Tuesday, October 18, 2011

Junk & Jonathan: Part 13—Chapter 10

This is part 13 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the links in Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

The title of Chapter 10 is "From Junk DNA to a New Understanding of the Genome." It's a very misleading title since the bulk of the chapter is an attempt to refute the arguments of various evolutionary biologists.
In this chapter, we return to the arguments based on junk DNA that we encountered in Chapter 2. Richard Dawkins, Kenneth Miller, Michael Shermer, Francis Collins, Philip Kitcher, Jerry Coyne and John Avise all claimed that most of our DNA is nonfunctional junk, and that this provides evidence for Darwinian evolution and against intelligent design (ID).
Wells' statement is very misleading. He's confusing the argument about conserved pseudogenes with a claim that most of our genome is junk. Several of these authors have pointed out that the presence of similar pseudogenes at the same location in the genomes of different species (e.g. humans and chimps) is powerful evidence of descent from a common ancestor. They also point out that the IDiots have a hard time explaining such observations [Creationist Logic]. (In fact, no IDiot has ever offered a satisfactory explanation.)

Speaking for Science?

Richard Dawkins is not a vocal proponent of massive amounts of junk DNA in our genome. As a matter of fact, he's most often thought of as a skeptic on this issue. He rarely talks about junk DNA in any of his books. It's not very nice of Jonathan Wells to proclaim that Dawkins is a proponent of massive amounts of junk DNA in our genome and it's posiviely criminal to suggest that he (Dawkins) would use this as evidence in favor of adaptation (Darwinism).

That doesn't stop Wells from saying ...
Dawkins studied bird behavior in the 1960s, but since then he has spent his career writing popular books and articles defending Darwinism and preaching atheism. Obviously, he is out of touch with recent genomics research. Yet from 1995 to 2008 he was Professor for the Public Understanding of Science at Oxford. As such, he should have made at least some attempt to familiarize himself with the evidence. Yet even now, he continues to defend the myth.
In addition to the seven men listed in the opening paragraph of this chapter, Wells adds Douglas Futuyma as a defender of the idea that "... pseudogenes are nonfunctional junk, providing evidence for Darwinism and against ID." This is a lie. Futuyma would never, ever, say that pseudogenes provide evidence of natural selection (Darwinism).

John Avise is a strong proponent of the idea that most of our genome is junk [Shoddy But Not "Junk"?]. I don't know if the other men in the list feel as strongly about this but I do know that most of them would never use the existence of junk DNA as evidence for evolution by natural selection (Darwinism.)

Wells, on the other hand, is sure he's right about this.
Coyne and Avise are professors of genetics at major universities, so they cannot claim ignorance of the genomic evidence without thereby admitting negligence or incompetence. In fact, one of Coyne's colleagues at the University of Chicago is James Shapiro, co-author of the 2005 article cited in Chapter 6 that listed over 80 known functions for non-protein-coding repetitive DNA. [The other author is Richard (von) Sternberg ... LAM] But if Coyne and Avise were not ignorant of the evidence, then they misrepresented it—and they continue to do so. Like Dawkins, Shermer and Kitcher they have forfeited any claim they might have to be speaking for science.
I didn't know whether to laugh, cry, or get angry when I first read this paragraph. Even now, after just typing it, I can't tell you which emotion is the strongest. What I can tell you is that this paragraph alone is enough to discredit Wells as a serious contributor to the debate over junk DNA. He's an IDiot.


& Junk DNA
How Darwinists Might Respond

Wells attempts to dismiss his opponents on the grounds that they don't know as much as he does about modern genomics. However, he is aware of the fact that some of us still might not agree with his characterization of junk DNA as a "myth." How does he think that people like me will respond to his book?
Now, in response to this book, some Darwinists might fall back on a tactic they used a few years ago—one that is based on misrepresentation and intimidation.
Wells is referring to something that happened nine years ago. In 2002 the Discovery Institute published a list of articles that questioned "neo-Darwinism." The National Center for Science Education (NCSE) then contacted the authors of those articles to see if they thought their work supported intelligent design creationism. Guess what? The authors denied that they were IDiots!
It's possible that the NCSE or others might resort to the same deceptive and intimidating tactic again in response to this book. So I want to make myself very clear: I am not claiming that the authors of articles I cite in this book on the functions of non-protein-coding DNA are pro-ID or anti-evolution. I argue only that their work provides evidence against the notion that most of our DNA is "junk."
Good for you, Jonathan. You deny that most of them are IDiots like you. Now, would you mind if we contacted them to see whether they agree with you that junk DNA is a myth?

Theology Masquerading as Science

Wells is very concerned about the criticisms leveled at Intelligent Design Creationism.
... there is another problem with the arguments of Dawkins, Miller, Futuyma, Shermer, Collins, Kitcher, Coyne, and Avise. In the books cited above, all eight of these authors rely on speculations about why a creator or designer would or would not have done certain things.
Boo hoo. You can't have it both ways, Jonathan. According to the IDiots, Intelligent Design Creationism predicts that junk DNA doesn't exist. Your own camp speculates that God the intelligent designer would never design a genome full of junk. That's why you wrote this book, IDiot.

Scientists point out that junk DNA exists, thereby refuting your speculations about the motives of God the intelligent designer. Deal with it.

The Logic of the Argument

According to Wells, the eight authors use the following argument.
  • If most human DNA is junk, then Darwinism is true and ID is false;
  • Most human DNA is junk;
  • Therefore Darwinism is true and ID is false.
This is nonsense. Wells is misleading his readers by pretending that anyone uses a silly argument of this form. Maybe we should contact those eight authors and ask them if Wells is correct? Or would that be unfair to Jonathan Wells?

This section of the chapter contains a statement that is widely quoted in the Intelligent Design Creationism world. It "explains" the purpose of the book.
Indeed, holding out for the nonfunctionality of large amounts or our DNA hardly seems like a promising strategy, given the rate at which new functions are being reported in the scientific literature. Junk DNA advocates have to retreat every time a new function is found. In effect, they are relying on an argument from ignorance—a sort of "Darwin of the Gaps"—that becomes less tenable with each new scientific discovery.
Wells and the other IDiots have been widely criticized for only explaining the functions of a small proportion of the genome—about 1% in each species.1 After the book was published they latched on to the idea that it's the "trend" that counts and not just the total amount of new functional DNA that has been discovered. As I've stated elsewhere, this is a very long-term trend (if it exists). At the rate of 1% every 20 years, we'll have to wait 2000 years before a function is found for all of the putative junk DNA.

Wells is also wrong about the argument from ignorance—or should I say he's wrong to suggest that it's the evolution side that's making such an argument. (We take it for granted that IDiots argue from ignorance.) There's plenty of positive evidence that much of our genome is junk. I'm sure that Wells meant to tell his readers about genetic load, the real data behind the C-value paradox, the fact that many humans carry deletions of junk DNA, and why we know that most transposon sequences are defective. I'm sure he meant to explain why junk DNA is perfectly compatible with non-Darwinian evolution. His intentions were honorable. He just ran out of time. That's got to be the answer, right?

Can the Genome Support a Design Inference?

No it can't, because most of it is junk. Wells disagrees. He quotes an argument made by Richard (von) Sternberg. You might recall that Sternberg collaborates with James Shapiro at the University of Chicago and Jerry Coyne was criticized for not paying attention to what they had to say about genomes.

I refer to Sternberg's argument as an argument from ignorance, not because it stems from lack of knowledge (although it does), but because it's made by people who are ignorant.
Sternberg argues that intelligent design suggests the following hypothesis: The organization of DNA strings along the genome is optimized for the establishment of multidimensional codes at all scales, and each species has a unique and elaborately ordered arrangement of chromosome regions that maximizes the information the genome can carry. The hypothesis is scientific, because it entails two predictions that can be empirically falsified: The first is that the genome of one species cannot be transformed into the genome of another species by random re-arrangements, since this would compromise the formatting, indexing, and punctuation of DNA files. The second is that any observed chromosome changes that result in normal fitness will be those that maintain genomic optimization.
Is this a prediction of Intelligent Design Creationism (i.e. design inference)? If so, it appears to be based on the assumption that there is no significant amount of junk DNA in our genomes. Many other IDiots have declared that this assumption (prediction) is a requirement of IDC. All we have to do now is find out how much junk DNA will falsify Intelligent Design Creationism and we can put an end to this nonsense once and for all.

Where Do We Go from Here?
Scientists make progress by testing hypotheses against the evidence. But when scientists ignore the evidence and cling to a hypothesis for philosophical or theological reasons, the hypothesis becomes a myth. Junk DNA is such a myth, and it's time to leave it behind—along with other discarded myths from the past.

As recent discoveries have demonstrated, we are just beginning to unravel the mysteries of the genome. Indeed, the same can be said of living organisms in general. But assuming that any feature of an organism has no function discourages further investigation. In this respect, the myth of junk DNA has been a science-stopper.

Not any more. For scientists willing to follow the evidence wherever it leads, these are exciting times.
Speaking of myths, the idea that junk DNA has been a science stopper is totally ridiculous. Ryan Gregory has written a series of posts debunking that myth [Quotes of interest]. Of course Wells doesn't mention any of this to his readers because that would be "evidence" against his claim and IDiots are very good at ignoring evidence.

1. They talk about other components such as regulatory sequences, centromeres, genes for RNAs, etc. as though these are also "new scientific discoveries" that refute junk DNA. Those don't count because they were never included in putative junk DNA to begin with. Wells "forgets" to mention this to his readers.


  1. On occasion when I've tried to discuss the topic with commenters over at Uncommon Descent, I've had the same response on junk DNA: they don't believe that ID makes any predictions one way or the other about it.

    This doesn't stop the very same commenters from paradoxically arguing vehemently that junk DNA doesn't exist all day and night, but I don't know of anyone formally making the claim that ID predicts no junk DNA.

    People like O'Leary and Wells isinuate that junk DNA is a prediction of "Darwinism", by which they mean evolutionary theory, and of course if the designer they had in mind just happened by chance to be God then the presence of junk is probably hard to explain, but I've still never seen anyone make a formal prediction about ID and junk DNA. I guess it's all part of their paradigm of never making predictions that can be tested so they can never be wrong.

  2. Wells:

    I argue only that their work provides evidence against the notion that most of our DNA is "junk."

    Nnnnggh .. it's that "most" thing again.

    Set a more rigorous bound on "most", and the best evidence against that notion will be the function that transgresses it. Of course, as it is approached, we can start to get a bit more excited. But while, on the basis of current knowledge, you are still deep in the region of "most", even "a fair chunk" can seem a long way off.

    No-one is more excited than the scientist when a new function is found, whatever their position on junk. They're always on the lookout for new stuff.

  3. There is one thing I don't understand about this. Michael Shermer has a PhD in the history of science and is not an expert on genetics or evolution. Why is he cited again and again along with Dawkins, Cyone, et al.? Surely it can.t be merely because he opposes ID? They might as well drag in Hitchens.