What a selfish little piece of...

"The Selfish Gene." "Selfish DNA." Oh, how such phrases can get people bent out of shape.  Stephen Jay Gould hated such talk (see a little book called The Panda's Thumb), and Richard Dawkins devoted more time to answering critics of his use of the term 'selfish' than should have been necessary. Dawkins' thesis was pretty straightforward, and he provided real examples of "selfish" behavior of genes in both The Selfish Gene and its superior sequel, The Extended Phenotype. But there have always been critics who can't abide the notion of a gene behaving badly.

Leaving aside silly bickering about the attribution of selfishness or moral competence to little pieces of DNA, let's consider what we might mean if we tried to imagine a really selfish piece of DNA. I mean a completely self-centered, utterly narcissistic little piece of DNA, one that not only seeks its own interest but does so with rampant disregard for other pieces of DNA and even for the organism in which it travels. Can we imagine, for example, a piece of DNA that deliberately harms its host in order to propagate itself?

Sure, we might picture genes acting in naked self-interest, perhaps colluding to create an organism that can fly and mate but can't eat. We can picture genes driving organisms to take outrageous risks in order to reproduce. And we can picture millions and millions of "jumping genes" that don't seem to care at all about the host's welfare while they hop about in bloated mammalian genomes. (If you are one who prefers to think of these transposable elements as beautifully-designed marvels of information transfer and storage, you can have a pass on that last one for now, because you won't like where we're going with this.) But can we picture a gene that actively harms its host in order to get ahead?

New reading on "junk DNA"

John Farrell runs an interesting blog at Forbes.com, and he regularly discusses genetics, design, and other topics of interest around here. His latest points to work by Larry Moran and Ryan Gregory, both of whom have debunked some of the "junk DNA" misinformation concocted by design theorists, then looks at some interesting new blogging from one Stanley Rice. It's interesting stuff.

Casey Luskin shows up in the comments. Nothing new there. Run over and check it out.

Alu need to know about parasitic DNA: telling the whole story about Alu elements and "design"

So, Alu elements are mobile DNA modules that can exert diverse influences on genomes and the organisms harboring them. They can affect genome function in constructive ways, by altering gene expression or supporting chromosome structure. And they can be damaging, even deadly. There are more than a million of them in the human genome, and we don't know what each one does. But, as I explained in the first post in this series, we do know that they can play both helpful and harmful roles, in the same way that other kinds of parasites can be good, bad, or indifferent.

Alu elements and other genome-wide repeats are a big problem for intelligent design (ID) theorists of some stripes. Any ID proponent who claims that genomes are carefully-designed, well-optimized systems must deal with the reality of the enormous numbers of mobile elements in (for example) the human genome. Now, I can think of various ways such an ID theorist might discuss Alu elements. She could propose that all of their characteristics (including their mobility) are part of their design, such that they can bring new design features quickly into being; she could propose that their mobility is a "bug" rather than a "feature," and perhaps speculate on how things went wrong; she could postulate that the damage caused by their expression and their mobility is being misattributed to the genome when it is instead caused by some other external process. (Or she could say, "We're still working on that one.")

Alu need to know about parasitic DNA: Alu elements and blindness

Age-related macular degeneration (AMD) is a leading cause of blindness in humans, and the leading cause of visual impairment during advanced age. The condition comes in two basic forms, the most severe of which is untreatable. Called geographic atrophy (GA), this condition involves the steady destruction of the retinal pigment epithelium, a layer of tissue in the eye that is essential for the health and maintenance of the photoreceptors in the retina. Loss of the pigment epithelium means certain death for the photoreceptors, and that means visual impairment and then blindness for the affected person.

A major publication in Nature last month (Kaneko et al., "DICER1 deficit induces Alu RNA toxicity in age-related macular degeneration," Nature 17 March 2011) now points to one likely cause of AMD, and in the process provides a chilling example of what can happen when the parasitic Alu elements in our genomes (see the previous post for an introduction) are left unrestrained.

Alu need to know about parasitic DNA: Introduction to Alu elements

Defenders of intelligent design theory often dwell on the topic of "junk DNA," which has been molded into a masterpiece of folk science. The ID approach to "junk DNA" involves a fictional story about "Darwinism" discouraging its study, and a contorted and simplistic picture of a "debate" about whether "junk DNA" has "function." The fictional story is ubiquitous despite being repeatedly debunked. But the picture of an ongoing "debate" about "function" is harder to sort out. Like most propaganda, that picture contains enough truth to sound plausible. (Browse my "Junk DNA" posts, and work by Ryan Gregory and Larry Moran, for more information on errors and folk science associated with these topics.)

There is, in fact, some scientific disagreement about functions of various elements in genomes, but it's not the crude standoff that ID apologists depict, and it has very little to do with "Darwinism." The debate, if we must call it that, is about at least two matters: 1) the extent to which certain genomic elements contribute to normal function or development of organisms; and 2) the means by which we might determine this. The debate is not about whether non-coding DNA can have function, or even about whether some segments of non-coding DNA do have function. That debate was invented by anti-evolution propagandists.

Introns. Let's think about this, people. Part IV.

So why is it that I and many other biologists hypothesize that introns are mostly non-functional?

(I'll assume that you've read the previous posts, and that you understand what it is that I mean when I challenge claims that introns are functional elements in an information-rich genome. And to avoid confusion, I'll speak only for myself, although I surmise that a tiny minority of biologists would agree with creationist characterizations of the human genome.)

Here are the basic data that lead me to conclude that intron sequences are mostly dispensable for biological function. I've provided links to key references, and we can go into more detail in further posts or in the comments.

Introns. Let's think about this, people. Part III.

What does it mean to claim that an intron has a function?

The question is obviously important, at least as long as there are disputes about whether introns have "functions" and whether science ignored them for decades.

Now, I can't help the ID people with their propensity for repeating falsehoods about the history of "junk DNA" and the role of "Darwinism" in its characterization. But I do think we can move a little closer together on this intron thing. So, first a discussion of the types of functions that are associated with introns then some comments on my specific dispute with Richard Sternberg.

Introns. Let's think about this, people. Part II.

Before we explore what introns are and how they work, let me correct the misuse of my words by one of the ID attack kittens. Months ago, referring to Steve Meyer's claim that introns "are now known to play many important functional roles in the cell," I sought to put intron "function" into context as follows:

The human genome contains at least 190,000 introns (though it's been recently estimated to contain almost 210,000). Together those introns comprise almost 1/4 of the human genome. One fourth. That's 768 million base pairs. And biologists have identified "important functional roles" for a handful of them. How many? Oh, probably a dozen, but let's be really generous. Let's say that a hundred introns in the human genome are known to have "important functional roles." Oh fine, let's make it a thousand. Well, guys, that leaves at least 189,000 introns without function, and gosh, they're snipped out of the transcripts and discarded before the darn things even leave the nucleus.

One critic has interpreted me as claiming that I know that 189,000 introns have no function. That's not my point, and I think most people know that.

Introns. Let's think about this, people. Part I.

It's time to talk about introns and function, so at least the ID people and I can agree on what we're disagreeing about. First, though, a little housecleaning.

When confronting the avalanche of misinformation on so-called "junk DNA" from intelligent design creationists, it can be hard to know where to start. In a previous series, I addressed many of the falsehoods that are employed by these folks, but the basic outline of the problem is easy to lose in the fog of confusion that ID advocates and other creationists purposefully generate around the issue. You can learn all you need to know by reading the previous series, and by reading the extensive work of Ryan Gregory. But here's a brief re-introduction.

In rage deaf as the sea, hasty as fire.

No one should take advice from this character, I'll grant you. But even King Richard II could see the obvious:

Then call them to our presence: face to face,
And frowning brow to brow, ourselves will hear
The accuser and the accused freely speak:
High-stomach’d are they both, and full of ire,
In rage deaf as the sea, hasty as fire.

--The Tragedy of King Richard the Second, Act I, Scene I, The Oxford Shakespeare

So Richard Sternberg, that aggrieved martyr of the Smithsonian Institution, butchered at the hands of Evil Darwinists and now among his people in Seattle, has posted a nasty rebuttal to a three-month-old post of mine on Signature in the Cell. I had resolved to ignore the minions of that awful place, but I'll grace Richard with a response since he's found a mistake that I do need to correct.

Introns and design

Mike Gene has posted an interesting series on introns that's worthy of a few comments. His thesis is that "introns facilitated the evolution of multicellular life."

A. The idea is interesting and rational but not novel. Research on introns and evolution is active and lively, and one prominent scientist in the field, Eugene Koonin, has proposed that introns drove many aspects of the evolution of eukaryotes (i.e., non-bacteria).

Signature in the Cell: Chapters 4 and 5 - errors and problems

Meyer's basic idea in chapters 4 and 5 is reasonably coherent. But I find further evidence in both chapters that Meyer is careless and underinformed on the subjects he addresses. (I explained before why I think this matters. If you think I'm not being nice enough to Meyer, consider providing me with the Rules of Engagement that apply when criticizing culture warriors who are proposing world-shifting new ideas.)

Signature in the Cell: beginning the review

So Stephen Meyer of the Discovery Institute, a founder of the ID movement, wrote a book called Signature in the Cell: DNA and the Evidence for Intelligent Design. It came out last summer, and I ignored it. I ignored it because it didn't seem interesting or important or new, and there's always something interesting and important and new to read. (I recently finished The Road. Wow.) It didn't matter to me that the ID people said it was "groundbreaking" or "seminal" or "a blueprint for twenty-first-century biological science" since they said things like that about Behe's last book. And that is a terrible book, one that reflects very poorly on its author. It seemed reasonable to assume that the ID movement wasn't going to generate any serious new arguments, and that if they did it would be obvious. Signature in the Cell gave no indication that it contained anything new.

Hugh Ross' shocking fairy tale

“I was to some degree trusting that the vetting process of a reputable book publisher was going to catch this level of duplicity.” But, he added: “Do I wish in retrospect that we had called L.A. child services and tried to run down the history of this person? I certainly do.”

That's Tom de Kay, editor of the Home & Garden section of the New York Times. Last week Thursday, that section ran a story, "A Refugee from Gangland," describing the life of Margaret B. Jones, the author of a just-released "heart-wrenching memoir" set in gangland L.A. The Times piece is fascinating, and the memoir probably is too. One little problem: the memoir has just been revealed to be a fraud. It was wholly fabricated.

In the aftermath, editors and publishers and even journalists are asking hard questions, and the book is being recalled.

It's surprising, jarring, in many ways incomprehensible, and it's just the most recent example of a "gritty memoir" that turned out to be a slick work of fiction.

Some folk science is truly fiction, but it's not that often that one uncovers a cynically fabricated bit of history. And maybe I'm too much of a moral relativist, but I do see a difference between, say, selective citation of the scientific literature in support of a weak or false proposition and, say, completely inventing a story of scientific discovery that paints one's opponents as fools and one's colleagues as brilliant heroes. Let's see if you agree.

IMPORTANT NOTE: this post, seeking to be harshly critical of Hugh Ross, refers to some of his statements as "lies." Please read the rest of this post in conjunction with a more recent post, "On folk science and lies: back to the basics." There I respond to some very important criticism, and agree that "lie" is not a useful or appropriate term here.

In Creation as Science (NavPress, 2006, pages 168-168), Hugh Ross relates a story of scientific discovery that is nothing other than a slick work of fiction. Here's how it begins:

The assumption that the non-protein-coding part of the genome served no purpose caused researchers to abandon study of its features for nearly three decades. Then a team of physicists made an observation that revived interest. They noticed that the quantity of "junk" in a species' genome was proportional to that species' degree of advancement.

You already know that the first sentence is a common falsehood. But here's an interesting new twist: a "team of physicists" somehow "revived interest" in the study of non-coding DNA. Ross claims that they "noticed" a proportional relationship between "junk DNA" and "degree of advancement."

The research to which Ross refers is reported in this brief paper: R.N. Mantegna et al., "Linguistic Features of Noncoding DNA Sequences," Physical Review Letters 73:3169-3172, 1994.

First, the authors of the article in question represent two departments: the physics department at Boston University, and the cardiovascular division of Beth Israel Hospital and Harvard Medical School. The group is truly interdisciplinary, evenly split between the two departments, but Ross elects to refer to it as a "team of physicists," and I think that says a lot about what might explain his egregiously error-filled forays into biology. In fact, one of the coauthors (Ary L. Goldberger) is quite well-known as a cardiologist and the director of the Margret & H. A. Rey Institute for Nonlinear Dynamics in Medicine at Beth Israel Deaconess and Harvard Medical School.

We'll soon see how the claim that this paper "revived interest" in "junk DNA" is an outrageous lie, but what about the proportional relationship between non-coding DNA and "advancement" that Ross associates with the authors of the 1994 paper? Well, it's a very short paper, but here's the only sentence that Ross could possibly have in mind:

An intriguing puzzle is related to the fact that in higher organisms, only a small fraction of the DNA sequence is used for coding proteins; the possible function – if any – of the noncoding regions remains unclear [5].

(The reference there, by the way, is to a review article on "Introns as Mobile Genetic Elements." It's a 37-page survey of one particular class of non-coding DNA, published more than a year before the "team of physicists" was able to "revive interest" in the "study of its features." This should make you laugh, but it's really not that funny.)

Note that the authors of the 1994 paper did not claim that the "quantity of 'junk' in a species' genome was proportional to that species' degree of advancement." Only an ignoramus would have written that, because it's not true; indeed, it's so far from the truth that precisely the opposite is actually the case.

"Degree of advancement" is not a phrase a biologist would use, but let's assume Ross means "complexity," in the way that a giraffe is more "advanced" than a worm, which is more "advanced" than an onion, which is more "advanced" than a mushroom, which is more "advanced" than a bacterium. For decades, biologists have known that the amount of DNA in an organism is utterly unrelated to its complexity. In fact, the very notion of "junk DNA" (referring specifically to pseudogenes, at the time) was invented as a hypothesis to account for the surprising lack of any correlation at all between an organims's DNA content and its size or complexity (or, for that matter, its phylogenetic position relative to other organisms). This observation was so surprising in its time that it was termed a paradox: the C-value paradox.

In other words, Hugh Ross begins his little story with a statement, falsely attributed to an interdisciplinary research group that he inaccurately calls a "team of physicists," that is so stunningly far from the truth that it is incomprehensible as anything other than an outright fabrication. I don't see how it could be a mistake, but perhaps when Reasons To Believe starts issuing retractions and apologies for its myriad falsehoods, Ross will attempt an explanation. (For the record, I'd settle for a correction, an apology, and a pledge to uphold at least minimal standards of academic integrity.)

Believe it or not, it gets worse. Here's the rest of Ross' fabricated fable:

The physicists decided to perform a computer analysis, and in 1994 they published their results. They found that what had long been labeled junk DNA carries the same complex patterns of communication found in human speech. In fact, they found that the junk DNA had an even higher linguistic complexity than did the protein-coding DNA. This breakthrough discovery drew teams of geneticists worldwide into a veritable frenzy to uncover the hidden designs and functions of the portion of DNA once thought useless.

This flurry of research has revealed five kinds of noncoding (for proteins) DNA, and each kind plays an important role in the vitality and function of the organisms in which they reside...

"Breakthrough discovery?" Well, according to Google Scholar, that paper has been cited 187 times, and when I examined this using Scopus, I found that about half of the paper's citations are from biology journals. Most of the remaining citations are from journals focused on physics, computation, and information theory, and most of those are mainly interested in the computational aspects of the 1994 study, not in its implications for genomics or genetics. According to Ryan Gregory, an actual expert in the area of genomic evolution and genome size, the report had no discernible impact on the study of genomes:

It would seem that other computer and physics types were interested, but few mainstream genetics authors picked up on it. Some people challenged it as being an artifact (Bonhoeffer et al. 1996a,b), but mostly I think people dismissed it as wishful thinking, if they even heard of it.
– Prof. T. Ryan Gregory, interviewed by email

And in case you're wondering whether 187 citations since 1994 is a lot, consider that my most cited paper, a 2001 article on p190RhoGAP on which I am co-first author with Madeleine Brouns, has been cited 108 times since then, all by biology journals. It's a very good paper, and it reported some very important results, but I don't think any of my colleagues would call the findings "breakthrough discoveries." What would a 1993-4 "breakthrough discovery" look like? Well, remember microsatellites? They comprise just one interesting class of non-coding DNA that was being intensively studied during the 30 years that Ross claims were lost to science. In 1993, a group from the Mayo Clinic in Minnesota reported that changes in microsatellite DNA are a frequent occurrence in colon cancer. Their paper has been cited almost 1500 times since then. And that review article on introns, which is cited by the "team of physicists" above? It's been cited 324 times since then.

It wasn't a breakthrough; it wasn't even an important or particularly useful result. But the most shocking and disturbing aspect of Ross' fairy tale is the full-blown lie at the end. Hugh Ross claims, falsely, that this insignificant little article launched a "veritable frenzy" of research "worldwide" on the functions of non-coding DNA. A quick look at the trajectory of research in any area of genomics or molecular genetics reveals this to be laughably untrue, but the final proof that Hugh Ross needs to re-examine his basic integrity is that last sentence. He actually claims, in print, that the "veritable frenzy" of research unleashed by the "team of physicists" led to the discovery of the various classes of non-coding DNA:

This flurry of research has revealed five kinds of noncoding (for proteins) DNA, and each kind plays an important role in the vitality and function of the organisms in which they reside...

Now, Ross' list is (you guessed it) not accurate; he doesn't even mention introns, for example. But the jaw-dropping lie, of course, is the claim that the imaginary impact of the "team of physicists" led to research that "revealed" these non-coding DNA elements. I'll leave you with a list of Ross' five classes of non-coding DNA, and references to the reports of their discovery.

Pseudogenes	1980
SINEs	before 1981
LINEs	1980
Endogenous retroviruses	1981
LTRs	1983

All of those non-coding elements were discovered more than 10 years before the little paper by the "team of physicists." (UPDATE: Ryan Gregory informs me that some of my dates are too generous: pseudogenes were known by 1977, and Alu elements (SINEs) were described by 1979.)

It's sad but true: you can't believe Reasons To Believe.

And if you work there, and you're reading this blog right now, please do something about this – for Christ's sake, if not for that of your own dignity.

Talking trash about "junk DNA": lies about "function" (part II)

The creator goes off on one wild, specific tangent after another, or millions simultaneously, with an exuberance that would seem to be unwarranted, and with an abandoned energy sprung from an unfathomable font. What is going on here? The point of the dragonfly's terrible lip, the giant water bug, birdsong, or the beautiful dazzle and flash of sunlighted minnows, is not that it all fits together like clockwork – for it doesn't, particularly, not even inside the goldfish bowl – but that it all flows so freely wild, like the creek, that it surges in such a free, fringed tangle. Freedom is the world's water and weather, the world's nourishment freely given, its soil and sap: and the creator loves pizzazz.

– from Pilgrim at Tinker Creek by Annie Dillard. Harper & Row (1974), p. 137.

Questions about the designs of the panda's thumb, the human appendix and tailbone, and male nipples should caution scientists against jumping too quickly to an evolutionary conclusion whenever some aspect of anatomy seems superfluous. The RTB creation model anticipates that future research into the anatomy of complex animal structures will reveal increasing, rather than decreasing, evidence for exquisite design and functionality.

– from Creation as Science by Hugh Ross, NavPress (2006), p. 170.

Can you tell which of the authors quoted above won a Pulitzer? Heh.

Back to the big lie about "junk DNA" as told by anti-evolution propagandists. The first theme in this cesspool of creationist folk science, as I described in the first installment of this series on "junk DNA", is this: that "junk DNA" is functional and therefore that evolutionary claims regarding its origin are mistaken. Two previous posts have tackled the first half of that howler, describing how creationist portrayals of "functions" for "junk DNA" are scandalously inaccurate. (The most disturbing installment, in which Hugh Ross is shown to have fabricated a bogus history of the study of "junk DNA," with physicists hilariously portrayed as heroes, will be posted separately this week.)

Now to the second half of this folk science fable. These deliberately misleading accounts of "function" for "junk DNA" are used by creationists in two ways.

1. After falsely claiming that "Darwinian" biologists left non-coding DNA unstudied for decades, they assert that scientists using design-based approaches would never have made this mistake. This claim is irrelevant, at least because the premise is untrue, if not because design proponents would have left the entire bloody genome unstudied while giving lectures and writing books on the impossibility of evolution.
2. After falsely claiming that non-coding DNA is "functional" despite "Darwinist" claims to the contrary, they assert that this evident "functionality" is evidence against common descent. This is a pretty ludicrous line of reasoning, but let's be clear on why it's wrong, because it's central to the folk science of "junk DNA."

Here's Fuz Rana of Reasons To Believe, summarizing an entire section of his discussion of "junk DNA" in Who Was Adam?

Evolutionary biologists maintain that the pseudogenes, SINEs, LINEs, and endogenous retroviruses shared among humans and the great apes provide persuasive evidence that these primates arose from a common lineage. The crux of this argument rests on the supposition that these classes of noncoding DNA lack function and arose through random biochemical events.

– From Who Was Adam? by Fazale Rana with Hugh Ross, NavPress (2005), p. 235.

That paragraph is excerpted from chapter 14, which is called "What About "Junk DNA"?" And Rana's claim throughout that chapter, as well as on the RTB website, is that a "supposition" of non-function is central to the explanation of common descent with regard to non-coding DNA.

I'm at a loss as to how to characterize Rana's misconduct here. As before, when I've confronted folk science on this blog, I'm struggling to understand how a Christian with even mediocre integrity would consider writing something like that. It can't be that he's stupid or ignorant enough to actually believe it. This is folk science, and it's bad.

To be brief: biologists make neither of those suppositions when they use non-coding DNA elements to establish common ancestry and particular evolutionary relationships. Whether or not a certain DNA element is "functional" doesn't make it any less an indication of common descent, nor have biologists ever assumed universal non-function of non-coding DNA in the first place. (The details of the reasoning actually employed by real scientists in this area will be the topic of the next post in this series.) Rana's continuous assertion that non-function is the "crux" of the phylogenetic argument is subtly disingenuous. (I think the subtlety of the ploy will be clearer as I continue the series and discuss specific types of non-coding DNA and what is known about them.)

Pseudogenes and mobile elements constitute overwhelming evidence for common ancestry, not because of "presumptions" regarding their function, but because they exhibit patterns of inheritance and location (within the genome) that are best explained by common descent. Even if a particular mobile genetic element has been put to work by the genome in which it is embedded, its conserved location in particular lineages (and not in others) presents an observation that is readily explained by common ancestry. In other words, even when it's true that a particular piece of non-coding DNA has a biological function, it's not true that this falsifies the basic explanation of common descent.

The fact that many non-coding DNA elements are known to be non-functional only makes Rana's position more laughable. Consider, for example, the GULO gene, which is necessary for the synthesis of vitamin C. You may be surprised to learn that, among mammals, only humans and their primate cousins, plus guinea pigs, require vitamin C in their diets. All mammals have a gene called GULO in the same general location in their genomes. But in primates, that gene has been mutated in a specific way, rendering it unable to make a functional protein. And in guinea pigs, the gene has been mutated differently. I'll present more examples in the final post in this series, but here's the point of including one in this post: primate species with the same dietary oddity (need for vitamin C) all display the same genetic oddity (mutation of a gene known to be essential for the manufacturing of vitamin C) in the same place in the genome. Think about it: that the outcome of the oddity is "non-function" of the gene is not actually central to the reasoning that identifies common descent as the only rational explanation. If the outcome had been the resurrection of a previously-dead pseudogene, the reasoning would have been the same, and it would be equally compelling.

Finally, the claim that the behavior of non-coding DNA elements such as LINEs or Alu elements (which are known to be mobile elements with sophisticated means of translocation) is due to "random biochemical events" is similarly dishonest. While the landing sites of many of these mobile elements are thought to be largely random (with some interesting and subtle exceptions), the process itself is non-random and fairly well understood. In fact, the combination of these two characteristics (largely known modes of mobility plus largely random or unpredictable landing sites) is exactly what establishes common descent as the only rational explanation for many remarkable genomic patterns.

In summary, creationist claims that non-coding DNA is largely functional are ludicrous, and the notion that a presumption of non-function underlies evolutionary explanations of genomic structure is very misleading. Other creationists are fond of this sort of argument, but at RTB they seem to be banking on it. Such misconduct is immeasurably corrosive to RTB's scientific and intellectual integrity, to say nothing of its witness as a public apologetics "ministry." I don't know what else to say.

Talking trash about "junk DNA": lies about "function" (part I)

Look, in short, at practically anything – the coot's feet, the mantis's face, a banana, the human ear – and see that not only did the creator create everything, but that he is apt to create anything. He'll stop at nothing.

There is no one standing over evolution with a blue pencil to say, "Now that one, there, is absolutely ridiculous, and I won't have it." If the creature makes it, it gets a "stet." Is our taste so much better than the creator's?

– from Pilgrim at Tinker Creek by Annie Dillard. Harper & Row (1974), p. 135.

God's creative work is ideal. If (as the songwriter David expressed in Psalm 8) the all-powerful, all-knowing Creator made the universe and all that's in it, then people can expect to see superior designs throughout the natural realm.

For those who agree with Darwin's view, any example of nature's imperfection contradicts the notion of a divine creation. As a result, many naturalists regard "junk" DNA as among the most potent evidences for biological evolution.

– from Who Was Adam? by Fazale Rana with Hugh Ross, NavPress (2005), p. 227.

Several weeks ago, I started this series on "junk DNA" by noting that the shoddy nature of anti-evolution folk science is rarely more clearly displayed than in discussions of genomic and genetic findings that are aptly explained by common descent. In that introduction, I noted three overall ways in which creationists – as typified by the apologists at Reasons To Believe (RTB) and the Discovery Institute (DI) – distort and/or ignore the facts about non-coding DNA. The first and most important of these errors regarding "junk DNA" is the claim that "junk DNA" is functional and that this therefore falsifies evolutionary hypotheses regarding its origin.

Hacking through the thicket of disinformation is going to be messy. We're not dealing with a single bogus idea or an isolated pseudo-factoid. We're approaching a quagmire of folk science, some of which is so grotesquely flawed that it's not even wrong. Like most well-designed folk science, the creationist "junk DNA" fables contain just enough factual information to give off the aroma of scientific credibility. As Obi-Wan once said [wink], "We must be cautious."

So what is "junk DNA"? It's a confusing term, and I am one of many scientists who never liked it and never used it. I'll have more on the history of the term elsewhere, but for now we'll use it the way anti-evolutionists (RTB/DI/AiG) use it: "junk DNA" is non-coding DNA, meaning that it is DNA that does not directly specify the code for making proteins. Here is a map of the makeup of the human genome, indicating the relative abundance of various categories of DNA:

Image from Molecular Biology of the Cell online, Alberts et al., 2002.

It's worth taking a few minutes to look at the diagram carefully. Notice that more than half (53%) of the human genome consists of "repeats," meaning certain types of sequences that occur multiple times in the genome. Notice also that relatively little of the genome is identifiably devoted to genes (pink + red in the diagram), and a very tiny proportion (1.5% or so) is devoted to the encoding of proteins (red).

Now, that means that 98.5% of the human genome is non-coding DNA. When creationists define "junk DNA" as non-coding DNA, they're referring to 98.5% of the human genome.

In the next two posts, I will comment extensively on this main error: the claim that "junk DNA" is functional and that this therefore falsifies evolutionary hypotheses regarding its origin. There are actually two falsehoods in that claim. This post, part I, will focus on the first one, and the next post will tackle the second.

Falsehood number 1. Evolutionists said that "junk DNA" has no function. But new evidence shows that "junk DNA" has important functions.

This kind of obfuscatory crap really annoys me. It's all over RTB and DI, and it's rampant in creationism in general right now. Both aspects of this claim are bogus.

First, it's just not true that biologists have ever claimed or assumed that 98.5% of the human genome has no function. Ryan Gregory is an evolutionary genomics researcher who has explained just how inaccurate this insidious claim really is, and his blog is required reading for anyone who wants to know more about "junk DNA" and evolutionary genetics. The short story is that biologists have adopted a range of stances toward non-coding DNA, from assuming that it is mostly functional to assuming that it is mostly parasitic. Those biologists, past and present, who would claim that it is mostly functional will readily note that useless parasitic DNA is likely to be abundant in most genomes; those who would emphasize the parasitic or artifactual nature of much of the human genome will readily (and eagerly) note the fact that such elements can and do get co-opted and put to work by the organism. To claim, as Hugh Ross does in Creation as Science (p. 168), that biologists assumed that the "non-protein-coding part of the genome served no purpose" is to promulgate a falsehood.

It's a falsehood, and it's not just irresponsible. It's downright silly. Biologists knew, for example – from very early on – that genetic control regions in the genome are not typically found in protein-coding segments. Only an ignoramus would have assumed or postulated that only protein-coding regions of a genome were functional.

Much worse, though, is this: many of the creationists cited here add another layer of dishonesty to this sick fable. They claim (DI / AIG) that because "Darwinists" assumed that much of the human genome had "no function," biologists failed to study it, and progress in understanding the genome was impeded. At DI, Casey Luskin even claims that this assumption hindered "research into understanding cancer and diabetes." This is how Hugh Ross puts it in Creation as Science (p. 192):

The assumption that naturalistic evolution governs the the history of life on Earth, for example, led to the deduction that the genomes for advanced species predominantly contain useless junk – the accumulation of millions of generations' worth of genetic accidents. This inference led to the 30-year abandonment of research into possible functions of non-protein-coding DNA, the so-called junk DNA.

I believe it is important for folks to understand that Ross and Luskin – and other creationists making this claim – are not telling the truth. If you take only one thing from this post, let it be this: the creationist claim that biologists ignored non-coding DNA for 30 years – because of the assumption that it was all non-functional – is a shameful lie.

Now, that's a pretty serious allegation, so you should expect me to present evidence. First, if you haven't already read Ryan Gregory on the history of the idea of "junk DNA," do it soon. Then, if you're interested and/or skeptical, check out this recent post in which I have a look into the scientific literature over the past 30 years.

The second aspect of this grand creationist lie is the claim that "junk DNA" is functional. And here's where things get a little sticky. Look carefully at a typical creationist argument of this type. It goes like this:

1. Evolutionists say (or said) that "junk DNA" has no function. (This is a lie, but we already covered that.)
2. But here is a paper describing a non-coding DNA element that has a biological function.
3. Therefore, "junk DNA" is functional.

The error here is pretty simple, but I think the argument typically exerts its influence first by virtue of the dishonest first premise, and then by an impressive-sounding (and usually perfectly accurate) discussion of a recent discovery in biology. The bogus conclusion is thus easier to smuggle in, especially if the audience isn't thinking carefully or is otherwise overly credulous.

Here's how to see the error (if it's not already obvious):

1. Insurance companies say that any 1989 Yugo is worthless and has no utility of any kind. They were crap when they were new, and they're worse than that now.
   
2. But let me tell you a story about a 1989 Yugo that is being used as a perfectly good mailbox (or church confessional, or shower).
3. Therefore, 1989 Yugos are valuable and useful.

Think about it: that first statement can't be right. Insurance companies probably don't say it just like that, and certainly they don't mean that an old Yugo can't be put to some good use. If you showed them one that actually runs, and proved that you drive it to work once a week, they would happily admit that it has some value. But who cares about that anyway? It's a red herring, and it's wrong to boot. Just forget about that silly first claim for a second, and follow the rest of the argument.

It's plain ludicrous. Of course some 1989 Yugos are valuable and useful, but that hardly means that 1989 Yugos are generally valuable at all. If you met someone who asserted that 1989 Yugos were "functional," and who claimed that those who say otherwise are involved in a nefarious conspiracy, you would probably take careful note of the locations of the exits.

There are several interesting types of non-coding elements found in animal genomes, existing in hundreds to thousands to millions of copies. Many of them have well-known properties (the subject of a future post), and many are like Yugos, or rocks, or logs, or roadkill: they're junk, but junk that may, occasionally, be put to use. Biologists have long known this, and suspected from the very beginning that even parasitic DNA elements would occasionally be co-opted by their hosts.

Once you understand what scientists really know about non-coding DNA, and how the history of its study has been systematically misrepresented by Hugh Ross, Casey Luskin, and other careless or unscrupulous creationists, you should see the "junk DNA" fable as inexcusably dishonest. And if you're a Christian, you should worry about your reputation.

I know I do.

Talking trash about "junk DNA": lies about genomic research

In another post in this ongoing series, we looked at creationist distortions of the nature of research into non-coding DNA, or "junk DNA." There I mention how creationists of all stripes are quite fond of the claim that "Darwinist" assumptions led to the labeling of all non-coding DNA as non-functional, and thereby to the neglect of research in the field for three decades. I've been in biology for most of those 30 years, and I know this claim to be dishonest. But if you want to see for yourself, it's easy enough to determine whether the claim is true (or reasonable, at least). One way to check is to ask someone who actually knows the field (as opposed to, say, a lawyer or a former physicist). Another approach is to look at the evidence in the scientific literature. That's what I did, and here's how it went.

I used PubMed, the standard online (free) database of the biomedical literature, to search for various terms during different time frames. I limited the searches to articles written in English. In each graph, the vertical axis indicates number of unique scientific articles containing the phrase, and the horizontal axis indicates publication date, in five-year intervals. First, let's see how often we find the phrase 'junk DNA' and the related phrase 'selfish DNA.'

Things to notice about this graph:

1. Neither phrase appears at all before 1970, and the phrase 'selfish DNA' doesn't appear till 1980.
2. The use of both terms has steadily increased over time.
3. The terms are extremely rare in the scientific literature. Total number of uses of 'junk DNA' in the past 40 years: 73.

Now, you might think this is pretty strong evidence in favor of the claim that the 'junk' assumption shut down research. Well, let's see. Ever heard of "satellite DNA?" That was an early term for a particular kind of non-coding DNA, composed of lots of small repeated sequences. Contrary to the dishonest claims of Ross and Co., satellite DNA was thought to be functionally relevant from its first description, and hypotheses regarding its roles were being vigorously tested before 1979. Folks, if all you did was read up on satellite DNA, you'd know enough to realize that neither RTB nor DI are telling you the truth about non-coding DNA. But let's see if it gets worse. (It does, of course.)

How much research has been focused on satellite DNA? Here's the graph:

If you look really hard you can see the little blue bars that show you the use of the term 'junk DNA.' And now you know why I am baffled as to why an honest person (much less a responsible Christian) would make a big deal out of the term 'junk DNA.' Biologists sure haven't. And now you know something else: research on satellite DNA was robust, and growing, throughout the 30 years following the first references to 'junk DNA.' Total number of papers that use the term: 4214. We could stop there. But we're just getting started.

You might have noticed that satellite DNA research seems to have peaked in the early 90's, and fallen off since. What's up with that? Heh. As methods for analysis of DNA and genomes improved, biologists recognized that satellite DNA could be categorized into two broad types: minisatellites and microsatellites. The technical differences don't concern us, but I think this graph will make it clear why the term 'satellite DNA' has become less prominent in the biomedical literature:
Got it? The new term was catching on, and replacing the old term. And what about microsatellites?

That's quite a different story, now isn't it?
Recapping so far – total numbers of articles, to date, using these phrases:

Junk DNA	73
Satellite DNA	4214
Minisatellite	2972
Microsatellite	25,582

What about introns? Those are the pieces of DNA interspersed in most genes (of organisms other than bacteria), pieces which are chopped out of the message before it's translated into protein. They're non-coding DNA, and therefore "junk" according to our creationist pundits. Question: how did research on introns fare during those 30 dark years of neglect?
Answer: pretty darn well. Total number of hits: 37,830.

Had enough? We could analyze research on ERVs, LINEs, SINEs, centromeres, telomeres... but I think it's clear enough that the fable about the evil Darwinists who killed an entire area of research, and with it countless victims of colon cancer and diabetes, is just a damned lie.

If you're just a Christian who's been reading this stuff, stop spreading the disease, and either give up the pointless opposition to common descent or find more respectable ways to defend your position.

If you're a Christian who's been writing this stuff, apologize, purge, re-orient, and maybe re-think. Your folk science is toxic, and our faith doesn't need "help" like that.

Talking trash about "junk DNA": Introduction

"Junk DNA" is a very popular subject among anti-evolution commentators. At the Discovery Institute (DI) and Reasons To Believe (RTB), as well as other creationist outlets, you can find ample discussion of "junk DNA" and why it matters to Christians who don't like evolution.

I've mentioned this topic several times myself, because I believe that the misuse of science by creationists is seldom more in evidence than when opponents of evolution confront genetics and genomics. As I've noted before, common descent provides a superior explanation for the extraordinary facts gleaned through comparative genomics (i.e., the examination and comparison of genome structure, overall and in detail, among different types of organisms), and there is no competing scientific explanation. As I see it, a knowledgeable Christian person considering these data has exactly two rational alternatives: 1) acknowledge the explanatory power of common ancestry and accept its reality; or 2) acknowledge the appearance of common ancestry but deny its reality. Any other choice is indicative of ignorance or of some form of intellectual dishonesty; I have advocated the use of the concept of folk science to account for the tendency of some apologists (e.g., the "scholars" at Reasons To Believe) to misrepresent science in defense of their preconceived interpretive framework.

Regarding so-called "junk DNA," the claims of the DI and RTB are quite similar, and I will consider them together here.

My assertion in these next 3 posts on "junk DNA" is this in a nutshell: the writing of the DI and RTB on the subject of "junk DNA" is a melange of half-truths, non sequiturs, quote-mined proof texts and outright fabrications that adds up to one of the clearest examples of folk science that I can imagine. My conclusion is that one would be very unwise to consult these sources for knowledge about developmental or evolutionary genetics, and that the architects of this deception are engaged in scholarly misconduct if not outright dishonesty.

When these apologists write about "junk DNA," they commit sins of commission and omission. I've identified 3 significant themes in this edifice of folk science, and the 3 posts will deal with each in turn.

1. Creationists insist that "junk DNA" is functional and therefore that evolutionary claims regarding its origin are mistaken.
2. Creationists systematically ignore fact and theory regarding the nature of vast numbers of non-coding genetic elements, which make up the bulk of the genetic material that is referred to as "junk DNA." Specifically, these apologists ignore (and sometimes deny) the fact that millions of chunks of DNA in the human genome alone are known to be mobile genetic elements.
3. Creationists distort the nature of ongoing research and debate concerning the evolutionary roles and fates of various "junk DNA" elements.

I'll deal with these 3 themes in 3 upcoming posts, but here are some teasers.

Creationists of various stripes commonly claim that because evolutionary biologists automatically assumed that non-coding DNA lacked function, little or no research on the subject occurred for decades. That claim is doubly false: biologists have always adopted various stances on the functional roles of non-coding DNA, and consequently research into its function has proceeded apace.

Enormous numbers of DNA elements that make up the bulk of the human genome -- and most of its non-coding "junk" segments -- have been identified and are being actively investigated by molecular biologists. These elements are anything but mysterious: they are so-called mobile genetic elements of various kinds, with well-known properties. Their properties, and their use in scores of analyses of evolutionary relationships, are systematically omitted from creationist writings on the subject.

The proteins that enable animals to smell are called olfactory receptors (ORs). The human genome contains about 800 OR genes, but more than half of them have been inactivated by mutation, yielding what are called pseudogenes. These "fossil genes" are found in precisely the same locations within the genome as are the fully-functional versions in other mammals (i.e., mice). Analysis of these genes and their properties has led to the construction of a highly coherent explanatory framework that accounts for the existence of these pseudogenes and the evolution of smell in vertebrates. Looking for a creationist approach to these data? The word 'olfactory' appears nowhere on RTB's website; at the DI, you'll find it in lots of articles...about stem cells.

So, stay tuned, or if you just can't wait go to Genomicron, a superb blog about nothing but genomes and evolution.

Which came first, the bird or the smaller genome?

It’s easy to think of a genome as a collection of genes, perhaps because so many of the metaphors used to explain genes and genomes (blueprint, book of life, Rosetta Stone) can give one the impression that everything in a genome is useful or functional. But genomes are, in fact, packed with debris. Many genomes contain huge collections of fossil genes: genes that have been inactivated by mutation but were never discarded, sort of like the old cheap nonfunctional VCRs in my basement. And many genomes contain even more massive collections of another kind of fossil-like DNA: mobile elements, or their remnants. The human genome, for example, contains over 1 million copies of a single type of mobile genetic element, the Alu transposon. Together, the various types of mobile genetic elements comprise nearly half of the human genome.

Think about that. Almost half of the human genome is made up of known mobile elements, pieces of DNA that can move around, either within a genome or between genomes with the help of a virus. This extraordinary fact -- and many of the specifics surrounding it -- constitutes one of the most compelling sources of evidence in favor of common descent, the kind of data for which only common ancestry provides a complete (or even reasonable) explanation. I’ll come back to this topic regularly.

Now it turns out, not surprisingly, that differences in genome size among types of organisms are determined primarily by the numbers of these mobile elements, and not by the number of genes. In fact, there is wild variation in genome size among types of organisms, and the variation has little to do with the numbers of genes expressed by those organisms. Consider birds, the subject of this week’s Journal Club (“Origin of avian genome size and structure in non-avian dinosaurs,” Organ et al., Nature 446:180-184, 8 March 2007).

Birds have remarkably small genomes, averaging 1/2 to 1/3 of the size of typical mammalian genomes. (The chicken genome, for example, is less than half the size of the mouse genome.) Why might this be? In other words, how might we explain this difference? The authors point to two important ideas. First, the chicken genome has been fully sequenced and analyzed, and it contains far less of the debris mentioned above. It seems that the processes that create (or multiply) mobile genetic elements are significantly less active in birds than in mammals and other vertebrates. Second, small genome size is intriguingly correlated with flight. Bats, compared to other mammals, have small genomes, and flightless birds, compared to other birds, have larger genomes. This has led to the proposal that small genome size might offer a selective advantage to flying animals, by reducing the energy cost associated with hauling all that debris around. So, it seems that a smaller genome is advantageous for flying vertebrates, and that genome size can be reduced by restraining the production of mobile genetic elements. And this raises several interesting questions, including this one: did the reduction in genome size accompany the origin of bird flight, or did it happen in advance? In other words, we can propose at least two alternative scenarios:

• 1) flight drove the genome change, by favoring small genomes, or
  
• 2) the genome change happened first, and helped to get flight off the ground. ;-)

How can we even hope to distinguish between these possible explanations? We would need, somehow, to look at the genomes of the ancestors of birds. And all evidence indicates that the relevant ancestors of birds are dinosaurs; in fact, today's birds are considered to be flying dinosaurs. The recent description of protein sequences from T. rex bone provided strong confirmation of the birds-from-dinosaurs hypothesis, but no DNA was recovered from the samples, and no information about genome structure can be inferred from those otherwise fascinating studies. If only, a la Jurassic Park, we could get some dino DNA...

Enter Organ et al. with a wonderfully creative idea. It turns out that, in organisms alive today, cell size is strongly correlated with genome size. In other words, organisms with large genomes tend to have larger cells. This relationship was first described in red blood cells, but Organ et al. show that it holds quite well in bone cells as well. Using bones from living species, they created a statistical model that enabled them to infer genome size by looking at the size of bone cells. Then they combined their model with measurements of bone cell size from fossilized bones of long-extinct animals, and were able to estimate the genome size of dozens of extinct species, including 31 dinosaur species and several extinct bird species. Their results are remarkable: small genomes are found in the entire lineage (with one interesting exception, Oviraptor) that gave rise to birds, all the way back to the theropod dinosaurs that are the typical reference point in the dinosaur-to-bird story. Here's how the authors put it: "Except for Oviraptor, all of the inferred genome sizes for extinct theropods fall within the narrow range of genome sizes for living birds." Even if you don't have access to Nature, you can have a look at the cool family tree in Figure 2, which shows small genomes in red and larger ones in blue. It's a compelling image.

The results suggest that small genomes arose long before dinosaurs took to the air, and raise some interesting questions about the interplay of physiological function (e.g., energy consumption associated with flight) and genome structure. Certainly scenario #1 above is not favored by these findings: flight apparently arose in organisms that already had much smaller genomes than many of their earthbound cousins. The relationship between flight and small genome size, then, remains unclear and even mildly controversial. Organ et al. acknowledge that the two characteristics did not arise together, but after reference to the larger genomes in flightless birds, they conclude their paper by noting that "the two may be functionally related, perhaps at a physiological level." And they postulate that small genome sizes may have been favored by warm-bloodedness and its associated energetic demands. But a minireview of the paper raises several criticisms of these hypotheses, and it is clear that the evolutionary forces acting on genome size are complex and yet poorly understood.

Notwithstanding the unanswered questions regarding genome evolution, this paper is the kind of scientific article that should be carefully considered by those who deny common descent. Following are some aspects of the story that create interesting questions for creationists and/or design advocates.

Consider the results presented in Figure 2. Outside of common ancestry, how are we to account for these data? The strong correlation between flight and small genome size in living organisms might look like some kind of "design" to someone who favors that sort of thinking, but Organ et al. have conclusively uncoupled genome size and flight. Of course those of us who see the universe as a creation will be happy to marvel at the advantages presented by small genomes to flying organisms, and perhaps we'll all think of these wonders as evidence of brilliant "design." But it seems to me that "design" does not serve a significant explanatory role here. On the contrary, I maintain that the work of Organ et al. demonstrates the following: in dinosaur lineages, the best way to predict genome size in an extinct species is to know the ancestry of the species. Common design aspects don't help. Common descent explains the pattern.

And yet, I think it gets much worse than that for anti-evolution thinkers. I regularly see certain old-earth creationists (e.g. the folks at Reasons To Believe) and design proponents (e.g. William Dembski) arguing that "junk DNA" (which includes, but is not limited to, the 45% of the human genome composed of mobile elements and their debris) is not "junk" but can have important functions. (The arguments of these critics are flawed in several ways, which I'll detail some other time.) While it's true that mobile elements have contributed to the formation of new genes from time to time, and are thought to be significant sculptors of genomic evolution, it's also true that mobile elements are indiscriminate in their jumping, and their continued hopping about is a documented cause of harmful mutation. Here, though, is a significant quandary for a design advocate considering a bird genome: if these mobile elements have important functions in the organism, then how is it that birds can get by with 1/4 as many of them as, say, squirrels? Why, if these elements have important functions in the organism, do bats seem to need far fewer of them than, say, rats? (The genome of the big brown bat is 40% the size of the genome of the aardvark. Hello!) It seems to me that these facts are best understood when one considers the possibility that most of this DNA is essentially parasitic, and that some types of organisms have benefited by restraining its spread. A "design" perspective with regard to genome size is just not helpful, and if that perspective insists on excluding common ancestry, then it's worse than worthless.

Article(s) discussed in this post: Organ, C.L., Shedlock, A.M., Meade, A., Pagel, M. and Edwards, S.V. (2007) Origin of avian genome size and structure in non-avian dinosaurs. Nature 446:180-184.