24 December 2007

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.

8 comments:

Martin LaBar said...

That's a great second paragraph!

Ben said...

The "appearance of common ancestry". I like it.

Stephen Matheson said...

Martin, glad you liked it, and thanks for the comment.
ArU, I'm really just paraphrasing Dawkins' infamous "ignorant/stupid/insane" quip. Believe it or not, there are some young-earth creationists who (to their credit) take the second door, often while acknowledging a significant amount of common ancestry. Anyway, thanks for the comment.

Anonymous said...

You said: 1) acknowledge the explanatory power of common ancestry and accept its reality; or 2) acknowledge the appearance of common ancestry but deny its reality.

This binary framework is too simplistic. For example, some old earth creationists (3) attribute genetic similarities and pseudogenes to God re-using and modifying existing genetic code and/or (4) add periods of some evolution to (3) in between period of direct intervention by God. As another example, some young earth creationists (5) accept rapid macroevolution after Noah's flood.

While it may be true that none of the above options work, it is not true that the only two options are accepting the evolutionary metanarrative or resorting to "appearance" arguments. Binary thinking usually suggests a lack of imagination.

I'm still looking for a philosophical and theological position here that isn't "folk" philosophy or theology. As I mentioned earlier, I'm not sure it does a great service to those of us in the evangelical community who want to confront this honestly to merely debunk popular creationist organizations. We need serious evangelical theological input on how all this relates to the doctrines of scripture, man, and the fall. Are there theologians at Calvin, for example, who will accept and contextualize your position? Otherwise it seems to me that there's a danger of debunking people's faith along with the folk science.

Stephen Matheson said...

dbecke:

First off, I recently realized I know who you are. I'm glad you're reading the blog and commenting forcefully. So thanks!

Re my claim that one must either "acknowledge the explanatory power of common descent" or "acknowledge the appearance of common ancestry but deny its reality," you assert that...

"...it is not true that the only two options are accepting the evolutionary metanarrative or resorting to "appearance" arguments."

Let me clarify the nature of my contention. I do not mean at all to suggest that anyone ought to advance an "appearance" argument, if by that we mean something akin to the claim of some YECs that the earth is very young but was made to appear old.

What I'm claiming is this: when faced with evidence indicative of common ancestry, a rational and knowledgeable person must acknowledge the excellence of the explanation. At that point, the person might accept the explanation, or acknowledge its apparent success (i.e., the appearance of common ancestry) but seek in its place an alternative explanation. Some creationists for whom I have very high regard do exactly this.

Admitting a little divine genetic tinkering here and "periods of evolution" there is, in my view, rejecting the explanation. That's fine with me: I'll honor any creationist preference (at least because I believe in an omnipotent God) when it comes to the seeking of alternative explanations, but find fault with creationists (of any stripe) who claim that common descent fails as an explanation. It doesn't.

Regarding your search for better theology and philosophy, have you read George Murphy and Robin Collins (among others) in Perspectives on an Evolving Creation? Does that qualify as "serious evangelical theological input"? Yes, some of my Calvin colleagues are working on some of these questions (with me included in one case). I'm not sure the vacuum is as complete as you seem to think.

But more importantly: I'm running a science blog here. I don't think my scant musings on theodicy are fairly characterized as "folk theology," and my post on Romans 5 was a commentary on a sermon by my excellent Christian Reformed pastor, but you would be unwise to seek a lot of "serious evangelical theological input" on Quintessence of Dust. For one thing, science is what I know. And for another, I'm not nearly as concerned about the "contextualization" of my positions as you are. (No disrespect intended here.) To gain a better view of my interest in these questions, consider my favorite quote from B.B. Warfield:

"In a word, the really pressing question with regard to the doctrine of evolution is not, on the one hand, whether it supplies in itself an adequate account of the origin of being and the differentiation of forms, nor, on the other, whether the old faith can live with this new doctrine. [...] The only living question with regard to the doctrine of evolution is whether it is true."

You end with this serious concern: "...it seems to me that there's a danger of debunking people's faith along with the folk science." I'll respond to that in a post. It's too important to hide in the comments.

Thanks again for the tough comments.

Agnosis00 said...

Prof. Matheson,

Great intro and I look forward to the rest of this series!

I also wanted to point out to your readers an article I found very helpful from Todd Wood, one of the creationists you referred to for whom you have 'very high regard.' It talks about the research into human-chimpanzee genetic/genomic comparisons: "The Chimpanzee Genome and the Problem of Biological Similarity."

Stephen Matheson said...

Agnosis--

Yep, that's a great example of neo-creationist work. Todd is, in many instances, a stronger critic of YECism than most, because he knows their literature so well. He's smart, honest, and generous.

Sometimes I try to picture reasons.org or discovery.org if either had been run by people with the kind of intellectual integrity that characterizes Todd Wood. It's not easy to picture, but I think both could advance their aims without folk science. (Uncommon Descent, I think, wouldn't even exist.)

Anonymous said...

Steve said: Admitting a little divine genetic tinkering here and "periods of evolution" there is, in my view, rejecting the explanation.

Why? I'm not suggesting this is the "right" answer, but I don't understand why this rejects common descent. It is in many ways indistiguishable from "standard" theistic evolution -- after all, TE wedded to an orthodox view of Providence is large scale genetic tinkering by God on an ongoing basis.

Steve said: Regarding your search for better theology and philosophy, have you read George Murphy and Robin Collins (among others) in Perspectives on an Evolving Creation?

Yes, along with George's longer book, and along with less "evangelical" stuff such as Ted Peters' work. I consider George a friend (by email). These are good efforts. But.... I get very concered that in this work the theological center often shifts too far. Perhaps part of the question is how we define "evangelical."

But more importantly: I'm running a science blog here.

Yes, and of course I can't presume to define what you want to do with your site.... but isn't it more than that? Isn't it in many ways a "science blog with a slant towards educating Christians about evolution?" If you publicly identify as a Christian who accepts evolution, don't you have some broader integrative responsibility?

I appreciate the Warfield quote,(I need to read it, but I also have Mark Noll's book on Warfield and evolution) but of course that quote is somewhat question begging. Whether it's "true" begs the question of how we justify knowledge claims, which begs the question of the relation of the book of scripture to the book of nature. And those questions are the heart of the concern of those of us evangelicals who want to engage this seriously and offer some kind of leadership to the Church.

It would be wonderful if you could share, or maybe even have some guest posts, on the theological work you mentioned at Calvin.

Glad you figured out who "dbecke" is BTW. I hope you don't take my probing as antagonistic and that we can continue a productive dialogue.