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Wednesday, June 13, 2007


Junk DNA is the DNA in your genome that has no function. Much of it accumulates mutations in a pattern that's consistent with random genetic drift implying strongly that the sequences in junk DNA are unimportant. In fact, the high frequency of sequence change (mutation plus fixation) is one of the most powerful bits of evidence for lack of function.

Catherine Shaffer is a science writer who describes herself like this on her website,
I am a writer specializing in biotechnology, genetics, genomics, and other molecular, biological sciences. I have experience with news and features. My strengths include a meticulous attention to detail, an absolutely fanatical devotion to scientific accuracy, and enthusiasm. Readers appreciate my clean, uncluttered prose; my crisp, novelistic style; and (sometimes) my zany sense of humor. I am a writer who always meets deadlines and is organized and dependable.

I studied biochemistry at the graduate level at the University of Michigan, and worked in the pharmaceutical industry for several years. I am especially knowledgeable about genomics, proteomics, biotechnology, drug discovery, and chromatographic separations.
She has written an article for WIRED on junk DNA [One Scientist's Junk Is a Creationist's Treasure]. Here's how the article begins,

Without your "junk DNA" you might be reading this article while hanging upside down by your tail.

That's one of the key findings of the opossum genome-sequencing project, and a surprising group is embracing the results: intelligent-design advocates. Since the early '70s, many scientists have believed that a large amount of many organisms' DNA is useless junk. But recently, genome researchers are finding that these "noncoding" genome regions are responsible for important biological functions.

The opossum data revealed that more than 95 percent of the evolutionary genetic changes in humans since the split with a common human-possum ancestor occurred in the "junk" regions of the genome. Creationists say it's also evidence that God created all life, because God does not create junk. Nothing in creation, they say, was left to chance.

"It is a confirmation of a natural empirical prediction or expectation of the theory of intelligent design, and it disconfirms the neo-Darwinian hypothesis," said Stephen Meyer, director of the Center for Science and Culture at the Discovery Institute in Seattle.

Advocates like Meyer are increasingly latching onto scientific evidence to support the theory of intelligent design, a modern arm of creationism that claims life is not the result of natural selection but of an intelligent creator. Most scientists believe that intelligent design is not science. But Meyer says the opossum data supports intelligent design's prediction that junk DNA sequences aren't random, but important genetic material. It's an argument Meyer makes in his yet-to-be-published manuscript, The DNA Enigma.
Hmmmm ... This is so confused that it's difficult to know where to begin. First, the connection between my junk DNA and whether I am an opossum completely escapes me. I don't know of any credible scientist who claims that it's changes in junk DNA that makes us so different from the common ancestor of opossums. (And none who claim that we are descended from opossums.)

Second, the implication that most junk DNA is turning out to have a function is completely false and the confusion about the difference between junk DNA and noncoding DNA is inexcusable from someone who claims to be an expert on genomics [see Noncoding DNA and Junk DNA, The Deflated Ego Problem].

Third, the idea that large amounts of evolution in junk DNA supports Intelligent Design Creationism is crazy. But, in fairness, I don't think Shaffer is making the connection between the sequence variation and Intelligent Design Creationism; instead, she's making the (factually incorrect) connection between the discovery of some functions in noncoding, nonjunk, DNA and Intelligent Design Creationism (IDC). I think Steve Meyer is suggesting that IDC predicts that junk DNA will have a function and that's why he's being quoted here in the article (see above).
Scientists have made several discoveries about what some call the "dark matter of the genome" in recent years, but they say the research holds up the theory of natural selection rather than creationism.
When sequences in noncoding DNA are conserved, this is taken as evidence of negative selection. In that sense, it supports the theory of natural selection. However, most of the sequence comparisons show that junk DNA is not conserved. This does not support the theory of natural selection. It supports Neutral Theory and the mechanism of evolution by random genetic drift.

The article then describes one recent study suggesting that some noncoding DNA is not junk (Lowe et al. 2007). It appears to be the justification for writing the article since it compares short stretches of sequences in the human and opossum genomes. This is not news so I won't bother commenting.
With scientists increasingly believing that so-called junk DNA regulates other genes, among other functions, creationists like Michael Behe, a biochemistry professor at Lehigh University in Pennsylvania and author of the controversial new book on intelligent design, The Edge of Evolution, are more than happy to point out their errors.

"From the very beginning Darwinism thought whatever it didn't understand must be simple, must be nonfunctional," Behe said. "It's only in retrospect that Darwinists try to fit that into their theory."
The concept of junk DNA is not based on ignorance in spite of what the IDiots say. It's based on good scientific evidence and deduction. Of course most IDiots wouldn't recognize scientific evidence even if it bit them on the ...

Is this just a way of getting in another quote from a prominent advocate of Intelligent Design Creationism? Why is Shaffer so interested in the IDiots? This seems to be more than just seeking out controversy since the proper way to do that would be to interview real scientists who can put the work into perspective and comment on it's significance (see below).
Part of the difficulty in studying junk DNA is that it's impossible to prove a negative, i.e., that any particular DNA does not have a function.

That's why T. Ryan Gregory, an assistant professor in biology at the University of Guelph, believes that nonfunctional should be the default assumption. "Function at the organism level is something that requires evidence," he said.
That's how a real scientist speaks [see A word about "junk DNA" and Comments on "Noncoding DNA and Junk DNA"].

This is getting to be a familiar pattern among science writers. Many of them seem to be incapable of sorting out the actual science from the rhetoric. In this case the problem is exacerbated by introducing IDiots as though their opinion had a bearing on the subject. Not only that, the poor science writing stands in sharp contrast to the claim that, "My strengths include a meticulous attention to detail, an absolutely fanatical devotion to scientific accuracy, and enthusiasm."

Lowe, C.B., Bejerano, G. and Haussler, D. (2007) Thousands of human mobile element fragments undergo strong purifying selection near developmental genes. Proc. Natl. Acad. Sci. (USA) 104:8005-8010. [PubMed]


Nick (Matzke) said...

Good post Larry. There almost needs to be a paper on the science reporting on the "junk DNA" question which assesses what proportion of it is junk...

T Ryan Gregory said...

I appreciate the post Larry -- I have expanded on my ultimately minor contribution to the article here.

Unknown said...

Wow, Shaffer sure demonstrated how "especially knowledgeable" she is about genomics. One would think that that a writer "knowledgeable" about genomics would know the difference between noncoding promoter/enhancer DNA and all of the repetitive junk in the genome.

Great post, Larry - and thanks for the links.

Steve LaBonne said...

The thing we've long known with certainty to be absolutely nonfunctional junk is the "science reporting" in WIRED.

Anonymous said...

What's infuriating is that the Wired author sought out creationists to discuss a complex biological issue, when those morons can't even get the simple biology right. Why would you seek out someone with no scientific credibility?

Science reporting is sinking to the level of political reporting....

Mark said...

If a writer wishes to impress me with her knowledge, she had damn well better present some convincing evidence about a topic making coherent points. That will go a lot farther than simply telling me she's smart.

llewelly said...

Thank you, Larry, for a clear explanation of how grievously wrong WIRED's garbage is.
But Mike, in WIRED's case, this not a sinking - WIRED's 'science reporting' has been junk since the late 1990s. (As steve said.)

James said...

I don't understand the dichotomy between junk DNA and non-coding DNA. In fact, today my Genetics professor referred to introns as "junk DNA," and said that they may play a role in catalyzing alternative splicing. Is he simply wrong?

Anonymous said...

Interesting stuff here about "junk DNA":

"A close-up view of the human genome has revealed its innermost workings to be far more complex than first thought.

The study, which was carried out on just 1% of our DNA code, challenges the view that genes are the main players in driving our biochemistry.

Instead, it suggests genes, so called junk DNA and other elements, together weave an intricate control network.

The work, published in the journals Nature and Genome Research, is to be scaled up to the rest of the genome."

The abstract of the paper

We report the generation and analysis of functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project. These data have been further integrated and augmented by a number of evolutionary and computational analyses. Together, our results advance the collective knowledge about human genome function in several major areas. First, our studies provide convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts, including non-protein-coding transcripts, and those that extensively overlap one another. Second, systematic examination of transcriptional regulation has yielded new understanding about transcription start sites, including their relationship to specific regulatory sequences and features of chromatin accessibility and histone modification. Third, a more sophisticated view of chromatin structure has emerged, including its inter-relationship with DNA replication and transcriptional regulation. Finally, integration of these new sources of information, in particular with respect to mammalian evolution based on inter- and intra-species sequence comparisons, has yielded new mechanistic and evolutionary insights concerning the functional landscape of the human genome. Together, these studies are defining a path for pursuit of a more comprehensive characterization of human genome function.

Anonymous said...

My first disappointment with american science reporting was discover magazine. It was my favorite mag as an adolescent, it brought aticles by carl Zimmer, contributions by scieentists..
Then it suddenly started oublishing apologies for ANIMAL TELEPATHY and INTELLIGENT DESIGN
and I was like.....WTF?????

Steve Reuland said...

Great post, other than the picture accompanying it. I don't know what that monstrous, soon-to-be roadkill creature you posted is called, but it looks nothing like Monodelphus domestica. :)

PZ Myers said...

It's all your fault, you know. Shaffer is complaining that you didn't help her out enough.

You might be interested to learn that I contacted Larry Moran while working on this article and after reading the archives of his blog. I wanted to ask him to expand upon his assertion that junk DNA disproves intelligent design. His response was fairly brief, did not provide any references, and did not invite further discussion. It's interesting that he's now willing to write a thousand words or so about how wrong I am publicly, but was not able to engage this subject privately with me. His blog post is inaccurate in a couple of ways. First, I did not make the claim, and was very careful to avoid doing so, that “most” DNA is not junk. No one knows how much is functional and how much is not, and none of my sources would even venture to speculate upon this, not even to the extent of “some” or “most.” Moran also mistakenly attributed a statement to Steven Meyer that Meyer did not make.

Anonymous said...

Shaffer sez: "I interviewed five scientists for this article. Dr. Francis Collins, Dr. Michael Behe, Dr. Steve Meyers, Dr. T. Ryan Gregory, and Dr. Gill Bejerano. Each one is a gentleman and a credentialed expert either in biology or genetics."

Steve Meyers, credentialed expert in biology? Give me a break...

Anonymous said...


Thank you for your detailed post. As an author on the opossum Nature paper, on two opossum repetitive element companion papers, and on the original white paper arguing to sequence the opossum, the Shaffer article pains me. The studies mentioned are based on evolutionary theory down to their core. To quote religious dogmatists saying otherwise is a perversion of reality.

PS: Steve is right: you need a picture of a South American Gray Short-Tailed Opossum, not a probable North American 'possum (Didelphis virginiana; aka roadkill). There are maybe 15-50 millions years separating the two.

Larry Moran said...

Dave Pollock says,

Thank you for your detailed post. As an author on the opossum Nature paper, on two opossum repetitive element companion papers, and on the original white paper arguing to sequence the opossum, the Shaffer article pains me. The studies mentioned are based on evolutionary theory down to their core. To quote religious dogmatists saying otherwise is a perversion of reality.

Thanks for speaking out. I've always wondered what the authors thought when their papers are misinterpreted.

PS: Steve is right: you need a picture of a South American Gray Short-Tailed Opossum, not a probable North American 'possum (Didelphis virginiana; aka roadkill). There are maybe 15-50 millions years separating the two.

I'm aware of the different species and I knew when I posted the photo that it wasn't Monodelphis domestica. What I was looking for was a good photo showing an opossum hanging upside down from its tail to illustrate the first line of Shaffer's article, "Without your "junk DNA" you might be reading this article while hanging upside down by your tail."

Unfortunately, that line got buried below the fold as my article evolved so its effectiveness was diminished. It used to be the very first line.

Greg Laden said...

It is inappropriate to bring in a discussion if intelligent design in relation to junk, non coding, and coding DNA. There is no connection. Perhaps they are just trying to sell newspapers.

I sometimes hang out in a coffee shop where there is a guy who carves wood and Styrofoam and other materials into inter-planetary flying machines that he feels very strongly are appropriate designs for NASA, and just can't understand why they never answer his queries. Maybe Wired should do piece looking at current thinking in interplanetary travel and interview this gentleman just to make sure his perspective is covered.

Let me know if you need to get hold of him. I have a guess as to which bridge he lives under this time of year.

Nice post, Larry.

Anonymous said...

Wait, people actually READ Wired and take them seriously? As far as I know, whenever I pick up Wired, it was for a good laugh...

Anonymous said...

The basic core plot of all movies, novels, comic books, etc. is 'Somebody wants something, someone or something is trying to stop them'. Most science writers use this as the basic 'plot' for their articles or as the 'hook' to bring the reader into caring about the subject. The Wired article lead was about 'Larry wants to do good science but the IDiots are stopping him with this oppossom paper'. That this is not the way science is done should be obvious to any educated person. That this is a cheap literary device used by a writer who is not creative enough to make her reader care about the real conflicts in research should also be obvious. As long as journalists can plausibly pit science against ID they will continue to take the quick way out and do it when the editor calls and says "Give me X hundred words about Y, and make it fun to read."