Recently I wrote an article explaining that both atheistic and theistic evolutionists have relied heavily on “junk DNA” — specifically pseudogenes — to argue against intelligent design (ID). In his 2006 book The Language of God, leading theistic evolutionist Francis Collins made such an argument, claiming that caspase-12 is a functionless pseudogene and asks, “why would God have gone to the trouble of inserting such a nonfunctional gene in this precise location?” (p. 139) Logan Gage and I responded citing research which suggested this purported “pseudogene” is functional in many humans. But Collins went much further in The Language of God. He claimed that huge portions of our genome are repetitive junk: “Mammalian genomes are littered with such AREs [ancient repetitive elements]” wrote Collins, “with roughly 45 percent of the human genome made up of such genetic flotsam and jetsam.” (p. 136) Collins frames his argument in theological terms, writing: “Unless one is willing to take the position that God has placed these decapitated AREs in these precise positions to confuse and mislead us, the conclusion of a common ancestor for humans and mice is virtually inescapable.” (pp. 136-137)

Such arguments are dangerous for those who make them, because they are based upon our lack of knowledge of these types of DNA. They amount to “evolution of the gaps” reasoning–because as we learn more and more about biology, we’re discovering more and more evidence of function for so-called “junk” DNA. The argument that much DNA is functionless junk, and thereby evidence for evolution, is relegated to gaps in our knowledge–gaps which are increasingly shrinking over time as science progresses.

But what if such DNA has function? If such DNA isn’t functionless junk, this may be another instance where, in Collins’ own words, a designer could have “used successful design principles over and over again.” (p. 111) In fact, as explained in this rebuttal to Collins, multiple functions have been discovered for repetitive DNA:

In 2002, evolutionary biologist Richard Sternberg surveyed the literature and found extensive evidence for function in AREs. Sternberg’s article concluded that “the selfish DNA narrative and allied frameworks must join the other ‘icons’ of neo-Darwinian evolutionary theory that, despite their variance with empirical evidence, nevertheless persist in the literature.” Reprinted from Sternberg’s paper, known genomic/epigenetic roles of REs include:

• satellite repeats forming higher-order nuclear structures;
• satellite repeats forming centromeres;
• satellite repeats and other REs involved in chromatin condensation;
• telomeric tandem repeats and LINE elements;
• subtelomeric nuclear positioning/chromatin boundary elements;
• non-TE interspersed chromatin boundary elements;
• short, interspersed nuclear elements or SINEs as nucleation centers for methylation;
• SINEs as chromatin boundary/insulator elements;
• SINEs involved in cell proliferation;
• SINEs involved in cellular stress responses;
• SINEs involved in translation (may be connected to stress response);
• SINEs involved in binding cohesion to chromosomes; and
• LINEs involved in DNA repair.

Other genetic research continues to uncover functions for allegedly functionless types of repetitive DNA, including SINE, LINE, and ALU elements. Sternberg, along with leading geneticist James A. Shapiro, concludes elsewhere that “one day, we will think of what used to be called ‘junk DNA’ as a critical component of truly ‘expert’ cellular control regimes.”

(Casey Luskin and Logan Gage, “ A Reply to Francis Collins’s Darwinian Arguments for Common Ancestry of Apes and Humans,” in Intelligent Design 101: Leading Experts Explain the Key Issues (Kregel, 2008) (internal citations removed.)

Collins wrote The Language of God in 2006, and it makes a number of other “junk” DNA-type arguments for common ancestry between humans and other species, many of which are rebutted here, showing much evidence of function for such so-called “junk” DNA. Suffice to say, after a closer analysis many of Collins’ “junk” DNA arguments for common ancestry turned out to be highly suspect, or simply inaccurate.

Collins Retreats on Junk DNA
Since writing The Language of God, Dr. Collins seems to have realized that it’s potentially dangerous and inaccurate to argue that much non-coding DNA is junk. As Jonathan M. explains here, Collins takes much softer tone towards junk DNA in his 2010 book The Language of Life:

The discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology. If you thought the DNA molecule comprised thousands of genes but far more “junk DNA”, think again.

(Francis Collins, The Language of Life: DNA and the Revolution in Personalized Medicine, pp. 5-6 (Harper, 2010).)

That sure sounds a lot different from his “45 percent of the human genome [is] made up of such genetic flotsam and jetsam” comment in 2006 in The Language of God. In fact, in his 2010 book, Collins seems to be strongly deemphasizing the amount of “junk” in the genome. Collins goes on to elaborate on just how much DNA isn’t junk–disavowing the notion that even “gene deserts” are junk:

The exons and introns of protein-coding genes add up together to about 30 percent of the genome. Of that 30 percent, 1.5 percent are coding exons and 28.5 percent are removable introns. What about the rest? It appears there are also long “spacer” segments of DNA that lie between genes and that don’t crowd for protein. In some instances, these regions extend across hundreds of thousands or even millions of base pairs, in which case they are referred to rather dismissively as “gene deserts.” These regions are not just filler, however. They contain many of the signals that are needed to instruct a nearby gene about whether it should be on or off at a given developmental time in a given tissue. Furthermore, we are learning that there may be thousands of genes hanging out in these so-called deserts that don’t code for protein at all. They are copied into RNA, but those RNA molecules are never translated–instead, they serve some other important functions.

(Francis Collins, The Language of Life: DNA and the Revolution in Personalized Medicine, p. 9 (Harper, 2010).)

But, it turns out Collins’ Darwinian viewpoint won’t allow him to completely divorce himself from junk-DNA thinking, as he makes an ambiguous statement that some unspecified portion of repetitive DNA remains junk:

Our genome is littered with repetitive sequences that have been inserted during a series of ancient assaults by various families of DNA parasites. Once they gain access to the genome, these “jumping genes” are capable of making copies of themselves, and then inserting those copies randomly throughout the genome. Roughly 50 percent of the human genome has had this history. However, in a nice demonstration of how natural selection can operate on all sorts of opportunities, a small fraction of these jumping genes have actually landed in a place where they have provided some advantage to the host. Thus, even some DNA we used to call “junk” is useful.

(Francis Collins, The Language of Life: DNA and the Revolution in Personalized Medicine, pp. 9-10 (Harper, 2010).)

If, according to Collins, natural selection explains function for junk-DNA, then perhaps this is a good example how Darwinian evolution both predicts we’ll find junk, and also predicts that we won’t find junk. Not exactly a very helpful theory. Moreover, as we saw above, much of the so-called repetitive “junk” is not functionless after all.

In the end, it’s clear that Collins’ 2010 book is a significant retreat on the claim that junk DNA dominates our genome. He even admits that noncoding DNA is “capable of carrying out a host of important functions”:

It turns out that only about 1.5 percent of the human genome is involved in coding for protein. But that doesn’t mean the rest is “junk DNA.” A number of exciting new discoveries about the human genome should remind us not to become complacent in our understanding of this marvelous instruction book. For instance, it has recently become clear that there is a whole family of RNA molecules that do not code for protein. These so-called non-coding RNAs are capable of carrying out a host of important functions, including modifying the efficiency by which other RNAs are translated. In addition, our understanding of how genes are regulated is undergoing dramatic revision, as the signals embedded in the DNA molecule and the proteins that bind to them are rapidly being elucidated. The complexity of this network of regulatory information is truly mind-blowing, and has given rise to a whole new branch of biomedical research, sometimes referred to as “systems biology.”

(Francis Collins, The Language of Life: DNA and the Revolution in Personalized Medicine, p. 293 (Harper, 2010).)

Collins Renews the Junk DNA Argument for Evolution
But Collins’ 2010 book The Langauge of Life is not his most recent book. His most recent book is The Language of Science and Faith, co-written with Biologos vice-president Karl Giberson, and it once again focuses on making junk-DNA arguments for evolution.

Collins and Giberson look at the vitamin C GULO ‘pseudogene’ found in humans and other primates (as well as some nonprimate species), and they contend that it is “not remotely plausible” that “God inserted a piece of broken DNA into our genomes.” They conclude that this “has established conclusively that the data fits a model of evolution from a common ancestor,” but has “ruled out” common design. (Karl Giberson and Francis Collins, The Language of Science and Faith, p. 43 (InterVarsity Press, 2011).)

Giberson also cited this same pseudogene in a recent op-ed on CNN.com where he argued:

In particular, humans share an unfortunate “broken gene” with many other primates, including chimpanzees, orangutans, and macaques. … How can different species have identical broken genes? The only reasonable explanation is that they inherited it from a common ancestor.

So it seems that Collins and Giberson still want to make junk-DNA arguments for evolution, but the discovery of function for so much so-called “junk” DNA in recent years has reduced them to citing a single example of a purported “broken” pseudogene in humans and other primates. Their gap in which to argue that noncoding DNA is “broken” has shrunk dramatically.

But as we’ve seen in recent posts, such as “Et tu, Pseudogenes? Another Type of ‘Junk’ DNA Betrays Darwinian Predictions,” “Is ‘Pseudogene’ a Misnomer?,” or “‘Junk’ RNA Found to Encode Peptides That Regulate Fruit Fly Development,” the notion that pseudogenes are merely “broken DNA” is coming under heavy fire from new scientific discoveries. Jonathan Wells has a whole chapter discussing functions for pseudogenes in his new book The Myth of Junk DNA. It seems that the gap is becoming so small that not even pseudogenes are a safe argument for “junk” DNA anymore.

Conclusion
Francis Collins and Karl Giberson are choosing to rely quite heavily on the argument that pseudogenes are junk, “broken DNA.” In fact, this singular pseudogene is their centerpiece evidence for common descent and macroevolution in their new book, The Language of Science and Faith. Giberson is so confident that this argument is right that in his recent CNN.com op-ed he’s betting “Jesus would believe in evolution and so should you.” But if history is to be our guide, then it would seem that this is a dangerous argument to make: The more we are learning about biology, genetics, and biochemistry, the more we are finding function for non-coding DNA, including pseudogenes.

Time will tell, but it’s revealing that Giberson and Collins are reduced to citing smaller and smaller gaps in our knowledge as regards “junk” DNA to argue for evolution. Professor Giberson may boast that “Jesus would believe in evolution and so should you” — but perhaps he should worry more about what direction the science is pointing rather than making religious arguments for evolution.