ENCODE at Last

Yes, this lot. It was inevitable, trust me.It’s taken longer than I expected and isn’t up to the quality (accuracy-wise at least) that I had been hoping from the delay, but Jeffrey Tomkins has finally written ENCODE Reveals Incredible Genome Complexity and Function. He opens:

Both the evolutionist and creationist communities are abuzz with the latest results from 30 simultaneously published high-profile research papers, proclaiming that the human genome is irreducibly complex and intelligently designed.

Poor quality though it may be, this article doesn’t waste any time. The primary ENCODE paper, stupid and misleading things though it may well have said, did not say that.

Tomkins goes on to say:

From an evolutionary perspective, this is yet another massive blow to the myth of “Junk DNA.” This evolutionary idea was exposed as a fraud from a scientific perspective in Jonathan Well’s recent book The Myth of Junk DNA.

The concept of ‘junk’ DNA is an ongoing – by no means dead – controversy. It is not by any streatch of the imagination a key doctrine of evolution, and from certain points of view should not even exist – if it is truly useless, why hasn’t natural selection weeded it out? Those who take a less adaptationalist line, emphasising the role of processes like genetic drift, beg to differ.

And for creationists, too, junk DNA is not some kind of God-killer. For the Intelligent Design crowd especially, the existence of junk DNA should not be problematic – nobody said that the design had to be perfect, after all. But their insistence that it does not exist betrays their underlying belief that it was their omnipotent omniscience God that did the designing, as He certainly would have done it properly. The Institute for Creation Research can more openly share that view, and for the purposes of this article we’ll take the devils advocate position on the grounds that if the ICR is swallowing a science news story whole then there is almost certainly something terribly wrong with it.

A large-scale international research effort, ENCODE (Encyclopedia of DNA Elements), began in 2003 as an expansion of the Human Genome project. The goal of ENCODE was to map and characterize the functionality of the entire human genome.

The Human Genome Project gave us the, or at least a, sequence of the human genome. This of course tells us nothing about what it all does, hence the ENCODE project. This is in reality a rather boring project to embark on, albeit a highly useful one, something which is being blamed for the hype surrounding the recent announcement. And yes it is hype – what else do you call a video narrated by Tim Minchin comparing the project to a cancer-killing robot?

Remembering Rosalind Franklin was a nice touch, however.

Before ENCODE, biologists understood that only a small fraction of the genome’s DNA actually codes for protein. They reasoned that the vast majority was therefore useless.

This is the usual ‘non-coding DNA is considered junk’ line that creationists like to spin, although Tomkins does not explicitly state it. It has been known for many decades that there was another “small fraction of the genome’s DNA” that regulates the other activities of the genome. There was no “junk of the gaps” logic used, and the argument for junk DNA is not one of ignorance.

The first piece of evidence in favour of the hypothesis is that genome size varies. Massively. Don’t delude yourself into thinking that that we’re at one of the extremes either – not even within mammals. The “Onion test” is a challenge for those opposed to the idea of junk DNA to explain why onions have a much greater quantity of genetic material than we do, and also why many other species have a much lower amount, if it’s all useful. There also seems to be a correlation between amount of DNA and metabolism, with animals like the hummingbird having a much shorter genome. This suggests that any advantage from the other elements is outweighed by the advantage of having a fast metabolism in those organisms – in other words, there isn’t much of one.

One of the oldest arguments is to do with the idea of mutational load: the extra DNA protects the more useful stuff from damage. If all our DNA was sequence-critical, that is it mattered what it said and not just that it was there, then we might be in trouble. But we know that a sizeable proportion is not sequence critical, as it can be mutated without obvious phenotypic change. In some cases we know we can even remove segments outright.

Having established that there are indeed positive arguments for junk DNA – and there are more than that – let’s continue with what Tomkins had to say:

But in the first round of ENCODE research results published in 2007, the authors in the lead paper reported that their “studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts.” With all that DNA being transcribed (activated and copied into RNA), the cell must use it for something. In other words—it’s not junk after all.

If you have a long memory for these things you might have noticed that junk DNA is ‘debunked’ on a regular basis, as if the discovery of function in a small segment changed the grand picture one iota. The 2007 release was of a different calibre, dealing with more of a (small) representative sample of the genome than a specific element. But the logic behind claims with this evidence that “it’s not junk after all” rely on the flawed logic that if it’s transcribed it must do something – and something useful at that. This needn’t be so, which may be why Tomkins glosses over it so quickly.

And what about the remaining 20 percent of the genome—is it functional too? According to Ewan Birney, ENCODE’s lead analysis coordinator, it’s probably not meaningless junk either. Birney said in an interview, “It’s likely that 80 percent will go to 100 percent” and “We don’t really have any large chunks of redundant DNA. This metaphor of junk isn’t that useful.”

This is cited to Ed Yong’s Discover Magazine blog post, ENCODE: the rough guide to the human genome. It would be nice if Tomkins provided an ‘accessed on’ date here, as this post has been modified at least the once in response to criticism. For example, the post now includes other quotes, like:

To include all such sequences within the bracket of “functional” sets a very low bar. Michael Eisen from the Howard Hughes Medical Institute said that ENCODE’s definition as a “meaningless measure of functional significance” and Leonid Kruglyak from Princeton University noted that it’s “barely more interesting” than saying that a sequence gets copied (which all of them are). To put it more simply: our genomic city’s got lots of new players in it, but they may largely be bums.

(Emphasis added.)

So what did ENCODE actually find? They found, in effect, that at least 80% (possibly even 100%) of your DNA ‘does something’ in a molecular sense – binds to a protein etc. But that doesn’t really make it all “functional.”

In fact, there is an obvious problem with that right away. One of the other arguments for junk DNA is that the genome is littered – if not mostly made up of – the decayed remnants of transposons (“jumping genes”). To carry out their work, which need not be “functional” (i.e. useful to you) by any reasonable definition of the term, these genes require the same kind of stuff that other genes do, which would show up in a test like ENCODE. What’s more, once a mutation causes the transposon to no longer be able to copy itself there will still be many of the components present that allowed it to take place, and these would still be caught by ENCODE. Worse, there have been suggestions that an entirely random base sequence would still register as functional by this definition! The 80% figure, therefore, is not very useful at all – and junk DNA lives on.

There is a more “conservative” number, ~20%, that the paper really should have run with. While from what I hear it may have problems of its own, it is not a number that challenges the idea of junk in the genome.

Birney expects that many critics will argue about the 80 percent figure and the definition of what is “functional.” Birney added, “[That figure] best [conveys] the difference between a genome made mostly of dead wood and one that is alive with activity” and “No matter how you cut it, we’ve got to get used to the fact that there’s a lot more going on with the genome than we knew.”

The problem is that while his project may have shown that there’s a lot going on – though how much more than we already knew I don’t know – it doesn’t follow that this is all productive. And it’s that aspect that is important here.

Some people will probably try to claim that these statements made by the scientists of ENCODE are merely hype. However, there is little to criticize since the 80 percent figure comes directly from a clearly written statement in an 18-page research paper in the prestigious secular journal Nature. Furthermore, this statement came from the lead paper of 30 other concurrently published ENCODE papers that were authored by hundreds of leading genomic scientists in multiple international laboratories worldwide.

Talk about an argument from authority! Next time something comes out of Nature that the ICR wishes to attack I will have to remind them how prestigious the journal is. It’s out of their league, I tell you.

Tomkins concludes:

While these startling comments about the newly discovered wonders of the human genome did not come from the mouths of creationists, they clearly demonstrate we are “fearfully and wonderfully made” by our Creator God who made us “in His image.”

There are a lot of logical jumps in this article. As Todd Wood remarked:

Me?  It’s cool science, no doubt about that.  Project leader Ewan Birney is to be commended.  No doubt about that either.  But I’m not sure the ENCODE results are worth all the attention they’re getting in the creation/evolution world.

On the one hand, I don’t think that function equates to design, nor do I think that design requires or predicts function.  They’re not the same thing.  So even if the 80% figure is right, I don’t think I care.  My understanding of genome design certainly didn’t predict functionality for every nucleotide in the genome, and my understanding of function does not require me to hypothesize God (or an anonymous designer, if you must) as the proximal cause.

Even if ENCODE were right, creationism is far from “clearly demonstrated.”

As I said at the start, Tomkins could have said a lot more here. One point I expected him to make, though he did in effect when he quoted Birney above, is that not all cells have been tested and thus the 80% could easily increase – there are a few other things as well, which I wont get into. Instead, however, Tomkins seems to think that simply acknowledging that other people will scoff is enough to be able to dismiss them. It is not.

At least, it shouldn’t be.

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2 thoughts on “ENCODE at Last

  1. “Next time something comes out of Nature that the ICR wishes to attack I will have to remind them how prestigious the journal is.”

    The original description of Tiktaalik was in Nature, for example. Ha ha.

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