Has Forbes.com Critic of <i>The Myth of Junk DNA</i> Read the Book? - Evolution News & Views

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Has Forbes.com Critic of The Myth of Junk DNA Read the Book?

Over at his Forbes.com blog, John Farrell has written a critique of Jonathan Wells' new book The Myth of Junk DNA. The only problem is that many of the arguments Farrell critiques aren't ones that Jonathan Wells makes in the book. Below is a comment I posted on Mr. Farrell's blog in response:

Dear Mr. Farrell,

Have you read Jonathan wells' book The Myth of Junk DNA? I don't mean to be cheeky, but frankly, it doesn't seem like you have. The Myth of Junk DNA either doesn't make the arguments you claim it does about a perfect mutation-free or disease-free genome, or it refutes the arguments you make in your post.

Regarding the latter problem, your post is logically incoherent because it tries to make two contradictory points, both of which are wrong:

(A) On the one hand, you try to rewrite history by arguing that evolutionary biologists never argued that the genome was full of junk.

(B) On the other hand, you then quote from a book by evolutionary biologist John Avise which argues that the genome is full of junk, and that this junk refutes intelligent design.

Your point (A) is an attempt to rewrite history, which is a predictable response to the overwhelming mass of evidence Jonathan Wells compiles in his book showing that evolutionary scientists have predicted that much of the genome is junk. In fact, John Avise's book from which you quote refutes your first point. As Jonathan Wells documents:

In 2010, University of California Distinguished Professor of Ecology & Evolutionary Biology John C. Avise published a book titled Inside the Human Genome: A Case for Non-Intelligent Design, in which he wrote that "noncoding repetitive sequences--' junk DNA'--comprise the vast bulk (at least 50%, and probably much more) of the human genome." Avise argued that pseudogenes, in particular, are evidence against intelligent design. For example, "pseudogenes hardly seem like genomic features that would be designed by a wise engineer. Most of them lie scattered along the chromosomes like useless molecular cadavers." To be sure, "several instances are known or suspected in which a pseudogene formerly assumed to be genomic ' junk' was later deemed to have a functional role in cells. But such cases are almost certainly exceptions rather than the rule. And in any event, such examples hardly provide solid evidence for intelligent design; instead, they seem to point toward the kind of idiosyncratic tinkering for which nonsentient evolutionary processes are notorious."


Avise also published an article in Proceedings of the National Academy of Sciences USA titled "Footprints of nonsentient design inside the human genome," in which he repeated the same argument. "Several outlandish features of the human genome," he wrote, "defy notions of ID by a caring cognitive agent," but they are "consistent with the notion of nonsentient contrivance by evolutionary forces." For example, "the vast majority of human DNA exists not as functional gene regions of any sort but, instead, consists of various classes of repetitive DNA sequences, including the decomposing corpses of deceased structural genes."


(Jonathan Wells, The Myth of Junk DNA, pp. 26-27 (2011).)

Wells provides many other examples of evolutionary scientists who predicted that most of the noncoding DNA in the genome would be junk. Here are just a couple he cites:

"The amount of DNA in organisms," 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, hitching a ride in the survival machines created by the other DNA."


In 1980, two papers appeared back to back in the journal Nature: "Selfish genes, the phenotype paradigm and genome evolution," by W. Ford Doolittle and Carmen Sapienza, and "Selfish DNA: The ultimate parasite," by Leslie Orgel and Francis Crick. The first paper argued that many organisms contain "DNAs whose only 'function' is survival within genomes," and that "the search for other explanations may prove, if not intellectually sterile, ultimately futile."15 The second argued similarly that "much DNA in higher organisms is little better than junk," and its accumulation in the course of evolution "can be compared to the spread of a not-too-harmful parasite within its host." Since it is unlikely that such DNA has a function, Orgel and Crick concluded, "it would be folly in such cases to hunt obsessively for one.


(Jonathan Wells, The Myth of Junk DNA, p. 20 (2011).)

And of course Wells cites multiple scientists who have used junk DNA as an argument against intelligent design. We already saw that Avise did this. Here are some other examples from my own notes:

"Our debris-laden genome Approximately half of the human genome consists of sequences that are obviously associated with transposable-element activity, and a large fraction of the remaining noncoding DNA might be a product of such activity but too divergent to be recognized as such. So much for intelligent design."[1]


"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."[2]

"In fact, 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. If the DNA of a human being or any other organism resembled a carefully constructed computer program, with neatly arranged and logically structured modules each written to fulfill a specific function, the evidence of intelligent design would be overwhelming. 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 to innovate, to test, and to discard what fails in favor of what succeeds. The organisms that remain alive today, ourselves included, are evolution's great successes."[3]

Your attempt to rewrite history and claim that evolutionary scientists largely haven't "asserted [the genome was full of] was functionless 'junk'" is also refuted by the following quotes, two from textbooks and another from Scientific American:

"Some of these integrated DNA segments are able to move around from site to site within host DNA molecules and are known as transposable elements or transposons. Other stretches of parasitic DNA are stuck permanently where they are and are probably the remains of once mobile gene creatures. They have degenerated into junk DNA. Much of the large human genome is comprised of these types of junk DNA that are no longer active."[4]


"Considering both the enormous amount of repetitive DNA in most eukaryotic genomes and the dearth of confirmatory evidence for any of the above proposals, a possibility that must be seriously entertained is that much repetitive DNA serves no useful purpose whatever for its host. Rather, it is selfish or junk DNA, a molecular parasite that, over many generations, has disseminated itself throughout the genome through some sort of transpositional process."[5]

"These regions have traditionally been regarded as useless accumulations of material from millions of years of evolution. ... In fact, the vast majority of genetic material in organisms from bacteria to mammals consists of noncoding DNA ... In humans, about 97 percent of the genome is junk."[6]

Many additional examples could be given. It's very convenient for T. Ryan Gregory to argue, in 2011, that the genome isn't full of useless junk. Good for him--he knows to jump off a sinking ship when he sees one. But that doesn't change the fact that for decades, evolutionary scientists presumed that non-coding DNA was largely junk. Your post is attempting to rewrite history.

But of course, Wells' book cites numerous papers which have found function for junk-DNA. In fact, his 170 page book has over 600 references--and that barely scratches the surface of the volume of literature which has found function for junk DNA.

In fact, the junk-DNA mindset, which was born and bred from the Darwinian paradigm, even stifled research into the function for junk DNA. The journal Science reported that the junk DNA mindset "repelled mainstream researchers from studying non-coding DNA." Fortunately some rogue scientists conducted research--"at the risk of being ridiculed"--that led to the overturning of the junk DNA paradigm.[7]

In 2003, Scientific American reported that one type of non-coding DNA called introns "were immediately assumed to be evolutionary junk." According to the article, "The failure to recognize the importance of introns may well go down as one of the biggest mistakes in the history of molecular biology."[8]

Junk DNA fell in spite of--not because of--Darwinian thinking.

Your point (B), that the genome is full of junk-DNA, is simply wrong on the facts. To understand why, you should read Jonathan Wells' book.

Much of the evidence he cites also is even finding function for pseudogenes. As one paper he cites from Annual Review of Genetics states: "pseudogenes that have been suitably investigated often exhibit functional roles."[9] As a recent 2011 paper in the journal RNA states:

Pseudogenes have long been labeled as "junk" DNA, failed copies of genes that arise during the evolution of genomes. However, recent results are challenging this moniker; indeed, some pseudogenes appear to harbor the potential to regulate their protein-coding cousins. Far from being silent relics, many pseudogenes are transcribed into RNA, some exhibiting a tissue-specific pattern of activation. Pseudogene transcripts can be processed into short interfering RNAs that regulate coding genes through the RNAi pathway. In another remarkable discovery, it has been shown that pseudogenes are capable of regulating tumor suppressors and oncogenes by acting as microRNA decoys. The finding that pseudogenes are often deregulated during cancer progression warrants further investigation into the true extent of pseudogene function. In this review, we describe the ways in which pseudogenes exert their effect on coding genes and explore the role of pseudogenes in the increasingly complex web of noncoding RNA that contributes to normal cellular regulation.[10]

Also, you make a third point stemming from John Avise's argument that the genome acquires mutations, making us prone to "genetic diseases," as if this refutes ID. You clearly have not read Jonathan Wells' book because he doesn't make any arguments that the genome must be mutation-free, disease-free, or mistake-free. The argument that pain or disease refutes intelligent design is an unscientific theological argument that has nothing to do with ID. (It's also theologically flawed, but that's a story for another day.) This has nothing to do with responding to Jonathan Wells' argument.

A final straw man argument you throw out is that somehow Jonathan Wells' book argues that if non-coding DNA isn't junk then therefore we should push "intelligent design into the public school science classrooms." Wells' book says nothing of the kind. His book says nothing about public education, and in fact Wells is affiliated with Discovery Institute, which opposes pushing ID into public schools.

I highly recommend that you read The Myth of Junk DNA because it will help you understand that your attacks are off-base.

Sincerely,

Casey Luskin

References Cited:

[1.] Michael Lynch, "The molecular natural history of the human genome," Trends in Ecology & Evolution, Vol. 16(8): 420-422 (August, 2001).

[2.] Michael Shermer, Why Darwin Matters: The Case Against Intelligent Design, p. 75 (Times Books 2006).

[3.] Kenneth R. Miller, "Life's Grand Design," Technology Review, Vol 97(2): 24-32 (February / March 1994).

[4.] David P. Clark, Molecular Biology: Understanding the Genetic Revolution, pp. 84-85 (Academic Press, 2005).

[5]. Donald Voet and Judith G. Voet, Biochemistry, p. 1138 (John Wiley & Sons, 2nd Edition, 1995).

[6.] Philip Yam, "Talking Trash," Scientific American, Vol. 272(3)W:24 (March 1995).

[7.] Wojciech Makalowski, "Not Junk After All," Science, Vol. 300(5623) (May 23, 2003)

[8.] Wayt T. Gibbs, "The Unseen Genome: Gems among the Junk," Scientific American (Nov., 2003) (quoting John Mattick, internal quotations omitted).

[9.] Evgeniy S. Balakirev, and Francisco J. Ayala, Pseudogenes, "Are They "Junk" or Functional DNA?," Annual Review of Genetics, Vol. 37:123-51 (2003)

[10.] Ryan Charles Pink, Kate Wicks, Daniel Paul Caley, Emma Kathleen Punch, Laura Jacobs, and David Paul Francisco Carter, "Pseudogenes: Pseudo-functional or key regulators in health and disease?," RNA, Vol. 17:792-798 (2011).

About two years ago when Stephen Meyer published Signature in the Cell, we saw that many early reviewers clearly hadn't read the book. We even saw Francisco Ayala review Signature in the Cell by attacking arguments Meyer hadn't made--including arguments about alleged imperfections in the genome.

It seems that even this soon after the release of The Myth of Junk DNA we're seeing a similar pattern from intelligent design critics. This is basically the approach taken by John Farrell.


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