Posted by 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.
June 27, 2007
June 27, 2007
June 27, 2007
June 27, 2007
June 27, 2007
June 27, 2007
June 27, 2007
June 27, 2007
June 27, 2007
June 27, 2007
June 28, 2007