The Current Creationist Abuse of ENCODE and “junk DNA”

The creationist blogosphere is set ablaze by the popular media claim that “biochemical functions for 80% of the genome”. For instance, Barry Arrington at the intelligent design creationist blog Uncommon Descent calls it a vindication of intelligent design proponents.

Not so fast! An article on Nature News Blog, aptly entitled “fighting about ENCODE and junk”, clarifies the situation in detail. To make a long story short, the researchers used an extremely broad definition of functional that included almost any biochemical activity.

Here is the creationist and media narrative:

That narrative goes something like this: scientists long thought the genome was littered with junk, evolutionary remnants that serve no purpose, but ENCODE has shown that 80% of the genome (and possibly more to come) does serve a purpose. That narrative appeared in many media reports on the publication. Many on Twitter and in online conversations bemoaned the rehashing of a junk-DNA debate that they considered imaginary or at least long-settled. Eisen, perhaps rightfully, puts the blame on press releases that touted the supposed paradigm shift: the one from Nature Publishing Group started thus: “Far from being junk, the vast majority of our DNA participates in at least one biochemical event in at least one cell type.” Eisen says that “the authors undoubtedly know, nobody actually thinks that non-coding DNA is ‘junk’ anymore. It’s an idea that pretty much only appears in the popular press, and then only when someone announces that they have debunked it.”

It is an old argument, but it’s not clear that it is a dead argument. Several researchers took issue with ENCODE’s suggestion that its wobbly 80% number in any way disproves that some DNA is junk. Larry Moran, a biochemist at the University of Toronto in Ontario argued on his blog that claims about disproving the existence of junk gives ammunition to creationists who like a tidy view of every letter in the genome having some sort of divine purpose. “This is going to make my life very complicated,” he writes.

So in other words, creationists think that evolutionary biologists long have believed that most of the genome was junk and so this discovery overturned it. They further claim that this corroborates the prediction of creationism, and not of evolution. They may even go so far as to claim that the belief in junk DNA has held back biologists due to what they claim is “darwinist dogma”. Nothing could be further from the truth.

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A quick search on the Pub Med database reveals that the phrase “junk DNA” only returns, at the time of this writing, only 127 results. Also note that a lot of these hits are due to the recent publications by ENCODE. Compare with evolution, which returns a little over 325000 hits. In other words, “junk DNA” has never been a major part of modern science. It is a fictitious construct by the media and some eccentric scientists of the past. The accurate term is “non-coding DNA” or “non-coding RNA”. Some of this non-coding DNA produces functional RNAs that have regulatory roles, whereas some are left-overs from transposons and viral infections.

So what is the reality between the popular 80% figure?

It’s a big number, to be sure. The protein-encoding portion of the genome — that which has historically been considered the most important part— represents a little more than 1%, and to imply that they found similarly important and interesting functions for another 79% is an extraordinary claim. Birney had said to me and reiterates in a Q&A-style blog post that it is also a loose interpretation of the word ‘functional’ that encompassed many categories of biochemical activity, from the very broad — such as actively producing or ‘transcribing’ RNA — to being attached to some sort of transcription-factor protein, all the way down to that narrow range of protein-encoding DNA within the 1%.

But hold on, said a number of genome experts: most of that activity isn’t particularly specific or interesting and may not have an impact on what makes a human a human (or what makes one human different from another). A blog post by Ed Yong discusses some of these critiques. It was already known, for example, that vast portions of the genome are transcribed into RNA. A small amount of that RNA encodes protein, and some serves a regulatory role, but the rest of it is chock-full of seemingly nonsensical repeats, remnants of past viruses and other weird little bits that shouldn’t serve a purpose.

Let us check out what the main article, called An integrated encyclopedia of DNA elements in the human genome says about what “functional” means to the researchers:

The vast majority (80.4%) of the human genome participates in at least one biochemical RNA- and/or chromatin-associated event in at least one cell type.

This is a far cry from how creationist portray the situation. Alright, what portion of the genome has a relevant function? The Nature News blog article continues:

The paper does drill down somewhat into what the authors mean by functional elements. And Birney does the same in his blog. Excluding all but the sites where there is very probable active binding by a regulatory protein, “we see a cumulative occupation of 8% of the genome,” he writes. Add to that the 1% of protein-encoding DNA and you get 9%.

Birney and his colleagues have estimated how complete their sampling is, and suspect that they will find another 11% of the genome with this kind of regulatory activity. That gets them to 20%. So, perhaps the main conclusion should have been that 20% of the genome in some situation can directly influence gene expression and phenotype of at least one human cell type. It’s a far cry from 80%, but a substantial increase from 1%.

So, to sum up, it is more like 20%, not 80%. The article also points out that maybe the should not have released all the articles at once. Sure, it maximizes impact, but that comes with the price of public misunderstanding and risking giving creationists a stronger ability to infiltrate their viewpoint, making it easier for them to pretend their position is scientific.