Dispatches from the Creation Wars

ID and Junk DNA, Part 2

The ID crowd has been all abuzz lately over junk DNA after a very bad article in Wired appeared on the subject. Whenever there is an article in the scientific literature proposing a possible function for some specific type of non-coding DNA, the ID advocates immediately jump up to make one of two types of arguments. Argument type one is this:

Scientists have always said that junk DNA is all useless and functionless and this proves them wrong. See how stupid those scientists are? You shouldn’t trust anything they say.

The last part is typically implied, of course, but that is exactly why they make this argument. The second form of argument is more specific:

Evolution says that junk DNA is all useless, but ID predicts that junk DNA has function. So now that this article shows that (some particularly type of non-coding DNA sequence) might have some particular function, ID has been shown to make accurate predictions.

Back in April I showed why this argument is hypocritical: it requires the kind of assumptions (or “side information”) about the nature of the designer that, in every other context of the ID dispute, they claim can’t be known or assumed. Yet here is Stephen Meyer making exactly that claim in the Wired article:

The opossum data revealed that more than 95 percent of the evolutionary genetic changes in humans since the split with a common human-possum ancestor occurred in the “junk” regions of the genome. Creationists say it’s also evidence that God created all life, because God does not create junk. Nothing in creation, they say, was left to chance.

“It is a confirmation of a natural empirical prediction or expectation of the theory of intelligent design, and it disconfirms the neo-Darwinian hypothesis,” said Stephen Meyer, director of the Center for Science and Culture at the Discovery Institute in Seattle.

Advocates like Meyer are increasingly latching onto scientific evidence to support the theory of intelligent design, a modern arm of creationism that claims life is not the result of natural selection but of an intelligent creator. Most scientists believe that intelligent design is not science. But Meyer says the opossum data supports intelligent design’s prediction that junk DNA sequences aren’t random, but important genetic material. It’s an argument Meyer makes in his yet-to-be-published manuscript, The DNA Enigma.

But here’s something very important that neither Meyer nor any other ID advocate will tell you: their argument requires that every single bit of non-coding DNA have a function. In human beings, only about 5% of our genome actually codes for traits in the phenotype. The rest of it is not just one thing called “junk DNA”, it is made up of a variety of other types of DNA including transposable elements, non-functional duplicates, retroviral insertions and much more. And yes, some types of non-coding DNA may well have function, as scientists have increasingly found. But as T. Ryan Gregory, an evolutionary biologist who specializes in genome size, points out, there has never been a time when scientists actually believed that all non-coding DNA had to be functionless:

In 1972, Susumu Ohno coined the term “junk DNA”. The idea did not come from throwing his hands up and saying “we don’t know what it does so let’s just assume it is useless and call it junk”. He developed the idea based on knowledge about a mechanism by which non-coding DNA accumulates: the duplication and inactivation of genes. “Junk DNA,” as formulated by Ohno, referred to what we now call pseudogenes, which are non-functional from a protein-coding standpoint by definition. Nevertheless, a long list of possible functions for non-coding DNA continued to be proposed in the scientific literature.

In 1979, Gould and Lewontin published their classic “spandrels” paper (Proc. R. Soc. Lond. B 205: 581-598) in which they railed against the apparent tendency of biologists to attribute function to every feature of organisms. In the same vein, Doolittle and Sapienza published a paper in 1980 entitled “Selfish genes, the phenotype paradigm and genome evolution” (Nature 284: 601-603). In it, they argued that there was far too much emphasis on function at the organism level in explanations for the presence of so much non-coding DNA. Instead, they argued, self-replicating sequences (transposable elements) may be there simply because they are good at being there, independent of effects (let alone functions) at the organism level. Many biologists took their point seriously and began thinking about selection at two levels, within the genome and on organismal phenotypes. Meanwhile, functions for non-coding DNA continued to be postulated by other authors.

As the tools of molecular genetics grew increasingly powerful, there was a shift toward close examinations of protein-coding genes in some circles, and something of a divide emerged between researchers interested in particular sequences and others focusing on genome size and other large-scale features. This became apparent when technological advances allowed thoughts of sequencing the entire human genome: a question asked in all seriousness was whether the project should bother with the “junk”.

Of course, there is now a much greater link between genome sequencing and genome size research. For one, you need to know how much DNA is there just to get funding. More importantly, sequence analysis is shedding light on the types of non-coding DNA responsible for the differences in genome size, and non-coding DNA is proving to be at least as interesting as the genic portions.

As I said, in order for the 2nd argument to be correct – if junk DNA has to be functional because “God doesn’t make junk” – then that means that all non-coding DNA has to prove to be functional. And Gregory points out just how ridiculous that claim is when you look at the radically differing genome sizes among different types of organisms. He proposes what he calls the Onion test:

The onion test is a simple reality check for anyone who thinks they have come up with a universal function for non-coding DNA1. Whatever your proposed function, ask yourself this question: Can I explain why an onion needs about five times more non-coding DNA for this function than a human?

The onion, Allium cepa, is a diploid (2n = 16) plant with a haploid genome size of about 17 pg. Human, Homo sapiens, is a diploid (2n = 46) animal with a haploid genome size of about 3.5 pg. This comparison is chosen more or less arbitrarily (there are far bigger genomes than onion, and far smaller ones than human), but it makes the problem of universal function for non-coding DNA clear.

Further, if you think perhaps onions are somehow special, consider that members of the genus Allium range in genome size from 7 pg to 31.5 pg. So why can A. altyncolicum make do with one fifth as much regulation, structural maintenance, protection against mutagens, or [insert preferred universal function] as A. ursinum?

His challenge will, no doubt, go completely unanswered by ID advocates. They cannot answer it and they know it. Nor will his argument that finding function for some types of non-coding DNA, far from being a prediction of ID, can only be done within an evolutionary framework:

Identification of function is done by evolutionary biologists and genome researchers using an explicit evolutionary framework. One of the best indications of function that we have for non-coding DNA is to find parts of it conserved among species. This suggests that changes to the sequence have been selected against over long stretches of time because those regions play a significant role. Obviously you can not talk about evolutionarily conserved DNA without evolutionary change.

Or without common descent, of course. The bottom line is this: when ID advocates start blathering on about junk DNA, the only real junk is in their arguments.

Comments

  1. #1 Fastlane
    June 27, 2007

    First, the ID advocates, as usual, are being dishonest in what scientists actually predicted, and what the IDists claim science predicted. You did a good job of pointing that out.

    I have a question, though, regarding ID’s ‘predictive power’ as trumpeted by S. Meyer. Did they actually make that prediction before the investigations yielded additional functions of the (poorly termed) junk DNA regions? I have may times seen retrodictions claimed as predictions, but then the IDists were completely unable to validate that they had made the prediction.

    Secondly, in science, predictions are usually made based on an increased understanding of the mechanisms (as is the case here, I think), or another observed data point that leads scientists to then look for more data in a similar region of other genomes, for instance.

    Did ID ever predict a mechanism that would be confirmed by thier ‘predictions’, or have they ever found anything else based on one of thier supposed predictions?

    Some of those last questions are obviously rhetorical. IDists don’t do any actual research, but I am curious about the actual prediction/retrodiction part if anyone knows.

    Cheers.

  2. #2 BobApril
    June 27, 2007

    Um. I hesitate to provide ammo for the ID crowd, but I find some issues here. Let’s do it this way – you guys poke holes in my lame counter-arguments, thus better preparing all of us when the IDers do it for real.
    1. “…their argument requires that every single bit of non-coding DNA have a function.” True. But it doesn’t require them to know what all those functions are. Saying so is an argument to ignorance, much like their argument that evolution can’t fill in all the details about how a specific mechanism evolved, and therefore evolution itself must be wrong. Or similarly, that we can’t build life in the lab today, therefore we must be completely wrong about how it arose. Since we call the IDers on it when they use it against us, I suggest we should avoid it ourselves.

    2. I may be misunderstanding the ID position here…but they seem to so many different things that I think I am quoting some of them. The junk DNA does not necessarily have to have a function within the species studied – it could have a function in a descendant species. Of course, this does indeed assume evolutionary change, and therefore won’t work with “young Earth” IDers, but I’ve heard others suggest that evolution only works because the Designer crafted the changes. Junk DNA in one species that is then expressed in another would serve as evidence for that notion.

    On the other hand, it doesn’t do much do explain why some of the junk DNA appears to be “left over” from earlier species – presumably the designer could have gotten rid of the excess along the way. If we assume that getting rid of leftovers isn’t required, though, it provides partial explanation for the “Onion Problem” – the onion has all that extra DNA because, as a plant, it is fairly low on the evolutionary scale. The many, many descendant species have uses for all that extra junk.

  3. #3 mark
    June 27, 2007

    “It is a confirmation of a natural empirical prediction or expectation of the theory of intelligent design, and it disconfirms the neo-Darwinian hypothesis,” said Stephen Meyer, director of the Center for Science and Culture at the Discovery Institute in Seattle.

    Did Meyer ever actually say what the “theory” of ID is? It seems he is here implying that ID is a scientific theory, but evolution is a mere speculative hypothesis. And just how does this disconfirm the “neo-Darwinian hypothesis?”
    For BobApril–Doesn’t this make the prediction untestable? Some stretches have been knocked out with no apparent ill effects; but if some “junk” DNA does not begin to function until some descendant generation, how can that be verified?

  4. #4 Sam the Centipede
    June 27, 2007

    There is an element of scientists shooting themselves in the foot early on. Given that geneticists called this stuff “junk DNA”, it is reasonable for any lay reader to infer that the geneticists think it’s grot stuck on the chromosomes. The word “junk” does not imply “oh, we haven’t worked out what it’s for yet”, it means “useless rubbish”! But I guess the lure of a catchy term was too strong. After all, “junk DNA” sounds so much more glamorous than “non-transcribed DNA” (or however it’s defined/described).

    And when “junk DNA” was first identified, I recall lots of discussions about its selective status, often assuming that it performed no useful role in the living cell — remember the Selfish DNA argument?

    Catchy terms are great for hooking grants (would chaos theory be as interesting if it was called non-linear system dynamics?), but can have long term impacts on (mis)understanding of science. Get non-specialists intrigued by catchy terms, and you will get more misunderstanding than if a field remains the exclusive province of its specialists.

  5. #5 MartinC
    June 27, 2007

    You might have thought that seeing as this is something they had predicted (they now claim) then perhaps one or two of them might have actually, well, how shall I put it………done an experiment to confirm it ?
    I get the feeling that it is the usual ID interpretation, that once a function for anything is found then ID is confirmed since anything functional must have been created by the Intelligent Designer.
    That leads to the question – Is there anything that is not intelligently designed ? I really can’t see how they can answer that one. Surely every single nucleotide MIGHT have a function. Indeed every drop of water or grain of sand, even every atom MIGHT have some intelligently designed function that we just havent worked out yet. Since that is the case they are able to claim every new discovery in science as evidence of the Designer. What a useful theory.

  6. #6 Dave S.
    June 27, 2007

    1. “…their argument requires that every single bit of non-coding DNA have a function.” True. But it doesn’t require them to know what all those functions are. Saying so is an argument to ignorance, much like their argument that evolution can’t fill in all the details about how a specific mechanism evolved, and therefore evolution itself must be wrong. Or similarly, that we can’t build life in the lab today, therefore we must be completely wrong about how it arose. Since we call the IDers on it when they use it against us, I suggest we should avoid it ourselves.

    Microbiologists do not say that something must be useless simply because they don’t know what it does. A finding of ‘functionless’ in biology is actually based on positive evidence. If sections of DNA can be excised and replaced with random sequences with no effect on the organism, that’s evidence of non-fuction in the original sequence. Some sequences are clearly corrupted copies (say they contain stop codons preventing transcription) of functional sequences, which makes them functionless. If one species has a much larger genome than a related species (Allium altyncolicum has a genome only one fifth the size of Allium ursinum), then the larger genome must have more functionless elements. Mutations on regions of the genome that show no evidence of being selected (accumulate at the background rate) also demonstate non-functionality.

    Of course, we’re not talking trivialities like ‘that piece of genome has to connect the bits on either side and so has function’. Or ‘the function of that bit of genome is to incorporate those nucleotides in the genome’.

    2. I may be misunderstanding the ID position here…but they seem to so many different things that I think I am quoting some of them. The junk DNA does not necessarily have to have a function within the species studied – it could have a function in a descendant species. Of course, this does indeed assume evolutionary change, and therefore won’t work with “young Earth” IDers, but I’ve heard others suggest that evolution only works because the Designer crafted the changes. Junk DNA in one species that is then expressed in another would serve as evidence for that notion.

    Does this explain why Allium altyncolicum has a genome only one fifth the size of the related extant species Allium ursinum)? How would such a notion be tested?

    On the other hand, it doesn’t do much do explain why some of the junk DNA appears to be “left over” from earlier species – presumably the designer could have gotten rid of the excess along the way. If we assume that getting rid of leftovers isn’t required, though, it provides partial explanation for the “Onion Problem” – the onion has all that extra DNA because, as a plant, it is fairly low on the evolutionary scale. The many, many descendant species have uses for all that extra junk.

    An unconstrained “Designer” could do absolutely anything. No data you could possibly find would be inconsistant with that notion. But this is precisely what makes such a notion scientifically vacuous. Indeed, there’s nothing at all in ID “theory” that says the designer can’t make as many functionless elements as he likes.

    Its like taking the chain of your bike off the sprockets. It makes peddling a whole lot easier, but you can’t get anywhere.

  7. #7 tacitus
    June 27, 2007

    In the words of William Dembski himself:

    But what about the predictive power of intelligent design? To require prediction fundamentally misconstrues design. To require prediction of design is to put design in the same boat as natural laws, locating their explanatory power in an extrapolation from past experience. This is to commit a category mistake. To be sure, designers, like natural laws, can behave predictably (designers often institute policies that end up being rigidly obeyed). Yet unlike natural laws, which are universal and uniform, designers are also innovators. Innovation, the emergence to true novelty, eschews predictability. Designers are inventors. We cannot predict what an inventor would do short of becoming that inventor. Intelligent design offers a radically different problematic for science than a mechanistic science wedded solely to undirected natural causes. Yes, intelligent design concedes predictability.

    When IDists claim that ID predicts “junk DNA” has function, they are assigning ID more power than they themselves claim is possible. The only thing ID is supposed to be able to do is detect design. Period. Any IDist claim about the functionality of “junk DNA” is breaking their own rules.

  8. #8 Ben Messer
    June 27, 2007

    My favorite part of this mess is that the original support actually fits perfectly into even a naive interpretation of evolution.

    “The opossum data revealed that more than 95 percent of the evolutionary genetic changes in humans since the split with a common human-possum ancestor occurred in the “junk” regions of the genome. Creationists say it’s also evidence that God created all life, because God does not create junk. Nothing in creation, they say, was left to chance.”

    Evolution and natural selection would actually predict that the majority of genetic differences appear in the non-functioning regions of the genome. Changes in the non-junk regions are subject to selective pressure, making casual changes in those regions unfavorable. All sorts of changes can happen in the junk region with little to no effect on the organism’s chances of survival. The same is obviously not true of the non-junk sections of DNA.

  9. #9 Hawks
    June 27, 2007

    2. I may be misunderstanding the ID position here…but they seem to so many different things that I think I am quoting some of them. The junk DNA does not necessarily have to have a function within the species studied – it could have a function in a descendant species. Of course, this does indeed assume evolutionary change, and therefore won’t work with “young Earth” IDers, but I’ve heard others suggest that evolution only works because the Designer crafted the changes. Junk DNA in one species that is then expressed in another would serve as evidence for that notion.

    No, I think you’re right onto it. The supposed function could have been active, be active or becoming active at some stage. There is, in fact, no end to ad hoc explanations the ID crowd could make – this includes accepting every single scientific explanation ever made since they can always claim that the designer set everything up with the Big Bang.

  10. #10 Tex
    June 27, 2007

    To a first approximation (and a second, and a third) most of this excess DNA is junk.

    Certain lilly species have 40 to 50 times more DNA than humans, but they are not 40 to 50 times more complicated than us. Because plants can make their own food, and because they may have slightly more genes than humans, some folks might quibble and say that plants maybe somewhat more complicated than animals like us. However, single celled amoebas can have 300 times more DNA than humans, and they are nowhere near more than 300 times more complicated than us.

  11. #11 P.A. Wahid
    June 28, 2007

    We have been all along propagating that genome is genetic program. The concepts of genetic program and molecular gene are chemistry-based. We say the DNA (including the junk) structure (base sequence) encodes genetic information and it is this information responsible for the biological activities (life) of an organism. Agreed. All these chemical structures are in tact at the instant death occurs to the organism. If DNA structure is genetic information certainly that information will also be in tact. But strangely the body does not function at death. Can a chemical structure lose its information (property)? Obviously biological program is not constituted by a chemical structure. It is nonphysical (corroborating the view of Wilhelm Johannsen who coined the term gene in 1911) like the program stored on computer disk. An organism is a natural biocomputer. The body structures (chemical structures) constitute the hardware and biological program stored on chromosome (storage device of the cell) forms the software. The program is stored in the cells (biochips) maybe as brain stores information in its cells. The manifestation of the execution of this program is the phenomenon of life. The deletion of this program is death. A dead body is like a computer without software. Our computers also have life (artificial life)as they run on man-made program. For more, see my book The Computer Universe: A Scientific Rendering of the Holy Quran, published (in 2006) by Adam Publishers and Distributors, New Delhi, India.
    P.A. Wahid

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