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The Receding Myth of “Junk DNA”

Charles Darwin’s 1859 theory that all living things are descended from one or a few common ancestors, modified by unguided processes such as natural selection, did not rise to its current prominence until it was supplemented by Gregor Mendel’s theory of heredity after 1900. By the 1940s, scientists had identified DNA as the carrier of Mendel’s heredity factors.

When James Watson and Francis Crick solved the structure of DNA in 1953, Crick formulated the “Central Dogma” of molecular biology, often stated as “DNA makes RNA makes protein makes us.” This implies that mutations in protein-coding DNA provide the raw materials for evolution. In the 1960s, however, biologists discovered that about 98% of our DNA does not code for protein. Some — including Crick — called the non-protein-coding DNA “junk” and attributed it to the accumulation of molecular accidents during evolution.
The Myth of Junk DNA

Since the mid 1990s, some defenders of Darwinian evolution — including Richard Dawkins, Kenneth R. Miller, Douglas J. Futuyma, Michael Shermer, Francis S. Collins, Philip Kitcher, Jerry A. Coyne and John C. Avise — have argued that “junk DNA” provides evidence for Darwinian evolution and against intelligent design. (Intelligent design, or ID, is the view that we can infer from evidence in nature that some features of the world, including some features of living things, are better explained by an intelligent cause than by unguided natural processes.)

By 2007, however, it was clear that most of the mammalian genome is transcribed into non-protein-coding RNA. Since organisms struggling for survival would presumably not invest so much energy in producing junk, this implied that most non-protein-coding DNA is probably not junk after all.

Since then, specific biological functions have been discovered for many non-protein-coding RNAs. Although functions have not yet been identified for many parts of our genome, the list of specific functions for so-called “junk DNA” is already long, and it grows longer every week. Defending Darwinism and criticizing ID on the grounds that most of our genome is junk amounts to a “Darwin of the gaps” argument that has to retreat with each new discovery.

I make these points and others in my recent book, The Myth of Junk DNA. Curiously, there has been no response from the authors I specifically criticize in it. On September 23, 2011, however, John Farrell reviewed it for the Huffington Post.

Mr. Farrell begins by impugning my credibility, on two grounds. First, he writes, I have “misread” history by claiming that Mendel “found Darwin’s theory unpersuasive,” when actually Mendel accepted “the fact of evolution (descent with modification)” and Darwin’s “theory of natural selection to explain it.” Farrell cites no references to support these claims.

Farrell does cite Daniel J. Fairbanks’ 2007 book, Relics of Eden, to support his statement that Mendel “not only read Origin of Species, he was aware of the significance that his own studies on garden peas meant for the evolutionary theory.” And this is true. Mendel read an 1863 German translation of Darwin’s Origin of Species, and he began his classic 1865 paper, “Experiments in Plant Hybridization“, by stating that his experimental approach might “be the only right way by which we can finally reach the solution of a question the importance of which cannot be overestimated in connection with the history of the evolution of organic forms.”

Yet in his copy of The Origin of Species, Mendel emphatically highlighted a statement by Darwin about hybridization with which Mendel substantially disagreed. And midway through his 1865 paper Mendel noted, “nothing justifies the assumption” that in cultivated varieties “the species speedily lose all stability, and their offspring diverge into an endless series of extremely variable forms.” Mendel concluded by citing botanist Karl Friedrich von Gärtner’s view that species are

fixed with limits beyond which they cannot change. Although this opinion cannot be unconditionally accepted, we find on the other hand in Gärtner’s experiments a noteworthy confirmation of that supposition regarding variability of cultivated plants which has already been expressed.

Second, Farrell is shocked by my statement in The Myth of Junk DNA that biologists have never observed speciation (the origin of a new species) by natural selection. He refers to “extensive work being done in the field” by two biologists, H. Allen Orr and Matthew L. Niemiller.

But Orr and Niemiller study the genetics of existing species and try to find evidence supporting hypotheses about their origins. As I documented in my 2006 book The Politically Incorrect Guide to Darwinism and Intelligent Design, there is nothing in the scientific literature showing that they or any others have ever observed the origin of a new species by natural selection.

In plants, new species have been observed to originate by chromosome doubling (polyploidy). But speciation by polyploidy is not due to natural selection (nor to genetic drift, another process mentioned by Farrell), and even evolutionary biologists acknowledge that polyploidy does not solve Darwin’s problem.

According to Farrell, “the reader is not encouraged by inaccuracies” such as my statements on Mendel and speciation “so early in the book.” But the inaccuracies are his.

Farrell then turns to the primary subject matter of The Myth of Junk DNA. He begins by defining pseudogenes as “no-longer functional duplicates of coding genes” — a clever move, since the issue is the functionality of pseudogenes. In my book, I describe several ways in which they do function, and soon after my book came out scientists reported in Proceedings of the National Academy of Sciences USA that functional pseudogenes “might be ubiquitous in eukaryotic organisms.” (Eukaryotic organisms are composed of cells with nuclei — unlike bacteria, which have no nuclei.)

Although pseudogenes constitute a relatively small proportion of the human genome (as I point out in my book), Farrell states that my chapter about them leaves the reader “with the misleading impression that biologists are well on their way to finding functions for the entire human genome.” Of course, my book also includes chapters about functions in various other forms of non-protein-coding DNA. In any case, I never claim that functions have been found for most non-protein-coding DNA, though as I stated above the list grows longer every week. It is the trend, more than the current total, that should worry any defender of junk DNA.

Farrell goes on to cite evolutionary biologist T. Ryan Gregory, “whose work on genome size Wells walks around very gingerly.” In my book, however, I address Gregory’s work in some detail — including his conclusion that the known correlation between genome size and cell size cannot be explained by invoking junk DNA.

The last third of Farrell’s review focuses on the vitamin C pseudogene, a topic that I relegate to an appendix because it is only peripherally connected with the issue of junk DNA. Defenders of Darwinian evolution assume that, because the vitamin C pseudogene does not participate in the synthesis of vitamin C, it performs no biological function. This assumption may be correct, but considering the rate at which scientists are finding functions for other pseudogenes it is questionable, at best.

Of the authors I criticize in The Myth of Junk DNA, Kenneth R. Miller and Jerry A. Coyne both rely on the vitamin C pseudogene as evidence that humans and chimpanzees are descended from a common ancestor. Miller also considers it evidence against ID. Common ancestry, however, is a separate issue from ID, and advocates of the latter have differing views on the former.

Farrell faults me for my “anti-science rhetoric and attacks on scientists [such as Miller and Coyne] who have provided some of the nicest confirmations based on evolutionary theory.” For example, I criticize Miller for claiming in 2008 that gorillas need vitamin C in their diet — even though Miller had no published scientific evidence for this. Farrell writes, “Wells may not have been able to find any published evidence on the need for vitamin C in the diet of the gorilla, but it exists” — he then cites a 1970 paper by Linus Pauling and a 1949 paper by G. H. Bourne. But both papers are about the possible health benefits to humans of an increased intake of vitamin C. Bourne refers to the gorilla’s vitamin-rich vegetarian diet; Pauling assumes that humans and gorillas are descended from a common ancestor and argues that in lieu of sufficient vegetables we should supplement our diet with more vitamin C. Neither author provides any scientific evidence whatsoever of how much vitamin C a gorilla needs.

“To close,” Farrell writes, “The Myth of Junk DNA cannot be recommended for anyone who takes evolutionary biology seriously,” but it will provide “rationalizations for creationists who loath[e] common ancestry, [and] who loath[e] natural selection.”

But I do not loathe natural selection. I have no doubt that it occurs, but Darwin’s theory that it produces new species lacks sufficient evidence. Nor do I loathe common ancestry. I have no doubt that it occurs within existing species, but Darwin’s theory that all species are descended from one or a few common ancestors also lacks sufficient evidence. And in science, it is ultimately the evidence that matters.