Rewriting History Won't Erase Bad Evolutionary Predictions
While many evolutionists adamantly maintain that the vast majority of the human genome is junk, even in the face of the ENCODE consortium's compelling experimental results, others have tried hedging their bets by embracing ENCODE's research. In fact, some of the latter even attempt to revise history by claiming that evolutionary biology expected all along to find what ENCODE found: mass functionality in the human genome.
Others are more forthright. They don't deny evolutionary biology's bad predictions, and they admit that new models are needed to accommodate ENCODE's data. In other words, they accept ENCODE's conclusions and admit they can't explain them in evolutionary terms.
This final installment of my four-part series on ENCODE will assess the responses of evolutionists who struggle to comprehend a junkless human genome in the post-ENCODE world.
Junky Predictions
First, let's review what evolutionists were saying prior to ENCODE's breakthrough papers in 2012, which showed that the vast majority of our genome is functional.
The April 17, 1980 issue of Nature contained two papers by influential biologists arguing that evolution predicted that our genomes should be full of junk DNA. One article 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,"1 while the other, co-authored by Nobel Prize laureate Francis Crick, concluded that "much DNA in higher organisms is little better than junk" and that "it would be folly in such cases to hunt obsessively" for function.2
Fifteen years later, the junk-DNA paradigm was still going strong, 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."3
Moving forward to 2007, we find Columbia University philosopher of science Philip Kitcher writing in his book Living with Darwin that "the most striking feature of the genomic analyses we now have is how much apparently nonfunctional DNA there is." Kitcher notes that "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."4
Just Kidding
With this background, it is no wonder that when ENCODE's findings were published in 2012, many evolutionists reacted harshly to them (see Salvo 31, 32, and 33). Others, however, realized that they had better switch their bets—or at least place some new ones.
Thus, a 2014 paper in Biology & Philosophy begins by noting that "junk DNA seems at odds with the view that the genome is . . . the work of an intelligent force or designer," but then switched gears, arguing that a junkless genome "is compatible with evolution by natural selection," because "we could expect natural selection to evolve lean genomes."5 Under this posturing, whether our genome is full of junk or devoid of it, evolution wins.
But first prize for betting on both horses goes to Richard Dawkins. In his 1976 book The Selfish Gene, he famously argued that "a large fraction" of our genome is useless, and that Darwinian evolution explains why:
The true "purpose" of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.6
In 2004 Dawkins suggested that it would behoove "creationists" to "spend some earnest time speculating on why the Creator should bother to litter genomes with untranslated pseudogenes and junk tandem repeat DNA."7 And as recently as 2009, he was still asserting that "the greater part (95 percent in the case of humans) of the genome might as well not be there, for all the difference it makes."8
A mere three years later, however, he completely changed his tune. In September 2012, just one week after ENCODE's results were published, in a debate against Britain's chief rabbi, Dawkins declared that ENCODE's results were precisely what Darwinism predicted: "There are some creationists who are jumping on [ENCODE] because they think it's awkward for Darwinism. Quite the contrary, of course; it is exactly what a Darwinist would hope for—to find usefulness in the living world."9
Previously, he went on to say, scientists had thought that "only a minority of the genome was doing something, namely, that minority which actually codes for protein." But now they realized that "actually the majority of it is doing something," for the portion of the genome that "had previously been written off as junk" was now understood to be "the program" that's "calling into action the protein-coding genes."10
Just like that, it was as if Dawkins's decades of arguing that our genome is full of junk had never happened.
Acceptance & Resistance
Other evolutionists have handled ENCODE's results more forthrightly. They acknowledge that the evidence now supports mass functionality in the genome and even concede that evolutionary models didn't anticipate this result. They are content to live with ambiguity until evolutionary models are developed to explain ENCODE's data.
For example, lead ENCODE researcher John Stamatoyannopoulos admits that "new models of evolutionary conservation are needed"11 to explain why so much human DNA is functional. And science writer Philip Ball concedes that, in light of ENCODE, "the current picture of how and where evolution operates, and how this shapes genomes, is something of a mess. . . . But we are grown-up enough to be told about the doubts, debates and discussions that are leaving the putative 'age of the genome' with more questions than answers."12
Perhaps so, but a number of biologists steadfastly refuse to accept ENCODE's results. Much of this resistance can be attributed to a fear of lending credence to intelligent design. Philip Ball acknowledges an "anxiety" among evolutionists "that admitting any uncertainty about the mechanisms of evolution will be exploited by those who seek to undermine it."13
Biochemists John Mattick and Marcel Dinger have written that "resistance to [ENCODE's] findings is further motivated in some quarters by the use of the dubious concept of junk DNA as evidence against intelligent design."14 Writing in a slightly different context, eight biologists published a Nature article in 2014 recognizing that scientists self-censor criticisms of neo-Darwinism because, "haunted by the spectre of intelligent design, evolutionary biologists wish to show a united front."15
But while evolutionary holdouts continue to attack ENCODE, the research goes on, and since 2012 it has continued to uncover additional specific functions for non-coding DNA. This means that those who have staked their careers and reputations on the premise that humans were created by purposeless processes that filled our genomes with useless junk now find themselves confronted with a growing threat to their paradigm. Thus, like University of Houston biologist Dan Graur, they fear that "If ENCODE is right, then Evolution is wrong," and their solution, like Graur's, is to "Kill ENCODE."16
Future Forecast
Where this attitude prevails, evolutionary biology is in an unhealthy state wherein devotion to the paradigm trumps the evidence. A 2003 paper in Science observed that "the term 'junk DNA' for many years repelled mainstream researchers from studying noncoding DNA,"17 but even now that junk DNA has largely been overturned, evolutionary dogmatism is still hindering scientific advancement.
The good news, however, is that most scientists aren't evolutionary ideologues. Rank-and-file biologists recognize compelling data when they see it, and many see it in ENCODE. Some of these biologists are now exploring what they call "post-Darwinian" models of evolution, often adopting the same critiques of Darwinism made by ID proponents.18 They still seek unguided, material explanations of life, and are resistant to design, but they don't put their evolutionary paradigm before the evidence.
And some are even beginning to understand how ENCODE's results represent a major coup for ID. As William Dembski eloquently put it some 14 years pre-ENCODE:
[D]esign 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. . . . Design encourages scientists to look for function where evolution discourages it.19
If scientists had embraced an ID paradigm when Dembski wrote those words in 1998, how much more advanced would molecular biology be today? We will never know, but this much is clear: ID boldly predicted ENCODE's results, and evolutionary biology did not. This puts ID in a strong position to lead science forward into a post-Darwinian world.
Casey Luskinis a scientist and an attorney with a PhD in Geology from the University of Johannesburg and a JD from the University of San Diego. In his day job, he works as Associate Director of the Center for Science and Culture at Discovery Institute, helping to oversee the intelligent design (ID) research program and defending academic freedom for scientists who support intelligent design. Dr. Luskin has written and spoken widely on the scientific mechanics and implications of both intelligent design and evolution. He also volunteers for the "IDEA Center," a non-profit that helps students to start IDEA Clubs on their college and high school campuses. He lives and works in Seattle, Washington, where he and his wife are avid enjoyers of the outdoors.
Get Salvo in your inbox! This article originally appeared in Salvo, Issue #34, Fall 2015 Copyright © 2026 Salvo | www.salvomag.com https://salvomag.com/article/salvo34/the-encode-embroilment-part-iv
