When I first got involved with the intelligent design debate in the late 1990s and early 2000s, one of the most common rebuttals we’d hear was, “If life was designed, then why is over 90 percent of the genome composed of junk DNA?” Critics thought this was a knock-down refutation of ID, and they used the argument frequently. But that was in the early days of genome sequencing, and very little was known at the time about non-coding DNA and whether it was truly junk or had useful and important functions. 

Many thinkers in the ID movement felt it would be imprudent to concede that most of the genome was junk when science had not yet established that this was in fact the case. Our response was therefore, “We don’t really know what most of the genome is doing. It’s better to adopt a wait-and-see approach. Let’s find out where research goes in the future before we conclude that the genome is mostly junk.” It’s incredible to see how things have changed since that time. 

The State of Research

Consider the state of research today, some 20 years later. As noted briefly yesterday by Evolution News, a new paper in the journal Genome Biology and Evolution — “Satellite-Like W-Elements: Repetitive, Transcribed, and Putative Mobile Genetic Factors with Potential Roles for Biology and Evolution of Schistosoma mansoni” — contains striking language documenting current thinking about junk DNA and how this thinking has shifted over time. The paper begins by observing how prevalent non-coding DNA is: 

A large portion of animal and plant genomes consists of noncoding DNA. This part includes tandemly repeated sequences and gained attention because it offers exciting insights into genome biology. 

The authors studied the platyhelminth worm, Schistosoma mansoni, and looked at repetitive DNA on the female W-chromosome. They investigated repetitive elements on the W-chromosome, called WEs, and identified 19 different families of WEs, called WEFs.

Did I Just Get Lucky?

As an aside, I happen to be vaguely familiar with this type of worm, as these parasites cause bilharzia, a common and unpleasant but treatable illness that one can contract in southern Africa after spending too much time in standing water. During my PhD studies in South Africa I spent a lot of time — I mean a lot — trudging through rivers, often drilling rock outcrops and collecting while standing knee-deep in water. I always took care to only do this in moving water where Schistosoma parasites, I was told, would not be a problem. Either I got lucky or I did something right because I never contracted bilharzia. 

In any case, the paper predicted that these WEs are functional, as they “challenge the classical view that repetitive DNA on the sex chromosomes is simply a by-product of heterochromatization and provide further evidence for their functional importance.” They found that these WEFs encode non-coding RNAs (ncRNAs), and these are involved in sex-determination in Schistosoma. After reviewing extensive evidence of function in these WEFs, they offer a striking finding:

The days of “junk DNA” are over. When the senior authors of this article studied genetics at their respective universities, the common doctrine was that the nonprotein coding part of eukaryotic genomes consists of interspersed, “useless” sequences, often organized in repetitive elements such as satDNA. The latter might have accumulated during evolution, for example, as a consequence of gene duplication events to separate and individualize gene function. This view has fundamentally changed, and our study is the first one addressing this issue with structural, functional, and evolutionary aspects for the genome of a multicellular parasite … Here, we provide conclusive evidence for WEF expression throughout schistosome development, from the miracidium to the adult stages.

[…]

From the data obtained in our study and against the background of recent literature, it is tempting to speculate that more of the WE “junk-DNA” than expected might be functional and relevant. WEs of all investigated WEFs exhibit a capricious incidence, and they are transcribed in a stage-, sex-, pairing-, gonad, and strain-specific or preferential pattern. From exemplary findings of features typical for the activity of mobile genetic elements, we hypothesize that WEs may have a mobile character. Together with previous findings of intraclonal recombination events of WEs, their presumptive role in sex chromosome emergence, their putative capacity to express regulatory RNAs, we propose that WEs might influence the biology of S. mansoni. Furthermore, based on the variable occurrence of WEFs in different schistosome strains, isolates, and even species, we hypothesize that the WEs represent one of the sources of heritable variability in the evolution of the family Schistosomatidae. [Emphasis added; internal citations removed.]

Back in the Day

What’s striking about this passage is not only that the evidence for function in junk DNA is so overwhelming that they declare “The days of ‘junk DNA’ are over,” but also that these authors remember a day when “the common doctrine was that the nonprotein coding part of eukaryotic genome” consisted of “’useless’ sequences, often organized in repetitive elements.” 

I remember those days as well. When I started the first IDEA Club at UC San Diego, we were hit over the head constantly with that “common doctrine” that non-coding DNA was junk, and we were told that it refuted intelligent design. But the authors go on to say that “This view has fundamentally changed.” I see no evidence that these authors are supportive of intelligent design. But it turns out we ID proponents were right all along to encourage critics to take a cautious “wait and see” approach, and let the evidence, rather than evolutionary “doctrine,” determine which paradigm was correct.