Junk & Jonathan: Part 9—Chapter 6

This is part 9 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links below. For other postings on junk DNA check out the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

• Junk & Jonathan: Part 1—Getting the History Correct
• Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?
• Junk & Jonathan: Part 3—The Preface: Preface
• Junk & Jonathan: Part 4—Chapter 1: The Controversy over Darwinian Evolution
• Junk & Jonathan: Part 5—Chapter 2: Junk DNA: The Last Icon of Evolution?
• Junk & Jonathan: Part 6—Chapter 3: Most DNA Is Transcribed into RNA
• Junk & Jonathan: Part 7—Chapter 4: Introns and the Splicing Code
• Junk & Jonathan: Part 8—Chapter 5: Pseudogenes—Not so Pseudo After All

Jumping Genes and Repetitive DNA
The title of Chapter 6 is "Jumping Genes and Repetitive DNA." Wells describes transposons as jumping genes and includes them in the category of "Repetitive Non-Protein-Coding DNA." This category makes up 50% of the genome, according to Wells. The breakdown is as follows. LINES 21%; SINES 13%; retroviral-like elements 8%; simple sequence repeats 5%; and DNA-only transposons 3%. These percentages are similar to those published in a wide variety of textbooks and scientific papers. [What's in Your Genome?] [Junk in your Genome: LINEs] [Junk in Your Genome: SINES]


Many LINES and SINES are Functional

Most of the transposons in the human genome are fragments or otherwise mutated versions of the original mobile elements. This is a good reason for assigning them to the junk DNA category. They are a form of pseudogene. What this means is that half of our genome is composed of defective transposons that can't "jump." This is non-functional DNA, otherwise known as "junk."

This conclusion is unacceptable to Jonathan Wells. In order to prove that junk DNA is a myth he must show that most of this DNA has a function. He begins with a section called "Many LINES and SINEs are functional.

Theme

Genomes
& Junk DNAThe first evidence for functionality comes from the data showing that most of the genome is transcribed—the main theme of Chapter 3. If most of these defective transposons are transcribed then it seems likely that they have a function. But the evidence for widespread transcription is not widely accepted and one of the main criticisms is that it's extremely difficult to tell which repeated sequences are actually transcribed and which ones just happen to be very similar to a family member that is transcribed. We know that active LINES and SINES have to be transcribed at some time and we know that many defective transposons will still be transcribed even if they are non-functional. The question is not whether any transposons are transcribed, it's whether all (or most) of them are. The answer is almost certainly that very few are transcribed on a regular basis. The pervasive transcription reported in some papers is most likely accidental transcription at a very low level or artifact.¹

Nishihara, H., Smit, A.F., and Okada, N. (2006) Functional noncoding sequences derived from SINEs in the mammalian genome. Genome Res. 16:864-874.

The first "function" paper Wells mentions is Nishihara et al. (2006). These workers characterized a new class of SINES in the human genome. They consist of a hybrid of 5S RNA and a tRNA (~300 bp). These SINES are found in most vertebrates (fish, amphibians, birds, mammals). There are about 1000 of these SINEs in the human genome and in 105 of them there seems to be more sequence conservation in the central portion of the sequence than expected from junk DNA. For example, the overall sequence similarity between human and zebrafish is about 59% in a stretch of 338 nucleotides. (The authors refer to these as regions that are "under strong selective constraint." That's a bit exaggerated.)

This section contains three other examples of sequence similarities in a small class of transposons. These are the only examples where he makes the case for widespread functionality of defective transposons.

Wells is happy to accept the arguments that sequence similarity is evidence of homology and also of function.² Several possible functions were ruled out in these studies but it's possible that they have some undiscovered function that results in moderate sequence conservation. If this turns out to be true it would mean that 0.01% of the genome should be moved from the "junk" category to the "functional" category.

Some Specific Functions of LINES and SINES

Wells then proceeds to a discussion of papers that demonstrate a function for individual transposon fragments. Before we look at those studies, it's worth keeping the big picture in mind. A typical eukaryotic genome has a million defective transposons and a dozen or so functional transposons that are still capable of jumping to new locations. If you examine the genomes of a dozen or so eukaryotes you can expect to find some examples where these bits of DNA have been co-opted to perform some new function. If you collect together all these examples from many different species then it looks like an impressive array of functional transposon sequences but impressions can be deceptive. It's still true that 99.9% of defective transposons are junk.

This section of the book consists of four pages of specific examples of presumed functional transposon-like sequences from mouse, rat, human, hamster, silkworm, fruit fly, and Arabidopsis (plant). There are 54 references to the scientific literature. Wells makes no attempt to asses the reliability of these studies, nor does he indicate whether the claims have been independently confirmed by other labs.

It's a typical ploy of creationists to focus on specific examples of unusual adaptations and ignore the context. In this case, all those specific individual examples don't amount to a hill of beans when compared to the vast majority of junk in eukaryotic genomes.

However, in fairness it's not just Jonathan Wells and the creationists who fail to see the forest for the trees. There are many scientists who also think that the evidence quoted by Wells is conclusive proof that junk DNA is a myth. Wells has no trouble finding such scientists whose views are expressed in the scientific literature.

Walters, R.D., Kugel, J.A., and Goodrich, J.A. (2009) Critical Review (sic): InvAluable Junk: The Cellular Impact and Function of Alu and B2 RNAs. Life 61:831-837.

Finding that Alu and B2 SINEs are transcribed, both as distinct RNA polymerase III transcripts and as part of RNA polymerase II transcripts, and that these SINE encoded RNAs indeed have biological functions has refuted the historical notion that SINEs are merely "junk DNA."

Endogenous Retroviruses

About 8% of your genome consists of endogenous retroviruses. Most of them are defective, usually because large parts of them have been deleted. Some are still capable of producing viable retrovirus, like HIV or hepatitis B. There are about 30,000 loci in your genome where endogenous retroviruses are located.

Endogenous retroviruses contain strong transcriptional promoters since they have to produce a lot of transcripts when they are induced. Some of these small promoter regions (called "LTRs") have become incorporated into the promoter regions of regular genes. What happened is that millions of years ago a retrovirus accidentally integrated into the genome near the 5′ end of a gene and when parts of the endogenous retrovirus were lost by deletion the remaining retroviral promoter region became active leading to enhanced transcription of the adjacent gene. Over time this piece of the retrovirus evolved to become an integral part of the regulation of the gene.

Wells describes several examples of such events in different mammals. He also describes a famous example where expression of a modified envelope protein from a defective endogenous retrovirus has taken on a role in the development of the mammalian placenta. Together, these examples of co-opted retroviral sequences account for about a dozen of the 30,000 copies in your genome. Naturally, this is assumed to be proof that none of the defective endogenous retroviruses are junk. That's the logic of creationists.

Francis Collins and Repetitive Elements

The last section of this chapter is pure rhetoric. Wells is upset because Francis Collins, a Christian, wrote the following in The Language of God (pages 135-136):

Even more compelling evidence for a common ancestor comes from the study of what are known as ancient repetitive elements (AREs). These arise from "jumping genes," which are capable of copying and inserting themselves in various other locations in the genome, usually without any functional consequences. Mammalian genomes are littered with such AREs, with roughly 45 percent of the human genome made up of such flotsam and jetsam. When one aligns sections of the human and mouse genomes, anchored by the appearance of gene counterparts that occur in the same order, one can usually also identify AREs in approximately the same location in these two genomes.

Some of these may have been lost in one species or the other, but many of them remain in a position that is most consistent with their having arrived in the genome of a common mammalian ancestor, and having been carried along ever since. Of course, some might argue that these are actually functional elements placed there by the Creator for a good reason, and our discounting them as "junk DNA" just betrays our current level of ignorance. And indeed, some small fraction of them may play important regulatory roles. But certain examples severely strain the credulity of that explanation. The process of transposition often damages the jumping gene. There are AREs throughout the human and mouse genomes that were truncated when they landed, removing any possibility of their functioning. In many cases, one can identify a decapitated and utterly defunct ARE in parallel positions in the human and mouse genome.

Wells is upset because this is a double-barreled attack on intelligent design. Not only does Collins describe these sequences as junk but he also uses them as evidence of common ancestry. This is one of the reason why creationists like Wells maintain that junk DNA is used to support evolution.

Wells says,

Collins's argument rests on the assumption that those repetitive elements ... are nonfunctional. Yet their similar position in the human and mouse genomes could mean that they are performing some function in both. Given the rate at which functions are being discovered, Collins's assumption seems foolhardy, and his argument could easily collapse in the face of new scientific discoveries.

As long as most of these repetitive elements remain non-functional they pose a serious problem for Intelligent Design Creationists. The IDiots have been wishing for evidence of function for 20 years but "wishing" isn't a very scientific argument. Given the rate at which functions are being discovered, it's going to be a long, long time before all those hundreds of thousands of repetitive elements are assigned a function (i.e. never!). The vast majority of them are junk and discovery of a few co-opted sequences isn't going to change that fact.

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1. As a general rule, Wells "forgets" to mention when one of his "facts" is disputed in the scientific literature. Like most creationists, he is delighted to quote any scientific studies that confirm his bias but he is somewhat more reluctant to quote papers that don't. In this case—pervasive transcription—the criticisms in the scientific literature are so well-known that he is forced to discuss them in Chapter 9.

2. This is a bit strange coming from someone who doesn't believe in evolution but logic has never been a strong point is Wells' writing. Note that Wells does not accept the corollary argument that lack of conservation implies lack of function.