11 February 2008

Talking trash about "junk DNA": lies about "function" (part I)

Look, in short, at practically anything – the coot's feet, the mantis's face, a banana, the human ear – and see that not only did the creator create everything, but that he is apt to create anything. He'll stop at nothing.

There is no one standing over evolution with a blue pencil to say, "Now that one, there, is absolutely ridiculous, and I won't have it." If the creature makes it, it gets a "stet." Is our taste so much better than the creator's?
– from Pilgrim at Tinker Creek by Annie Dillard. Harper & Row (1974), p. 135.
God's creative work is ideal. If (as the songwriter David expressed in Psalm 8) the all-powerful, all-knowing Creator made the universe and all that's in it, then people can expect to see superior designs throughout the natural realm.

For those who agree with Darwin's view, any example of nature's imperfection contradicts the notion of a divine creation. As a result, many naturalists regard "junk" DNA as among the most potent evidences for biological evolution.
– from Who Was Adam? by Fazale Rana with Hugh Ross, NavPress (2005), p. 227.
Several weeks ago, I started this series on "junk DNA" by noting that the shoddy nature of anti-evolution folk science is rarely more clearly displayed than in discussions of genomic and genetic findings that are aptly explained by common descent. In that introduction, I noted three overall ways in which creationists – as typified by the apologists at Reasons To Believe (RTB) and the Discovery Institute (DI) – distort and/or ignore the facts about non-coding DNA. The first and most important of these errors regarding "junk DNA" is the claim that "junk DNA" is functional and that this therefore falsifies evolutionary hypotheses regarding its origin.

Hacking through the thicket of disinformation is going to be messy. We're not dealing with a single bogus idea or an isolated pseudo-factoid. We're approaching a quagmire of folk science, some of which is so grotesquely flawed that it's not even wrong. Like most well-designed folk science, the creationist "junk DNA" fables contain just enough factual information to give off the aroma of scientific credibility. As Obi-Wan once said [wink], "We must be cautious."

So what is "junk DNA"? It's a confusing term, and I am one of many scientists who never liked it and never used it. I'll have more on the history of the term elsewhere, but for now we'll use it the way anti-evolutionists (RTB/DI/AiG) use it: "junk DNA" is non-coding DNA, meaning that it is DNA that does not directly specify the code for making proteins. Here is a map of the makeup of the human genome, indicating the relative abundance of various categories of DNA:

Image from Molecular Biology of the Cell online, Alberts et al., 2002.

It's worth taking a few minutes to look at the diagram carefully. Notice that more than half (53%) of the human genome consists of "repeats," meaning certain types of sequences that occur multiple times in the genome. Notice also that relatively little of the genome is identifiably devoted to genes (pink + red in the diagram), and a very tiny proportion (1.5% or so) is devoted to the encoding of proteins (red).

Now, that means that 98.5% of the human genome is non-coding DNA. When creationists define "junk DNA" as non-coding DNA, they're referring to 98.5% of the human genome.

In the next two posts, I will comment extensively on this main error: the claim that "junk DNA" is functional and that this therefore falsifies evolutionary hypotheses regarding its origin. There are actually two falsehoods in that claim. This post, part I, will focus on the first one, and the next post will tackle the second.

Falsehood number 1. Evolutionists said that "junk DNA" has no function. But new evidence shows that "junk DNA" has important functions.

This kind of obfuscatory crap really annoys me. It's all over RTB and DI, and it's rampant in creationism in general right now. Both aspects of this claim are bogus.

First, it's just not true that biologists have ever claimed or assumed that 98.5% of the human genome has no function. Ryan Gregory is an evolutionary genomics researcher who has explained just how inaccurate this insidious claim really is, and his blog is required reading for anyone who wants to know more about "junk DNA" and evolutionary genetics. The short story is that biologists have adopted a range of stances toward non-coding DNA, from assuming that it is mostly functional to assuming that it is mostly parasitic. Those biologists, past and present, who would claim that it is mostly functional will readily note that useless parasitic DNA is likely to be abundant in most genomes; those who would emphasize the parasitic or artifactual nature of much of the human genome will readily (and eagerly) note the fact that such elements can and do get co-opted and put to work by the organism. To claim, as Hugh Ross does in Creation as Science (p. 168), that biologists assumed that the "non-protein-coding part of the genome served no purpose" is to promulgate a falsehood.

It's a falsehood, and it's not just irresponsible. It's downright silly. Biologists knew, for example – from very early on – that genetic control regions in the genome are not typically found in protein-coding segments. Only an ignoramus would have assumed or postulated that only protein-coding regions of a genome were functional.

Much worse, though, is this: many of the creationists cited here add another layer of dishonesty to this sick fable. They claim (DI / AIG) that because "Darwinists" assumed that much of the human genome had "no function," biologists failed to study it, and progress in understanding the genome was impeded. At DI, Casey Luskin even claims that this assumption hindered "research into understanding cancer and diabetes." This is how Hugh Ross puts it in Creation as Science (p. 192):
The assumption that naturalistic evolution governs the the history of life on Earth, for example, led to the deduction that the genomes for advanced species predominantly contain useless junk – the accumulation of millions of generations' worth of genetic accidents. This inference led to the 30-year abandonment of research into possible functions of non-protein-coding DNA, the so-called junk DNA.
I believe it is important for folks to understand that Ross and Luskin – and other creationists making this claim – are not telling the truth. If you take only one thing from this post, let it be this: the creationist claim that biologists ignored non-coding DNA for 30 years – because of the assumption that it was all non-functional – is a shameful lie.

Now, that's a pretty serious allegation, so you should expect me to present evidence. First, if you haven't already read Ryan Gregory on the history of the idea of "junk DNA," do it soon. Then, if you're interested and/or skeptical, check out this recent post in which I have a look into the scientific literature over the past 30 years.

The second aspect of this grand creationist lie is the claim that "junk DNA" is functional. And here's where things get a little sticky. Look carefully at a typical creationist argument of this type. It goes like this:
  1. Evolutionists say (or said) that "junk DNA" has no function. (This is a lie, but we already covered that.)
  2. But here is a paper describing a non-coding DNA element that has a biological function.
  3. Therefore, "junk DNA" is functional.
The error here is pretty simple, but I think the argument typically exerts its influence first by virtue of the dishonest first premise, and then by an impressive-sounding (and usually perfectly accurate) discussion of a recent discovery in biology. The bogus conclusion is thus easier to smuggle in, especially if the audience isn't thinking carefully or is otherwise overly credulous.

Here's how to see the error (if it's not already obvious):
  1. Insurance companies say that any 1989 Yugo is worthless and has no utility of any kind. They were crap when they were new, and they're worse than that now.
  2. But let me tell you a story about a 1989 Yugo that is being used as a perfectly good mailbox (or church confessional, or shower).
  3. Therefore, 1989 Yugos are valuable and useful.
Think about it: that first statement can't be right. Insurance companies probably don't say it just like that, and certainly they don't mean that an old Yugo can't be put to some good use. If you showed them one that actually runs, and proved that you drive it to work once a week, they would happily admit that it has some value. But who cares about that anyway? It's a red herring, and it's wrong to boot. Just forget about that silly first claim for a second, and follow the rest of the argument.

It's plain ludicrous. Of course some 1989 Yugos are valuable and useful, but that hardly means that 1989 Yugos are generally valuable at all. If you met someone who asserted that 1989 Yugos were "functional," and who claimed that those who say otherwise are involved in a nefarious conspiracy, you would probably take careful note of the locations of the exits.

There are several interesting types of non-coding elements found in animal genomes, existing in hundreds to thousands to millions of copies. Many of them have well-known properties (the subject of a future post), and many are like Yugos, or rocks, or logs, or roadkill: they're junk, but junk that may, occasionally, be put to use. Biologists have long known this, and suspected from the very beginning that even parasitic DNA elements would occasionally be co-opted by their hosts.

Once you understand what scientists really know about non-coding DNA, and how the history of its study has been systematically misrepresented by Hugh Ross, Casey Luskin, and other careless or unscrupulous creationists, you should see the "junk DNA" fable as inexcusably dishonest. And if you're a Christian, you should worry about your reputation.

I know I do.


Jim Lemire said...

An excellent follow-up to your previous "junk DNA" post.

It's amazing to me how important semantics are to the creationist arsenal - especially when "everyday" words, like 'junk' and 'theory', are used. Everyone thinks they know what these words mean and thinks we're all talking about the same thing when in fact we're using the same words to mean vastly different things.

And then, to top it off, when scientists try to specify just what exactly they mean, well, they're just showing off how much smarter they are then everyone else - why can't they just use "regular" words. The general public is willing to conceptualize "junk DNA", that's easy, but introns, LINEs, retroviral elements, and transposons? No way. So, we're back to arguing semantics about "junk DNA".

Stephen Matheson said...

Thanks Jim, and thanks for the comment on the previous post and the link at your blog.

Semantics is definitely a tool of anti-evolution apologists, and many of them are highly skilled at moving seamlessly between tech-talk and simplistic everyday terms, turning facts into folk science right before the eyes of the awestruck audience.

Hence the blog (and the bloodshot eyes). :-)

Doppelganger said...

Just discovered this blog via Genomicron - EXCELLENT work. I have not had time ot read all of the junk DNA related posts yet, so you may be aware of John Woodmorappe's paper on pseudogenes, wherein he first re-defines ALL transposable elements as pseudogenes, then points out that a couple of pseudogenes appear to have a function, and concludes that therefore ALL pseudogenes, to include things like LINES and SINES, therefore have function, therefore 1. evolution is wrong and 2. phylogenies built using pseudogenes are also wrong.

Yeah, I don't get it either...

As an aside - I used to live in Grand Rapids many years ago. Is "The Something Better News" still available? :)