DNA Trash Talk

Questions for Jonathan Wells on The Myth of Junk DNA

Materialists have a longstanding love affair with the notion that life is a poorly constructed kluge. For decades, they have argued that since only about 2 to 3 percent of human DNA codes for proteins, most noncoding DNA is useless genetic junk.

As their argument goes, no designer would put such genetic garbage in our genomes, and therefore so-called junk DNA refutes intelligent design (ID). Random evolutionary mutations, on the other hand, might be expected to produce a genome full of what Francis Collins called "genetic flotsam and jetsam."

Proponents of intelligent design respond that we're just beginning to understand the workings of the genome, and we ought not to assume that noncoding DNA is unimportant. In fact, as scientists discover more and more about the workings of the genome, it is becoming evident that noncoding DNA performs many vital cellular functions. Far from being useless genetic garbage, "junk" DNA might be as important—or even more important—than the gene-coding DNA itself.

In his new book The Myth of Junk DNA, pro-ID biologist Jonathan Wells documents the recent avalanche of scientific studies that have discovered functions for "junk" DNA. He concludes not only that the idea of junk DNA is a myth, but that this whole area is Exhibit A where predictions of neo-Darwinism failed while ID's predictions were confirmed. We caught up with Jonathan Wells and asked him about his new book.

What is "junk DNA" and why did you write a book debunking it as a myth?

According to Charles Darwin's theory, all living things are descendants of common ancestors that have been modified solely by unguided processes such as accidental variations and natural selection. In modern neo-Darwinism, genes control embryo development, variations are due to differences in genes, and new variations originate in genetic mutations. In the 1950s, neo-Darwinists equated genes with DNA sequences and assumed that their significance lay in the proteins they encoded. By 1970, however, biologists knew that about 98 percent of our DNA does not code for proteins. Some called this non-protein-coding DNA "junk" and attributed it to molecular accidents that have accumulated in the course of evolution.

"The amount of DNA in organisms," neo-Darwinist Richard Dawkins wrote in 1976,

is more than is strictly necessary for building them: A large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the "purpose" of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. 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. (The Selfish Gene, p. 47)

Since the 1980s, however, and especially after completion of the Human Genome Project in 2003, biologists have discovered many functions for non-protein-coding DNA. In light of the evidence, the notion that most of our genome consists of "junk DNA" is not science, but myth.

How have Darwin's defenders used junk DNA as an argument against intelligent design?

In 1994, Brown University biologist Kenneth R. Miller wrote:

The human genome is littered with pseudogenes, gene fragments, "orphaned" genes, "junk" DNA, and so many repeated copies of pointless DNA sequences that it cannot be attributed to anything that resembles intelligent design. . . . In fact, the genome resembles nothing so much as a hodgepodge of borrowed, copied, mutated, and discarded sequences and commands that has been cobbled together by millions of years of trial and error against the relentless test of survival. It works, and it works brilliantly; not because of intelligent design, but because of the great blind power of natural selection. ("Life's Grand Design," Technology Review, February/March 1994)

Twelve years later, Skeptic Magazine publisher Michael Shermer wrote:

We have to wonder why the Intelligent Designer added to our genome junk DNA, repeated copies of useless DNA, orphan genes, gene fragments, tandem repeats, and pseudo­genes, none of which are involved directly in the making of a human being. In fact, of the entire human genome, it appears that only a tiny percentage is actively involved in useful protein production. Rather than being intelligently designed, the human genome looks more and more like a mosaic of mutations, fragment copies, borrowed sequences, and discarded strings of DNA that were jerry-built over millions of years of evolution. (Why Darwin Matters, pp. 74–75)

The same year, Human Genome Project director Francis Collins (now director of the U.S. National Institutes of Health) published a book titled The Language of God that argued (ironically, given the book's title) that much of our genome consists of "junk DNA"—repetitive elements that provide evidence for Darwinian evolution and evidence against intelligent design.

In 2009, University of Chicago geneticist Jerry A. Coyne wrote: "Perfect design would truly be the sign of a skilled and intelligent designer. Imperfect design is the mark of evolution." Based on neo-Darwinian theory, "we expect to find, in the genomes of many species, silenced, or 'dead,' genes: genes that once were useful but are no longer intact or expressed." These are called "pseudogenes." According to Coyne, "the evolutionary prediction that we'll find pseudogenes has been fulfilled—amply." Indeed, "our genome—and that of other species—are truly well populated graveyards of dead genes" (Why Evolution Is True, pp. 67, 81).

If non-protein-coding DNA isn't junk, then just what is it doing?

Most of our DNA is transcribed into RNA. Since an organism struggling to survive would presumably not waste precious resources on making "junk," widespread transcription suggests that non-protein-coding RNAs are functional. Indeed, we now know that many of them help to regulate gene expression. For example, some genes are needed during embryo development but must be turned off in the adult. Other genes are needed in certain tissues but would cause disease if expressed in others. Non-protein-coding RNAs play essential roles in regulating those genes.

Some pseudogenes regulate protein production by producing RNAs that protect or interfere with the RNAs transcribed from the genes they resemble. Repetitive DNA produces RNAs that help to inactivate the extra X chromosome in human females. Mammalian embryos depend on products of repetitive DNA to implant themselves in the uterus.

Non-protein-coding DNA can also perform functions that do not depend on transcription into RNAs. For example, in the eyes of nocturnal mammals, non-protein-coding DNA forms liquid-crystal lenses in certain cells to focus scarce rays of light at night.

To be sure, there is much DNA for which no specific functions have yet been identified. But new functions for non-protein-coding DNA are being reported every week. Anyone who claims that most of our genome consists of "junk DNA" is relying on a "Darwin of the gaps" argument—one that must constantly retreat as gaps in our knowledge are filled by new evidence.

If you could have lunch with Francis Collins and Richard Dawkins, what would you say to them about their use of the "junk DNA" argument?

Actually, Collins no longer relies on "junk DNA." In 2007 he announced in an interview for Wired magazine that he had "stopped using the term." In 2010 he wrote that "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" (The Language of Life, pp. 5–6). Unfortunately, his followers at the BioLogos Institute (which he founded) seem to be unaware of this, because they continue to promote the myth that most of our DNA is junk. I would encourage Collins to set them right.

Unlike Collins, Dawkins seems utterly oblivious to recent developments in genomics. I would encourage him to read some of the scientific literature.

What do you say to those who claim there may yet be junk hiding out in some unstudied portion of the genome?

There may be, but saying that some of our DNA might be junk is a far cry from claiming that most of our DNA is junk—and that this junk provides evidence for Darwinism and against intelligent design. I would add: Calling something in a living cell "junk," just because no one knows its function, is a science-stopper. Biologists make progress not by closing their eyes to "junk" but by looking for new functions. •

From Salvo 18 (Autumn 2011)
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