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Sep 27 2012

Jonathan Wells talks about history

Oh, boy. Jonathan Wells explains why some of us reject the outrageous interpretations made from the ENCODE work claiming 80%+ functionality of the genome. It was really an effort to get past this sentence.

Some historical context might help.

Bwahahahahaha! First sentence, he makes a joke. Wells is a creationist clown notorious for his tortured abuse of the history of science. He doesn’t have a merely whiggish view of history — it’s more of a Burke&Hareish perspective, where if History isn’t conveniently dead to permit him to commit ghoulish atrocities on it, he’s willing to take a cosh to it’s skull and batter it into extinction. When Wells announces that he’s going to provide “historical context”, brace yourself for a graceless exercise in ugly alternative histories.

After James Watson and Francis Crick discovered the molecular structure of DNA in 1953, Crick announced that they had found "the secret of life," a popular formulation of which became "DNA makes RNA makes protein makes us."

What? I don’t even…OK, second sentence is wrong. That looks like a mangled version of the Central Dogma of molecular biology, with a weird appendage tacked on to claim that it “makes us”. Crick did not discover the secret of life. What the Central Dogma is about is the irreversibility of information flow: nucleotide sequence specifies the order of amino acids in a protein, but there is no mechanism to translate a sequence of amino acids back into a sequence of nucleotides in RNA/DNA. It’s an important concept, but not the secret of life.

But biologists discovered that about 98% of our DNA does not code for protein, and in 1972 Susumu Ohno and David Comings independently used the term "junk" to refer to non-protein-coding DNA (though neither man excluded the possibility that some of it might turn out to be functional).

More garbage. NO. No one equated non-protein-coding DNA with junk. Unless it was a creationist. In 1972, we knew about lots of non-coding DNA that wasn’t just functional, it was essential — genes for tRNAs and regulatory sequences, for instance. The term “Junk DNA” was initally coined to describe pseudogenes — gene duplicates that had been rendered nonfunctional by mutation. We knew that gene duplication was common, but that successful gene duplications, that is events that resulted in a copy with novel functions that would be maintained by natural selection, were going to be rare. So Ohno expected large quantities of such relics to be found in the genome.

Why didn’t biologists simply call non-protein-coding sequences "DNA of unknown function" rather than "junk DNA?" For some, it was because "junk DNA" seemed more suited to the defense of Darwinism and survival of the fittest.

No, because the term was initially applied to a specific class of sequences that were recognized as failed duplications. They weren’t of unknown function…they were the debris left over from unsuccessful natural experiments.

Now we know of other mechanisms that produce repetitive, non-functional sequences. There are transposable elements that have no purpose but to replicate themselves over and over in the genome, there are viral insertions, for instance. We know how they get there, and it’s not because their existence confers greater fitness on the bearer, or because they make active contributions to the phenotype. They’re just splatters of DNA.

The term “Junk DNA” is perfectly reasonable to apply to such mostly-useless sequences. I think the only legitimate argument against the term is that we have so many different classes of the material that more specific labels would be more useful…but the argument that these sequences are functional is a nonstarter.

In 1976, Richard Dawkins wrote in The Selfish Gene that "the true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus [i.e., non-protein-coding] DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA."

Hey, Wells gets something mostly right! Yes, that’s correct, and it’s the explanation born out by observations of things such as LINEs and SINEs, which code for enzymes (or sequences recognized by such enzymes) that insert copies of themselves back into the genome. This isn’t just a supposition, we know how this works.

He gets the motivation behind the dispute completely wrong, however. We aren’t calling some sequences “junk” because we don’t know what they do: to the contrary, it’s because we know where those sequences come from and what they do. It’s also not because, somehow, it is a Darwinian prerequisite that “junk” exist in the genome. Again, to the contrary, there was initially resistance to the idea of junk because of a Darwinian bias towards seeing adaptedness in everything. The idea of non-functional DNA sequences that don’t contribute significantly to the phenotype emerged from observations of what we actually found when we started taking apart the components of the genome.

That’s why a lot of us are irritated with the ENCODE interpretation that the whole genome is ‘functional’. It’s not because of a philosophical predisposition, or because we apply the label by default to sequences we don’t understand, but because that conclusion rides roughshod over a lot of well-established evidence.

Oh. Right. In addition to history, evidence is another of those esoteric concepts that Jonathan Wells can’t comprehend.

24 comments

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  1. 1
    JohnnieCanuck

    What, he’s still here? Why wouldn’t Jesus-Moon have taken him with Him at the end of His Second Coming?

    Perhaps he didn’t live up to expectations with that disproving evolution task he was given.

  2. 2
    Lars

    Now we know of other mechanisms that produce repetitive, non-functional sequences.

    My brain expected the next sentence to be “Creationists with typewriters”. Instead you confused me. Poopyhead.

  3. 3
    Pierce R. Butler

    Maybe Jonathan W. can follow in the footsteps of his higher-achieving namesake H.G. and present us with a magnum opus entitled The Out-and-Out Lying of History.

  4. 4
    sadunlap

    I realize sometimes there’s just too much fail and wrongness for PZ to catch it all in one post.

    After James Watson and Francis Crick discovered the molecular structure of DNA in 1953

    Let’s see…

    After James Watson and Francis Crick discovered stole Rosalind Franklin’s research with the collusion of her research “partner,” which led them to take credit for her work in the discovery of the molecular structure of DNA in 1953…

    There, that’s better.

    BTW, history trivia: back in that time Franklin was barred from eating in the same commissary as her male colleagues at Cambridge. She had to eat with the cleaning staff.

  5. 5
    Reginald Selkirk

    Wells: After James Watson and Francis Crick discovered the molecular structure of DNA in 1953, Crick announced that they had found “the secret of life,” a popular formulation of which became “DNA makes RNA makes protein makes us.”
    .
    What? I don’t even…OK, second sentence is wrong. That looks like a mangled version of the Central Dogma of molecular biology, with a weird appendage tacked on to claim that it “makes us”. Crick did not discover the secret of life…

    Watson & Crick actually did discover something very close to the ‘secret of life.’ The base pairing double helical nature of DNA explains replication, transcription and about half of translation. So the value of the discovery goes way beyond the ‘Central Dogma’ which Wells mis-stated.

  6. 6
    Funny Diva

    And now I’ve got an earworm…

    “my name is John Wellington Wells
    I’m a dealer in magic and spells
    In blessings and curses And ever-filled purses
    In prophecies, witches, and knells”

    That is to say, NOT a dealer in actual facts…

  7. 7
    Crissa

    Umm, I’m pretty sure ‘makes’ is a verb that also means ‘constructs’, as in, DNA constructs RNA which constructs proteins which are assembled to create a human.

    Which I think isn’t quite right, either, but really, yelling and screaming at this point is possibly going to lose anyone who hasn’t passed college biology recently. Dumbed down language is going to be clumsy.

  8. 8
    jose

    It’s interesting creationists think Ohno advanced the idea of useless DNA to support darwinism. Isn’t what actually happened the opposite of that? It went against the time’s view of darwinism, with its excessive focus on adaptation and optimization. The presence of a bunch of useless stuff would challenge this purported power of natural selection to shape efficiently all aspects of organisms.

  9. 9
    jose

    …Right. Forget previous post.

  10. 10
    robro

    Incidentally, the current issue (October) of Scientific American has an interview with Ewan Birney on this subject. As the subtitle says, “What was once known as junk DNA turns out to hold hidden treasures, says computational biologist Ewan Birney.”

  11. 11
    Ant (@antallan)

    @ sadunlap #4

    Why am I more aghast at her being forced to eat elsewhere than about her research being stolen?

    /@

  12. 12
    Ant (@antallan)

    … except:

    Sayre states “that while the male staff at King’s lunched in a large, comfortable, rather clubby dining room” the female staff of all ranks “lunched in the student’s hall or away from the premises”.[92][93] Elkin states that most of the MRC group typically ate lunch together (including Franklin) in the mixed dining room discussed below.[94]

    [Wikipedia]

    What’s the truth of the matter here?

    /@

  13. 13
    Glen Davidson

    We could call any DNA that makes lying jerks like Wells “junk DNA.”

    Except that it doesn’t seem to be something caused by DNA (or only one possible outcome out of many). That it’s a junk brain writing complete BS for the dead Moon (why hasn’t he been resurrected, moron?) is certain, no matter that it could have been useful at one time.

    Glen Davidson

  14. 14
    Ichthyic

    just for the people who don’t know Wells’ OWN history…

    I was in grad school with this guy. He was in molecular and cell bio, and I in zoology. I used to have lunch with him.

    …he lies as easily as you might talk about your favorite TV show around the water cooler. Hell, he fooled me into thinking he was just a confused grad student trying to “reconcile his religious beliefs with his science research”.

    BULLSHIT. I later saw him make a presentation a about this “reconcilation effort” at a museum lunch, and saw the lies pop one after another. just amazing. I think my major prof actually blew a gasket; his face turned red and he actually started heckling Wells DURING his presentation.

    don’t ever think Wells doesn’t know better. He and I TAUGHT freshman bio at Berkeley as grad students; that had all the basics of genetics and evolution in it. That, aside from the fact that there is no way he could have passed his GRE’s without knowing this stuff in and out.

    so, just stressing… never think the man ignorant or confused. He is deliberately and with malice, lying. This is what he has been paid to do for decades now.

    *sigh*

  15. 15
    andrewriding

    I’m kind of impressed that he went to the trouble of exempting Susumu Ohno and David Comings from claims that junk DNA must be completely useless.
    My expectations for creationists are adequately low, but in this regard the guy has slightly exceeded expectations. Guess I let an argument with an IDiot on sandwalk over-colour my perception. Was a nightmare trying to get that one to recognize the selective force could be too slow to “optimize” a genome and get rid of the failed duplications and transposable elements- well he never showed signs of understanding what we were saying solved his problem, but we did eventually get to the point where he was rejecting it at the final stage of explanation instead of the moron material he began with.

    That said, none of my biology courses seem to have conveyed the whole junk DNA issue very well. My professors and textbooks all seemed content to act as though it was a great mistake of scientists past. The way they presented the central dogma was almost as bad, but I vaguely recall one professor trying to make some point about the portrayal of it being too simple; I can’t recall if he explained this as the original idea being complete or if he let the students think this was some later modification. Is it common for college education to get history quite so wrong?

  16. 16
    JohnnieCanuck

    For some given level of detail, all history is wrong. All you need to see this is to compare two accounts of an event. They will not agree, even if the two observers are on the same side.

    A person with one watch knows what time it is. A person with two watches isn’t quite so sure.

    It took quite a while for the dust to settle about ‘junk’ DNA. The last word on it may still be yet to come. That makes for confusion in the lecture halls.

  17. 17
    PZ Myers

    No, Watson & Crick did discover the structure of DNA. Rosalind Franklin didn’t. Franklin had the crystallographic data that contained critical information for determining that structure, but there was more to putting together the whole story than just the crystallography.

  18. 18
    Rolan le Gargéac

    PeeZee …

    take a cosh to it’s skull

    FFS its dangnabbit !

  19. 19
    haslar53

    A three word rebuttal: The onion genome

  20. 20
    nooneinparticular

    Thanks, PZ. As ever, thoughtful and clear. Best explanation of “junk DNA” I’ve seen.

  21. 21
    Worldtraveller

    Jonathan Wells speaks, stupid comes out. Can’t explain that! (Well, yes we can….)

  22. 22
    timmyson

    Well, thanks for setting me straight. I’m sure if I worked hard enough at it, I could blame my mistaken understanding of “junk” DNA on some or other science popularization from the 90′s, but I had thought that it referred to non-protein chunks. Now I know.

  23. 23
    andrewriding

    The term does seem to be used for DNA that doesn’t contribute in the protein production process, rather than exclusively sequences of known origin. Hard to tell if that’s just because journalists keep trying to use it that way or not though.

  24. 24
    mattdavies

    Hi all, may sound a bit cheeky but can anyone help me out with poit 9 on the following?

    http://www.biblicalpublishing.org/Debate/Is%20Evolution%20a%20Fact%20-%20Rebuttal.pdf

    sounds like a creationist cherry picking, mis-represeting etc but i don’t quite have the science.

    thanks

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