Disposable DNA

Addendum in light of recent developments

As you are probably aware there has been an important new development in that intervening period: the announcement of the results (though not the final results, they haven’t quite finished yet) of the ENCODE project. If you believe the hype – and, for that matter, the abstract of one of the papers – at very least 80% of the genome is functional, and the concept of Junk DNA is dead in the water.

Now is probably a good time to talk about the significance of junk DNA to the Controversy. Evolution does not actually require said junk, a point often lost in these arguments. Creationism, too, could at least survive if it were proven beyond a shadow of doubt that junk DNA did exist. The crucial difference here, however, is that for said creationists the idea that their God elegantly designed their DNA such that an appreciable proportion is entirely useless is too bitter a pill to swallow, hence the vehement opposition to the concept from that quarter evidenced by the previously discussed Tomkins post. The reason why this non-critical concept is defended equally strongly by anti-creationist bloggers is a little more complex.

Toronto biochemistry Professor Larry Moran, of Sandwalk, is perhaps the strongest proponent of junk DNA in the blogosphere. He published a post earlier today/yesterday/whatever the configuration of timezones makes it for you, called ENCODE Leader Says that 80% of Our Genome Is Functional. He opened, referring to this blog post:

Ed Yong is a science journalist and usually he’s a very good one. This time, however, he should have gotten the other side of the story.

As you can tell he’s not in agreement. He doesn’t actually give any specific reasons why, so we will probably have to wait until tomorrow. But other people have been a little less prepared to wait. For example, this tweet:

Yes, what does ‘functional’ actually mean in this context? It turns out that it’s not all that simple. Ewan Birney, a scientist involved in the ENCODE project, has a detailed Q&A blogpost for the curious. He says:

[I]n ENCODE we define our criteria as “specific biochemical activity”.

That’s a fairly broad definition, absurdly so according to many criticisms – there is a lot of what you might think of as ‘bological noise,’ but Birney would rather you call ‘biologically neutral,’ that this will pick up but any reasonable layman definition of ‘functional’ would exclude. What’s more, 80% isn’t the only number:

Q. Ok, fair enough. But are you most comfortable with the 10% to 20% figure for the hard-core functional bases? Why emphasize the 80% figure in the abstract and press release?
A. (Sigh.) Indeed. Originally I pushed for using an “80% overall” figure and a “20% conservative floor” figure, since the 20% was extrapolated from the sampling. But putting two percentage-based numbers in the same breath/paragraph is asking a lot of your listener/reader – they need to understand why there is such a big difference between the two numbers, and that takes perhaps more explaining than most people have the patience for. We had to decide on a percentage, because that is easier to visualize, and we choose 80% because (a) it is inclusive of all the ENCODE experiments (and we did not want to leave any of the sub-projects out) and (b) 80% best coveys the difference between a genome made mostly of dead wood and one that is alive with activity. We refer also to “4 million switches”, and that represents the bound motifs and footprints.

We use the bigger number because it brings home the impact of this work to a much wider audience. But we are in fact using an accurate, well-defined figure when we say that 80% of the genome has specific biological activity.

In other words, it’s correct to say that 80% ‘does something’ in a biological sense. But it’s questionable that that’s a useful number when it comes to junk DNA.

A blog post by T. Ryan Gregory gives 4 reasons why junk DNA still exists, including:

3) The onion test. Maybe 80% of the human genome is “functional”, even in a biologically meaningful sense of that word. Even so, we’d still be left with the question of why onions need so much more non-coding DNA than humans, or how pufferfishes can get by just fine with only 1/10 as much.

There is evidence in favour of the existence of junk DNA – we just went over some of it, remember? – and it hasn’t suddenly gone away with the publication of these papers. As an update to the Ed Yong post previously mentioned says, “Barely five hours after publication, and a backlash against the 80 percent figure has predictably begun.” Will it go the way of the famous ‘arsenic life’? We can’t say yet. (I should add that even if so this shouldn’t belittle the achievements of the ENCODE project.)

“This is going to make my life very complicated.” — Larry Moran, on the inevitable creationist reaction.

What can be said with complete certainty is that the creationists will be all over this – Evolution News and Views already is. We will see a DpSU on this in the near future, most likely accompanied by a Tomkins blog post of some form (perhaps only just a repost of said DpSU), and possibly many other articles and blogposts from the ICR’s various websites crowing about the demise of junk DNA.

The timing is unfortunate, as I have exams coming up very shorty (September 12 though to the 19th). Thank goodness these aren’t the real ones, and merely ‘practise.’ Nevertheless they are going to have to lead to a hiatus over that week, probably starting sooner. It would be nice if the ICR stuck with their usual fortnight delay before publishing articles, which would be exactly perfect in this case, but judging by their reaction to the Higgs announcement we could see something as soon as tomorrow – I’m pessimistic.

I’ll keep you posted.

3 thoughts on “Disposable DNA

  1. It seems to me that there is still plenty of DNA that looks, waddles and quacks like “junk” and thus may indeed be actual junk. Plus, exerting “biological function” does not necessarily mean “vitally important.” Let us not toss old paradigms in favor of new ones prematurely; be patient and if indeed warranted then in due course empirical data will out.

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