Intelligent design creationists think junk DNA is a placeholder for ignorance

Paul Nelson is a Senior Fellow of the Discovery Institute—the most important source of intelligent design propaganda. Paul and I have been disagreeing about science for many years. He is prone to interpret anything he finds in the scientific literature as support for the idea that scientists have misunderstood their subject matter and failed to recognize that science supports intelligent design. My goal has always been to try and explain the actual science and why his interpretations are misguided. I have not been very successful.

The photo was taken in London (UK) in 2016 at a meeting on evolution. It looks like I'm holding my breath because I'm beside a creationist but I assure you that's not what was happening. We actually get along quite well in spite of the fact that he's wrong about everything. :-)

The latest example is a recent post on Evolution News (sic) concerning junk DNA [With One Short Rule, Philip Ball Explains Why “Junk DNA” May Be a Placeholder for Ignorance]. Intelligent design creationists have a lot invested in the junk DNA debate. They have admitted that if the human genome is really full of junk then that will cause serious problems for their claim that humans are intelligently designed. They have been fighting desperately to hold on to the idea that most of our genome must be functional and the standard tactic is to advertise any little bit of DNA with a newly discovered function.

This is part of a larger campaign designed to misrepresent junk DNA proponents by claiming that the junk DNA argument is based on ignorance. They assume, contrary to the evidence, that junk DNA is just DNA that hasn't yet been assigned a function. That view gives rise to Paul's explanation for why his cherry-picking tactic is a valid argument.

Two Containers — With Only One-Way Traffic Between Them

Out on the lawn sit two containers: a large waste bin and a smaller treasure chest (see the illustration). The bin is labelled “DNA with no known function, aka junk DNA.” The treasure chest has the label “DNA with functions.” Curious, we inspect these two containers daily for months. We notice that DNA sequences are regularly being moved from the larger into the smaller container — but never in the other direction. DNA labeled as non-functional may on closer investigation turn out to have functions. Once a role has been assigned to a sequence, however, and it is placed in the functional treasure chest, there it stays. All the traffic flows in one direction.

I know that Paul has read my book because he mentions it in his post. He knows that the argument for junk DNA is based on mutation load and conservation (purifying selection) both of which show that about 90% of our genome is junk. He knows that junk DNA explains the C-value paradox and no other explanation, including intelligent design, can account for the wide variations in genome size. He knows that half of our genome consists of pseudogenes and fragments of degenerate transposons and viruses that look like junk by any reasonable criteria. He read my summary of the data on introns showing that most intron sequences are junk. (Introns make up about 40% of the genome.) He knows that it's easy to refute all claims that there is evidence to support a function for most of our genome.

Paul Nelson knows that junk DNA proponents claim that about 90% of our genome is junk and we have good reasons to back up this claim. For example, he surely read my description of the comparison between the human and chimpanzee sequences showing that the differences are consistent with a genome that's 90% junk evolving at the neutral rate from an ancestor that lived about six million years ago (p. 86). He knows that Intelligent Design Creationists can't explain this data and that's why they haven't tried—it would require them to admit that they don't understand evolution.¹

He knows that there is evidence that 10% of our genome is functional and since he's read my book he knows that we've only discovered function for about 4% so far. That means we still have to move about 6% of the genome from unknown to functional and the bin on the left of his diagram contains 90% junk DNA and 6% of the genome that has an unknown function.

If Paul knows all this then why is he misrepresenting his opponents?

This brings us to the reason why Paul wrote this post a few weeks ago (Feb. 20, 2024). He's quoting an article by Philip Ball that appeared on Chemistry World. Philip Ball is a science writer with some strange ideas that were recently expressed in a new book (How Life Works). It's a horrid book but I'll deal with it later. The article that caught Paul Nelson's attention is "An unprecedented supramolecular structure brings new complexities to life."

Ball describes a protein that binds to short tandem repeats (STRs). These are regions of DNA containing an array of short repetitive sequences such as CAGCAGCAGCAG etc. There are about 350,000 STRs in the human genome and their length and locations are highly variable from one individual to another. In fact, they are so variable that they are used in DNA fingerprinting to distinguish one person from another.

Here's what Philip Ball wrote.

It’s weird that FOXP3 has this alternative, biologically relevant mode of action. It’s doubly weird that the five dimer units stick to sections of DNA previously thought to be meaningless junk: ‘microsatellites’ in which short sequences of a G base and a few T’s (TnG, such as T3G) repeat several times. TnG repeats ‘are usually considered non-functional and are discarded by sequence-analysis programs’, say immunologists Zhi Liu and Ye Zheng in a Nature commentary, which prompts me (not least because this isn’t an isolated example) to propose a new year’s resolution for molecular biologists: stop assuming we know which parts of DNA matter and which don’t.

That's music to the ears of creationists like Paul Nelson who are desperately looking for any examples of someone who challenges junk DNA. The challengers don't have to be experts on the subject—and Philip Ball falls into this category with a loud thump—as long as they look like authorities.

We already know that some STRs are functional. Telomere sequences are a good example and there's evidence that some STRs might be required for the proper function of centromeres. (Most of the DNA in centromeres consists of various classes of satellite DNA where most of these classes consist of somewhat longer repeats than STRs.) Paul must know this because he read my book. He knows that junk DNA proponents never dismissed ALL STRs as junk but we have good reason to be suspicious of most STR regions.

So what we have here is the possible identification of some STR with some (unknown) function. That's possibly a little tiny bit more DNA moved from the unknown 6% into the functional 10%. Big deal.

I get why Intelligent Design Creationists are all over this but Philip Ball's motives are much more difficult to understand. Why would he lecture molecular biologists by telling them to "... stop assuming we know which parts of DNA matter and which don’t." I can understand why he would admonish ENCODE researchers this way but those people aren't his target. (This becomes clear in his book.) He's referring to junk DNA proponents who, for the most part, are trying very, very hard to base their claims on scientific evidence. Most of us are strongly opposed to statements like "all non-coding DNA is junk" or "all STRs are junk" or even "all intron sequences are junk."

Philip Ball doesn't know this. Paul Nelson knows this but prefers to ignore it when he's writing for his creationist friends.

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1. That last point requires a bit of explanation. It would perhaps be slightly more accurate to say that creationists have "tried" to account for the data but have consistently failed to come up with arguments that conform to the facts. We have an interesting example from 10 years ago when Vincent Torley tried to refute the human/chimp data but got hopelessly confused. I give you a link to one of my last posts in that debate—it contains links to the earlier ones [Vincent Torley apologizes and claims that he is not a liar]. There's an interesting aside to that exchange. Vincent Torley has subsequently been drummed out of the intelligent design movement for challenging some of its dogma.