Pharyngula

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.

Comments

  1. #1 oicur12
    September 28, 2012

    Huh? What? No negative doubled unthought, is never disproven invalid or not. Tautologically speaking magic monkeys are evolving magic freaking spelling fairies non-heating. Processing the carbon, man, of Little Earth.

  2. #2 djlactin
    Pohang, South Korea
    September 28, 2012

    “…such as LINEs and SINEs, which code for enzymes (or sequences recognized by such enzymes) that insert copies of themselves back into the genome…” Grammar problem? Here, “themselves” = “enzymes”; i.e., that the genome includes protein sequences. I think you mean “such as LINEs and SINEs, which code for enzymes (or sequences recognized by such enzymes) that insert copies of the LINEs and SINEs back into the genome”
    (Sorry to be such a pedant; in a parallel life I am a technical editor.)

  3. #3 Piotr Gąsiorowski
    September 28, 2012

    Why is it so important to creationists what percentage of the human genome is or is not “functional’? After all, no-one infers the existence of an Inteligent Designer from the fact that prokaryotes have no junk DNA. If humans had none either, or if they had less of it (like bats, hummingbirds or pufferfish), would that matter at all?

    Creationists act as if ID *predicted* the nonexistence of junk DNA. This is absurd. First, predictions logically follow from a theory, and there is no theory behind ID to base a prediction on. Secondly, supposing for the sake of the argument that there is a virtually omnipotent designer who created life on Earth, how do creationists know that he can’t have created junk as well? Can they read God’s own mind?

  4. #4 Monty
    September 29, 2012

    In response to Piotr: The reason creationists latch on to the nonexistence of junk DNA is because they (for some odd reason) believe of the ridiculous notion of irreducible complexity. This same line of thinking was a key argument used by the defendents in the Kitzmiller v. Dover Area School District case in the state of Pennsylvania in 2005. Junk DNA doesn’t fit into the idea of irreducible complexity because their supposition is that an organism could function without junk DNA. Therefore, because the Designer obviously wouldn’t design something with junk DNA, it must not exist.
    It’s just another example of idiots clinging to bad science/explanations of science.

  5. #5 Monty
    September 29, 2012

    Excuse me,
    *believe in the ridiculous notion

  6. #6 Piotr Gąsiorowski
    September 29, 2012

    @Monty: Well, an organism as complex as a mouse can be fine without at least *some* of its junk DNA:
    http://www.nature.com/nature/journal/v431/n7011/abs/nature03022.html
    irrespective of whether the non-junk part is “irreducibly complex” or evolvable. It strikes me as presumptuous of religiously motivated freaks to tell their God what he obviously shouldn’t have done. What if he had a queer aesthetic taste and liked to season his products with useless junk?

  7. #7 AnswersInGenitals
    September 29, 2012

    If you have ever had the joyous opportunity to read some computer program code you would have noticed that it has a fair percentage of “junk code”, code that in no way contributes to the functioning of the program – mostly annotation, but also spaces and line feeds that make the code more conveniently readable. Since the programmer was made in the image of god and therefore has many thought processes derived from god, it is only rational to presume that any code that god created, such as DNA, would have nonfunctional code included. God would certainly include in such code nonfunctional (as far as the organism is concerned) annotation sequences to remind him of what the hell he was trying to accomplish and to help analyze what went wrong with the program (for we know that the “program” went horribly wrong at least twice).

  8. #8 Greg Uncles
    October 1, 2012

    80%? Pardon, but doesn’t the general viability of human fetuses make that pretty much impossible?

  9. #9 RDees
    Denmark
    October 1, 2012

    PZ,
    Panda Antivirus is denying me access to your freethought blog site, because it’s been labelled as a malware site. Any idea what’s up with that?

  10. #10 David Marjanović
    Museum für Naturkunde, Berlin
    October 1, 2012

    Creationists act as if ID *predicted* the nonexistence of junk DNA. This is absurd. First, predictions logically follow from a theory, and there is no theory behind ID to base a prediction on.

    You’ve caught one of the many places where they say “ID” and mean “Christianity”. It doesn’t make a lot of sense that a perfect, omniscient and omnipotent creator, as opposed to some incompetent little demiurge, would litter genomes with trash (or annotations for that matter), so junk DNA must not exist!

    That’s also why Stupid Design upsets them so much.

    Secondly, supposing for the sake of the argument that there is a virtually omnipotent designer who created life on Earth, how do creationists know that he can’t have created junk as well? Can they read God’s own mind?

    Trying to do that is the whole point of religion, isn’t it?

  11. #11 James
    U.S
    October 3, 2012

    PZ, It is such a shame to see a beautiful mind like yours believe in such fairy tales such as evolution – the belief that everything popped into existence by chance – uncaused and without the help of a conscious intelligent designer who created the blueprint for the remarkable design that we see in nature, and implemented that blueprint – creating all the beautiful and complex natural machines that we see today.

    In my philosophy class at Liberty University we talked about how atheists – are not actually looking for evidence of god’s existence or evidence that there is a supreme designer of this myriad of beauty that is called nature, but are just trying to turn there back on god, like rebels, in order not follow his commands which he has called us to follow and keep.

    I urge you, Dr. Myers that you stop this nonsense, that you get on your nears and pray to God to save you from this stupidity, it has infected your mind, evolution is not true, it will never be true, god exists, whether you agree with this idea or not. Just because you may be angry and annoyed at god doesn’t mean you can discount his existence, because he exists irrespective of whether a mere peasant such as yourself believes in him or not.

    I know my comment will be mocked and ridiculed, but I’m not afraid of you, or your atheist disciple since I am the epitome of courage.

  12. #12 Piotr Gąsiorowski
    October 3, 2012

    In my philosophy class at Liberty University…

    The Burning Book university? How very apt!

  13. #13 MattD
    October 3, 2012

    @ James

    The world is glad you decided (after much thought and study, I’m sure) that your religious views are the right ones, because there’s quite a few religions out there that contradict yours. Glad to hear you’ve done your homework on all of them, and decided that’s the right one, because it’s quite confusing for the rest of us who use more then one of our senses to perceive the world around us.

  14. #14 TimM
    October 4, 2012

    James –

    Evolution 150+ yrs and counting. Courtesy: Genetics, Paleontology, Physics, Geology, Astrophysics, Biology, Nuclear Sciences, to name a few all agree on an old universe and the tree of life. We’d rather you were properly educated in the sciences than afraid.

    Afraid is how creationists keep their flocks in ignorance. Believe or Else!

  15. #15 David Marjanović
    Museum für Naturkunde, Berlin
    October 4, 2012

    evolution – the belief that everything popped into existence by chance

    No. Evolution is descent with heritable modification; it’s an observed fact that is explained by the theory of evolution by mutation, selection and drift.

    Now give me a reason why I should read the rest of your comment, when you so clearly don’t even know what the basic terms mean.

    …Oh yeah, here’s a reason: fun.

    the remarkable design that we see in nature

    So, how do you explain stupid design? You know, like the fact that vertebrate eyes are inside-out (remember that cephalopod eyes aren’t), the fact that you were born through a ring of bone that can’t become much wider even though birds don’t need it at all, or the fact that DNA falls apart when kept in water, so that all organisms spend lots of energy on constantly repairing it (remember that alternatives have been made in the lab, for instance a protein backbone instead of a sugar/phosphate backbone).

    but are just trying to turn there [sic] back on god, like rebels

    LOL. Pretending something doesn’t exist would be a very stupid way to rebel indeed!

    There is no evidence for anything supernatural, no reason to think any such thing exists. That’s why most atheists are atheists.

    that you get on your nears [see, that comes from using a spellchecker!] and pray to God

    Waaaait. Which god?

    “But what if we’ve picked the wrong church? Every week we’re just making Him madder and madder!”
    – Homer Simpson, wiser than all of “Liberty” “University” together

    I am the epitome of courage

    (…Isn’t that blasphemous to say? … Never mind.)

    Do you have the courage to research the bases of your own convictions? Are you prepared to learn?

    Let’s find out!