyDelete
  48. So it is confirmed that there are two different standards.
    One standard for people you agree with and another standard for those you disagree with.

    ReplyDelete
  49. I don't know who Atheistoclast is. I am interested in the points he makes. Are those points valid or not?
    But I notice that people here do not want to deal at that level but rather at the level of the man himself.
    This is an Alinsky method as well.
    Rule number 11.

    The method is to focus on the person and discredit him personally rather than deal with what he is saying.

    ReplyDelete
  50. Anonymous, after 6 separate comments in this thread alone on the topic of ridicule in public life, do you have any substantive comment to make about the actual topic of Dr. Moran's post?

    ReplyDelete
  51. Anonymous,

    "Atheistoclast" happens to be someone who has published 3 peer reviewed articles in the past 6 months on the subject of evolutionary biology:

    Gene duplication and the KPNA family

    A review of gene duplication and biological complexity

    An analysis on the opportunism of natural selection


    Larry won't tell you that - only reporting vicious gossip that I am an antisemitic holocaust denier and an international arms dealer.

    I am respectable scientist and not some Bond Villain!

    ReplyDelete
  52. Re Anonymous

    It is hard for Mr. Anonymous to admit that Karl Rove and the late and unlamented Lee Atwater are front and center in rubbing raw the sores of discontent, as advocated by Saul Alinsky. Quite typical of his ilk.

    ReplyDelete
  53. "...Jonathan Wells offers over 600 references to recent peer-reviewed literature."

    And I'll bet EVERY ONE of those 600 refs indicates that all DNA is functional, right Mr.Klinghoffer?

    Of course, this is the same Jonathan Wells that claimed in his Icons book that a Jain, Lake and Rivera paper showed that molecular phylogenetics was "in crisis" when in fact their paper was on the clonal theory of the origin of eukaryotes, and Wells lopped off half a sentence that he quoted indicating this.

    IOW - Wells is indeed a documented liar. Not sure why anyone puts so much stock in what he says.

    Anonymous X

    ReplyDelete
  54. "...I can recognize the exceptional level of ridicule that has infected the public discourse in recent years..."

    You've never watyched Fox News or listened to AM radio, have you? Read the Weekly Standard or perused Michelle Malkin's blog?

    I get a kick out of how easily right wingers get their panties in a bunch over 'the incivil discourse' when they apparently think all of the vile hatred and insulting nonsense from THEIR side somehow doesn't count - this is true for YEC/ID types as well.

    Anonymous X

    ReplyDelete
  55. Anonymous,

    I don't know who Atheistoclast is. I am interested in the points he makes. Are those points valid or not?

    Then you can't read, because I answered those points. If the answers were not clear enough for you, you could have asked. But you claim you want to know if the points are valid, yet you jumped the answers. That's interesting to say the least.

    ReplyDelete
  56. Anonymous,

    And you seem to have skipped other people's answers to atheistoclast too. Some much easier to grasp for a layperson than mine.

    ReplyDelete
  57. If SLC is upset about what he believes about Lee Atwater and Karl Rove then he must be even more upset that the Alinsky tactics are being used by a man who is the President of the United States!
    And there is no doubt that Obama who knows the Alinsky methods like the back of his hand has been continuing to use those tactics right up to today.

    But I am only claiming so far that people here are using Alinsky rules #5 and #11.

    ReplyDelete
  58. "Most intelligent design proponents wouldn't write a piece of diatribe and pass it off as scholarship"

    Did you read 'Icons of Evolution'?

    ReplyDelete
  59. Bozo:
    "DNA repair mediated by endonuclease-independent LINE-1 retrotransposition.

    http://www.ncbi.nlm.nih.gov/pubmed/12006980

    Gee, I'm such an IDiot!"

    I would agree - did you even bother to read the abstract? The LINE-1 inserts at damaged DNA sites - lesions. They see a hole and fill it because it is easier for them to insert at such sites.

    Wow - clearly a Designer made it so DNA accrues lesions such that LINE-1 can insert itself to 'fix it'....

    That is some serious creIDiot logic at work...

    Anonymous X

    ReplyDelete
  60. Bozo's "peer reviewed papers":

    1 is in the Journal of Bioeconomics

    1 is in the 'essays &commentary" section of an online 'multidisciplinary' journal

    1 makes spurious and rather absurd extrapolations

    A 'serious scientist'?

    Not so much - more like a guy taking advantage of lax reviewing standards in a couple of low-level journals hard up for submissions.

    ReplyDelete
  61. Jud asks:

    Do you have any substantive comment to make about the actual topic of Dr. Moran's post?

    I have a lot of respect for Professor Moran because he is of Irish descent (like me) and is one of the few evolutionary biologists whom you actually learn something from, and who is not an ideological Darwinist.

    But he refuses to entertain my hypothesis that much of "junk DNA" is *potentially* functional and whose sequences are not random gibberish. Just because it is not essential does mean it is "junk". He simply doesn't understand this distinction.

    ReplyDelete
  62. Joseph Esfandiar Hannon Bozorgmehr

    The Genetic code and the Latin language

    The genetic code and the biological information it makes possible are a profound engima for scientists studying the origin of life. However, a link to natural human language, in this case Latin, is found when the frequency distribution of characters is analyzed.



    Dean Yeager: This university will no longer continue any funding for any of your group's activities.

    Dr. Peter Venkman: But the kids love us!

    Dean Yeager: Doctor... Venkman. The purpose of science is to serve mankind. You seem to regard science as some kind of dodge... or hustle. Your theories are the worst kind of popular tripe, your methods are sloppy, and your conclusions are highly questionable! You are a poor scientist, Dr. Venkman!

    ReplyDelete
  63. We hope you are not comparing Dr. Moran to your Dr. Venkman.
    That would be improper, but still funny.

    ReplyDelete
  64. Atheistoclast writes: But he refuses to entertain my hypothesis that much of "junk DNA" is *potentially* functional and whose sequences are not random gibberish. Just because it is not essential does mean it is "junk".

    (missing "not" in that last sentence?).

    Any DNA is *potentially* functional. I'm a *potential* millionaire. But you seem to be saying that junk is there because it is potentially functional. That's its function, to be potentially functional. Translated into evolutionary genetic terms, you are saying that organisms or species with this reservoir of potential function have, in the past, had more offspring than those without it, via a causal link.

    So rather than being a consequence of weak selection against insertions and stronger selection against deletions - a ratchet - or the result of a battle between selfish elements and the interests of the wider genome, your hypothesis is that it is useful for genomes to turn a blind eye to the depradations of their many genetic parasites, or to make their meiotic alignments a little more sloppy than the strict demands of accuracy.

    It's certainly not impossible, but I don't see any evidential support.

    ReplyDelete
  65. Atheistoclast said:

    I have a lot of respect for Professor Moran because he is of Irish descent (like me)

    Well in that case, I'm actually an Irish citizen, so you should REALLY póg mo thóin. ;)

    ReplyDelete
  66. @Anonymous said...

    We hope

    We wonder why you are speaking in the first person plural.

    ReplyDelete
  67. Alan,

    My point is that retrotransposons are a unique case in that they are "mobile elements" when active.

    When they insert in promoter and regulatory regions near genes they serve to modulate gene expression. They have also been known to donate short exons to coding regions and to help with DNA repair.

    However, they only become useful when this happens. So, their utility is potential rather than actual. There may be no immediate benefit to their existence.

    But it is better in evolutionary terms for the organism to have them than not have them.So the appellation of "junk" by Larry et al is not fair at all.

    I am exploring a way in which I could test my hypothesis. I would appreciate it if someone could propose a way to do this.

    ReplyDelete
  68. Bozorgmehr (Atheistoclast) says,

    But he refuses to entertain my hypothesis that much of "junk DNA" is *potentially* functional and whose sequences are not random gibberish. Just because it is not essential does mean it is "junk". He simply doesn't understand this distinction.

    If the DNA is required for the survival of the individual, it's immediate descendants, or the species, then that DNA is essential. The rest is junk.

    Is that distinction clear enough for you?

    ReplyDelete
  69. From steve oberski:
    "We wonder why you are speaking in the first person plural."

    Likewise we wonder why you are speaking in the first person plural.

    Two can play these stupid games you like to indulge in. You are desperate to find something to criticize. But go ahead. Continue if you must.

    All these insults and ridicule are directly from the Alinsky playbook.

    ReplyDelete
  70. Prof. Moran:
    If the DNA is required for the survival of the individual, it's immediate descendants, or the species, then that DNA is essential. The rest is junk.


    There is a picture "Variabilität Coecinela (Adalia) 10-punctata".

    There are 109 color patterns to be found on this ladybird. Apart from the fact that it posits a problem for Darwinists how it comes along with aposematic warning coloration the question is:

    Let us presume that in variation
    79 is involved a gene or switch X. We can clearly imagine that the species can thrive without this variation. In your definiton the gene X is now junk, isn't it?

    The picture is on my blog here:

    http://cadra.wordpress.com/2009/06/29/franz-heikertingers-dismissal-of-natural-selection/

    ReplyDelete
  71. Bozorgmehr (Atheistoclast) says,

    I am exploring a way in which I could test my hypothesis. I would appreciate it if someone could propose a way to do this.

    If your hypothesis is correct then you would expect all modern species to have lots of junk DNA in their genome because they are the end result of successful evolution. Presumably, they will have out-competed their cousins that had less DNA.

    Here's some data on the range of genome sizes in animals [Animal Genome Size Database]. Does it fit with your hypothesis that larger genomes are selected in most groups?

    ReplyDelete
  72. Thanks, Larry.

    In eukaryotes, I would consider the likes of amoebae and algae to be the most successful organisms because of their ability to survive and adapt in most environments. There is a difference between biological complexity and viability.

    It is no small wonder that they also exhibit very large genomes in spite of the metabolic cost (not insignificant) of maintaining them.

    I really don't buy into your argument about evolution by accident. It seems to me to be a cop-out that precludes further research and investigation.

    ReplyDelete
  73. Larry says:

    If the DNA is required for the survival of the individual, it's immediate descendants, or the species, then that DNA is essential. The rest is junk.

    I am gobsmacked. Many duplicate genes can be knocked out and with no phenotypic consequences. Are these duplicates "junk" because they are non-essential and only provide a redundant functionality?

    Come on,Larry, you are not thinking.

    ReplyDelete
  74. Bozorgmehr (Atheistoclast) says,

    In eukaryotes, I would consider the likes of amoebae and algae to be the most successful organisms because of their ability to survive and adapt in most environments. There is a difference between biological complexity and viability.

    It is no small wonder that they also exhibit very large genomes in spite of the metabolic cost (not insignificant) of maintaining them.


    Interesting. The vast majority of modern (successful) protozoa and algae have genomes that are an order of magnitude smaller than mammalian genomes.

    How does that fit in with your speculation?

    ReplyDelete
  75. Bozorgmehr (Atheistoclast) says,

    I am gobsmacked. Many duplicate genes can be knocked out and with no phenotypic consequences. Are these duplicates "junk" because they are non-essential and only provide a redundant functionality?

    Yes, if that "redundant functionality" is never required for survival of the individual, it's immediate descendants, or the species.

    Come on,Larry, you are not thinking.

    :-)

    ReplyDelete
  76. Larry,

    How many genomes have been sequenced from protozoa and algae? Don't make such sweeping statements.

    However, "metabolic minimalism" is a feature of many single-celled organisms as much as "adaptive potentiality". Therefore one should expect to find both small and huge genomes in these types of organisms depending on their ecology.

    I would focus on why a particular species has amassed so much ncDNA rather than just dismiss this as a freakish accident as you do.

    ReplyDelete
  77. Larry says:

    Yes, if that "redundant functionality" is never required for survival of the individual, it's immediate descendants, or the species (it is junk).

    Interesting. Perhaps you would explain why selection retains duplicate genes precisely as "backups" in thale cress?

    Evolutionary Persistence of Functional Compensation by Duplicate Genes in Arabidopsis

    The authors conclude:

    One reason why many duplicated genes are retained in the Arabidopsis genome is because some or many of them contribute to genetic robustness and are retained by natural selection.

    In other words, the redundant utility of gene duplicates to compensate for potential failures not in the immediate present is why they have been retained.

    Junk today, useful tomorrow.

    ReplyDelete
  78. How many genomes have been sequenced from protozoa and algae? Don't make such sweeping statements.

    You don't need to sequence a genome in order to know its size. Did you not know that?

    There's a list of several hundred alga genome sizes at the Plant DNA C-values Database on the KEW Gardens website.

    The genomes of 19 protists have been sequenced. You can see their genome sizes at: List of sequenced eukaryotic genomes. Note that all of these genomes are quite small. The genome size of Amoeba was reported to be very large but that report is probably wrong. The cells are likely polyploid (see Ryan Gregory).

    I'm surprised that you seem to know so little about genomes.

    ReplyDelete
  79. @Anonymous All these insults and ridicule are directly from the Alinsky playbook.

    We are sorry we hurt your (2nd person plural) feelings.

    We furthermore hasten to assure you (all) that the insults (those not self inflicted) are entirely of our own invention and that the ridicule was copy and pasted from The Internet Movie Database and a very interesting paper by Bozorgmehr (Atheistoclast) on the Genetic code and the Latin language (we are not making this stuff up).

    Bozorgmehr (Atheistoclast) may want to consult the works of Cicero in his current quest since they seemed to stand him in good stead in the aforementioned paper.

    ReplyDelete
  80. VMartin, you made a very good point. I hope it does not get lost. Perhaps Dr. Moran could respond to it.

    ReplyDelete
  81. Note that all of these eukaryotic genomes are quite small.

    The exception being the maize plant which is a major case for research into ncDNA and retrotransposons that comprise about 2/3 of its genome.

    It has 63,000 genes (polyploid) and is roughly the same size as that of humans (2.8Mb). This is more than 10 times more than thale cress which has about 30,000 genes.

    So clearly ncDNA is a major factor in the biology of the maize plant.

    I think there is a reason for this while you think it is just accidental.

    ReplyDelete
  82. steve oberski keeps trying. Oh well - continue if you must.
    The Alinsky methods work for Obama. Perhaps they will work for you here.
    No doubt you will have some ridiculing (and ridiculous) comeback.
    Each time you do you prove my point.

    ReplyDelete
  83. Anonymous writes:

    Each time you do you prove my point.

    Which would be...? (I'm quite serious. I really can't tell what you're driving at, with all sorts of comments about ridicule, Obama, and Alinsky, but precious little to the point of the post.)

    ReplyDelete
  84. Anonymous writes:

    VMartin, you made a very good point. I hope it does not get lost. Perhaps Dr. Moran could respond to it.

    Ooh, ooh, let me.

    VMartin's example is coding DNA. If the coding DNA changes, you eventually get a different species. And Dr. Moran said whatever's necessary for survival of the species isn't junk. So coding DNA isn't junk.

    That's for all coding DNA. For this particular example, the coloration could drive away predators or attract mates, so it could assist in species survival in other ways.

    ReplyDelete
  85. VMartin writes:

    There are 109 color patterns to be found on this ladybird. Apart from the fact that it posits a problem for Darwinists how it comes along with aposematic warning coloration....

    Let's suppose Heikertinger actually demonstrated what you say he did regarding insect coloration. It might cause extreme adaptationists to go looking for some other advantage conferred by the patterns, e.g., sexual selection, but if these were simply examples of neutral variation, I don't think it would cause evolutionary theory in general, or Dr. Moran in particular, any problems whatever.

    ReplyDelete
  86. It's #4 per Amazon. Scroll to the "Product Details" section

    * ISBN-10: 1936599007
    * ISBN-13: 978-1936599004
    * Amazon Bestsellers Rank: #7,316 in Books (See Top 100 in Books)
    o #4 in Books > Professional & Technical > Medical > Basic Sciences > Genetics

    ReplyDelete
  87. Anonymous:
    VMartin, you made a very good point. I hope it does not get lost. Perhaps Dr. Moran could respond to it.

    Thank you. Polymorphism refutes his claim in my humble opinion. It is hard to imagine that all those color morphs or races of ladybirds are inevitable for surviving of the species.

    ReplyDelete
  88. Jud said:
    "I don't think it would cause evolutionary theory in general, or Dr. Moran in particular, any problems whatever."

    No matter what the evidence, it always is interpreted as supporting evolution theory.

    ReplyDelete
  89. I sincerely hope that Larry reads "The Myth of Junk DNA" and writes a book review of it for some journal.

    Btw, on the subject of essential function, how much of the 5' and 3' UTRs can be deleted with no consequence? How much of the protein-coding sequence in many genes can be deleted with no effect on survival and reproduction?

    Should all non-essential DNA be regarded as "junk"? If we deleted all of the SINEs and LINEs in our genome, as Larry recommends, would we be at a biological and evolutionary advantage?

    I suspect we have cornered Larry into defending the indefensible.

    ReplyDelete
  90. The same VMartin that is good pals with John Davison? Humble opinion, indeed.

    Anonymous X

    ReplyDelete
  91. I hope at some point in his book Wells explains how "no junk DNA" is a prediction of Intelligent Design since supposedly nothing can be known about the designer; neither his competence nor his intentions nor methods. In fact, I hope he explains how ID can generate any predictions when starting from such a vague assumption.

    ReplyDelete
  92. VMartin has made an interesting point. Instead of addressing it in an intellectually honest way, "Anonymous X" attacks him personally.
    That is a technique that is practiced here very often.
    Have people noticed that?

    ReplyDelete
  93. Anonymous writes:

    No matter what the evidence, it always is interpreted as supporting evolution theory.

    Translation: "If I, who know nothing about evolution, cannot figure out what is wrong with it, then certainly that must indicate a problem with evolution!"

    Err, no. That's simply what happens when you try to poke holes in a firmly corroborated scientific theory that you know nothing about. You could substitute "Einstein's theory of gravitation" or "quantum mechanics" for "evolution" and the outcome would be exactly the same.

    ReplyDelete
  94. Jud seems to be confused.

    ReplyDelete
  95. Anonymous writes:

    Jud seems to be confused.

    How remarkably cryptic.

    About many things I may be confused. However, the lack of knowledge of the theory of evolution you've indicated in your comments thus far is quite clear. Let's just take your latest plaint as one example:

    No matter what the evidence, it always is interpreted as supporting evolution theory.

    Would you be at all surprised to see this in a sentence about the theory of gravitation? All it indicates is that the theory has been so well corroborated and refined over a century or more that it has taken into account all the relevant evidence of which researchers (much less laypeople) are aware.

    The same is true of the theory of evolution. You and a handful of other relatively uninformed laypeople raise what you think are "issues" (but in fact are not), and are shocked - shocked! - that 150 years of careful scientific research in multiple disciplines doesn't immediately fall before your oh-so-keen minds.

    Get over it.

    ReplyDelete
  96. It looks like Dr. Moran will not be addressing what VMartin posted.
    Pity.

    ReplyDelete
  97. VMartin the electrician:

    There are 109 color patterns to be found on this ladybird. Apart from the fact that it posits a problem for Darwinists how it comes along with aposematic warning coloration the question is:


    Wow... OBVIOUSLY designed - only a super intelligence could find a reason for 109 coloration patterns in one kind of beetle...

    ReplyDelete
  98. Vmartin:
    Thank you. Polymorphism refutes his claim in my humble opinion. It is hard to imagine that all those color morphs or races of ladybirds are inevitable for surviving of the species.

    Ah, the old argument from personal incredulity, a creationist classic. I guess the old 'whim of the creator' all purpose escape clause suits you better?

    ReplyDelete
  99. Anon:
    VMartin has made an interesting point. Instead of addressing it in an intellectually honest way, "Anonymous X" attacks him personally.
    That is a technique that is practiced here very often.
    Have people noticed that?



    Well, Mr.Wizard, lets take a look at a couple of facts.

    1. You ASSUME that VMartin made an interesting point, as is personal incredulty is interesting.

    2. You apparently failed to realize that this is the comments section on a blog, not a meeting of the Oxford Debate Team.

    3. Looking at the sorts of things a person believes are good points, valid points, good science, etc. is a good way to assess how much they actually understand about the concepts/claims/issues they are lauding or denigrating. If you are familiar with the inane rants of John Davison, you would understand why so many folks find those impressed with his claims to be functionally scientifically illiterate.

    Get over yourself.

    AnonX

    Anonymous X

    ReplyDelete
  100. Anon:
    It looks like Dr. Moran will not be addressing what VMartin posted.

    Pity


    Why? Were you oh-so-impressed by it?

    How about you explain why it is so pertinent?

    ReplyDelete
  101. Anonymous X does his best to justify attacking those he disagrees with.

    I am still wondering if Dr. Moran will respond to what VMartin has posted.

    ReplyDelete
  102. Anonymous writes:

    I am still wondering if Dr. Moran will respond to what VMartin has posted.

    I'm sort of curious whether you or VMartin will respond to what VMartin has posted, regarding what it means for Jonathan Wells in particular and ID in general, since although evolution really has no problem with this surfeit of forms, ID does have one in absolute spades.

    You may not have noticed the following: You have not only the 109 pattern variations resulting from coding and regulatory genes to explain, you have the existence of all the DNA in these beetles that apparently does absolutely nothing - the "junk" - to explain as well. And you have to find some essential design purpose for it, while evolutionary theory easily admits of both "junk" and neutral coding DNA. While you've been pushing VMartin's point, you've entirely failed to realize he's making a much better argument against design than he is against evolutionary theory.

    ReplyDelete
  103. "Can you imagine Jonathan Wells or anyone else prominent in the ID community replying in kind, designating Professor Moran as "Larry Moron" or similar?"

    Translation: I get to call Larry Moran Larry Moron without doing it explicitly. I am so wily!

    ReplyDelete
  104. JUD:
    "you have the existence of all the DNA in these beetles that apparently does absolutely nothing"

    The key word is "apparently".
    The function has not yet been discovered.
    That is what science is all about.
    Exciting isn't it? Or do you suggest no further study of what their function(s) might be?

    ReplyDelete
  105. I completely agree with Anonymous' latest comment that searching for new knowledge is incredibly exciting, and studies that may lead to new knowledge are to be encouraged.

    With regard to what are the sensible choices on which to spend research dollars, let freedom of choice reign. Anyone who wishes research to be done searching for functionality in DNA that acts as a template for products that are thrown away before proteins are made is welcome to spend money in an effort to prove it.

    ReplyDelete
  106. Jud posted:
    "DNA that acts as a template for products that are thrown away before proteins are made"

    Can you give us references for that?
    What does it mean to be thrown away? Is it ejected from the cell as waste?
    Links we can follow would be great.

    ReplyDelete
  107. Anonymous asks:

    Jud posted:
    "DNA that acts as a template for products that are thrown away before proteins are made"

    Can you give us references for that?
    What does it mean to be thrown away? Is it ejected from the cell as waste?
    Links we can follow would be great.


    Definition of an intron:

    An intron is any nucleotide sequence within a gene that is removed by RNA splicing to generate the final mature RNA product of a gene.

    Understand? The RNA that is made from the DNA template has large regions that must be deleted (thrown away) before what remains is spliced together to make the RNA template for a protein. The DNA regions corresponding to the RNA that must be thrown out, as well as the deleted RNA regions, are called introns.

    Link: http://en.wikipedia.org/wiki/Intron

    Also, from our host:

    Protein-encoding genes: (9.6% junk)
    transcribed region:
    essential 1.8%
    intron junk (not included above) 9.6%

    Introns sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.

    Link: http://sandwalk.blogspot.com/2008/02/theme-genomes-junk-dna.html

    ReplyDelete
  108. In response to this:

    Can you imagine Jonathan Wells or anyone else prominent in the ID community replying in kind, designating Professor Moran as "Larry Moron" or similar?

    Jeffry Shallit says:

    "Right, because ID supporters, as we know, are morally flawless and would never resort to ridicule of any kind."

    You, chaps, need no ridicule from outside. You are derising yourselves with your evolutionary arguments. There is no evidence of random error-accumulating incrementality leading to formal functionality, error correction, noise reduction or semantics proper. You, guys, will never accept the evident existence of the cybernetic cut: spontaneous low-information redundant regularity vs. choice-contingent control proper.

    ReplyDelete
  109. Hmmm. So the new ID tactic is to wait until a comment thread is cold, and then to make ridiculous claims, such as Anonymous December 28, 2011 9:01:00 AM, in the hope it looks like you came out this a cracker of an argument?

    ReplyDelete
  110. Yes what about all the junk DNA floating about the primordial muddy pool - then it just came together - just like that - (as tommy cooper used to say) to form the first living cell - then went on from their to a fish then an animal then flew like a bird - if you believe this you need certified.

    ReplyDelete
    Replies
    1. What the hell are you babbling about, Charles Allan?

      Delete