Intelligent Design

Who believed in the myth of junk DNA? – Michael Shermer, for one

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In 2006, Skeptic Magazine publisher Michael Shermer wrote: “We have to wonder why the Intelligent Designer added to our genome junk DNA, repeated copies of useless DNA, orphan genes, tandem repeats, and pseudogenes, none of which are involved directly in the making of a human being. In fact, of the entire human genome, it appears that only a tiny percentage is actively involved in useful protein production, It looks as though Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragment copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution.”- Jonathan Wells, The Myth of Junk DNA, p. 23

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27 Replies to “Who believed in the myth of junk DNA? – Michael Shermer, for one

  1. 1
    Elizabeth Liddle says:

    Michael Schermer is not a biologist, he’s a journalist. I think his scientific training was in experimental psychology.

    The really interesting thing about pseudo genes (and ERVs, and some other stuff) is what they tell us about lineages, and, in some cases, like the broken GULO gene in primates, what kind of environment our shared ancestors might have lived in (probably rich in vitamin-C bearing fruit).

    Trying to fit the GULO gene data into an ID hypothesis seems to me to be fairly difficult.

    As for non-coding regulatory genes, Schermer should have known better, in 2006, that genes involved in “useful protein production” are a relatively small part of what the genome does, and, indeed, that “making” a human being is itself only a small part of what the genome does.

    Or rather, that “making” a human being is a continuous process that includes enabling that human being to function flexibly in his/her environment, largely governed by cell signalling processes that are mediated by non-coding DNA.

    The protein-making part is just building materials supply logistics. What really matters is which proteins are produced where in response to what.

  2. 2
    Arthur Hunt says:

    (Sorry for the repetition, but these numbers always seem to bear repeating):

    Some (very round) numbers to keep in mind when discussing this subject:

    # of protein-coding genes in the human genome – 30,000

    Average size of a protein – 1000 amino acids

    Average protein-coding capacity of a typical gene – 3000 nucleotides

    1. Total number of protein-coding nucleotides – 10^8 nucleotides

    Total number of introns – 200,000

    Average intron length – 6000 bp

    Total intronic content – 1.2*10^9 bp

    “functional” intronic sequences (these include splicing signals and intronic enhancer and suppressor elements) – 600 bp per intron (a very generous overestimate, since most introns probably have a fraction of this extent of functional sequence)

    2. total “functional” intronic sequence content – 1.2*10^8 bp

    promoter elements per gene – 100 (this is probably a huge overestimate, but I have decided to round up to the nearest order of magnitude)

    size of a typical promoter element – 100 bp (another huge overestimate, made to give every benefit of the doubt to supporters of Wells et al.; in particular, it assumes that every human gene includes promoter elements derived from repetitive DNA, that could conceivably be as large as 100 bp)

    3. total content of functional DNA in promoters – 3*10^8 bp

    upper range of estimates of non-coding RNAs (outside of stable RNAs) – 10,000

    size of non-coding RNAs (another huge overestimate) – 10,000 nts

    4. total content of non-coding RNAs – 10^8 bp

    total of “functional” DNA – sum of #’s 1-4 = 6.2 *10^8 bp

    fraction of the human genome that is functional (assume a haploid genome of 3*10^9 bp) – 20%

    So, even when we grant Wells et al. their each and every wish when it comes to functionality of non-protein-coding DNA, we can only account for 20% of the human genome. (Readers should note that this is a wild over-estimate, but it serves as a baseline for discussion.)

    So, for readers here who have looked through Well’s book – what specific and tangible data do Wells point to (or describe – maybe he has been doing some actual experiments) that support the standard ID assertion that there is no such thing as junk DNA? Not vague reference to experiments not done, not hopeful or wishful thinking, but solid experimental results that allow us to state that the remaining 80% of the human genome has some specifiable (and specific) function.

    Some more things:

    total size of the RNA polymerase II “transcriptome” – 1.3*10^9 bp (from the preceding comment, assuming that these are released from moderation in the order in which I posted them)

    total size of the “stable” transcriptome (that which is not thrown away) – 10^8 bp

    percentage of all polII-transcribed RNA that is thrown away – 92%

    Again, readers who have looked through Wells’ book might tell us just how much of this 92% Wells proves to have function. (This is a tough one, since the RNA actually is not present in the cell, except transiently). Please be as specific and quantitative as possible.

  3. 3
    Mung says:

    Trying to fit the GULO gene data into an ID hypothesis seems to me to be fairly difficult.

    Why?

    Designed things frequently break.

    Designed things often become obsolete.

    What is the difficulty for ID?

  4. 4
    DrREC says:

    “Designed things frequently break.”
    “Designed things often become obsolete”
    “What is the difficulty for ID?”

    Complex=designed
    Simple=designed
    Functional=designed
    Broken=designed
    Required=designed
    Obsolete=designed

    Heck, I’ve even seen arguments here for Evolved=designed?

    No problem, seems like design explains all. Might be a bit hard to detect/define/quantify/test/falsify, but don’t let that get in the your way!

  5. 5
    DrREC says:

    And secondly, the GULO pseudogene contains mutations/deletions that precisely align with common descent.

    So the “designed things frequently break” argument fals short of explaining the appearance of common descent.

    Unless common descent flies at ‘uncommon descent.’

  6. 6
    nullasalus says:

    Unless common descent flies at ‘uncommon descent.’

    It does.

    No problem, seems like design explains all. Might be a bit hard to detect/define/quantify/test/falsify, but don’t let that get in the your way!

    Speaking for myself, I would be more than happy if scientists flatly said ‘whether or not life – and anything else – is designed is a question science cannot answer. For all we know, all organisms, the origin of life and evolution itself is designed. Those questions are beyond science.’

    Seems reasonable, eh?

  7. 7
    DrREC says:

    “Unless common descent flies at ‘uncommon descent.”
    “It does.”

    I could take that as a mere irony, if it weren’t for the history (wedge) and current political discussions of ID as a replacement for evolutionary biology.

    “I would be more than happy if scientists flatly said ‘whether or not life – and anything else – is designed is a question science cannot answer.”

    Umm…isn’t intelligent design supposed to be the science that DOES demonstrate life is designed? Kinda shooting yourself in the foot here, Mr. none-but-Catholics-are-saved.

    As for me, I can say the hypothesis that a designer that equally includes broken bits, non-optimal design, obsolete bits, in a manner that precisely gives the appearance of common descent and natural evolution is non-falsifiable. It is outside of science. It is also essentially theistic evolution.

    If we accept this, doesn’t that leaves the ID movement a sad shell of what it claimed to be?

    I thought it was supposed to show the falseness of evolution in short order, not relegate itself to some non-scientific sideshow.

  8. 8
    nullasalus says:

    DrREC,

    I could take that as a mere irony, if it weren’t for the history (wedge) and current political discussions of ID as a replacement for evolutionary biology.

    How about you take it as what’s stated on the very FAQ itself? And who’s recommending that ID is a ‘replacement for evolutionary biology’? How could it be, when ID proponents such as Behe defend the possibility of both design and evolution being true, along with accepting common descent?

    Umm…isn’t intelligent design supposed to be the science that DOES demonstrate life is designed? Kinda shooting yourself in the foot here, Mr. none-but-Catholics-are-saved.

    I see you’re back to that insult. But I’ll forgive both your bigotry and your penchant for lying. You can’t help yourself, clearly.

    I disagree that ID is science, nor do I think that science is the only way to infer, even strongly infer, that life is designed.

    As for me, I can say the hypothesis that a designer that equally includes broken bits, non-optimal design, obsolete bits, in a manner that precisely gives the appearance of common descent and natural evolution is non-falsifiable. It is outside of science. It is also essentially theistic evolution.

    Theistic evolution and ID are compatible in principle, even if not always in practice.

    And what is ‘natural evolution’? It can’t be ‘something that isn’t designed’, scientifically. Science can’t determine whether something is or isn’t designed, remember?

    ID has always accepted the possibility of non-optimal design, obsolescence, and the like. It’s concerned with design, full stop.

    I thought it was supposed to show the falseness of evolution in short order, not relegate itself to some non-scientific sideshow.

    You thought wrong. Not really a surprise given your track record.

  9. 9
    DrREC says:

    “I disagree that ID is science,”

    Great, we’re in perfect agreement.

    Can we then agree that something that isn’t science shouldn’t be taught in science class?

  10. 10
    nullasalus says:

    Great, we’re in perfect agreement.

    Doubtful. There’s that track record again.

    Can we then agree that something that isn’t science shouldn’t be taught in science class?

    The moment it’s stated clearly that science is utterly incapable of determining whether or not evolution is guided and therefore whether or not organisms are designed, that science is silent on teleology’s presence or lack in nature, and that it becomes acceptable to point out the flaws in Neo-Darwinism as well as the areas that are still a mystery or a looming question in evolutionary theory, I’ll be more concerned about that.

  11. 11
    DrREC says:

    So you want a sticker saying:

    1) Science isn’t religion, though it may conflict with certain beliefs
    2) Science isn’t infallible–you are being taught the consensus as scientists understand it today

  12. 12
    nullasalus says:

    So you want a sticker saying:

    Nope. I said what I wanted, and that’s not an accurate translation. Nor do I think a ‘sticker’ is a solution. Do you think a sticker saying ‘scientists right now think evolution is true’ as the complete coverage of evolutionary theory would be sufficient?

  13. 13
    Elizabeth Liddle says:

    I want every science textbook to have sticker with the url of Isaac Asimov’s essay, The Relativity of Wrong.

    http://chem.tufts.edu/AnswersI.....fWrong.htm

  14. 14
    Joseph says:

    DrREC,

    ID, as with all design inferences, can be falsified just by demonstrating necessity and/or chance can account for what we are investigating.

    THAT is how the EF works and it is also follows Newton’s First Rule.

    As for universal common descent, well, if all you have as “evidence” is similarities then you don’t have anything as it is teh physiological and anatomical differences your position must account for.

  15. 15
    DrREC says:

    “ID, as with all design inferences, can be falsified just by demonstrating necessity and/or chance can account for what we are investigating.”

    No-that would show chance and necessity are apparently sufficient conditions. That a designer also played a role could not be ruled out. see below:

    “THAT is how the EF works and it is also follows Newton’s First Rule”

    Dembski: (1) I’ve pretty much dispensed with the EF. It suggests that chance, necessity, and design are mutually exclusive. They are not. Straight CSI is clearer as a criterion for design detection.

    http://www.uncommondescent.com.....ent-299021

    Setting aside that there seem to be differing opinions on how to calculate CSI–I think it is fairly easy to conclude CSI has been observed to increase in natural processes.

    “As for universal common descent, well, if all you have as “evidence” is similarities then you don’t have anything as it is teh physiological and anatomical differences your position must account for.”

    Of course we consider the differences. In the molecular phylogeny of primates, for example, it is the small percent differences that allow the formation of a phylogenetic tree. I don’t understand this criticism.

  16. 16
    Mung says:

    And secondly, the GULO pseudogene contains mutations/deletions that precisely align with common descent.

    So what?

    You can add:

    common descent = designed

    So far you haven’t given me any argument against design based on the presence of that (pseudo-)gene.

  17. 17
    Mung says:

    DrREC:

    Kinda shooting yourself in the foot here, Mr. none-but-Catholics-are-saved.

    A bit of gratuitous ad hominem never hurt anyone, right?

  18. 18
    Mung says:

    DrREC:

    Setting aside that there seem to be differing opinions on how to calculate CSI–I think it is fairly easy to conclude CSI has been observed to increase in natural processes.

    Nice to see how evolutionary processes can increase something that’s already there.

    How does that explain how the CSI got there in the first place?

  19. 19
    Elizabeth Liddle says:

    Mung:

    DrREC:

    Setting aside that there seem to be differing opinions on how to calculate CSI–I think it is fairly easy to conclude CSI has been observed to increase in natural processes.

    Nice to see how evolutionary processes can increase something that’s already there.

    How does that explain how the CSI got there in the first place?

    It doesn’t. Darwinian theory doesn’t explain that.

    Darwinian theory is about how it increases once you’ve got it (although given that it’s a threshold measure, it could boost it from subthreshold to supra-threshold).

  20. 20
    DrREC says:

    “DrREC:

    Kinda shooting yourself in the foot here, Mr. none-but-Catholics-are-saved.

    A bit of gratuitous ad hominem never hurt anyone, right?”

    I call out extreme religious bigotry when I see it. An avatar based on the Catholic doctrine “extra ecclesiam nulla salus” is hurtful to all non-Catholics, no matter how your try to sugar coat the doctrine that we, outside the church, are hell-bound.

    Even Vatican II affirms, “They could not be saved who, knowing that the Catholic Church was founded as necessary by God through Christ, would refuse either to enter it, or to remain in it.”

    I’m sorry, but I’ll continue to point this out. I would do the same for someone whose name was any sort of slur against others.

  21. 21
    DrREC says:

    Mung:
    “So what?

    You can add:

    common descent = designed

    So far you haven’t given me any argument against design based on the presence of that (pseudo-)gene.”

    I don’t know how to make this any clearer. NO argument can ever be made against design! This is particularly true when you start explaining away broken bits, common descent, novel genes arising by tractable and *apparently* non-design processes by saying a designer could have been involved.

    How do I argue against that!

    There is no argument to be made. But you move the design hypothesis out of testability and into a faith statement when you do this.

  22. 22
    Mung says:

    NO argument can ever be made against design!

    Well now, that just isn’t true.

    So there.

  23. 23
    DrREC says:

    Ok Mung, indulge me.

    Present a way to falsify your hypothesis of a designer, acting in some unperceived way that gives the appearance of common descent where:

    Complex=designed
    Simple=designed
    Functional=designed
    Broken=designed
    Required=designed
    Obsolete=designed

    and

    Common descent=designed

    Or more simply perhaps, how would I demonstrate the
    GULO pseudogene is not designed?

  24. 24
    Mung says:

    DrREC:

    Present a way to falsify your hypothesis of a designer, acting in some unperceived way that gives the appearance of common descent where:

    Well, that explains your confusion I suppose.

    ID theory doesn’t consist of a hypothesis about a designer acting in ways, perceived or unperceived, that give the appearance of common descent.

  25. 25
    Mung says:

    Or more simply perhaps, how would I demonstrate the GULO pseudogene is not designed?

    However you like.

    ID isn’t about what is not designed. ID is about cases in which ID is the best explanation.

    Possible explanations include:

    Chance
    Necessity
    Chance + Necessity
    Intelligent Design

  26. 26
    DrREC says:

    Mung-don’t dodge the question.

    How would you falsify a design hypothesis (of your choosing, since you’ll dance around mine ad nauseum)?

  27. 27
    Mung says:

    Well, we could take the GULO pseudo-gene. If it is true that it serves no actual function, then the design hypothesis for it would be falsified.

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