Tuesday, May 29, 2012

Watch Jonathan Wells Screw Up

Here's Jonathan Wells attacking the concept of junk DNA during a lecture at Biola University in October 2010. It's remarkable because he repeats a false history that he knows is untrue because many people have corrected him. Pay attention to what he says about four minutes into the presentation.


Wells is talking about the history of junk DNA. He begins by falsely describing the Central Dogma of Molecular Biology, which, he says, is "DNA makes RNA, makes protein, makes us." He then quotes Jacques Monod as a supporter of this concept (4 minutes, 23 seconds).
With that, and the understanding of the random physical basis of mutation that molecular biology has provided, the mechanism of Darwinism is at last securely founded, and man has to understand that he is a mere accident.
Jacque Monod (1970) quoted in "The Eight Day of Creation" by Horace Freeland Judson (p. 192)
I looked up this passage and guess what I found? I discovered that when Monod said "with that" he was referring to the real Central Dogma—the one that Crick actually formulated. Only a few sentences earlier Monod is quoted as saying ...
This was what Francis Crick called the Central Dogma: no information goes from protein to DNA.
This is followed by a brief description of Lamarckism and why it conflicts with the Central Dogma. So Monod has it exactly right, the Central Dogma says that information can only flow from nucleic acid to protein and not vice versa. That rules out the inheritance of applied characteristics and makes "the mechanism of Darwinism ... securely founded."

Why is this important? Because Wells immediately follows this by claiming that ...
... biologists discovered that most human DNA does not code for proteins. Based on the Central Dogma that "DNA makes RNA makes protein makes us," this non-protein-coding DNA was dubbed "junk."
This is nonsense. Not only did the concept of junk DNA have nothing to do with the Central Dogma, it also had nothing to do with "non-coding DNA." By 1970, all knowledgeable molecular biologists knew that there was lots of perfectly functional DNA that did not encode protein. It's simply not true that the consensus opinion among the experts at the time was that all noncoding DNA was junk [Junk & Jonathan: Part 3—The Preface].

There are legitimate debates about the quantity of junk DNA in our genome. What I just don't understand is why IDiots feel they have to distort history in order to make their point. Wouldn't they be a lot more credible if they at least got the simple things right?

Are they pathological liars?


21 comments :

  1. Replies
    1. Me too.

      That's two votes for pathological liar, zero votes for "scientist."

      Delete
    2. Your knowledge of the scientific method is practically zero. You can do a bit of programming, but that's about it.

      Delete
  2. It was not until 1977 that it was realized that eukaryotic genes were split up by non-coding regions now knowns as "introns". In spite of all the evidence to the contrary, Larry regards the vast majority of intronic sequences to be "junk".

    Is Larry Moran a pathological denier?

    ReplyDelete
    Replies
    1. Genes are not "split up" by introns. They CONTAIN introns between exons within the transcribed region that are spliced out during RNA processing, resulting in the contiguous chain of exonic sequences in the mature mRNA that are translated into proteins. Genes are "split up" by intergenic (non-coding) DNA that contains regulatory sequences that bind regulatory proteins (which control gene transcription), and other DNA, some of which is "junk" (i.e. completely non-functional, rich with dead transposable elements and simple repeats). Indeed, some introns actually contain cis-acting regulatory sequences that affect transcription of the gene. Intron splicing itself also affects RNA stability, and thus ultimate protein levels. I'm sure Larry Moran knows all of this, and does not consider introns to be "junk" DNA (no one does).

      Delete
    2. It was not until 1977 that it was realized that eukaryotic genes were split up by non-coding regions now knowns as "introns".

      Most of us in the field at the time knew about intervening sequences by 1974. And by 1977 we knew that some protein encoding eukaryotic genes did NOT have introns.

      In spite of all the evidence to the contrary, Larry regards the vast majority of intronic sequences to be "junk".

      Let me correct your typo. I think you meant to say "Because of abundant evidence, Larry regards the vast majority of intronic sequences to be junk."

      You're welcome.

      Delete
    3. Anonymous says,

      I'm sure Larry Moran knows all of this, and does not consider introns to be "junk" DNA (no one does).

      Yes, Larry knows all this and he also knows that most of the intron is junk.

      There also seem to be cases where replacing an intron-containing gene with one that has no introns (i.e. derived from cDNA) has no obvious effect. That suggests that, at least in some cases, the introns aren't necessary.

      There are also many intronless paralogues in large multicellular eukaryotic genomes. The intronless paralogues are often expressed at very high levels or in certain tissues (i.e. spermatocytes). This tells us that introns are not essential for gene expression.

      Delete
    4. I agree with everything you say. Most intronic sequences are junk, in the sense that even if splicing affects message stability of that particular gene, the nucleotide sequence per se is non-functional (except when containing a binding site for a regulatory protein, which I admit is a rare scenario), and splicing is not universal among genes in eukaryotes. I was arguing against the position that introns were necessarily junk DNA (i.e. by definition).

      Delete
  3. Are they pathological liars

    The answer to that question is absolutely positively, and unequivocally yes.

    ReplyDelete
    Replies
    1. That's four votes for pathological liars. I think Jonathan Wells is about to become the first survivor to be eliminated.

      Delete
  4. "Wouldn't they be a lot more credible if they at least got the simple things right?"
    If they were going for credibility, then yes. But it's not an academic exercise, so what does it matter for credibility?

    ReplyDelete
  5. Since they cling to a worldview that is diametrically in opposition to reality, they're forced to lie.

    ReplyDelete
  6. Well -- WordPress is certainly giving me fits. Let's try for the third time, then I'm giving up.

    Yes, pathological liars.

    This is in service to the false dichotomy logical fallacy, which lies at the very heart of the creationist movement.

    If "X" is false, then "Y" is true.

    If junk DNA is false, then Jesus rode dinosaurs.

    Kevin

    ReplyDelete
  7. Unfortunately, Larry is faced with some very disturbing evidence as far as he is concerned. He has to address the following facts:

    1) Many intronic sequences are heavily conserved. Why would that be if the sequences are mostly junk?

    High intron sequence conservation across three mammalian orders suggests functional constraints.

    http://palumbi.stanford.edu/manuscripts/Hare%20and%20Palumbi%202003.pdf

    This level of intron sequence conservation is above that expected by chance and strongly suggests that intron sequences are playing a larger functional role in gene regulation than previously realized.

    2) Functions continue to be found for introns other than for alternative splicing (as mentioned by Wells).

    Comparative and functional analysis of intron-mediated enhancement signals reveals conserved features among plants

    http://nar.oxfordjournals.org/content/early/2011/03/22/nar.gkr043.long

    Introns in a wide range of organisms including plants, animals and fungi are able to increase the expression of the gene that they are contained in.

    No matter how many papers in the literature I cite, nothing seems to evoke an iota of curiosity in Larry Moran's mind. I, along with the rest of the scientific community, might as well live on Mars.

    ReplyDelete
  8. Atheistoclast, just for the sake of discussion, let's say that you're right and that there is no junk DNA in any organism.

    With that in mind:

    What is your ultimate point?

    Do you think that no junk DNA would automatically confirm that organisms are or were intelligently designed?

    Are or were the diseases/defects/disabilities in organisms intelligently designed?

    Is or was death intelligently designed? How about decay?

    Who or what is "the designer"?

    ReplyDelete
    Replies
    1. I have never claimed that there is no junk in the eukaryotic genome. Actually, unlike Larry, I maintain that some of that junk is in the protein-coding sequences themselves that he regards as essential - I will explain why if you need to know.

      It is clear to me that introns, integenic regions and many transposable elements (both active and defective) do appear to be play a role in maintaining genomic stability, gene expression,regulation, repair and replication. This fact has really little to do with ID because Darwinian adaptationists can also see this. But Larry believes in "evolution by accident" which I find to be intellectually offensive.

      If you look at the yeast genome, it contain far less non-coding DNA than the human genome. But it nonetheless contains all of the elements (introns, retrotransposons etc). Why has the yeast genome accumulated so little "junk" when Larry supposes that this process is inevitable given enough time? Or could it be, more likely, that complex multicellular organisms need lots of ncDNA?

      Larry is correct, and Wells is wrong, however, about pseudogenes. Wells maintains that some pseudogenes regulate the expression of functional genes just by getting transcribed into RNA. That may be so, but it is hardly the case that their "function" is "designed" and is not merely incidental to the fact of their nonfunctionalization.

      Delete
    2. "But Larry believes in 'evolution by accident' which I find to be intellectually offensive"

      I hope poor Larry doesn't lose too much sleep over your disappointment in him.

      Delete
  9. Wells: pathological liar 100% certified.

    ReplyDelete
  10. Atheistoclast, you seem to have missed the point of my questions. Here they are again, with some rewording:

    Atheistoclast, just for the sake of discussion, let's say that you're right and that there is less junk DNA in some or all organisms than Larry or some other scientists posit.

    And, just for the sake of discussion, let's assume that it's possible that there is no junk DNA in any organism and never has been any.

    With all that in mind:

    1. What is your ultimate point?

    2. Do you think that less or no junk DNA would automatically confirm that organisms are or were intelligently designed?

    3. Are or were the diseases/defects/disabilities in organisms intelligently designed?

    4. Is or was death intelligently designed? How about decay?

    5. Who or what is "the designer"?

    ReplyDelete
  11. It's not just the IDists constant repetition of false, previously corrected claims, but their avoidance of having an actual discussion with their critics, that makes them liars.

    ReplyDelete