Laying the Junk DNA Hypothesis to Rest

The ENCODE Project Yields Yet More Falsification of Neo-Darwinism

In his 2009 book Why Evolution is True, University of Chicago emeritus professor Jerry Coyne predicted that human genome research in the coming years would find confirmation of the evolutionary origins of mankind in the form of “vestigial genes” (pp. 66-67). Indeed, the prediction that future research would prove that there was “junk DNA” floating throughout the genetic code was deemed by many science professionals to be so vital to the credibility of evolutionary theory that any suggestion to the contrary led to immediate and sometimes vehement conflict.

In fact, the prediction that much useless genetic material would be found had already been subjected to significant skepticism in the early 2000s. The key idea behind the doctrine of “Junk DNA” was that we should expect to see evolutionary leftovers proving that man, and by extension every other animal, was a product of a mindless, undirected process. Interestingly, Coyne´s term “vestigial genes” echoes the term “vestigial organs,” a concept that has been often invoked in the defense of Darwinism. It is the idea that, as products of an unguided process that did not have humans in mind, we would have retained functionless anatomical relics from previous stages in our evolutionary history in our bodies. It is a concept that had long since been debunked by the time his tendentious tome appeared and has been dealt further blows since then. Unsurprisingly, the thesis has fared no better in the years since Coyne´s prediction. The first release of project ENCODE was one of the most significant bodies of evidence refuting this suppositional argument invoked by the defenders of neo-Darwinism. So, what is ENCODE?

The ENCODE Project

ENCODE stands for “ENCyclopedia Of DNA Elements.” It began in the year 2000 as a project of the National Human Genome Research Institute (NHGRI) and has gone through three distinct phases since them. Its objective was to map all approximately 3 billion base pairs or 20-25,000 genes in the human genome. In 2000, at the outset of ENCODE, the science to date seemed to support a naturalistic account of human origins, as it indicated that only 2 percent of the genome coded for functional proteins. So, the initial release of information from ENCODE made quite a splash in the international media when it announced that a lot more than 2 percent of the genome was functional. This quote from The Guardian´s September 5, 2012 article on ENCODE Phase 1´s findings is typical:

Long stretches of DNA previously dismissed as "junk" are in fact crucial to the way our genome works, an international team of researchers said on Wednesday.

It is the most significant shift in scientists' understanding of the way our DNA operates since the sequencing of the human genome in 2000, when it was discovered that our bodies are built and controlled by far fewer genes than expected. Now the next generation of geneticists have updated that picture.

The results of the international ENCODE project will have a huge impact for geneticists trying to work out how genes operate….

For years, the vast stretches of DNA between our 20,000 or so protein-coding genes – more than 98% of the genetic sequence inside each of our cells – was written off as "junk" DNA. Already falling out of favor in recent years, this concept will now, with ENCODE´s work, be consigned to the history books….

The researchers found that [non-protein-coding DNA] is far from useless: within these regions they have identified more than 10,000 new "genes" that code for components that control how the more familiar protein-coding genes work. Up to 18% of our DNA sequence is involved in regulating the less than 2% of the DNA that codes for proteins. In total, ENCODE scientists say, about 80% of the DNA sequence can be assigned some sort of biochemical function.

Since then, even more function has been found in the non-coding stretches of the human genome. Contrary to Richard Dawkins’s assertion in his book The Greatest Show on Earth (also 2009) that as much as “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,” the ENCODE researchers have found, from the initial results of Phase 1 to the newest results of Phase 3, that at least 80 percent and perhaps much more of the genome is biologically functional. The “much more” is indicated by the newest findings from Phase 3, some of which were published in the scientific journal Nature in 2020:

It has become apparent that, by virtually any metric, elements that govern transcription, chromatin organization, splicing, and other key aspects of genome control and function are densely encoded in many parts of the human genome sequence. However, most of these elements are actualized sparingly in a cell type or state selective manner, complicating assessment of the completeness of the ENCODE Encyclopedia, or what remains to be discovered.

As Casey Luskin pointed out in an article first published in 2015 and revised in 2021, the findings of ENCODE Phases 1-3 are very much in line with predictions that have been made by intelligent design advocates since the 1990s. The discovery of biological function in DNA sequences previous thought to be non-functional is clearly evidence against an unguided, undirected, unintelligent origin of man (or any other life-form). It is at least understood to be evidence of this kind by scientists such as University of Houston professor Dan Graur. He famously and succinctly stated that “If ENCODE is right, then evolution is wrong.”

In light of the fact that after nearly a quarter-century of research into the human genome, the evidence against the very existence of junk-DNA has only grown, it seems that Dr. Graur´s framing of the issue is helpful to ID proponents. It is not helpful, though, to the defenders of the “Blind Watchmaker” hypothesis. Many of them are now disingenuously claiming that they never made predictions that junk DNA would predominate in the human genome. Unfortunately for them, they made almost a habit of recording those predictions for posterity back before the weight of evidence turned against them. Predictions are a key indicator of the explanatory power of a theory, and good theories lead to good predictions. Bad theories lead to bad predictions.

Good theories lead to good science.

And consequently, bad theories lead to bad science. The commitment and dedication with which advocates of the junk DNA theory have persisted in defending it in the face of mounting evidence against it is admirably fanatical, but it certainly has nothing to do with defending science from the influence of knuckle-dragging creationists like myself. Wait, sorry. I seem to have internalized the rhetoric of my oppressors there. You see, when they enter the public arena to attack the ENCODE results, philosophical materialists like Graur have a standard line of attack. First, they bring out the ad hominem by impugning both the character and intellect of those who are convinced that we will see more and more function to DNA once thought to be useless. Then they move on to denigrating the research itself as being a tool for “pseudoscience” or giving cover to “creationists”.

But the problem here is not only that this debate is about the worldview implications of the science, but that those implications will impact practice. When one assumes that “95 percent of the human genome could be done away with,” then there is no reason to study that 95 percent and look for, say, the possible gene expression triggers or structural elements that make the difference between a person who has a predisposition to contract ALS and one who does not. Adhering to the materialist rejection of the evidence from ENCODE would therefore be a hindrance to medical research that could improve or save lives.

If, on the other hand, one assumes that elements in the human genome should be functional, even if their functions have been degraded through defective mutations, then there is a warrant to conduct that research and expect results. The latter assumption flows right out of intelligent design theory, and it is the one making predications that are borne out by observed findings. Indeed, if one assumes that the function of genes might be affected by the non-coding elements around them, this would lead to caution in future research, such as research on genetically modifying human embryos. The human race, it is clear, would be better served if medical researchers read and understand the genetic encyclopedia that the Creator wrote before they try to edit it. The real answer to “how many genes in the human genome are necessary?” may be "all of them."  That would certainly be what intelligent design theory would predict.