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.")

BioLogos and Christian unity. Part I: The cost of artificial unity

Christian unity is not something to take lightly. Famous biblical proof texts urge us to pursue it. Basic theological commitments establish it as a primary goal of believers. Basic human nature would seem to drive us to seek solidarity with those who share fundamental beliefs. So when a Christian – especially a Christian in the midst of a dispute or disagreement with another Christian – makes an appeal for unity, only a fool would rise to disagree. Considered in isolation, talk of unity is powerfully persuasive to Christian believers. "Considered in isolation." That's where I will focus as I try to explain (again) why talk of unity can be inappropriate and even dangerous when it is offered outside of context. In short, I take the following to be evident: unity is not an end in itself, and is not achieved by wishful thinking or gushy happy talk. I'll look at those two points in two posts on BioLogos and Christian unity.

So, I'm occasionally frustrated by the stance of my friends at BioLogos when it comes to Christian unity. Consider a recent and widely-discussed piece by Darrel Falk, on the question of why BioLogos is co-sponsoring a conference (called The Vibrant Dance) with two organizations known to regularly misrepresent science: Reasons To Believe (RTB) and the Discovery Institute (DI). Falk notes that this choice has been criticized by believers and skeptics alike. In my opinion, his defense of that choice misses the most important criticisms. His defense amounts to a claim that Christian unity matters more than just about anything else. Specifically, he asserts that "what we have in common far outweighs the differences we may experience." And "we" is BioLogos, RTB, The DI, and an interesting group of other organizations, one of which is my employer (Calvin College). I will have words for Calvin in the near future. Here are some comments on his reasoning and his claims in that post.

Love. Peace. Unity. Or?

Last month, I read that Biologos (a Christian "think tank" that advances evolutionary creation) and Reasons To Believe (a Christian "think tank" that advances old-earth creationism) were reporting on a dialogue between their two organizations that was intended "to discuss areas of agreement and disagreement" with a particular focus on "the biological record of the past 700 million years."

This is very interesting to me. My position is very closely aligned with that of Biologos, so naturally I often disagree with the opinions of Reasons To Believe (RTB). But as I've explained in detail before, my big problem with RTB has nothing to do with their preference for miraculous intervention during biological evolution. It has to do with their proclivity for the crafting and promulgation of falsehoods, and I have asserted that their statements on various aspects of evolutionary science amount to misconduct that calls for intensive reform.

And so I'm quite curious about how Biologos and RTB interacted. The joint statement reports that "significant progress was made in clarifying similarities and differences" and that the two groups seek to model Christian disagreement that is characterized by "civility, grace, and unity." The comments are full of joyous praise for the effort, and the statement cites classic proof texts calling for Christian unity and mutual respect.

And who could disagree with that? Well, I'm going to try.

Weekly sampler 20

Wow, lots going on lately.

1. So, what is a species? The concept is much abused by creationists, so that an already-challenging topic is turned into an abyss of confusion and obfuscation. John Wilkins is a philosopher of science who runs a superb blog over at ScienceBlogs, Evolving Thoughts. He's an expert on this whole species thing, and he recently provided a fascinating commentary on the issue and on a Scientific American essay on the topic by the dashing Carl Zimmer. Warning: spoiler ahead!

So my answer to the question Carl proposes: what is a species? is that a species is something one sees when one realises that two organisms are in the same one. They are natural objects, not mere conveniences, but they are not derived from explanations, but rather they call for them...

2. Oh, speaking of Carl Zimmer, check out this deliciously disturbing story of manipulation in nature, starring some of the creatures that drove Charles Darwin to agnostic distraction: parasitic wasps. Don't read this one at night.

3. Okay, so I've been a little hard on Jim Watson around here. He was "forced out" of his position at Cold Spring Harbor after he was reported to have made some plainly racist statements. Richard Dawkins was indignant, probably because Watson is a fellow atheist who Dawkins fawns over in The God Delusion. I had mixed feelings. On one hand, I was outraged by Watson's nakedly disgusting racist remarks; on the other, I was concerned about the likelihood that his comments on evolution and cognition would be ignored (or worse, rejected) in the uproar.

Well, Watson was recently interviewed by Henry Louis Gates, Jr., at an interesting site called The Root. Watson says that he is "mortified" by "those three sentences in the Sunday Times article." I'm pretty sure all three sentences appear in this paragraph:

He says that he is “inherently gloomy about the prospect of Africa” because “all our social policies are based on the fact that their intelligence is the same as ours – whereas all the testing says not really”, and I know that this “hot potato” is going to be difficult to address. His hope is that everyone is equal, but he counters that “people who have to deal with black employees find this not true”. He says that you should not discriminate on the basis of colour, because “there are many people of colour who are very talented, but don’t promote them when they haven’t succeeded at the lower level”. He writes that “there is no firm reason to anticipate that the intellectual capacities of peoples geographically separated in their evolution should prove to have evolved identically. Our wanting to reserve equal powers of reason as some universal heritage of humanity will not be enough to make it so”.

It seems to me that a discussion of the last two sentences could be quite fruitful; Watson is right about evolution, but wrong about what that must mean about the "equality" of "them."

4. Here's an interesting place to hang out: The Galilean Library. When I first followed a link there, I assumed it was a repository along the lines of Darwin Online. But no: here's how the community is described:

The aim of TGL is to provide a venue for people interested in the sciences and humanities and the possibility of learning more about them in community with others. Its rules are strict, relative to other discussion forums, and standards of expected behaviour are high, but all users need to do is demonstrate a genuine commitment to friendly and respectful dialogue with others in good faith. It consists in a Library of essays, at both introductory and more advanced levels, alongside a Discussion Forum where members of our community meet to converse and debate.

Cool. And yes, they do have stuff by Galileo, including that masterpiece of science-faith dialogue, Letter to the Grand Duchess Christina.

5. Kevin Corcoran unearths ancient secrets of scientific explanation. Now I get it.

6. A slick new Tangled Bank is up at Syaffolee.

7. A recent post in Steve Martin's ongoing series on "Evangelicals, Evolution, and Academics," by Karl Giberson, led to a lengthy and robust discussion there and on the ASA listserv. And a new post in the series, by Gordon Glover, just went up. It has this in-your-face title: "Why Evolution should be taught in Christian schools." Required reading.

8. Hey! My wife and I are looking for scholars (or just friends) in Scotland and/or London who would be willing to help us with our January trip to London and Edinburgh to study Christianity and the Scottish Enlightenment. Doesn't that sound like a great time? Please get in touch if you agree.

9. Reasons To Believe is a morass of misinformation about biology and evolution, but this is a new low: some "guest scholars" have contributed a series on "Evolution as Mythology" which is a rancid concoction of dishonest quote mining and fallacious reasoning that should make any informed Christian seethe. So much for RTB's claim to respect science and scientists; that series is a tour de force of the kind of arrogance-fed ignorance that forms the backbone of the young-earth creationism that RTB claims to eschew. Here's a typically nauseating morsel:

Even though macroevolution seems improbable via the traditional pathway (and regulatory genes are a strong argument for creationism) the myth-like character of neo-Darwinism continues to keep it as the dominant theory. As Behe says, “Most biologists work within a Darwinian framework and simply assume what cannot be demonstrated.”²³ Evolutionists even claim regulatory genes make neo-Darwinism more plausible because punctuated equilibrium is more easily explained by regulatory genes, but this only emphasizes how the myth of macroevolution must be protected with religious zeal.

Note to RTB: your intellectual integrity is mediocre at best, and your failures are magnified, not hidden, by your attempts to claim moral high ground in "debates" involving science and faith. Your organization desperately needs reform.

Now this is a documentary you don't want to miss!

Via John Farrell.

On folk science and lies: Back to the basics

Months ago, I was worrying about how to characterize creationist statements that are untrue or misleading. The claims in question are not merely false (mistakes of various kinds can generate falsehood) and are not statements of opinion with which I disagree. They are claims that are demonstrably false but have been asserted by people who are certain (or likely) to know this. In other words, they bear the marks of duplicity. I said:

As a Christian, I am scandalized and sickened by nearly all creationist commentary on evolution. But I'm not a misanthrope, and so I find it hard to believe that so many people could be so overtly dishonest.

So I proposed the term 'folk science' as a way to refer to belief-supporting statements that sound scientific but do not seek to communicate scientific truth. I have two goals in my practice of using this phrase: 1) I recognize folk science as a particular type of argumentation, and I want to be able to accurately identify it as such; and 2) I want to create space within which I can identify falsehood, and especially falsehood that seeks to mislead, without making unwarranted accusations.

Not everyone was all that excited by this. One example I used, in which Fuz Rana presents a completely inaccurate — and wholly misleading — summary of evolutionary theory, led one commenter (Henry Neufeld) to reflect as follows:

But I'm still having a hard time wrapping my brain around the idea that someone with any sort of education in biology could manage to say some of the things creationists say. For example, in the blog post you cited from RTB, there are huge areas of evidence for common descent (everything related to the genome, for example) that are simply omitted. It would seem to me that even a person who had read only the popular literature would at least be aware of such evidence.

I can understand those poorly educated in science falling for folk science — it's easier and it makes you feel better! But I have a hard time understanding how a biologist could do so.

And Steve Martin of An Evangelical Dialogue on Evolution, had this to say:

I think there is a different level of accountability for those in leadership. We all need to take seriously the words in James 3:1. (And I’m speaking for myself here too — even if my own role is virtually insignificant in the larger debate). For those in leadership that ignore data that contradicts their teaching, I’m not sure the appeal to “folk science” cuts it. Integrity is just way too important.

Some people noted that the moral and intellectual milieu within which folk science is generated is not amenable to simplistic moral analysis. But I surmise that many of my respondents back then were concerned about going soft on crime, as I put it.

Lately, as I've been describing the folk science of "junk DNA," I have run across examples of falsehood that stretch the limits of the term 'folk science,' in that they resemble what many people would refer to as 'lies.' And I started to describe these disheartening and regrettable falsehoods as 'lies,' even as 'outrageous lies.' These are descriptors that I had deliberately avoided in my earlier posts, and I'm sorry to say that I drifted into this habit rather than making a specific decision to use this more serious language.

My friend and colleague Kevin Corcoran is urging me to reconsider this practice in a St. Patrick's Day post on his blog, Holy Skin and Bone. Now would be a good time to read his post, and the intense discussion that it generated. Come on back here when you're done.

Now, I don't buy Kevin's argument about the implications of the word 'lie'; he asserts that to call a statement a 'lie' is to call the speaker a liar, and I disagree. I don't see any problem with separating the statement from the speaker, and I think many English speakers would agree. If you read that the Holocaust never happened, you're reading a lie, no matter how you end up characterizing the motivations or competence of the writer. How else could we refer to the sinful practice of "repeating lies?" Moreover, I think a lie can evolve, such that it can come to be through careless repetition (with modification), subtly transformed into a perniciously misleading statement when full-grown. In other words, I believe that a lie can exist without being traceable to a specific liar. In fact, I think it's likely that Hugh Ross' sickening fable about the "team of physicists" arose through some sort of evolutionary process, and not through a spasm of malicious dishonesty at a keyboard in Glendora, CA.

But what's the difference between a lie and a falsehood? Unlike Kevin, I label a statement a 'lie' after making a judgment regarding intentionality. If a statement is being used to deceive, or was conceived to deceive, then I will judge it to be a lie, whether or not the person who most recently uttered it – or who forwarded the email in which it was found or whatever — meant to deceive. In this vein, I regularly deem the behavior of some people to be the repeating or spreading of lies, without necessarily assuming that those people are dishonest in any way.

The problem, though, is that some people (Kevin, at the least) don't see things this way at all. And if, as I suspect, Kevin speaks for others as well, then some of my readers have reached the conclusion that I believe Hugh Ross to be a malicious liar. This is not the case, and I have explicitly stated as much in previous posts on this subject. But it just won't do to have confusion regarding character judgments. I will henceforth commit myself to complete avoidance of the word 'lie' in describing folk science. If I think something is really an actual lie, I'll show it to Kevin before I write anything about it. (Seriously.)

Now let me be clear: I will continue to refer to certain examples of RTB's behavior as misconduct, and I will not hesitate to identify the promulgation of falsehood by Ross and Rana as irresponsible, indefensible, and even dishonest. I will not hesitate to question Hugh Ross' intellectual integrity, and I think he should not be considered trustworthy as long as he persists in the reckless dissemination of fabricated nonsense that serves only to direct Christians away from basic facts of biology. The fabricated fable about the "team of physicists" is deeply troubling to me, and it should be troubling to anyone who claims the name of Christ. If I knew Hugh Ross, I would urge him to do whatever is necessary to change course, and I would encourage RTB to invest in mechanisms designed to establish and maintain basic integrity. But I won't call him a liar, or refer to his falsehoods as lies, and I won't assume that he seeks only to mislead or misinform Christians.

Please provide me with some feedback, and feel free to be as critical as you can.

Weekly sampler 10

The sun came out this week and the temperature soared to almost 50. In Phoenix, such a temperature is called 'cold'; here, it inspired us to have a cookout, though it didn't happen because the snow and ice on the deck precluded access to the blessed Weber kettle. But tomorrow, we're there.

And I've been back on my bike this week, dodging cell-phone-wielding buffoons driving alone in SUVs. I wear one of these iridescent yellow-green visible-from-space bike jackets, but I know it's just a matter of time before something terrible happens and I use the F-word on Lake Drive. FOOL!

1. Check out the National Evolutionary Synthesis Center. They sponsor lots of integrative research, and host fellows under various arrangements. (A sabbatical there sounds like a blast.) The Education & Outreach section is pretty meager, but I assume that it will continue to grow, and the Center is a co-sponsor of the new journal Evolution: Education and Outreach.

2. There's a very interesting (and large) collection of pieces on Richard Dawkins at the Times (London).

3. The RATE project is an attempt by young-earth creationists to provide a credible response to the overwhelming evidence for the great age of the earth. The project took several years, and millions of dollars, and generated a two-volume report.

As I always say, it's one thing to believe that the earth must be young, and it's quite another to assert that science backs such a claim. The RATE project, of course, takes the latter route. It's inevitable that the outcome of such an effort will involve the production of comforting folk science, cherry-picked and massaged with care. But does it have to include outright duplicity?

I'm pleased to report that the ASA has undertaken a major response to RATE, and the extent of the discussion exceeded the capacity of the ASA's journal, Perspectives on Science and Christian Faith. So the ASA has put together a web site containing the complete set of reports and articles, which includes responses from RATE and responses thereto. Related: Randy Isaac is the Executive Director of the ASA, and he has a series of articles on scientific integrity on his ASA blog.

4. Scott Carson has some interesting thoughts on miracles and explanation.

5. Every now and then I get questions about whether I'm on thin ice as a Calvin College professor who openly affirms common descent and evolutionary explanations, even for humans. Some people know that my denomination, the church that owns and operates the college, has made statements that seem hostile to common ancestry of humans and other animals. I recently commented on this over at An Evangelical Dialogue on Evolution. While you're there, check out Steve's new post on the Darwin exhibit, now in Toronto. We missed it when it was at the Field Museum in Chicago, but that's okay: we'll try to catch it in London. :-)

6. Today's issue of Nature includes an interesting book review. The book is Creationism and its Critics in Antiquity, in which the author details debates surrounding the argument from design, played out not in Victorian England or 21st-century Pennsylvania, but in ancient Greece. Here's an excerpt from the review:

The brilliance of this book is that Sedley lets the Greeks talk to us and, surprisingly, we can understand what they’re saying. Listen to Empedocles describing a time when the world was filled with a diversity of creatures with improbable combinations of features, most of which were then winnowed out, and you hear the late Stephen Jay Gould illuminating the body plans of the Burgess Shale fossils. Listen to Aristotle heaping scorn on Democritus for supposing that living things self-assemble from accidental combinations of atoms, and you hear Fred Hoyle’s gambit that “a tornado sweeping through a junkyard might assemble a Boeing 747 from the materials therein”. Truly it has been, as Darwin said, just “one long argument”.

7. Watch this weekend for a fun quiz regarding DNA content in different organisms, and my long-promised commentary on Howard Van Till's recent address to the Grand Dialogue.

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.

When it's not just a disagreement

Now this is interesting. I can think of plenty of interesting Shakespearean scenes involving conflict and disputation. [Takes a bow] But I couldn't recall the word 'disagree' anywhere in, say, Hamlet or Romeo and Juliet, or even Macbeth. So to a quick search of the Oxford Shakespeare, which unearthed exactly one use of the word, in King Henry VI, Part I:

King Henry. Henceforth I charge you, as you love our favour,
Quite to forget this quarrel and the cause.
And you, my lords, remember where we are;
In France, amongst a fickle wav’ring nation.
If they perceive dissension in our looks,
And that within ourselves we disagree,
How will their grudging stomachs be provok’d
To wilful disobedience, and rebel!

– King Henry VI, Part I, Act IV, Scene I, The Oxford Shakespeare

Interesting scene, and reminiscent of the kind of talk one might hear in any community that is facing opposition: we mustn't disagree, or at least reveal our disagreement, because it will signal weakness (real or not) to our enemies. Christians often talk like this. So do Democrats, and Republicans, and sports teams, and I'm sure we could find examples in much odder places than those.

There is much that I could say about this aspect of dissent and disagreement in Christian communities, but I have a different goal here. I want to distinguish mere disagreement from more substantive forms of conflict, because the deliberate smearing of these moral distinctions is a tactic oft employed by propagandists and their defenders.

First off, it should be obvious by now that I have significant and substantive disagreements with most creationists. We disagree about the meaning of large sections of the Old Testament. We probably disagree about the concept of biblical inerrancy, and we probably disagree on the proper role of scripture itself. We almost certainly disagree about the importance of natural vs. supernatural causation, and we surely disagree on the meaning and roles of Christian apologetics. Perhaps we further disagree on various questions regarding human nature, and I'm sure we would disagree on several topics related to the Christian life.

Those are significant disagreements. They're important topics, every one. Some have come up on this blog before, and they'll come up again. But this post isn't about disagreement. It's about confronting dishonesty.

I've already written about folk science and dishonesty; what I want to do here is to close what looks like a loophole. It's the "we just disagree" loophole. (Some think that my substitution of 'folk science' for 'recklessly dishonest propaganda' is loophole enough, and I agree.)

At Reasons To Believe (RTB), Hugh Ross and Fuz Rana believe that all of the species that have ever lived have been separately and miraculously created de novo, and thus they reject the notion of common ancestry. They further propose that the purpose of 3+ billion years of life preceding the advent of humans was largely to create fossil fuels and other raw materials needed for human civilization. (No, I'm not joking.) (I said NO, I'm not joking.) Now, those proposals are completely preposterous, and I'm embarrassed for Ross and Rana, and for their organization and its supporters. But while I think that theologians can probably identify outright errors in their scriptural analyses, I nevertheless view our differences as disagreements. It's an outrage to assert with any theological confidence that God made dinosaurs to provide us with petroleum, but it's not necessarily dishonest to say that. Besides, and this is important: the omnipotent God we both worship could have miraculously created species without common ancestry. So, at least on the surface, RTB and I are merely disagreeing.

Ditto for young-earth creationists, who believe that Genesis commits them to a cosmos created less than 10,000 years ago. I'm certain that they're wrong, and our disagreement is profound, but it's a disagreement. Could the scripture be telling a yet-unintelligible history of a very young universe in the Old Testament? Yes, I think it could. We just disagree on whether it does.

What about the ID folks? Again, lots of disagreement, on most of the same questions as above. (Because the ID movement is, of course, a creationist movement.)

The point is this: yes, of course, I disagree with RTB, and with Answers in Genesis, and with the Discovery Institute. But my most serious criticism of these outfits will be questions about their integrity. At least in principle, you can disagree with me on the historicity of Genesis without lying. But you can't claim that "junk DNA" was ignored by scientists for 30 years without disseminating falsehood. You can disagree with me on the importance of supernatural explanation without even a hint of dishonesty. But you can't claim that biologists have never observed "a measurable change within a species" without lying. You can dislike evolutionary theory as much as you want, and refuse to accept it as an explanation, all without engendering any accusation from me. But you can't talk about a "lack of transitional fossils" without revealing yourself to be either ignorant or duplicitous.

Here's a specific example. At RTB, Fuz Rana seems to be reasonable and thoughtful most of the time. His writing on biology is far more accurate than Hugh Ross' (which is scandalously irresponsible), and he seems to be steering clear of many of Ross' most idiotic notions. Sadly, though, Rana engages in some truly inexplicable behavior that looks for all the world like full-blown dishonesty. I've already mentioned Rana's sickeningly inaccurate portrayal of evolutionary theory on the comment-free RTB "blog." I think this indicates that Rana is willing to write things he knows to be false in defense of his peculiar natural theology. But there's more.

When writing about the interesting topic of convergent evolution, Rana confirms that truth-telling is a secondary priority at RTB. Convergent evolution, or convergence, is the phenomenon in which two apparently unrelated lineages of organisms develop very similar characteristics. On the PBS Evolution site, for example, you can see the extraordinary comparison of ant-eating animals from around the world, all of which independently developed long snouts and other adaptations. Such convergent evolution is not uncommon, and evolutionary theory must of course seek to explain it.

Fuz Rana thinks that convergence is a problem for evolutionary theory. He claims that "the evolutionary paradigm cannot accommodate 'repeatable' evolution." Now, no evolutionary biologist would agree with him, but if all he claimed was that he found convergence to be inadequately explained, or that he was certain that evolutionary theory would never explain convergence to his own satisfaction, I might think he's ignorant, but I wouldn't be justified in saying that he's dishonest. I'd just say, "We disagree." But here's what Rana actually wrote, in a 2000 article found on the RTB website:

The evolutionary paradigm cannot accommodate “repeatable” evolution. When evolutionists observe a tree frog ideally suited for its environment, they assert that natural selection––environmental, predatory, and competitive pressures repeatedly operating on random inheritable variations for long periods of time––has led to this relationship. Chance governs the evolutionary process at its most fundamental level. Because of this, it is expected that repeated evolutionary events will result in dramatically different outcomes.

Rana correctly identifies this idea with Stephen Jay Gould and his 1989 book Wonderful Life. In that book, Gould discusses this famous thought experiment: let's replay life's tape. We'll go back to, say, the Precambrian, and run the whole simulation again. What would we see? Rana continues:

Gould’s metaphor of “replaying life’s tape” asserts that if one were to push the rewind button, erase life’s history, and let the tape run again, the results would be completely different. The very essence of the evolutionary process renders evolutionary outcomes as nonreproducible (or nonrepeatable). Therefore, “repeatable” evolution is inconsistent with the mechanism available to bring about biological change.

This paragraph is perniciously dishonest. Rana moves smoothly from Gould's assertion (about the 'tape of life' and historical contingency) to a characterization of "the very essence of the evolutionary process." And in the previous quote, Rana carefully asserts that "it is expected that repeated evolutionary events will result in dramatically different outcomes." The question he's hoping you won't ask him is this: "'Expected'? By whom, Fuz?"

Gould's ideas on contingency, in fact, have always been hotly disputed. Simon Conway Morris, for example, has written entire books repudiating Gould on this subject. (Conway Morris once held to the contingency view, then changed his mind.) And most prominently, Gould's position has always been utterly rejected by strict adaptationists – those who postulate that natural selection is the predominant force acting in evolution. When adaptationists – such as Richard Dawkins or Daniel Dennett – see convergent evolution, they see strong evidence for the power of natural selection. And they wholly contradict Gould on the "tape of life" experiment, expecting that because organisms adapt to their environments in roughly predictable ways, the trajectory of evolution should be roughly predictable. (Go to Laelaps for an excellent account of these controversies.)

Fuz Rana knows this. But when he sat down to construct another rancid piece of folk science, he apparently elected to deliberately mislead his readers about the real status of contingency ideas in evolutionary theory. He constructed a fictional world in which evolutionary theory is somehow committed to thoroughgoing historical contingency, then proceeded to knock over that pitiful strawman by pointing to examples of convergence.

When Fuz Rana claims to doubt common descent, all I can say is that I disagree. But when he claims...

If life is exclusively the result of evolutionary processes, then biologists should expect to see few, if any, cases in which evolution has “repeated” itself.

...then I can say that's a dishonest claim made by a purveyor of folk science who ought to know better. It's not just a disagreement.

Crossing the divide

I recently recommended a very nice new blog by Mike Beidler called The Creation of an Evolutionist. It's subtitled "My journey from young earth creationism to evolutionary creationism," and it's downright fun to read. Mike is engaging and bright. He writes with enthusiasm and joy, so it's hard to imagine that his journey might have been difficult in places. But I'm sure it was.

Others have shared here and elsewhere about the trauma that many experience when considering the abandonment of creationism, an experience I mostly avoided because I never fully embraced creationism, and certainly never adopted a young-earth position. But it's easy for me to understand the emotional environment in which such struggles occur, and that's why I'm glad commenters like David O. have insisted on pointing out that the debunking of crude folk science (like the Reasons To Believe train wreck) is not helpful in the absence of a sound theological framework. Why? Because the obstacles that keep most Christians from embracing evolution and an ancient creation are not merely (or even mostly) academic in nature. They're deeper, much deeper than that: they're emotional, tied to the most basic ways by which Christians define themselves.

In the newest issue of Science, a remarkable News Focus piece tackles this very subject. You need a subscription to access the article online. I'll quote it extensively here, but if you are at all interested in this topic, I urge you to get a copy and read it. I find the article remarkable not just for its coverage of the issue, but for the fact that it is published in Science, one of the most prominent science journals in the world.

The article is "Crossing the divide," written by Jennifer Couzin, and it displays this tagline: "Like others who have rejected creationism and embraced evolution, paleontologist Stephen Godfrey is still recovering from the traumatic journey." Godfrey works at the Calvert Marine Museum in Chesapeake Bay; he was raised in a "fundamentalist" Christian environment but came to a "staunch acceptance of evolution."

Godfrey's "anguished path" began with his study of fossils. 'Anguished' sounds right:

With this shift came rejection from his religious community, estrangement from his parents, and, perhaps most difficult of all, a crisis of faith that endures.

After noting the immense emotional appeal of creationism and the cruel God-or-science choice it typically presents, Couzin observes:

People like Godfrey tend not to advertise their painful transition from creationist to evolutionist, certainly not to scientific peers. When doubts about creationism begin to nag, they have no one to turn to: not Christians in their community, who espouse a literal reading of the Bible and equate rejecting creationism with rejecting God, and not scientists, who often dismiss creationists as ignorant or lunatic.

Gosh, that paragraph about sums up one of my main goals as a Christian biologist: to offer fellow Christians at least one other choice. I hope it saddens you as much it does me, and it oughtn't matter whether you believe or not.

There are some rough spots and simplifications in the piece: Couzin refers to the "fateful apple" in Eden, for example, and seems to suggest that only "biblical literalists" hold that "belief is generally an all-or-nothing proposition." (Though I think I know what she means.) The descriptions of the harrowing journey from YECism to evolutionary creation, however, are raw and jarring. Woven into Godfrey's story are quotes from Denis Lamoureux, Brian Alters, and Christopher Smith, Godfrey's brother-in-law who is a Baptist pastor here in Michigan. But it is Godfrey's "anguished path" that is laid out in disheartening detail. Examination of fossil strata (and footprints therein) finally leads to the "explosion" of his YEC ideas.

Godfrey ran through bitterness, anger, and disappointment about having been deceived for so many years. He sought out creationists and confronted them. Late in graduate school, he and his devout Christian wife, mother-in-law, and mother attended a weekend symposium at a Bible school in New York state, where Godfrey says he angrily stood up at the end of a talk and argued passionately with the speaker.

Well...gulp. That reaction is understandable, even laudable, but I think Dr. Godfrey would agree that it's not the way that things should go for long. Indeed, he identifies at least some times when one ought to let sleeping dogs lie.

But sometimes, former creationists believe, changing minds is not worth the heartache it brings. Godfrey no longer considers evolution worth mentioning to his parents, now 78 and 79 years old, and he asked that they not be contacted for this article. “You can live your life just fine and not know squat about evolution,” he says.

The hardest parts of the story for me to read were those that described his parents' distress, convinced as they are that "their afterlife depends on embracing creationism." But before you conclude that he (or I) would embrace laissez faire, consider his passion here:

Just as he longs for biblical literalists to be more receptive to evolution, Godfrey also wishes that biologists would join the discussion. He was incensed 5 years ago when, participating in an evolution-creationism debate at Bishop’s University, where he once argued against the fossil record, no one from the biology department attended.

Ouch! Not in my house.

According to Couzin, "Godfrey is conflicted about how, and how forcefully, to press his case." He co-wrote a book with his brother-in-law; his father prayed that it would fail to be published at all, and Godfrey seems unconvinced that the book had any impact.

I want to hear voices like Godfrey's, and David Opderbeck's, and others who have traveled this "anguished path." I've explained elsewhere why I don't think laissez faire is always – or even usually – the right approach. But my path was far less anguished, and I never knew the complete isolation that so many of these wise people experienced. (Thank God.) So I'm listening.

Christendom cannot continue to construct and support folk science and desperate dishonesty. It must not continue to employ falsehood in the "defense" of the gospel. But the dismantling of these corrupt and toxic structures has to be done for the sake of the gospel, and not for any other reason.

That's my pledge. Hold me to it.

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.

The real danger in anti-Darwinism is...

Here at Calvin we used to have a super-cool club called SNUH, which sought to discuss and enjoy The Simpsons. I was a guest speaker there twice, but their biggest catch by far was Prof. Tony Campolo, who came to Calvin three years ago, specifically in response to an invitation from the wacky SNUH. I generally like Tony Campolo, mostly because he's good at uncoupling evangelical Christian faith (yay) from American evangelical politics (ick).

But Campolo really stepped in it a week and a half ago, when he put his name on a screed in the Philadelphia Inquirer called "The real danger in Darwin is not evolution, but racism." It's a weird little rant, riddled with red herrings. For example, referring to those (like me) who oppose the teaching of "the intelligent design theory of creation" in public schools, Campolo writes:

Arguing for what they believe is a nonprejudicial science, they contend that children in public schools should be taught Darwin's explanation of how the human race evolved, which they claim is value-free and depends solely on scientific evidence.

Huh? "Value-free?" Who says that? It's a pretty simplistic and unsophisticated view, and while I'm sure quote miners can dig up examples of commentators who say stuff like that, I'm very suspicious of Campolo here. It's not just that he's wrong; his claims about Darwin's racism – and Darwin's alleged influence on (of course) the Nazis – are very nicely dispatched in a piece by Joshua Rosenau at Thoughts from Kansas. Rosenau shows just how wrong Campolo is on the facts, and on the moral implications of common descent. (And readers of the Inquirer did some good work, too.)

But there's something else I don't like about the piece. It seems to be crafted as an argument in a case for "the intelligent design theory of creation." Campolo chides young-earth literalists, but links ID to the "suggestion" that "the evolutionary development of life was not the result of natural selection, as Charles Darwin suggested, but was somehow given purposeful direction and, by implication, was guided by God." That's a pretty soft view of ID, and though Campolo has expressed reservations about the ID program elsewhere, it looks to me like he's bought some of its most intellectually damaging claims.

Anyway, check out the Campolo piece, and don't miss Rosenau's excellent work at Thoughts from Kansas. He cites another hero of mine, Mark Noll. Superb.