Evolution vs. Intelligent Design Watch: Junk DNA is Not Junk

This is in the New York Times today:

The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as “junk” but that turn out to play critical roles in controlling how cells, organs and other tissues behave. […]

The findings, which are the fruit of an immense federal project involving 440 scientists from 32 laboratories around the world, will have immediate applications for understanding how alterations in the non-gene parts of DNA contribute to human diseases, which may in turn lead to new drugs. […]

As scientists delved into the “junk” — parts of the DNA that are not actual genes containing instructions for proteins — they discovered a complex system that controls genes. At least 80 percent of this DNA is active and needed. The result of the work is an annotated road map of much of this DNA, noting what it is doing and how. It includes the system of switches that, acting like dimmer switches for lights, control which genes are used in a cell and when they are used, and determine, for instance, whether a cell becomes a liver cell or a neuron.

“It’s Google Maps,” said Eric Lander, president of the Broad Institute, a joint research endeavor of Harvard and the Massachusetts Institute of Technology. In contrast, the project’s predecessor, the Human Genome Project, which determined the entire sequence of human DNA, “was like getting a picture of Earth from space,” he said. “It doesn’t tell you where the roads are, it doesn’t tell you what traffic is like at what time of the day, it doesn’t tell you where the good restaurants are, or the hospitals or the cities or the rivers.”

And the discovery that junk DNA is not junk is contrary to what researches anticipated:

Human DNA is “a lot more active than we expected, and there are a lot more things happening than we expected,” said Ewan Birney of the European Molecular Biology Laboratory-European Bioinformatics Institute, a lead researcher on the project. […]

“Most of the changes that affect disease don’t lie in the genes themselves; they lie in the switches,” said Michael Snyder, a Stanford University researcher for the project, called Encode, for Encyclopedia of DNA Elements.

And that, said Dr. Bradley Bernstein, an Encode researcher at Massachusetts General Hospital, “is a really big deal.” He added, “I don’t think anyone predicted that would be the case.”

Isn’t that interesting? Reigning theory, and what you would predict from reigning theory, doesn’t match what is actually observed.

And what might that reigning theory be? Isn’t it evolutionary theory? Hasn’t it long been assumed that there are elements within DNA that are the junk remnants of our evolutionary history, and that there must be a lot of them? And weren’t they supposed to be located in the 95% of our DNA that does not produce proteins?

Surprise, surprise! At least 80% of our junk DNA is not junk. There may be junk remnants in the 95% of our DNA that doesn’t produce proteins, but there may not be nearly as many of them as supposed.

I’m not advocating intelligent design here (though it certainly doesn’t hurt the case that one might make for it), but noting that when we make broad assumptions based on a crude extrapolation of a rather general theory, we can find ourselves far from reality. There’s nothing in the above discovery that an evolutionary biologist can’t account for, of course, but the fact that it’s surprising on the standard evolutionary narrative heretofore ought to be remarked upon, and not swept under the rug.

Mark a point for intelligent design proponents here. They’ve long predicted that junk DNA would prove not to be junk. It’s only fair to notice it.

Here’s a biologist briefly explaining junk DNA and speculating on the future of research into it.

__________

And here’s an intelligent design book trailer, made over a year ago, that professes to doubt what, until quite recently, has been the consensus among biologists as to what junk DNA is.

About Santi Tafarella

I teach writing and literature at Antelope Valley College in California.
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28 Responses to Evolution vs. Intelligent Design Watch: Junk DNA is Not Junk

  1. “The human genome is packed with at least four million gene switches that reside in bits of DNA that once were dismissed as “junk” but that turn out to play critical roles in controlling how cells, organs and other tissues behave.”

    And not all of us need the New York Times or a government study to tell us this.😉

    • Santi Tafarella says:

      Well, actually, if you’re not a scientist, how could you know this apart from reading about it in a place like the New York Times? The design inference is far from obvious, and if God exists it may be that (s)he used evolution to bring about things (in which case, some of the DNA in existing creatures may well be junk from long extinct ancestors). Indeed, 20% of the DNA that isn’t used for making proteins may well be junk.

      –Santi

      • God doesn’t make “junk.” Common sense.

      • And I wasn’t referring to you, I was referring to so-called “scientists” and supposed intellectuals who look to the media or “studies” to tell them what should be common sense. “Junk” DNA was a term created by supposed “scientists” who didn’t want to admit how little they know about life, creation, genes, and how we are designed. And if they don’t know, they’ll never admit it and simply say, “functions unknown at this time,” they just audaciously dismiss them as being “useless” or without function. How arrogant. How ignorant.

      • Santi Tafarella says:

        Synapt:

        How do you know God doesn’t make junk? God made Hitler, and Hitler was a pretty junky piece of flabby matter in the universe.

        What’s arrogant and ignorant is your presumption, absent evidence, about what God’s up to. Evolution occurred and continues to occur, and evolution makes lots of extinction wreckage. It would be hardly surprising if some of that wreckage can be charted in DNA.

        Who told you existence is a rose garden?

        –Santi

  2. Alan says:

    This says absolutely zip about ID. Just says that we have a lot to learn about life.

    • Santi Tafarella says:

      Absolutely zip? Really? What are you trying to cordon off by saying that?

      • Alan says:

        Thanks for the post. Interesting and informative – should also be sobering for folks who jump to conclusions. DNA is more than currently meets the eye! Learning is like that – we think we know something, then we learn a little more and see our previous mistakes – then move on to new ones.
        It is good for science to get a little egg on its face from time to time to help reign in the hubris.
        Irrelevant at this point still are those lucky guesses from the ID camp: their intelligent designer could have designed it any way it chose to, with or without lots of junk. What they (still) need to show is how evolution/natural selection could not have achieved this formation – the same challenge they will have for a long time to come through many more generations of our advancing knowledge of life. So some biologists guessed wrong about this junk, a lot of guesses are wrong regardless how educated.
        Interesting, but nothing to jump to conclusions over.

  3. You can call it “evolution” all you want, but the fact is that adaptation will always occur. As long as there is changes in the environment and changes in what we are exposed to, we (all living organisms) will make the proper homeostatic changes in order to adapt and will make LIMITED changes in order to adapt and resist. We will NEVER evolve into something else entirely.

    We (human beings) should be grateful that we were designed for such resiliency.

    • Santi Tafarella says:

      I don’t feel resilient at all. I feel pretty vulnerable in the furnace of this world. Nobody gets out alive. If God exists, I have no idea what (s)he is up to.

  4. People really should take spectacular scientific anouncements in the press with a little (more than a little actually) grain of salt. That means to check with actual experts who nowadays have blogs.
    T. Ryan Gregory at Genomicron, for instance, have a slightly different response to today’s ENCODE hype. As well as Larry Moran at Sandwalk. Both have benn writing on the subject of the so called Junk DNA way before these ENCODE anouncement, as a search on “junk dna” on their blogs can show. Anyone interested should really digg in but to give just a glance of what is wrong with the bells and wistles, just 2 things.
    One is that the ENCODE results seem to rely on a very very loose definition of function. A definition that it’s not the one widely used in the field. If I understand it, applying their criteria we could say that salt water have a “function”. Not very impressive.
    And two, the claim that 80% of the genome is functional still leave us with the problem of the onion. The onion test, originarily devised by T. Ryan Gregory to test claims on the funtionality of non-functional DNA can be put like this: If 80%, or more, of the genome is functional as it’s clamed by the ENCODE team, having regulatory roles, then why the f* an onion (an onion been a more or less arbitrary choice as there are other species with even bigger genomes) needs 5 times more DNA than humans do?
    In Inteligent Design terms it’s as if the set of instructions to assemble a 747, or a supercomputer, were very very smaller than the ones needed to assemble a glider, or an abacus. As far as I know ID “theorists”, who are so found of complexities, are oblivious to this. They keep talking that ALL DNA must be functional because it’s “inteligently designed”, but never ever adress the fact that there is no correspondence between genome size and organism complexity. Ironicaly they are in the same boat as the real darwinians who claim that ALL DNA must be functional because of natural selection.
    BTW, as it seems to be the case of all anti-evolutionists synapticcohesion don’t understand what evolution is. Organisms don’t “make the proper homeostatic changes in order to adapt”, organisms, individuals don’t adapt, populations of organisms do. Biological evolution is a population process. Populations evolve, change, individuals don’t.

    • Santi Tafarella says:

      Gato,

      Thank you for bringing in this other perspective. I’ll look into the links you direct the reader to.

      –Santi

    • “Organisms don’t “make the proper homeostatic changes in order to adapt”, organisms, individuals don’t adapt, populations of organisms do. Biological evolution is a population process. Populations evolve, change, individuals don’t.”

      OK…
      We are all capable of adapting. When our body temperatures change according to the environment, we are making homeostatic changes in order to adapt. When we tan, we are adapting. When we build an immunity to pathogens and a resistance to drugs, we are adapting. Individual freshwater fish can adapt to salt water if you introduce salt into their water supply slowly and gradually. They did not “evolve” into superfish, they simply adapted to their changing environments. They did not “gain” any additional information or ability because if you place them into their former freshwater environment, they will die. So I don’t know where you’re getting the idea that individuals do not adapt and change, but that is untrue.

    • Santi Tafarella says:

      Synaptic,

      Gato, I believe, is referring to genetic change that gets passed to offspring. Obviously, individual organisms adapt to temperature by sweating or shivering, etc. but these don’t change the genome and get passed to offspring. That would be Lamark not Darwin. You sweat or shiver well, or you don’t. Your personal environmental exposure and your reaction to it does not get passed onto offspring as “knowledge” on which they can build.

      Darwin’s insight is that offspring differ from parents, and in a competition for mates and resources, nature selects those offspring in a population that most fit it.

      • Santi

        Exactly. Synaptic is confounding acclimatization with adaptation.
        “When we build an immunity to pathogens and a resistance to drugs, we are adapting.”
        If this was true we wouldn’t need vaccines, and contagious diseases wouldn’t be such a threat. What happens in a lethal epidemic is that some people die, some people don’t. Those that survive do so because they already have some level of resistance to the disease, so the population became dominated by disease resistant people, as the not resistant have gone. But resistant to that particular strain only, not to subsequent mutated ones.
        “So I don’t know where you’re getting the idea that individuals do not adapt and change”
        The point I’m making is that this is not what biologists are talking about when they talk about Biological Evolution. At all. So it’s pointless the keep saying that individuals make “homeostatic changes in order to adapt” but that they “will NEVER evolve into something else entirely” because this is not what it’s meant by the expression Biological Evolution. So you are atacking a strawman, and an old and since long debunked one btw.

      • “”Organisms don’t “make the proper homeostatic changes in order to adapt, organisms, individuals don’t adapt, populations of organisms do. Biological evolution is a population process. Populations evolve, change, individuals don’t.”

        Gato may be talking about more radical adaptive changes that take longer to see, but his saying that, ”Organisms don’t “make the proper homeostatic changes in order to adapt” is completely false. We all go through homeostasis (a word you should all be familiar with because it DOES happen to all of us individually) as is necessary. And yes, when our body adjust to an environment, these homeostatic changes does effect the offspring in ways that may not be obvious to us until several generations later. Changes happen in increments.

        Evolutionists claim that these changes that are undeniable can also result in changes from unicellular to multicellular, and from knuckle-dragging apes into bipedal human beings over millions and billions of years. There is absolutely NO evidence of that. Only evidence of our ability to change–within limits–over time because of our natural ability to adapt to our environment. We never gain NEW genetic information in order to be able to change as much as evolutionist claim, we only able to express the genetic information we already have in different ways in order to survive changing environments.

        I mentioned skin color changes–with the immediate homeostatic change being tanning in a hot, sunny environment. Over the long term (perhaps thousands of years), this could result in a population with darker skin compared to many other parts of the world because over time, the homeostatic changes that occurred resulting in extra melanin production in which the offspring is expose to in utero. This would obviously be more beneficial to a child in this environment as he/she will already have the proper amounts of chemicals and hormones needed for protection from the sun. And this will continue to be passed on to generations over time. But as you can see (as with all other experiments claiming to prove evolution) this is simply adaptive changes WITHIN LIMITS). They are still human beings that over all that time, only have a change as superficial as skin pigmentation. And again, this population is not superhuman–they did not gain any additional genetic information, they were only able to express the genetic information that they already had (and that was more useful to them) in a more obvious way. Though they have their bodies had adjusted over time to produce extra amounts of melanin, there will have to be something else that is traded off in order to have this greater gene expression–perhaps a muting of the body’s production other hormones (which can have some disadvantages as well).

        This trade off is why it is so ridiculous to assert that we could all evolve from a “magic molecule” (as Dawkins asserts). That requires a LOT of gaining of NEW genetic information–that goes against all the rules of homeostatic balance.

  5. This post by Ryan Gregory is very informative: Function, non-function, some function: a brief history of junk DNA.
    And the original Onion Test.
    Both are from 2007.

  6. Synaptic
    You insists in atacking a strawman even after it was pointed to him.

    Evolutionists claim that these changes that are undeniable can also result in changes from unicellular to multicellular, and from knuckle-dragging apes into bipedal human beings over millions and billions of years.

    NO. This IS NOT what evolutionists claim. No evolutionist claim that a single unicellular organism changes to a multicellular one.

    There is absolutely NO evidence of that…They are still human beings that over all that time, only have a change as superficial as skin pigmentation

    Do you realize that life has been around this planet for about 3.8 billion years, but humans (homo sapiens) only in the last 200 thousand? Maybe if I put the zeros you can grasp the order of magnitude:
    Life= 3.800.000.000
    Us= 200.000

    I would like to point out as well that you are far away from the topic, and ignoring the observations I did, and the links I pointed. I would like to hear what explanation ID have for the konwn lack of correlation between genome size and organism complexity, or at least an aknowledgment of the problem.

    • “When we build an immunity to pathogens and a resistance to drugs, we are adapting.”
      If this was true we wouldn’t need vaccines, and contagious diseases wouldn’t be such a threat. What happens in a lethal epidemic is that some people die, some people don’t. Those that survive do so because they already have some level of resistance to the disease, so the population became dominated by disease resistant people, as the not resistant have gone. But resistant to that particular strain only, not to subsequent mutated ones.

      We DON’T need vaccines. But that is beside the point. We resist disease (with limited and varying ability), but so do pathogens–that is a fact of life and you don’t need evolution to know this and to study this in depth.

      Pseudoscientists are the ones who claim that there are “lower” and “higher” organisms and “simple” and “complex” ones. In fact, Darwin subscribed to the idea that there are “lower” and “higher” apes and that blacks and aboriginals are closer link between to the so-called “higher apes” that whites are. Talk about ignorance, idiocy, and pseudoscience. Those who accept intelligent design, however, it is known that even the tiniest prokaryotes are incredibly complex (with their specialized organelles) and efficient–better than anything man can create.

      • We DON’T need vaccines

        Oh boy…I’ve been giving you the benefit of the doubt synaptic. Maybe you’re just an ignorant, who knows? But it’s clear now that you are just an ordinary creationist troll living somewhere in Lunacy Land.

        who claim that there are “lower” and “higher”

        Claim who exactly? Nobody here is this comment thread. So what? You still didn’t acknowledge the fact that an onion have 5 times more DNA than humans. How ID explain that? Does it at least acknowledge it? Why “The Designer[TM]” needed to pack 5 times more “genetic information” in onions than in humans? Or, if you don’t like onions particularly, why the lungfish “design” need 40 (FORTY) times more “genetic information” than humans? if you don’t like fish either some species of salamander “need” 4x more than humans.
        So stop the creationist trolling and get back to the topic. Come on. This is not new stuff. This have been known for at least 60 years. ID Theory[TM] must have something to say about it.

        Over the long term (perhaps thousands of years), this could result in a population with darker skin compared to many other parts of the world because over time, the homeostatic changes that occurred resulting in extra melanin production in which the offspring is expose to in utero.

        Two things. One: “perhaps thousand of years”? You don’t know? Not sure? Humans have been here for two hundred thousand years. And still have acumulated such (yet superficial) differences in the very short time they (the various human sapiens groups) have lived isolated form each other. What to say about populations of organisms that have diverged hundreds of millions of years ago?
        And two: do you realize that you have just thrown the whole Genetics out the window with this ‘extra melanin production exposition in utero’ bullshit? Do you?

      • “Maybe you’re just an ignorant, who knows?”

        “do you realize that you have just thrown the whole Genetics out the window with this ‘extra melanin production exposition in utero’ bullshit? Do you?”

        Let’s be fair here: I was the one who needed to enlighten you on what homeostasis is.

    • Correction: “Darwin subscribed to the idea that there are “lower” and “higher” apes and that blacks and aboriginals are closer link between to the so-called “higher apes” THAN whites are.”
      I wrote “that” instead of “than,” which completely changes the meaning of the sentence.

  7. Let’s be fair here: I was the one who needed to enlighten you on what homeostasis is.

    Sigh..No you don’t. And what you’re talking about skin color inheritance is bullshit, btw. You don’t know what you’re talking about. But even if you did, so what? As I already said homeostasis/acclimatization have nothing to do with Biological Evolution. Nobody says it does, except you. So what you are saying is that something that nobody claims it happens actually don’t happen. Wow!

    He can have any ignorant belief of his choosing, but when it is applied directly to his “scientific studies,” it is no longer science, but PSEUDOSCIENCE.

    What fits nicely for you and your creationist friends. This is what they call “projection” I think. Talk about irony.

  8. zzap says:

    Darwinian evolution is a lie. A lie from the pit of hell. It dwells in the cesspool of atheism and homosexual bondage. It’s proponents are fools and are far away from God’s glory and majesty.

    “For my thoughts are not your thoughts, neither are your ways my ways,” declares the Lord. “As the heavens are higher than the earth, so are my ways higher than your ways and my thoughts than your thoughts. Isaiah 55:8-9

  9. andy plant says:

    Please don’t refer to people as ‘fools’ – if you knew the gospels you would know that – to do so is judgemental. Paul tells us that the God’s work has always been visible all around and some people refused to accept it. The same is true today. Christ performed miracles and people doubted them, and wanted to see other miracles on demand, which of course he denied them. It doesn’t matter how much of the genome is mapped out, and so on and so forth – nobody will ever ‘prove’ the Truth. The Truth will be ‘proved’ on your passing from this life or the second coming, otherwise there would be no such thing as Faith and hope (in what cannot be seen) – which is what God requires.
    I hope we can all accept that we are the lump of clay, not the potter, and that the scientists do a wonderful job in using the gift given to them by God to help their fellow man.
    I hope we can also all accept the words of Isaiah 55.

  10. Pingback: At Least 80% Of Our Junk DNA Is Not Junk | Prometheus Unbound

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