Junk DNA

In 1979, a biology professor at the University of California Berkeley named Thomas Jukes wrote to Francis Crick, the Nobel laureate and co-discoverer of the helical structure of DNA: 

Dear Francis, I am sure that you realize how frightfully angry a lot of people will be if you say that much of the DNA is junk. The geneticists will be angry because they think that DNA is sacred. The Darwinian evolutionists will be outraged because they believe every change in DNA that is accepted in evolution is necessarily an adaptive change. To suggest anything else is an insult to the sacred memory of Darwin.

In his new book What’s in Your Genome?, Laurence A. Moran shows that all the research done in the decades since that letter was written has confirmed what Crick, Jukes, and other specialists believed all along: much of our DNA is indeed a kind of “junk.”

Moran is professor emeritus of biochemistry at the University of Toronto. While he has been a science textbook co-author through five editions of the highly regarded Principles of Biochemistry, What’s in Your Genome? is the first book he has written for the general public. In addition to his teaching duties, Moran has since 2006 run his own blog, “Sandwalk”—named after Darwin’s favorite walking path. Beautifully organized, it’s a comprehensive resource for anyone who wants to learn more about the many complicated aspects of evolution that don’t always get covered in the popular press.

It goes without saying that Moran has tangled with creationists of all stripes for years. Indeed, his blog grew out of the need to carefully defend each and every aspect of the science they attacked. “There is no simple way to explain evolution correctly,” he writes, “but there are many simple ways to explain it badly.”

Moran is not shy about chastising celebrity science authors such as Richard Dawkins who, in Moran’s judgment, ignore or play down the crucial random processes involved in evolution while placing too much emphasis on natural selection and adaptation as the primary drivers of change.

Junk DNA is one of the more complicated examples of how randomness permeates the history of life. Few topics are more misunderstood and deliberately garbled in the press. The evidence that up to 90 percent of the human genome consists of useless DNA, repeatedly copied over the eons alongside all the most important genes that make us who we are, upsets a number of evolutionary biologists who believe—mistakenly, in Moran’s view—that natural selection simply wouldn’t have tolerated the accumulation of so much wasted code. And yet, as Moran shows in eleven detailed chapters, it’s precisely the existence of junk DNA in the genomes of most species that serves as one of the most powerful lines of evidence in support of evolution.

But what exactly do scientists mean by “junk”? First, it’s important to remember what they mean by a gene: a DNA sequence that’s transcribed to produce functional products (proteins) that constitute the body of an organism. Put another way, functional DNA is any stretch of DNA whose deletion from the genome would reduce the fitness of the individual organism (causing illness or death). Junk DNA, by contrast, is any stretch of DNA whose deletion from the genome makes absolutely no difference to the fitness or survival of the individual organism. And it appears we have a lot of it.

The term began to circulate back in the early 1970s (possibly coined by Benjamin Lewin, the editor of the journal Cell), but by then scientists had long been faced with a puzzle about human DNA: given the rate of harmful mutations that scientists estimated took place throughout the genome, the percentage of DNA that was actually responsible for producing a healthy human body could only be a fraction of the total DNA, otherwise humans would go extinct. A second puzzle had to do with the wide variation in the amounts of DNA that different and related species possessed. Since mammals displayed a greater developmental complexity than, for example, primitive fish, it was assumed they must have more DNA. In fact, it turned out many simpler species had more DNA than humans. The lungfish (Protopterus aethiopicus) has one of the largest genomes known, more than forty times larger than the human genome. The common house mouse (Myotis mystacinus) has a genome similar in size to ours. But the Venezuelan spiny rat (Proechimys trinitatus) has a genome almost twice the size of ours. There was no obvious explanation for such variation when the data began to emerge, a problem that became known as the C-Value Paradox: there appeared to be no correlation between the size of a genome and the complexity of an organism.

The answer seemed to be that the vast amounts of repetitive DNA scientists were discovering throughout various animal genomes were simply not necessary to the survival of the organism. Still, many scientists continued then, and continue now, to resist the evidence for junk DNA, and expect that further investigation will lead to the discovery of some kind of important function for it. Moran considers several examples of these efforts and explains why none of them are ultimately convincing.

While What’s in Your Genome? is intended for a general audience, its author does expect the reader to be able to digest some fairly dense sections on how genes are transcribed, the various kinds of no-longer-functioning DNA (transposons, pseudogenes), population genetics, and the role of genetic drift in evolution. There are helpful illustrations throughout the book, and Moran provides copious notes and a thorough bibliography. Still, a glossary of terms would have made it easier to keep track of the many different processes discussed.

Given that humans are the inheritors of a “sloppy genome,” resulting not only from natural selection but also, and no less importantly, from random processes such as genetic drift, the question arises: Is it really a shock to discover we carry so much empty genetic baggage?

Randomness in the structure of creation is not an unfamiliar problem to theologians over the centuries, nor is the idea that God’s designs could be realized through chance and contingency. The 2004 International Theological Commission’s “Communion and Stewardship” document emphasizes that, according to the Catholic understanding of divine causality, “true contingency in the created order is not incompatible with a purposeful divine providence. Divine causality and created causality radically differ in kind and not only in degree. Thus, even the outcome of a truly contingent natural process can nonetheless fall within God’s providential plan for creation.” This is in keeping with Aquinas’s thinking. In his Summa Theologiae he writes that the effect of divine providence is not only that things should happen somehow, but that they should happen either by necessity or by contingency. “Therefore, whatsoever divine providence ordains to happen infallibly and of necessity happens infallibly and of necessity; and that happens from contingency, which the divine providence conceives to happen from contingency” (I, 22,4 ad 1). 

Still, it can be disquieting to realize how much our own genetic makeup is steeped in the wreckage of what lived before. The Dominican priest and scientist Raymond Nogar (1916–1967) thought deeply, and perhaps somewhat ruefully, about the chaotic nature of the physical world he had spent his life studying, and how it frustrated the human desire to project order onto the universe. “What is far more obvious to me is the disorder, the waste, the hectic disorganization of the fragments of the universe of reality,” Nogar wrote in his book The Lord of the Absurd. Such a view is a painful one, he acknowledged, but we could now be confident, he believed, that the old idea of cosmic harmony was an illusion. “The universe may, in point of fact, be one; when God looks upon the universe He may see it to be one; but when I look out upon the universe of matter, of man and of God’s handiwork, I do not see it as one.”

What’s in Your Genome? is a powerful account of how the human genome was assembled at the most basic level, why it’s so sloppy and prodigal, and why that isn’t necessarily a bad thing.

What’s in Your Genome?
90% Of Your Genome is Junk
Laurence A. Moran 
University of Toronto Press
$39.95 | 392 pp.