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Thursday, December 22, 2011

Do the IDiots Understand Biochemistry and Molecular Biology?

We've been discussing whether Intelligent Design Creationists understand enough about biochemistry, molecular biology, and evolution to warrant their criticisms of these fields. The answer is clearly "no" as they demonstrate time and time again.

This time it's an anonymous posting on the premier IDC website, Evolution News & Views [Long Non-coding RNA Punches Another Hole in "Junk Genome" Myth]. The anonymous poster links to a recent paper in Genes & Development that shows a function for a particular long non-coding (lnc) RNA. The paper implies that many of these lncRNAs (up to 400) are expressed in mouse erythroid cells.

Regulatory RNA have been known and studied for at least four decades and various lncRNAs have been characterized over the past twenty years. The IDiot at Evolution News & Views seems to think that this is a new discovery proving that there's no junk in our genome. The facts are quite different.

As I pointed out in my review of The Myth of Junk DNA, the amount of the genome devoted to producing lncRNAs is about 0.1% [Junk & Jonathan: Part 6—Chapter 3]. So, not only have we known about regulatory RNAs for many years, we also know that their genes don't account for very much of the genome, I figure it can't be more than 2% even when you include all of the most optimistic estimates of regulatory RNAs [see What's in Your Genome?].

But the ignorance of the IDiots is much more profound than just being incapable of calculating percentages. The latest posting reveals the depth of their ignorance.
These findings have two important implications. First, non-coding regions of the genome were assumed to be leftover evolutionary relics that no longer play a functional role. The assumption was not due to extensive studies of non-coding regions of the genome, but rather to a commitment to what is known as the central dogma of molecular biology: DNA is transcribed into RNA and RNA is translated into amino acids to make proteins. This was considered the primary purpose of DNA. The non-coding regions were assumed to have no function, and were dismissed as the natural consequence of genetic "junk" accumulating over time. This paper is one among an accumulating corpus of papers discussing new and interesting functions of the non-coding regions of the genome. (See The Myth of Junk DNA by Jonathan Wells for a history of "junk" DNA and additional references describing the function of so-called "junk" DNA. See here for a discussion on the regulatory role of introns.)
There was never a time in the past fifty years when knowledgeable biochemists and molecular biologists thought that all non-coding DNA was nonfunctional junk. This was never an assumption of the Central Dogma of Molecular Biology which states that "... once (sequential) information has passed into protein it cannot get out again" [Basic Concepts: The Central Dogma of Molecular Biology]. There are many scientists who have misconceptions about the Central Dogma [The Central Dogma Strawman] but the IDiots go one step farther by misunderstanding the misconception!

We've known about functions in non-coding DNA since the early 1960s as anyone who has ever glanced at a textbook would know. It's hard to tell whether the IDiots are just butt-ignorant of basic science or whether they are lying. This is an especially tricky problem when the silly strawman argument is popularized by Jonathan Wells because he's supposed to know the science [Junk & Jonathan: Part 1—Getting the History Correct] [Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?].

We know that most of our genome is junk because we know a great deal about genomes, genes, biochemistry, molecular biology, and evolution. We know which parts are likely to be functional and which parts are likely to be broken genes and other kinds of junk. We know this because we understand the subject, not because we are covering up our ignorance.

The IDiots are ignorant of the science and they assume that everyone else is as well. That's a very bad assumption.


  1. The IDiots are ignorant of the science and they assume that everyone else is as well. That's a very bad assumption.

    If your target audience is limited to other IDiots and the credulous of religious and other sorts then this is probably a pretty good assumption.

  2. Wow, misrepresenting the central dogma that way is a new low. It betrays them for what they are: quacks deluding their public. They took advantage of the way the misnomer of the central dogma sounds. The way they managed it shows that their expertise is rhetorical bullshit. They are masters of bullshit. I have to wonder how can they sleep at night, how can they live with themselves.

  3. You said in an earlier thread:
    It gives you a very good idea of what Intelligent Design Creationism is all about. It's about nothing ... there's not a single mention of what IDC stands for and not a single bit of evidence for the existence of a designer.
    I understand that you are interested in biochemistry and molecular biology, and can't miss the opportunity of sharing that enthusiasm with us, but isn't it overkill to point out the scientific failures of IDC in their criticism of evolution? Maybe even giving them the unmerited honor of a scientific response?
    Don't get me wrong - I welcome the opportunity to learn about biochemistry.

  4. Larry, you're operating under the misapprehension that they have at least some level of scruples. Some IDiots may understand it perfectly well, others may not even be able to spell 'biochemistry'. But to them it doesn't matter, it's all about promoting their agenda, and to do that they will lie and obfuscate in order to try to bamboozle those who are easily led into their trap. They simply don't care what they do, never have and never will.

  5. Larry advances an argument from ignorance and personal incredulity:

    I can't believe something could possibly be functional, if not now in the future, so that means it is "junk".

    Now, is that a rational and scientific position to take? I think not. The progress of science will undermine such flawed arguments.

  6. @Atheistoclast

    When I attribute a quote to someone I indicate this by putting it in italics or blockquotes. Based on my experience this appears to be a common convention in venues of this sort.

    I don't see the quote you attribute to Larry in his post nor can I infer it from contents of the post.

    You appear to have dispensed with the (bending over backwards to be charitable here) very thin veneer of rationality you have (all too infrequently) displayed in the past and your true persona of pathological liar is revealed apparently without the least vestige of embarrassment.

  7. Steve,

    Larry is on the wrong side of scientific progress and history. Just because he is incapable of understanding the subtle function of retrotransposons, does not mean others are not.

    The simple fact is that more complex organisms seem to require more ncDNA rather than merely produce it.

    Notice how he refuses to engage with me any longer because he realizes he has no valid arguments.

  8. Larry is on the wrong side of scientific progress and history. Just because he is incapable of understanding the subtle function of retrotransposons, does not mean others are not. - Atheistoclast said...

    That is so funnily wrong it has cheered me up from my festivity induced hang-over.

  9. "Notice how he refuses to engage with me any longer because he realizes he has no valid arguments."

    No. I suspect he's following the old adage that says 'never wrestle with a pig, you just get dirty and the pig enjoys it.' Please, if you wish to keep tilting at windmills learn to duck, your head has obviously taken a few too many hits from the vanes. That tired old "they won't debate us" whine that creationists constantly drag out shows a persecution complex that is entirely unjustified and undignified. We're also tired of the false dichotomy, the idea that if you can show evolution to be false then your alternative is correct. Wrong. Present your evidence for ID (creationism in a shabby cloak) without reference to the claims of evolutionary theory.

    We're waiting...

  10. I have here repeatedly pointed out the growing evidence of functions attributed to seemingly "defective" (inactive) retrotransposons. Larry just ignores it all being a true science denier.

    I am particularly enthused at the functional relationship between transposons and the chromatin:

    LINE Retrotransposon RNA Is an Essential Structural and Functional Epigenetic Component of a Core Neocentromeric Chromatin

    The authors report that:

    "Although the great majority of L1s are inactive due to 5′ end truncations, active transcription and translation of these retrotransposons has recently been detected in a variety of cell types and implicated to be a potential regulator for cellular processes.

    I am shocked at the level of intellectual disinterest by a Toronto university professor of biochemistry. It is really maddening and saddening.

    Btw, I am happy to debate Dr. Moran on the sidelines of the Evolution 2012 conference in Ottawa. But I suspect he would prefer to avoid such an event.

  11. Atheistoclast displays the typical persecution complex of the deluded conspiracy theorist. He probably won't debate me because he's scared. It's in league with the government won't release data on alien visitations because they say there isn't any. Therefore they must be hiding something.

  12. One thing that puzzles me is this. Suppose that 50 years ago scientists did assume that all non-coding DNA is junk. Or assume that Larry Moran is proved wrong in his belief that most of the non-coding DNA is junk. So what? How does this disprove evolution? Wouldn't science just move forward with a deeper understanding of how the world works? This ongoing argument srtikes me as a bit pointless. What do the IDiots hope to gain?

  13. Anonymous said: "What do the IDiots hope to gain?"

    What they hope to gain is converts to their side from those who are easily swayed by bullshit.

  14. Dear Clast:
    Others have made the prediction that sometimes some previously irrelevant sequences can get functions by hitchhiking. Random functions. Randomness is the signature of hitchhiking.

    In that Chueh paper they describe several L1 sequences in that portion of a chromosome: 13 sequences. Including 6 non-defective, full-length, sequeneces. But only ONE and only ONE is transcribed. And it is transcribed also in the original chromosome (where it do not form a neocentromere).

    This cannot be an example of a general and widespread function for these L1 elements. The sentence you hihglight is taken from paper's introduction, and is not an accurate reflection of paper's results and conclusions.

    Please, we all are eager to see you providing evidence that many other centromeres or neocentromeres form around active L1 retrotransposons.

    Just to make my position clear, active L1 retrotranspons may have an effect in evolution/genetic mechanisms. They promote variability. But that not means that L1 elements per se have a definite and specific function other than autoreplication.

    See Han&Boeke BioEssays 27:775 (2005)