Science Magazine‘s reporter Yudhijit Bhattacharjee tells about "The Vigilante," Dan Graur of the University of Houston, who has made it his campaign to keep "junk DNA" in the junkyard. "When the ENCODE Project declared that there is no such thing as junk DNA, Dan Graur counterattacked," Bhattacharjee begins. "But does he go too far?"
Graur, a tall, imposing man who wears his sarcasm on his sleeve, is not the only scientist who objected to ENCODE’s conclusion that at least 80 percent of the human genome is functional. But he is the most vocal. Some have considered his criticism "so over-the-top it is not worthy of a response." A staunch atheist, Graur uses inelegant analogies and metaphors to make his point, and rub it in. In a presentation in Chicago last year, he "showed a photograph of dollar bills taped together in the shape of a toilet paper roll — his view of what ENCODE had achieved with the $288 million spent on the project so far," after six years of detailed study. Even those who agree with him have asked Graur to tone down his "furious attacks."
The basis of his attack is a logical flaw he sees in the interpretation of the data: "We know that some functional regions are transcribed. Ergo, all transcribed regions are functional." By that definition, gum stuck on a shoe is functional. Is this criticism valid?
Obviously, criticism is a necessary part of science. Even if you dislike Graur’s tone, we should take his critique of ENCODE seriously, just like we want our critiques of the Darwinian consensus to be considered seriously. "We simply do not do enough debunking in science these days," W. Ford Doolittle, who agrees with Graur, says. "We have moved into a very positivist mode where everybody is expected to simply get with the program." That’s not good. So let’s take Graur seriously. It’s fair game, however, to glance into his background.
Bhattacharjee learned about Graur’s life during a personal meeting at the University of Houston. Dan Graur grew up in Romania but moved to Israel where he served in the army, then earned a doctorate from the University of Houston, then taught in Israel, then returned to Houston.
The move brought him back to Houston, where he has spent the past decade producing papers on genomic evolution, with a focus on the comparative study of genomes. His other passion is collecting modern art, including a number of creations made from household junk. He wears his atheism on his sleeve: One of his pastimes is needling a devout Christian in his department with questions about the veracity of various biblical stories. Another is challenging antiabortion campaigns run by religious groups on campus. (Emphasis added.)
Bhattacharjee goes on, telling about Graur’s apparent glee at debunking "whatever he finds silly or stupid or wrong." These glimpses, while providing context, do not mitigate the need to examine his criticisms, but it’s instructive to look at his worldview motivations.
Graur’s atheism inflamed his anger at ENCODE. He perceives an echo of intelligent design in the consortium’s "80% claim," which he takes to imply that most of the genome exists because it serves a purpose. "What ENCODE researchers did not take into account," he contends, "is that everything is shaped by evolution." And evolution is slow to weed out useless features. Genetic mutations — the drivers of evolution — occur at random, and those that are deleterious are weeded out, sometimes over many generations. Other mutations, salubrious and inconsequential alike, get passed down to progeny. As a result, species like humans and elephants that have a small effective population size are expected to accumulate a lot of junk in their genomes.
So, Graur sees a suggestion of intelligent design in ENCODE’s results. Interesting.
It’s only fair we repeat this part of Science Magazine’s coverage. After all, Graur himself questioned others’ motives: "ENCODE leaders made such broad claims because they wanted to create a media splash that would justify the project’s cost," he alleged. They published "the 30-some-odd articles on the same day" because they wanted "public relations impact." Graur is upset that the $288 million on this one project kills careers of young scientists by not funding "500 other projects." It’s "a scandal," he opines in his "combative" way.
What we find in the passage quoted above is more than just atheism or hatred of intelligent design. His argument begs the question when he "contends" (merely stipulates) that "everything is shaped by evolution." But of course! Why wouldn’t we expect to hear a story about how evolution produced the observations? One would not expect actual design in such a picture.
In support of his story, Graur points to the paradox of there being no correlation between genome size and an organism’s complexity. "The onion’s genome is five times larger than ours," Bhattacharjee relates. Then there are the ubiquitous transposable elements that are mostly inactive, and defunct genes (pseudogenes). Graur uses these to bolster his claim that DNA is mainly junk, as evolutionists have long believed. To him, conservation is the metric that geneticists should use to measure function: i.e., if evolution conserves something, it most likely is important. By his measure, then, only 5 to 15 percent of the human genome is functional.
Before analyzing these criticisms, let’s see what the article relates about ENCODE’s counter-arguments. For one, "To ENCODE researchers like Bernstein, conservation is too narrow a criterion for pronouncing a region of the genome to be functional." One might expect conserved sequences to be functional, but that does not mean others are not.
Brushing aside their displeasure at Graur’s "uncivil discourse" and "combative approach" (which are matters of style, to which Graur retorts, "Science is not about abiding by a code of behavior put forward by Miss Manners"), what of his critique? After all, Birney appears to have backed off from use of the word "function," stating instead that 80 percent of the genome shows "specific biological activity."
Graur and other critics place undue emphasis on the 80% figure, says John Stamatoyannopoulos, an ENCODE principal investigator at the University of Washington, Seattle. The real take-home lesson, he says, is that "there is a tremendous amount of activity encoded in the genome — much more than researchers had suspected.
Bhattacharjee leaves the situation at a standoff. The ENCODE leaders consider Graur’s provocations rude; Graur considers them guilty of self-promotion and self-delusion. Graur asks, "How do you know it’s functional?" ENCODE responds, "How do you know it’s not?" Graur’s null hypothesis is "assume no function"; ENCODE thinks the opposite: "specific biological activity" indicates that something interesting is happening.
By assuming that "everything is shaped by evolution," Graur begs the question of evolution. Not only that, he mixes metaphors: intelligent agents shape things. His argument is contradictory: he says that evolution is "weeding out" junk, but he knows that the cell continues to expend wasted energy by transcribing all that alleged junk. He discounts the "tremendous amount of activity" ENCODE found in non-coding DNA. Finally, his choice of null hypothesis is dependent on his worldview: "assume no function" fits his belief that the genome is filled with junk.
Why not "assume function" as the null hypothesis? We see from history that the evolutionary teaching about "vestigial organs" held science back for a century or more. More recently, we have seen the "junk DNA" myth to be a science stopper. And now, the modENCODE project is showing the same pattern of pervasive biological activity in the fruit fly genome that was found in the human genome.
With these counter-arguments in hand, we can only wonder what makes Dan Graur so doggone angry at the suggestion that the gene is not primarily junk. Since he questions ENCODE’s motives, he opens himself up for having his own motives questioned.
Science’s understanding of biology would have progressed much faster had biologists thought the way Paul Nelson puts in in Illustra’s Flight film: "If something works, it’s not happening by accident." The sleek power of a cheetah on the chase, the precision aerodynamics of a hummingbird hovering motionless at a flower, the nearly flawless operation of molecular machines proofreading DNA during cell duplication — these are not expectations of systems believed to be cobbled together with junk by unguided processes. On the contrary, they are witnesses to the proposition that in biology, intelligent design deserves to be the default explanation.