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September 20, 2012 | By:  Jack Scanlan
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The Designer's Detritus: ENCODE, Junk DNA, and Intelligent Design Creationists

Where to start? It's unlikely that you've missed any of the extensive media coverage the Encyclopedia of DNA Elements (ENCODE) project has received over the past two weeks, after the international team of scientists responsible published 30 papers in high-profile journals detailing their efforts in mapping the activity of the human genome in over 100 cell types. Nearly every newspaper, online news site and vaguely science-y blog has written something about the accomplishment, with most focusing on what has become, unarguably, ENCODE's most controversial "finding": that over 80% of the genome is functional.

A good proportion of the biology community hit back at the claim, with the blogs of biochemist Larry Moran and evolutionary geneticist T. Ryan Gregory providing some of the more comprehensive critiques (which are spread across multiple posts on their blogs - have a look through their archives if you're interested in the details). The consensus amongst the critics is that the leaders of ENCODE have a very loose definition of "functional", under which it is likely most possible DNA sequences will fall, including those uncontroversially deemed "junk DNA", simply due to the noise and imprecision inherent in various biological processes like transcription. Some critics have even gone so far as to propose the Random Genome Project, a null hypothesis test for the "80% functional" claim essentially based around the question "What proportion of a randomly generated genome, on average, would be assigned function based on ENCODE's criteria?" If the answer turned out to be around the 60-80% mark, it would cast serious doubts on the claim that most of our genome is functional.

That's all well and good, but what I've just told you is only representative of the responses to ENCODE from the scientific community. There are two other classes of responses: those from the mainstream media, and those from the intelligent design (ID) creationism movement. While the mainstream media's responses are worthy of discussion in their own right (including claims that ENCODE has ended all disease forever), my area of expertise - if you use the word loosely - is ID and there certainly haven't been a lack of responses from their side of the tracks.

Intelligent Design Is Neutral On Genomic Junk

ID, according to the website (owned by conservative think-tank the Discovery Institute), "holds that certain features of the universe and of living things are best explained by an intelligent cause, not an undirected process such as natural selection". That's a pretty good synopsis of what is essentially a negative claim about the inability of evolution to produce the diversity of life at worst and a very weak positive claim about the actual cause of the diversity of life at best. The ID movement is infamous for its unrelenting, yet largely ineffectual, attacks on the science of evolutionary biology, yet being completely unable to produce valid scientific evidence for ID, their favoured hypothesis. Add to that the well-established fact that ID as an idea grew out of young-earth creationism in the 1980s as a way to circumvent the US court system, and you have a faux-academic movement in a reasonably embarrassing state of affairs, to put it mildly.

But despite this, the central hub of the movement - the aforementioned Discovery Institute - continues to have a life online, albeit one that seems to exist in its own little bubble of self-importance and victimisation. Of the handful of blogs that continue to push ID forward, Evolution News and Views is the most active and, unsurprisingly, has had the most to say about ENCODE - although strangely, it has barely commented on criticism of the project's conclusions:

"We will have more to say about these blockbuster findings from ENCODE researchers in coming days, but for now, let's simply observe that it provides a stunning vindication of the prediction of intelligent design that the genome will turn out to have mass functionality for so-called "junk" DNA. ENCODE researchers use words like "surprising" or "unprecedented." They talk about how "human DNA is a lot more active than we expected." But under an intelligent design paradigm, none of this is surprising. In fact, it is exactly what ID predicted."

Huh? What does junk DNA and ENCODE have to do with ID? It's hard to find an explicitly reasoned answer, which is strange in the light of how loudly proponents of ID have announced some sort of victory based on the "80% functional" claim. Of course, intuitively there's the feeling that if the human genome was designed by an "intelligent" being, it should be as functional as possible, but this feeling is never laid out in any formal way. One of the closest times we ever got to this was in 2007, when ENCODE's preliminary results for a select 1% of the genome were released:

"Proponents of intelligent design have long maintained that Neo-Darwinism's widely held assumption that our cells contain much genetic "junk" is both dangerous to the progress of science and wrong. As I explain here, design theorists recognize that "Intelligent agents typically create functional things," and thus [Discovery Institute fellow] Jonathan Wells has suggested, "From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much 'junk'." Design theorists have thus been predicting the death of the junk-DNA paradigm for many years."

Hmm. "Designers typically create functional things" isn't a very reasonable statement, I think you'll agree. ID is continually hung up on analogies to human design to drive its argument forward, a logical tactic recognised as flawed by philosopher David Hume in his Dialogues Concerning Natural Religion (1779) and by many subsequent philosophers thereafter, but it's hard to look at the world of designs humans have produced without coming across some truly terrible ones. A car designed by yours truly would probably be grossly inefficient, considering I know next to nothing about mechanical engineering - but it'd still be designed. Why should we expect that life on Earth, if it were designed, to be any better than my bloated, hypothetical car?

ID proponents go out of their way to deny that the Designer they have in mind is necessarily a perfect, all-powerful deity, which quite obviously leaves the doors open to any old extraterrestrial species with a bureaucratic tendency to design lifeforms by committee to share the explanatory podium with the ID proponent's God of choice. It may sound like a concept straight from the work of Douglas Adams, but the point is no less meaningful because of it. If the Designer they hypothesise could have any level of competence, why should they expect that junk DNA does indeed have a function? It's not a question I've ever heard answered satisfactorily.

Evolutionary Biology's View Of Junk Has Evolved

On the other side of the coin, ID proponents wouldn't be ID proponents if they didn't use ENCODE's results as an attack on evolutionary biology. From the same 2007 post on Evolution News and Views:

"It seems beyond dispute that the Neo-Darwinian paradigm led to a false presumption that non-coding DNA lacks function, and that this presumption has resulted in real-world negative consequences for molecular biology and even for medicine. Moreover, it can no longer seriously be maintained that intelligent design is a science stopper: under an intelligent design approach to investigating non-coding DNA, the false presumptions of Neo-Darwinism might have been avoided."

It's not clear that ID predicts functional (non-)junk DNA, as I think I've established. But does evolutionary biology - here deemed "the Neo-Darwinian paradigm" - predict the opposite, that genomes should be rife with junk? The short answer is yes, but the long answer is a bit more complex. ID proponents use the term "Neo-Darwinism" to mean modern evolutionary theory, but the term is rarely used by modern evolutionary biologists to refer to the current state of their field.

Before the 1960s and 70s, Neo-Darwinism, which emphasised the role of natural selection above all other processes, was indeed the dominant view of evolution, and given its tendency towards panselectionism (that all aspects of organisms have been fine-tuned by selection), the idea that some genomes contained significant amounts of junk DNA was considered highly implausible, if not impossible.

In the 1960s and 70s however, appreciation of the power of neutral (non-adaptive) evolution grew, and it soon became clear that non-functional DNA sequences could accumulate in genomes under certain conditions. Add increased knowledge of the composition of genomes and today, amongst biologists with a good understanding of population genetics and nearly-neutral evolutionary theory, the idea that junk DNA is common in many genomes is uncontroversial and in many ways expected, although the exact amount of junk we should expect is still being debated.

Back to the quoted statement above from the Discovery Institute. Notice how they use the term "non-coding DNA", presumably to mean "junk DNA"? This is a sneaky trick. Although all junk DNA is non-coding DNA, not all non-coding DNA is junk DNA! Geneticists have long known that some of the DNA that doesn't code for proteins must have roles, at the very least, in regulating when and where genes turn on and off. Non-coding RNA transcripts have been discovered that regulate protein levels, control selfish DNA elements and even help in the production of polypeptides (tRNA and rRNA are vital to translation). Other DNA sequences, which aren't transcribed, are necessary for chromosome structure, DNA replication and cell division. All of these discoveries took place against a background of evolutionary thought - it's extremely dishonest for ID proponents to characterise evolution as opposing exciting discoveries in molecular genetics over the last 60 years.

ID, Evolution And The Bigger Picture

So where does ENCODE leave intelligent design? As the "80% functional" claim is at best wildly exaggerated, ID proponents have little to celebrate about. But even if it were true that most of the human genome is functional, it wouldn't provide any good evidence for ID, even if it would force biologists to rethink ideas about the evolutionary origins of genome structure and composition. Evidence against (a specific version of) evolution isn't evidence for design. ID still has to own up to the fact that it won't get anywhere as a scientific hypothesis without evidence or respect for its opposition.

While the Discovery Institute's unscientific output is grossly inaccurate, the ID movement luckily has very little to no influence in the scientific realm. However, the real problem is at the school and household level, where students and the general public have a significant deal of exposure to the ideas of creationists through churches, the Internet and word of mouth. Scientists and science communicators have a responsibility to put accurate, pro-science messages on topics such as ENCODE and evolutionary biology into the public sphere through traditional media outlets and the Internet, in order to counter the ID movement's attempts at misinformation.

1 Comment
September 22, 2012 | 09:03 PM
Posted By:  Eric Sawyer
It's easy to overlook or disregard that the scientific literature is distorted and just plain lied about by ID proponents and others. Most scientists don't care enough to read the ID literature (I don't), but in fact a lot of people are seeing current science news through the ID filter. Thanks for this excellent summary of the ID response to ENCODE. --Eric
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