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Already Outdated: Will Carl Zimmer Update His New Evolution Textbook on Junk DNA?

Carl Zimmer.jpgBack in July, we saw how Discover Magazine blogger Carl Zimmer tried to manufacture a controversy and score some points for the Darwin side in the evolution debate. He refused to buy or read our book, Science and Human Origins, yet confidently asserted that we lacked a credible reference backing our argument that the genetic evidence for chromosomal fusion (bearing on the question of human common descent with apes) isn't as strong it's often claimed to be. He was wrong, but that didn't stop him from pressing his accusation in one blog post after another--as if somehow by repeating it that would make it valid.

Now Zimmer has co-authored a new evolution textbook with Douglas Emlen, Evolution: Making Sense of Life. Unlike Zimmer, who sees nothing amiss in criticizing a book without reading it, I immediately shelled out $100+ to purchase a new copy of his book--just as I have done for a number of Zimmer's other books. Over the years I've found that buying and reading books is one of the best ways to stay informed about what people -- whether I agree with them or not -- are saying about evolution and intelligent design. I commend Carl Zimmer and other Darwin advocates that it's vital to keep up with the relevant scientific literature.

So how is Zimmer's new textbook? Well I was pleasantly surprised to learn it contained a short but nice discussion of functions for non-coding DNA and "RNA genes" (see p. 130). This surprised me because I had expected Zimmer to defend the notion that our genome is full of useless genetic junk. Then I kept reading, and found this passage two pages later:

Over half of the genome is composed of neither genes, nor vestiges of human genes, nor regulatory regions. Instead, it is made up of parasite-like segments of DNA, known as mobile genetic elements, with the capacity to make new copies of themselves that can then be reinserted into the genome. Some mobile genetic elements originated as viruses that integrated their genes into the genome of their host. The origins of other mobile genetic elements are more mysterious. Once they become established in their host genome, mobile genetic elements can proliferate into thousands of copies and take up large amounts of space. (p. 132)
So there you have it: According to Zimmer, "[o]ver half of the genome" is "parasite-like DNA" which, since it's parasitic, isn't there to perform a useful function. As a general rule, that's what makes a "parasite": it is of no use to the host. Contrast Zimmer's view with the findings of the molecular biologists who head the international consortiums that study this "parasite-like DNA," as reported by Discover Magazine (where, as I mentioned, Zimmer himself blogs):
According to ENCODE's analysis, 80 percent of the genome has a "biochemical function." More on exactly what this means later, but the key point is: It's not "junk." Scientists have long recognized that some non-coding DNA has a function, and more and more solid examples have come to light [edited for clarity -- CL]. But, many maintained that much of these sequences were, indeed, junk. ENCODE says otherwise. "Almost every nucleotide is associated with a function of some sort or another, and we now know where they are, what binds to them, what their associations are, and more," says Tom Gingeras, one of the study's many senior scientists.

And what's in the remaining 20 percent? Possibly not junk either, according to Ewan Birney, the project's Lead Analysis Coordinator and self-described "cat-herder-in-chief." He explains that ENCODE only (!) looked at 147 types of cells, and the human body has a few thousand. A given part of the genome might control a gene in one cell type, but not others. If every cell is included, functions may emerge for the phantom proportion. "It's likely that 80 percent will go to 100 percent," says Birney. "We don't really have any large chunks of redundant DNA. This metaphor of junk isn't that useful."

Mr. Zimmer, call your office!

Saying that "it's likely" that "100 percent" of our genome will turn out to have "function of some sort or another" sure sounds different from what Carl Zimmer claims in his new evolution textbook. But that's how science goes -- sometimes it progresses so quickly that a book is outdated before it's even published. That's awkward for publisher and author alike. The lesson, I think, is always to be careful about keeping up with the relevant scientific literature. For the sake of students who read his textbook, let's hope Carl Zimmer is doing that.

Image: Carl Zimmer, Wikipedia.