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New Long Story Video Tackles “A Battle of Predictions: Junk DNA”

Image source: Discovery Institute.

In the previous Long Story Short: The Codes of Life video, we learned how our bodies are chock-full of amazing information. Since information comes from a mind, this has major positive implications for intelligent design (ID). The evolutionist immediately objects that our genomes are actually full of huge amounts of “junk DNA,” showing that our DNA evolved by random mutation and was not designed. 

But is it true that the human genome contains huge amounts of junk DNA? We’ve just now released a new Long Story Short: Codes of Life video titled “A Battle of Predictions: Junk DNA.” It shows that the concept of junk DNA — long espoused by evolutionists — has overall been refuted by mountains of data and is no longer even considered valid by many biologists. 

Bad Evolution-Based Predictions

First, we must document where the concept of junk DNA came from in the first place. The idea came 100 percent from evolutionary biologists. Let’s review some history. 

As far as my research can tell, the concept of junk DNA first came into the literature in the 1960s and early 1970s. The earliest example I’ve found is a 1963 paper in the Journal of Ultrastructure Research which vaguely alluded to the possibility that some DNA might not be “competent genetic material” and would be “’junk’ DNA.” That paper didn’t speculate about just what proportion of DNA is “junk,” but a 1969 paper in Science made a much bolder prediction that “99 percent of mammalian DNA is not true genetic material.” The concept really got going in 1972 when Japanese evolutionary biologist Susumu Ohno wrote a chapter in a book titled “So much ‘junk’ DNA in our genome” and also published a paper in the Journal of Human Evolution arguing, “At least 90% of the mammalian genomic DNA appears to represent ‘nonsense’ DNA base sequence of various kinds.” 

From there the idea really caught on among evolutionary scientists. The April 17, 1980, issue of Nature published papers by influential biologists arguing that evolution predicts our genomes should be full of junk DNA. The first article, “Selfish Genes, the Phenotype Paradigm and Genome Evolution,” by W. Ford Doolittle and Carmen Sapienza, maintained that “Natural selection operating within genomes will inevitably result in the appearance of DNAs with no phenotypic expression whose only ‘function’ is survival within genomes.” A second paper, “Selfish DNA: the ultimate parasite,” was by Francis Crick, who won the Nobel Prize for determining the structure of DNA, and the eminent origin-of-life theorist Leslie Orgel. They concluded, “much DNA in higher organisms is little better than junk,” and “it would be folly in such cases to hunt obsessively for” its function.  

Fifteen years later in 1995, the junk-DNA paradigm was alive and well, as Scientific American reported: 

These regions have traditionally been regarded as useless accumulations of material from millions of years of evolution … In humans, about 97 percent of the genome is junk. 

This idea lived on into the 2000s. In 2007 Columbia University philosopher of science Philip Kitcher wrote an Oxford University Press book titled Living with Darwin citing “masses of genomic junk” that “litters the genome.” Kitcher pronounced that “The most striking feature of the genomic analyses we now have is how much apparently nonfunctional DNA there is.” In his view, “From the Darwinian perspective all this is explicable,” but “if you were designing the genomes of organisms, you would certainly not fill them up with junk.” 

In his 2009 book The Greatest Show on Earth, Richard Dawkins stated that “the greater part (95 per cent in the case of humans) of the genome might as well not be there, for all the difference it makes.” Even as recently as last year, University of Toronto biochemistry professor Laurence Moran wrote a book titled What’s in Your Genome? 90% of Your Genome Is Junk. You read that right — in 2023 people were still saying that some “90% of Your Genome is Junk.” 

According to a a 2021 article in American Scientist co-authored by University of Chicago evolutionary biologist and geneticist Manyuan Long, Professor Moran’s view has historically been the consensus of the field. Long co-wrote: 

[W]ith the conclusion of the Human Genome Project, a monumental 13-year-long research effort to sequence the entire human genome, approximately 98.8 percent of our DNA was categorized as junk. … What is the function of all that junk DNA? To most geneticists, the answer was that it has no function at all.

A summary of Long’s article at American Scientist states the following: “Close to 99 percent of our genome has been historically classified as noncoding, useless ‘junk’ DNA. Consequently, these sequences were rarely studied.”

Good ID-Based Predictions

Meanwhile, ID proponents have long made a very different set of predictions about junk DNA. In 1994, ID proponent Forrest Mims predicted that non-coding “junk” DNA would have function, writing a letter to Science, “Those supposedly meaningless strands of filler DNA that molecular biologists refer to as ‘junk’ don’t necessarily appear so useless to those of us who have designed and written code for digital controllers.”

Science rejected the letter, but in 1998, long before the “junk DNA” revolution was in full swing, William Dembski predicted function for non-coding “junk” DNA based upon intelligent design:

But design is not a science stopper. Indeed, design can foster inquiry where traditional evolutionary approaches obstruct it. Consider the term “junk DNA.” Implicit in this term is the view that because the genome of an organism has been cobbled together through a long, undirected evolutionary process, the genome is a patchwork of which only limited portions are essential to the organism. Thus on an evolutionary view we expect a lot of useless DNA. If, on the other hand, organisms are designed, we expect DNA, as much as possible, to exhibit function. And indeed, the most recent findings suggest that designating DNA as “junk” merely cloaks our current lack of knowledge about function. For instance, in a recent issue of the Journal of Theoretical Biology, John Bodnar describes how “non-coding DNA in eukaryotic genomes encodes a language which programs organismal growth and development.” Design encourages scientists to look for function where evolution discourages it.

William Dembski, “Intelligent Science and Design,” First Things, Vol. 86:21-27 (October 1998)

Then in 2004 Jonathan Wells wrote, “research shows that ‘junk DNA’ does, indeed, have previously unsuspected functions. Although that research was done in a Darwinian framework, its results came as a complete surprise to people trying to ask Darwinian research questions. The fact that “junk DNA” is not junk has emerged not because of evolutionary theory but in spite of it. On the other hand, people asking research questions in an ID framework would presumably have been looking for the functions of non-coding regions of DNA all along, and we might now know considerably more about them.”

What the Data Says

Something happened in 2012 that changed the entire debate in favor of the ID-based prediction that DNA would be largely functional. A major Nature paper by the ENCODE consortium reported evidence of “biochemical functions for 80%” of the human genome. Lead ENCODE scientists predicted that with further research, “80 percent will go to 100” since “almost every nucleotide is associated with a function.” In the wake of this research, the journal Science published an article titled “ENCODE Project Writes Eulogy for Junk DNA” which stated that these findings “sound the death knell for the idea that our DNA is mostly littered with useless bases.”

The subsequent decade saw further serious erosion of the concept of junk DNA. A 2021 article in Nature reported that over 130,000 specific “genomic elements, previously called junk DNA” have seen specific functions identified, followed by a paper in Genome Biology and Evolution which concluded, “The days of ‘junk DNA’ are over.” A 2022 paper in Nature Methods stated that “The genome is constantly being transcribed; isoforms emerge; there’s splicing; genes interleave with other genes. The genome is far from what was once called ‘islands of genes among intergenic deserts.’” Most recently, last fall a paper in BioEssays described a Kuhnian “paradigm shift” away from the concept of junk DNA. The author, John Mattick, had striking things to say about the failure of the evolutionary paradigm. As he and a co-author wrote in a 2023 book published by Taylor & Francis:

While the story is still unfolding, we conclude that the genomes of humans and other complex organisms are not full of junk but rather are highly compact information suites that are largely devoted to the specification of regulatory RNAs. These RNAs drive the trajectories of differentiation and development, underpin brain function and convey transgenerational memory of experience, much of it contrary to long-held conceptions of genetic programming and the dogmas of evolutionary theory.

John Mattick and Paulo Amaral, RNA: The Epicenter of Genetic Information (CRC-Taylor & Francis, 2023), p. vii

Read that quote carefully — again from a book just published last year. They say that “the genomes of humans and other complex organisms are not full of junk” and this runs “contrary to … the dogmas of evolutionary theory.” Mattick and Amaral are evolutionists, but this is a huge admission of a failed prediction coming out of the standard evolutionary paradigm.

Evolutionists Respond

Many evolutionists remain recalcitrant in their refusal to let go of the idea of junk DNA. We’re ready for their objections — in fact we’re already far along producing a second junk DNA video that addresses many objections to these arguments. Objections to these arguments come down to getting angry, denying the data, rewriting history, hiding out in the unknowns, pretending that evolutionary speculation is “data,” as well as quite badly misrepresenting our arguments. The most amusing responses are those which — in the same breath — simultaneously say they predicted all this function for junk DNA (that’s revisionist history), and then contradict themselves by asserting that most of our genome is still junk after all. Stay tuned for responses to critics. 

Of course there is still much we do not understand about the genome and many specific genetic elements for which no function has yet been discovered. Nonetheless, there is a strong trend in biology away from non-functionality for “junk” DNA — and this trend was predicted by ID and not predicted by the evolutionary paradigm. Enjoy our new Long Story Short video which provides an overview of this fascinating story!