Intelligent Design Creationists Attempt to (re)Define Junk DNA

Paul McBride is causing quite a stir among the creationists. His review of Science & Human Origins was so devastating that they couldn't ignore it.

Jonathan McLatchie (Jonathan M) is the latest creationist to attempt a defense of the home team. He concentrates on defending the Intelligent Design Creationist position on junk DNA [A Response to Paul McBride on Junk DNA].

On this topic (junk DNA), the IDiots make a lot of errors. One of them is to deliberately conflate "junk DNA" and "noncoding DNA" so that when they come up with evidence for function in noncoding DNA they can tout this as evidence against junk DNA. This error is so pervasive in the IDiot literature that Paul McBride even predicted that Casey Luskin would make this mistake in the book.

Casey Luskin's latest take on junk DNA—is he lying or is he stupid?

Some of us have been trying to educate the IDiots for over twenty years. It can be very, very, frustrating.

The issue of junk DNA is a case in point. We've been trying to explain the facts to people like Casey Luskin. I know he's listening because he comments on Sandwalk from time to time. Surely it can't be that hard? All they have to do is acknowledge that "Darwinians" are opposed to junk DNA because they think that natural selection is very powerful and would have selected against junk DNA. All we're asking is that they refer to "evolutionary biologists" when they talk about junk DNA proponents.

We've also pointed out, ad nauseam, that no knowledgeable scientist ever said that all noncoding DNA was junk. We just want the IDiots to admit that there were some smart scientists who knew about functional noncoding DNA—like the genes for ribosomal RNAs, origins of replication, and centromeres.

Theme: Genomes & Junk DNA

Junk in Your Genome

Transposable Elements: (44% junk)

      DNA transposons:
         active (functional): <0.1%
         defective (nonfunctional): 3%
      retrotransposons:
         active (functional): <0.1%
         defective transposons
            (full-length, nonfunctional): 8%
            L1 LINES (fragments, nonfunctional): 16%
            other LINES: 4%
            SINES (small pseudogene fragments): 13%
            co-opted transposons/fragments: <0.1% ^a

^aCo-opted transposons and transposon fragments are those that have secondarily acquired a new function.

Viruses (9% junk)

      DNA viruses
         active (functional): <0.1%
         defective DNA viruses: ~1%
      RNA viruses
         active (functional): <0.1%
         defective (nonfunctional): 8%
         co-opted RNA viruses: <0.1% ^b

^bCo-opted RNA viruses are defective integrated virus genomes that have secondarily acquired a new function.

Pseudogenes (1.2% junk)
      (from protein-encoding genes): 1.2% junk
      co-opted pseudogenes: <0.1% ^c

^cCo-opted pseudogenes are formerly defective pseudogenes those that have secondarily acquired a new function.

Ribosomal RNA genes:
      essential 0.22%
      junk 0.19%

Other RNA encoding genes
      tRNA genes: <0.1% (essential)
      known small RNA genes: <0.1% (essential)
      putative regulatory RNAs: ~2% (essential) Protein-encoding genes: (9.6% junk)
      transcribed region:  
            essential 1.8%  
            intron junk (not included above) 9.6% ^d

^dIntrons sequences account for about 30% of the genome. Most of these sequences qualify as junk but they are littered with defective transposable elements that are already included in the calculation of junk DNA.

Regulatory sequences:
      essential 0.6%

Origins of DNA replication
      <0.1% (essential) Scaffold attachment regions (SARS)
      <0.1% (essential) Highly Repetitive DNA (1% junk)
      α-satellite DNA (centromeres)
            essential 2.0%
            non-essential 1.0%%
      telomeres
            essential (less than 1000 kb, insignificant)

Intergenic DNA (not included above)
      conserved 2% (essential)
      non-conserved 26.3% (unknown but probably junk)

Total Essential/Functional (so far) = 8.7%
Total Junk (so far) = 65%
Unknown (probably mostly junk) = 26.3%

For references and further information click on the "Genomes & Junk DNA" link in the box

LAST UPDATE: May 10, 2011 (fixed totals, and ribosomal RNA calculations)

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November 11, 2006
Sea Urchin Genome Sequenced

The sea urchin genome is 814,000 kb or about 1/4 the size of a typical mammalian genome. Like mammalian genomes, the sea urchin genome contains a lot of junk DNA, especially repetitive DNA. The preliminary count of the number of genes is 23,300. This is about the same number that we have in our genomes. Only about 10,000 of these genes have been annotated by the sea urchin sequencing team.

See the IDiots Gloat over Jonathan Wells

This is part of my discussion about The Myth of Junk DNA by Jonathan Wells. I still haven't read the book—it won't be released in Canada until May 31st.

Over on Evolution News & Views (sic) David Klinghoffer is already counting his chickens [Junk DNA and the Darwinist Response so Far].

Over the weekend, Jonathan Wells's The Myth of Junk DNA broke into the top five on Amazon's list of books dealing with genetics -- a list normally dominated at its pinnacle by various editions of Richard Dawkins' The Selfish Gene. Not bad, Jonathan.

Not bad indeed, except I can't tell if it's true. When I check the top selling recently published books I don't see The Myth of Junk DNA in the top five. Never mind, I'm sure there will be many skeptics like me who will buy the book just for a good laugh.

UPDATE: The latest information shows that Wells' book is ranked 23rd under "Genetics." I'm sure the IDiots just made a simple arithmetic error when they said it had broken into the top five.

The juxtaposition with Dawkins' Selfish Gene is appropriate, notwithstanding the demurrals of biochemist Larry Moran et al. Dawkins and other Darwinists, such as Jerry Coyne, have indeed posited that neo-Darwinian theory predicts that swaths of the genome will turn out to be functionless junk. The Junk DNA argument has been a pillar of the Darwin Lobby's efforts to seduce public opinion and influence public policy. Professor Moran wants to imagine that Dawkins never held that neo-Darwinism predicts junk DNA. But that's not how other Darwinists see it. (Compare, for example, Dennett's Darwin's Dangerous Idea, page 316.)

The IDiots have a bit of a problem. In order to make this book look important they have to first establish that the concept of abundant junk DNA in our genome was a "pillar" of support for evolution. That's hard to do when their understanding of evolution is so flawed that they don't see the difference between "Darwinism" and evolution by random genetic drift.

Their claim that evolutionary theory PREDICTED the presence of huge amounts of junk DNA in our genome is just plain false. They been told this but they keep repeating their error. There's a word for that kind of behavior.

It's easy to see how they got confused. It's because they're IDiots. It's partly because they don't understand that an argument for inheritance of a few pseudogenes is not the same as an argument that more than 50% of our genome is junk. There are plenty of scientists who will use the pseudogene argument to challenge Intelligent Design Creationism but who don't believe that MOST of our genome is junk.

It's also partly because the IDiots don't know the difference between selfish DNA and junk. Here's what Daniel Dennett says on page 316 of Darwin's Dangerous Idea.

The presence of functionless DNA in the genome is no longer regarded as a puzzle. Dawkins (1976) selfish-gene theory predicts it, and elaborations on the idea of "selfish DNA" were simultaneously developed by Doolittle and Sapeinza (1980) and Orgel and Crick (1980) (see Dawkins 1982, ch. 9, for the details).

Selfish DNA is not junk DNA. The classic examples of selfish DNA are active transposons and integrated viruses. These bits of DNA have a function—even if it's only to propagate themselves. As you can see from my summary [What's in Your Genome?]. I don't count them as junk.

It's remarkable that Klinghoffer quotes Chapter 9 of The Extended Phenotype (1982) since Dawkins take pains to point out that much of the junk DNA in our genome could have a function. This is exactly the sort of skepticism one would expect from a Darwinist.

This does not mean, however, that the so-called junk DNA is not subject to natural selection. Various 'functions' for it have been proposed, where 'function' means adaptive benefit to the organism.

He goes on to describe several of the proposals that are common arguments against junk DNA. If the DNA has a function and it's adaptive, then it is not junk. Selfish DNA is not junk.

Let's be very clear about one thing. The scientific dispute is not over the existence of junk DNA. That's well established. The dispute is over how much of our genome is junk (DNA with no function). In order to refute the idea that MOST of our genome is junk, you have to show that most of it has a function of some sort. I'm looking forward to Jonathan Wells' book where he is going to prove to us that >50% of our genome has a function. (Not holding my breath!)

So far, with none of them having actually read the book (though P.Z. Myers threatens to do so), the Darwin apologists' response to The Myth of Junk DNA has followed along four lines of defense.

1) The usual insults. In his blog Larry Moran of the Department of Biochemistry at the University of Toronto, a grown man and from the looks of him not a young one either, repetitively derides Jonathan as an "IDiot." (How embarrassing for this mature gentleman, you might think. Can you imagine Jonathan Wells or anyone else prominent in the ID community replying in kind, designating Professor Moran as "Larry Moron" or similar? The question is self-answering and tells you a lot about how desperation kindles anger among these people.)

You know, there's one sure way to prove you're not an idiot. The IDiots have been trying for over twenty years to show that they understand science. I'll gladly stop calling them idiots as soon as they deserve it.

Speaking of insults. There's one sure way to ensure that you aren't going to be insulted and that's to stop calling evolutionary biologists "Darwinists" and stop saying that they don't understand their own discipline. I find that extremely insulting and I'm not going to refrain from responding in kind.

I don't know what Jonathan Wells is going to say in his latest book but here's a few examples of insults in Icons of Evolution.

There is a pattern here, and it demands an explanation. Instead of continually testing their theory against the evidence, as scientists are supposed to do, some Darwinists consistently ignore, explain away, or misrepresent the biological facts in order to promote their theory. One isolate example of such behavior might be due simply to overzealousness. Maybe even two. But ten? Year after year? (p. 230)

Fraud is a dirty word, and it should not be used lightly. In the cases described in this book, dogmatic promoters of Darwinism did not see themselves as deceivers. Yet they seriously distorted the evidence—often knowingly. If this is fraud when a stock promoter does it, what is it when a scientist does it? (p. 234)

If dogmatic promoters of Darwinian evolution were merely distorting the truth, that would be bad enough. But they haven't stopped there. They now dominate the biological sciences in the English-speaking world, and use their position of dominance to censor dissenting viewpoints. (p. 235)

The truth is that a surprising number of biologists quietly doubt or reject some of the grander claims of Darwinian evolution. But—at least in America—the must keep their mouths shut or risk condemnation, marginalization, and eventual expulsion from the scientific community. This happens infrequently, but often enough to remind everyone that the risk is real. (p. 239)

Klinghoffer continues with his four lines of defense that we "Darwinists" apparently use to defend the existence of abundant junk DNA (>50%) in our genome.

2) Denying that junk DNA ever figured preeminently in the Darwinist's quiver of arguments against design. Moran, for example, asserts, "There was never a time when knowledgeable molecular biologists equated 'junk' DNA and 'noncoding' DNA." Huh, that's strange. I'm not aware of anyone who has scientifically polled the community of professional biologists on the subject. But I do know that in the struggle for public opinion over the question of Darwin versus Design, junk DNA has again and again been employed, by all the most eminent protagonists on the Darwinian side, as a bludgeoning weapon against intelligent design. Never mind The Selfish Gene, in his most recent book, The Greatest Show on Earth (2009), Dawkins observed that "the greater part...of the genome might as well not be there, for all the difference it makes," and that this fact is "useful for...embarrassing creationists."

Similarly, in Why Evolution Is True (2009), Jerry Coyne offers it, again, as a "prediction" of neo-Darwinian theory that we'll find the genome littered with useless "vestigial genes."

I said that knowledgeable scientists never said that all non-coding DNA is junk. Klinghoffer says, blah, blah, blah, not even addressing my statement.

You can't make this stuff up. At every single opportunity the IDiots demonstrate that they deserve the title.

3) When not denying that junk DNA is a prime, staple argument for Darwin apologists, Professor Moran wants to have it the opposite way. In the same series of blog posts attacking "the IDiot" Jonathan Wells, Moran maintains his own belief that the genome is indeed overwhelmingly useless junk. "Some (I am one)," he writes, "still think that as much as 90 percent could be junk." He insists that "it's not sufficient to show that a few bits of repetitive DNA have gained a function in some species."

Dr. Moran's problem is that he has neither read Jonathan's book nor, it seems, followed the cascade of evidence from the scientific publications. It's a heck of a lot more than just "a few bits of repetitive DNA" that have been shown to be functional. In a brief (and enviably readable and accessible) 115-page book, Jonathan Wells offers over 600 references to recent peer-reviewed literature.

Twenty-five thousand studies further down the road from where we are now, no one knows how much of the genome will turn out to be truly functionless and therefore genuinely worthy of the appellation "junk." But for Darwinists, the speedily mounting evidence against junk DNA is an ominous portent. As Casey Luskin and others have put it, it's the trend that stands out prominently here, on which the likes of Larry Moran have so far been in denial.

Theme

Genomes
& Junk DNAI've tried and tried to get the IDiots to have a serious, scientific, discussion about the evidence for and against abundant junk DNA in our genome. Some of them have tried but their arguments soon degenerate into insults about my lack of knowledge of the scientific literature. This is in spite of the fact that I have dozens of postings on the subject over the past few years and nobody has ever shown that I've been ignorant of the science behind the controversy. We may disagree about the interpretation but that's not what I'm being accused of here.

As soon as I read the book I'll post a bunch of articles pointing out why it's wrong. That will give the IDiots, like Jonathan Wells, a chance to debate the points I make and show that he is right and I am wrong. I'm looking forward to it.

4) Finally, in my own small contribution to this debate, I made a facetious comment here about how the identification of Osama bin Laden's corpse by DNA fingerprinting, using his "junk DNA" as the media habitually referred to it, provided a welcome news hook for the publication of Jonathan's book. This provoked braying responses from the Darwin Lobby. For example, our journalist friend Lauri Lebo, challenged as ever in her reading-comprehension skills, somehow understood that I was saying the usefulness of non-coding DNA for this forensic purpose proved it isn't junk.

P.Z. Myers tried to show that the usefulness of non-coding DNA for genetic fingerprinting is another demonstration that the stuff really is junk, being "subject to random changes at a higher rate than coding DNA, because it is not subject to functional constraints."

Every now and them some IDiots get something right—even if it's just by accident. One example is when Klinghoffer describes his posting as "my own small contribution."

But whether "junk DNA" is functional is exactly the question at issue, isn't it? The fact that our DNA is pervasively transcribed, as Jonathan Wells points out in Chapter 3 of his book, itself suggests pervasive functionality. As has become clear, too, DNA may serve in various functions even if it does not code for functional RNA.

It will be fun to read how Wells deals with the issue of spurious transcription based on his understanding of how RNA polymerase and transcriptional activators bind to DNA. I'm certainly looking forward to learning about the reliability of those genome studies on transcription and I'm sure Wells is going to discuss conflicting data in the scientific literature. After all, Wells has a Ph.D. in molecular biology so he must know about the real scientific controversy, right?

As for functions that don't require transcription, I highly recommend my short summary of these in What's in Your Genome. We've known about them for decades but apparently the IDiots think this is a new discovery.

So far, the Darwinist response fails to appreciate that Jonathan is in the act of very seriously blunting a Darwinian icon. What, in this context, is an icon? It's a mainstay in the public debate about Darwinian evolution that turns out, on inspection, to be based not on solid science but on puffery, illusion or deception.

This is another icon that, as Jonathan shows, was in the process of being blunted by biologists who are not ID advocates, well before Dr. Wells gathered the evidence together so concisely and conveniently in these pages.

Whatever. Wells' first book, Icons of Evolution was full of lies and I suspect this one will be too. Only one of the ten so-called icons was "blunted" by Wells and that one was the Haeckel drawings. Even then, Wells seriously distorted the significance of those fake drawings by claiming that there was now no evidence of similarities in the development of all mammals.

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Nessa Carey doesn't understand junk DNA

Nessa Carey is a science writer with a Ph.D. in virology and she is a former Senior Lecturer in Molecular Biology at Imperial College, London.

She has written a book on junk DNA but it's not available yet (in Canada). Judging by her background, she should be able to sort through the controversy and make a valuable contribution to informing the public but, as we've already noted Nessa Carey and New Scientist don't understand the junk DNA debate.

Casey Luskin has a copy of the book so he wrote a blog post on Evolution News & Views. He's thrilled to find someone else who dismisses junk DNA and "confirms" the predictions of Intelligent Design Creationism. I hope Nessa Carey is happy that the IDiots are pleased with her book [New Book on "Junk DNA" Surveys the Functions of Non-Coding DNA].

Note to David Klinghoffer, When You find Yourself in a Hole, Stop Digging

Some of you might recall the recent Chromosome 2 kerfuffle. It started when Carl Zimmer asked David Klinghoffer a simple question. Zimmer asked him to describe the evidence to support his claim that the fusion site didn't look like it should if two primitive ape chromosomes had fused to produce human chromosome 2.

Rather than simply answer the question, the IDiots circled the wagons then went into attack mode. Eventually, after a lot of pressure, they got around to answering the question; apparently there is no evidence to support their claim [And Finally the Hounding Duck Can Rest].

Of course by then they were so deep in their hole that the sun don't shine.

Why do Intelligent Design Creationists lie about junk DNA?

A recent post on Evolution News (sic) promotes a a new podcast: Casey Luskin on Junk DNA’s “Kuhnian Paradigm Shift”. You can listen to the podcast here but most Sandwalk readers won't bother because they've heard it all before. [see Paradigm shifting.]

Luskin repeats the now familiar refrain of claiming that scientists used to think that all non-coding DNA was junk. Then he goes on to list recent discoveries showing that some of this non-coding DNA is functional. The truth is that no knowledgeable scientist ever claimed that all non-coding DNA was junk. The original idea of junk DNA was based on evidence that only 10% of the genome is functional and these scientists knew that coding regions occupied only a few percent. Thus, right from the beginning, the experts on genome evolution knew about all sorts of functional non-coding DNA such as regulatory sequences, non-coding genes, and other things.

Pwned by lawyers (not)

A few days ago I mentioned a post by Barry Arrington where he said, "You Should Know the Basics of a Theory Before You Attack It. I pointed out the irony in my post.

Barry Arringotn took exception and challenged me in: Larry Moran's Irony Meter.

OK, Larry. I assume you mean to say that I do not understand the basics of Darwinism. I challenge you, therefore, to demonstrate your claim.

This was the kind of challenge that's like shooting fish in a barrel but I thought I'd do it anyway in case it could serve as a teaching moment. Boy, was I wrong! Turns out that ID proponents are unteachable.

I decided to concentrate on Arrington's published statements about junk DNA where he said ...

ENCODE, Junk DNA, and Intelligent Design Creationism

andyjones has replied to my earlier posting on ENCODE and junk DNA. You can read his response at: (More) Function, the evolution-free gospel of ENCODE. Here's part of what he says ...

Larry Moran has sort-of replied to my previous blogpost but disappoints with only one substantive point. And even that one point is wrong: ID is not committed to the idea that individual genomes be well-designed; that is just an expectation some of us derive based on belief in a designer which is established on other evidence. ID would still be true if only globular proteins were designed (lookup Axe), or even if only the flagellum was designed (lookup Behe), or even if only the first life form was designed (lookup Meyer – and please read their actual work, not cheap reviews, because reviewers often dont pick up on the salient points – more below). I just say this lest readers get the impression that this is ID’s strongest point, or in any sense a weak point. It is neither.

It's true that there are some IDiots who are distancing themselves from a commitment to junk DNA. There are probably some who claim that they could live with the fact that 90% of our DNA is junk.

But let's not forget that Jonathan Wells is a prominent IDiot and he wrote a book on The Myth of Junk DNA. It sounded very much like Intelligent Design Creationism is staking its reputation on finding function for most of our genome.

Casey Luskin on Junk DNA and Junk RNA

 
Intelligent Design Creationists can't abide junk DNA. Its very existence refutes the idea that living things are designed by some intelligent being. This is why the IDiots go out of their way to make up stories "disproving" junk DNA.

The latest attempt is by Casey Luskin [Nature Paper Shows "Junk-RNA" Going the Same Direction as "Junk-DNA"]. Having failed to explain why half of the human genome is composed of defective transposons, he now pins his hope on the idea that most of the genome is transcribed. Luskin seems particularly upset by my statement that most of these transcripts are junk [Junk RNA].

Luskin thinks that a recent paper in Nature supports his view that a large fraction of the genome isn't junk. The paper by Guttman et al. (2009) says no such thing. Here's the important part ...

Genomic projects over the past decade have used shotgun sequencing and microarray hybridization1, 2, 3, 4 to obtain evidence for many thousands of additional non-coding transcripts in mammals. Although the number of transcripts has grown, so too have the doubts as to whether most are biologically functional5, 6, 13. The main concern was raised by the observation that most of the intergenic transcripts show little to no evolutionary conservation5, 13. Strictly speaking, the absence of evolutionary conservation cannot prove the absence of function. But, the markedly low rate of conservation seen in the current catalogues of large non-coding transcripts (<5% of cases) is unprecedented and would require that each mammalian clade evolves its own distinct repertoire of non-coding transcripts. Instead, the data suggest that the current catalogues may consist largely of transcriptional noise, with a minority of bona fide functional lincRNAs hidden amid this background. Thus, to expand our understanding of functional lincRNAs, we are faced with two important challenges: (1) identifying lincRNAs that are most likely to be functional; and (2) inferring putative functions for these lincRNAs that can be tested in hypothesis-driven experiments.

In other words, most of the transcripts are probably transcriptional noise, or junk, just as I said. This is the consensus opinion among informed¹ molecular biologists.

Guttman et al. wanted to identify the small subset that might be functional. They identified 1,675 transcripts that show evidence of conservation. The average transcript has six exons averaging 250 bp. Thus, each transcript has about 1500 bp. of conserved exon sequence.

Even if every single one of these lincRNAs have a biological function they will only account for 1675 × 1500 = 2.5 million bp. This represents less than 0.1% of the genome. Casey Luskin ain't gonna disprove junk DNA using this paper.

Luskin ends his article with ...

As an ID proponent, I'm still waiting for Darwinists to let go of their precious "junk" arguments for blind evolution and common descent and learn the lesson that you can't assume that if we don't yet see function for a biomolecule, then it's probably just "junk."

This is a point of view that creationists share with many scientists who haven't studied the subject. They assume that the only reason for labeling most of our DNA junk is because we don't know what it does. That's just not true. There's plenty of good evidence that most of our genome can't be functional. We know a lot about the part that consists of transposons and defective transposons, for example [Junk in Your Genome: SINES and Junk in your Genome: LINEs]. That's 44% of our genome.

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1. I added the qualifier "informed" after a commenter pointed out that most molecular biologists probably don't know enough about the topic to have an opinion. Thus, according to this commenter, the consensus opinion would be "I don't know."

Creationist Logic

Help me out, dear readers. I can't for the life of me figure out the logic behind the latest posting at Uncommon Descent: If you make a prediction and it doesn’t happen ….

I'm serious. Although I often make fun of the IDiots, I usually try hard to understand the points they are trying to make so I can expose them as nonsensical. But this one has me completely stumped. On the surface the author seems to be saying that "Darwinism" made a prediction "based on core principles" that wasn't fulfilled. This is bad for "Darwinism."

What is that prediction?

The author ("News") starts with a quotation from The Myth of Junk DNA.

In 2010, University of California Distinguished Professor of Ecology & Evolutionary Biology John C. Avise published a book titled Inside the Human Genome: A Case for Non-Intelligent Design, in which he wrote that "noncoding repetitive sequences–'junk DNA'–comprise the vast bulk (at least 50%, and probably much more) of the human genome." Avise argued that pseudogenes, in particular, are evidence against intelligent design. For example, "pseudogenes hardly seem like genomic features that would be designed by a wise engineer. Most of them lie scattered along the chromosomes like useless molecular cadavers." To be sure, "several instances are known or suspected in which a pseudogene formerly assumed to be genomic ‘ junk’ was later deemed to have a functional role in cells. But such cases are almost certainly exceptions rather than the rule. And in any event, such examples hardly provide solid evidence for intelligent design; instead, they seem to point toward the kind of idiosyncratic tinkering for which nonsentient evolutionary processes are notorious."

Jonathan Wells, The Myth of Junk DNA (Seattle: Discovery Institute Press, 2011), pp. 26-27

This is a pretty accurate representation of what John Avise actually says except that it juxtaposes two separate facts. It's true that repetitive DNA sequences—mostly defective transposons—make up about half our genome. Then there's pseudogenes. They are found in the other half and they make up about 1% of the human genome.

Avise, and many others, point out that the presence of pseudogenes is inconsistent with good design and therefore poses a problem for Intelligent Design Creationism.¹ I note that the IDiots have consistently refused to address this problem. Instead, they try and convince their followers that pseudogenes don't exist.

Here's what Avise says in his book Inside the Human Genome: A Case for Non-intelligent design (p. 115). You can see that Wells accurately represented the actual argument that he (Avise) was making.

At face value, pseudogenes hardly seem like genomic features that would be designed by a wise engineer. Most of them lie scattered among the chromosome like useless molecular cadavers. This sentiment does not preclude the possibility that an occasional pseudogene is resuscitated such that it contributes positively to cellular operations, several instances are known or suspected in which a pseudogene formerly assumed to be genomic "junk" was later deemed to have a functional role in cells. But such cases are almost certainly exceptions and not the rule. And in any event, such examples hardly provide solid evidence for intelligent design; instead, they seem to point toward the kind of idiosyncratic genetic tinkering for which nonsentient evolutionary evolutionary processes are notorious.

It's important to make sure you understand the argument that Avise and others are making. When looking at the big picture the presence of thousands of pseudogenes in the human genome is a challenge for those who argue for Intelligent Design Creationism. The fact that a handful of these regions were misidentified as pseudgenes and now turn out to have a function cannot be taken as evidence that all of the 20,000 known pseudogenes have a function.

So, how does Wells deal with this challenge to his belief? On the next page of his book (p. 27) he says ...

But Is It True?
The arguments by Dawkins, Miller, Shermer, Collins, Kitcher, Coyne and Avise rest on the premise that most non-coding DNA is junk, wihout any significnat biological function. Yet a virtual flood of recent evidence shows that they are mistaken. Much of the DNA they claim to be "junk" actually performs important functions in living cells.

The following chapters cite hundreds of scientific articles (many of them freely accessible on the Internet) that testify to those functions—and those articles are only a small sample of a large and growing body of literature on the subject. This does not mean that the authors of those articles are critics of evolution or supporters of intelligent design. Indeed, most of them interpret the evidence within an evolutionary framework. But many of them explicitly point out that the evidence refutes the myth of junk DNA.

This is a classic "bait-and-switch." The argument from Avise and the others is mostly about the presence of pseudogenes. There is solid evidence that many pseudogenes are completely non-functional. There is evidence that non-functional pseudogenes have been inherited from common ancestors, strongly suggesting that the genes were inactivated in ancient ancestors and passed down to modern species as the evolved.

This argument is NOT about "most noncoding DNA." It's about that 1% of the genome that contains known pseudogenes. Unless that point is addressed directly (it isn't) then Wells is guilty of ignoring one of the main arguments of his critics.

But that's not the point of this posting. I'm concerned about the point that "News" makes in the recent posting on Uncommon Descent. He/she says ...

Darwinism predicts something, based on its core principles, and it doesn’t happen. And there are no consequences? Only on planet Darwin. Where all correct predictions originate in Darwin’s theory and are grandfathered as such by his loyal heirs. All incorrect predictions are “proved” to have originated elsewhere, no matter where they actually originated.

What are these predictions of "Darwinism"? It's surely not pseudogenes since no evolutionary theory that I know of predicted pseudogenes. Bacteria don't have many pseudogenes and that's perfectly consistent with evolutionary theory. Plant genomes have lots of pseudogenes and that's perfectly consistent with evolutionary theory. Yeast has a few pseudogenes but not nearly as many as plants and that's perfectly consistent with modern evolutionary theory.

Is "News" referring to junk DNA in general? That's not a prediction of "Darwinism" or any evolutionary theory that I know of. The fact that bacteria have very little junk DNA has never been taken as a fact that overthrows modern evolutionary theory. I'm unaware of any evolutionary biologist who predicted back in the 1960s that most of the mammalian genome would be junk and that this prediction was a requirement of modern evolutionary theory. The arguments of Avise et al. are not based on the "premise" that most of our genome is junk, they're based on the evidence that pseudogenes exist.

No prediction was made so no prediction has been refuted. The point that "News" is making seems illogical.

Unless I'm missing something obvious.

What about the predictions of the IDiots? Casey Luskin explains it [Intelligent Design and the Death of the "Junk-DNA" Neo-Darwinian Paradigm].

Proponents of intelligent design have long maintained that Neo-Darwinism's widely held assumption that our cells contain much genetic "junk" is both dangerous to the progress of science and wrong. As I explain here, design theorists recognize that "Intelligent agents typically create functional things," and thus Jonathan Wells has suggested, "From an ID perspective, however, it is extremely unlikely that an organism would expend its resources on preserving and transmitting so much ‘junk'." [4] Design theorists have thus been predicting the death of the junk-DNA paradigm for many years: ...

and in Another Intelligent Design Prediction Fulfilled: Function for a Pseudogene ...

Darwinists have long made an argument from ignorance, where our lack of present knowledge of the function for a given biological structure is taken as evidence that there is no function and the structure is merely a vestige of evolutionary history. Darwinists have commonly made this mistake with many types of "junk" DNA, now known to have function. In contrast, intelligent agents design objects for a purpose, and therefore intelligent design predicts that biological structures will have function.²

Here's another prediction, according to Barry Arrington on Uncommon Descent [FAQ4 is Open for Comment].

ID does not make scientifically fruitful predictions.

This claim is simply false. To cite just one example, the non-functionality of “junk DNA” was predicted by Susumu Ohno (1972), Richard Dawkins (1976), Crick and Orgel (1980), Pagel and Johnstone (1992), and Ken Miller (1994), based on evolutionary presuppositions. In contrast, on teleological grounds, Michael Denton (1986, 1998), Michael Behe (1996), John West (1998), William Dembski (1998), Richard Hirsch (2000), and Jonathan Wells (2004) predicted that “junk DNA” would be found to be functional.

The Intelligent Design predictions are being confirmed and the Darwinist predictions are being falsified. For instance, ENCODE’s June 2007 results show substantial functionality across the genome in such “junk DNA” regions, including pseudogenes.

Thus, it is a matter of simple fact that scientists working in the ID paradigm carry out and publish research, and they have made significant and successful ID-based predictions.

It seems like it's the IDiots that have hitched their star to a prediction about junk DNA. If any genome turns out to have a substantial amount of junk DNA then Intelligent Design Creationism is refuted. As it turns out, many genomes do have a lot of junk DNA in spite of what Jonathan Wells would have you believe. Thus, Intelligent Design Creationism is no longer a credible scientific hypothesis.

But you knew that already, didn't you?

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1. Most scientists actually argue a more specific point; namely, that the conservation of specific pseudogenes in different species is an especially serious problem for Intelligent Design Creationists.

2. It's interesting that Casey Luskin seems to know something about the motivations of the intelligent designer because when scientists point out that the genome doesn't look like it was designed this is not taken as an argument against the IDiot position. Instead it's taken as illegitimate science as pointed out by Wells in his book (p. 103), "Do arguments based on speculations about a creator or designer have a legitimate place in science? Not according to Canadian biologist Steven Scadding, who once wrote that although he accepted evolutionary theory, he objected to defending it on the grounds that a creator would or would not do certain things. 'Whatever the validity of this theological claim,' Scadding concluded, 'it certainly cannot be defended as a scientific statement, and thus should be given no place is a scientific discussion of evolution."

ENCODE/Junk DNA Fiasco: The IDiots Don't Like Me

Casey Luskin has devoted an entire post to discussing my views on junk DNA. I'm flattered. Read it at: What an Evolution Advocate's Response to the ENCODE Project Tells Us about the Evolution Debate.

Let's look at how the IDiots are responding to this publicity fiasco. Casey Luskin begins with ...

University of Toronto biochemistry professor Larry Moran is not happy with the results of the ENCODE project, which report evidence of "biochemical functions for 80% of the genome." Other evolution-defenders are trying to dismiss this paper as mere "hype".

Yes that's right -- we're supposed to ignore the intentionally unambiguous abstract of an 18-page Nature paper, the lead out of 30 other simultaneous papers from this project, co-authored by literally hundreds of leading scientists worldwide, because it's "hype." (Read the last two or so pages of the main Nature paper to see the uncommonly long list of international scientists who were involved with this project, and co-authored this paper.) Larry Moran and other vocal Internet evolution-activists are welcome to disagree and protest these conclusions, but it's clear that the consensus of molecular biologists -- people who actually study how the genome works -- now believe that the idea of "junk DNA" is essentially wrong.

Casey Luskin doubles down on junk DNA

Intelligent Design Creationists are committed to the idea that most of our genome is functional. They oppose the idea that a significant proportion is junk. It's easy to see why a junky genome is incompatible with intelligent design but there's something more to their opposition than that.

I think they've painted themselves into a corner. They are so opposed to evolution and modern science that they will take any opportunity to discredit it. They saw a chance to do so about twenty years ago when they became aware of the controversy surrounding junk DNA. This was their chance to (pretend to) rely on real science to back their position. By taking a stance against junk DNA they could seen to be supporting the latest evidence ... or so they thought.

Intelligent Design Creationists claim that they "predicted" that most our genome would be functional. They claim that "Darwinists" predicted junk DNA. The second part isn't true since evolutionary theory is silent on whether some genomes could become bloated with junk DNA or not. However, the ID proponents are sticking to their guns in spite of the growing consensus that most of our genome is junk.

Casy Luskin Gets it Wrong (Again)

 
This is getting to be really annoying. What is it about the concepts of junk DNA and Darwinism that confuse the IDiots? It's not rocket science.

In today's posting on the Discovery Institute anti-science website, Casey Luskin leads off an anti-evolution posting with,

It’s beyond dispute that the false “junk”-DNA mindset was born, bred, and sustained long beyond its reasonable lifetime by the neo-Darwinian paradigm.

Let me try and make this simple for the IDiots.

1. Junk DNA is here to stay. It's a lie to claim that the concept has been abandoned by scientists. True, there are some stupid scientists who don't understand what's going on but they do not represent the consensus.


2. The concept of junk DNA is anti-Darwinian. There's no possible way that a true Darwinist could accept junk DNA. It is incredibly ignorant to claim that the idea of junk DNA was "born, bred, and sustained" by the neo-Darwinian paradigm. On the contrary, it has helped overturn that paradigm, replacing it with a more pluralistic approach to evolution.

It goes without saying that Intelligent Design Creationists think they have a better "paradigm" than real scientists. Luskin is amazed by recent discoveries that some heritable diseases are caused by mutations in regulatory sequences, which he, in his ignorance, thinks are equivalent to junk DNA.

How much earlier might these non-coding “junk” DNA causes of disease have been recognized had scientists operated under an intelligent design paradigm rather than a Neo-Darwinian one?

Me, me, me (pumping his hand in the air). I know the answer ...

What do pseudogenes teach us about intelligent design?

The human genome has about 14,000 pseudogenes that are derived from protein-coding genes and an unknown number derived from genes that specify functional noncoding RNAs. There is abundant evidence that the vast majority of these pseudogenes are nonfunctional by all measurable criteria.

• Different kinds of pseudogenes - are they really pseudogenes?
• Different kinds of pseudogenes: Processed pseudogenes
• Different kinds of pseudgogenes: Duplicated pseudogenes
• Different kinds of pseudogenes: Unitary pseudogenes
• Different kinds of pseudogenes: Polymorphic pseudogenes

It would be perverse to deny the existence of pseudogenes. Almost all of them are junk DNA with no known function. Anyone who claims otherwise can be dismissed as a kook and it's not worth debating those people.

The presence of a single well-characterized pseudogene at the same locus in the genomes of different species is powerful evidence of common descent. For example, Ken Miller has long argued that the existence of common pseudogenes in chimpanzees and humans is solid evidence that the two species share a common ancestor. He uses the β-globin pseudogene and the gene for making vitamin C as examples in Only a Theory: Evolution and the Battle for America's Soul.

Advice from Jonathan Wells on Junk DNA

 

Copied from Uncommon Descent (Denyse O'Leary): What advice, on junk DNA, would Jonathan Wells give Francis Collins or Richard Dawkins?.

From the Salvo Magazine interview with Jonathan Wells, by Casey Luskin. Wells is the author of The Myth of Junk DNA:

If you could have lunch with Francis Collins and Richard Dawkins, what would you say to them about their use of the “junk DNA” argument? [that there is no design in life]

Actually, Collins no longer relies on “junk DNA.” In 2007 he announced in an interview for Wired magazine that he had “stopped using the term.” In 2010 he wrote that “discoveries of the past decade, little known to most of the public, have completely overturned much of what used to be taught in high school biology. If you thought the DNA molecule comprised thousands of genes but far more ‘junk DNA,’ think again” (The Language of Life, pp. 5–6). Unfortunately, his followers at the BioLogos Institute (which he founded) seem to be unaware of this, because they continue to promote the myth that most of our DNA is junk. I would encourage Collins to set them right.

UD News does not think Collins would succeed. They are not Collins’s followers, they are Darwin’s men. They do not seek more knowledge than Darwin had. They seek to make what he knew part of the bedrock of Christianity.

Unlike Collins, Dawkins seems utterly oblivious to recent developments in genomics. I would encourage him to read some of the scientific literature.

Why? Dawkins can command international attention for not keeping up to date – because millions of tax burdens feel he speaks for them – and they don’t need to keep up to date either. Their champions are fronts for the dead orthodoxies that keep them in place.

Dear Jonathan Wells and Denyse O'Leary,

I have read The Myth of Junk DNA and I have read the scientific literature. What advice would you give me?

Why don't you respond to my review of The Myth of Junk DNA? What are you afraid of?

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The IDiots Don't Understand Junk DNA

So what else is new?

The chief IDiot (Casey Luskin) over at Discovery Institute claims that junk DNA is a science-stopper. This is such old news.

Every time scientists find a function for some non-coding DNA we are treated to another diatribe against junk DNA. In fairness, it's not just the IDiots who do this. Some so-called scientists are just as guilty. They don't understand junk DNA.

Here's a clue. Junk DNA is DNA that has no function. It is not non-coding DNA. Lots of non-coding DNA has a function (regulatory sequences, origins of replication, centromeres, telomeres, SARs, etc. etc). But, in mammals, most of it doesn't. Most of the human genome is junk.

Just because we discover a function for some little bit of non-coding DNA does not mean that all of it has a function. Use your head. This is elementary rationalism. Oops, I almost forgot, that's not their strong point.

Think of pseudogenes or degenerative alu sequences, for example. They will always be junk DNA.

Why Do the IDiots Have So Much Trouble Understanding Introns?

Most eukaryotic genes have introns. Introns make up about 18% of the DNA sequences in our genome. Most of these sequences are junk but introns are functional and up to 80bp of each intron is required for proper splicing. The essential sequences contain the 5′ splice site (~10 bp); the 3′ splice site (~30 bp): the branch site (~10 bp); and enough additional RNA to form a loop (~30 bp). The branch site and the splice sites are where specific proteins bind to the mRNA precursor [Junk in Your Genome: Protein-Encoding Genes]. It turns out that within introns about 0.37% of the genome is essential and about 17% is junk.

Pseudogenes Are Pseudogenes and They Are Almost Always Junk

The IDiots have found a paper by Wen et al. (2012) with a very provocative title, "Pseudogenes are not pseudo any more."

Naturally, lawyer Casey Luskin is all over this: Paper Rebuffs Assumption that Pseudogenes Are Genetic "Junk," Claims Function Is "Widespread". And just as naturally, the folks at Uncommon Descent (probably lawyer Barry Arrington) jump on the bandwagon: Junk DNA: Yes, paper admits, it WAS thought to be junk.

The authors of the paper, including Templeton Prize winner Francisco J Ayala, claim that pseduogenes exhibit two puzzling properties: (a) similar processed pseudogenes occur in mouse and humans suggesting that they are conserved, and (b) many pseudogenes are transcribed.

Processed pseudogenes arise when mRNA transcripts are reverse transcribed and inserted back into the genome. They usually come from genes that are highly expressed in germ line cells. Such genes tend to be highly conserved in related species. Mammals are closely related on the scale that were talking about. It's not surprising that a few new pseudogenes in such lineages are very similar in sequence. They're still pseudogenes. The vast majority of known pseudogenes are evolving at a rate that approximates the rate of mutation indicating that they are not constrained by negative selection.

Many pseudogenes are derived from gene duplications followed by mutations in one of the copies that make them incapable of producing a functional product. There's no reason to suspect that the first of these debilitating mutations will prevent transcription; therefore, one expects that many pseudogenes will be transcribed.

Some pseudogenes have been co-opted to provide a different function. There aren't very many examples but that doesn't stop the IDiots from making the fantastic leap from 0.0001% to 100%. (Pseudogenes represent about 1% of the genome [What's in Your Genome? ] so even if we assume that every single pseudogene is not a pseudogene, it hardly makes a dint in the amount of junk DNA.)

I discussed all this when I reviewed Jonathan Well's book The Myth of Junk DNA. The relevant chapter is Chapter 5 [Junk & Jonathan: Part 8—Chapter 5]. That review was posted in May 2011. It seems clear that the lawyers on the IDiot websites haven't read it.

Here's what one of them says on Uncommon Descent.

Darwin’s followers considered junk DNA powerful evidence for their theory, which is really a philosophy (often a cult), and that they often expressed that view, often triumphantly. Others insist it is true anyway.

The problem they hope to suppress is that if lots of junk in our DNA is such powerful evidence for their theory, then little junk throws it into doubt. That is, if it is such a good theory, why was it wrong on a point that was announced so triumphantly?

So it is a good thing that the science-minded public is reminded of the historical fact that Darwinism was supported by junk DNA. And it will be fun when the squirming editorials come out in science mags, warning people not to read too much into this, Darwin is still right.

I'm not even going to bother pointing out how stupid that is. If you're reading Sandwalk, chances are high that you could detect the lies¹ with your eyes closed.

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1. Yes, "lies." At this point there's no other explanation.

Wen, Y-Z., Zheng, L-L., Qu, L-H., Ayala, F.J., and Lun, Z-R. (2012) Pseudogenes are not pseudo any more. RNA Biology 9: 27 - 32. [doi: 10.4161/rna.9.1.18277]

Is Intelligent Design Creationism a Scientific Theory?

You should recall that Casey Luskin is one of those "serious science bloggers" who strikes fear into the hearts of evolutionary biologists. In fact, we are so afraid of people like Casey Luskin and Jonathan M that we go out of our way to avoid responding to their posts [see: A Reason to Doubt the IDiots].

Luskin's latest posting on Evolution News & Views (sic) is: How Do We Know Intelligent Design Is a Scientific "Theory"?. Here's the main argument ...

ID is a theory of design detection, and it proposes intelligent agency as a mechanism causing biological change. ID allows us to explain how aspects of observed biological complexity, and other natural complexity, arose. And it uses the scientific method to make its claims.

The scientific method is commonly described as a four-step process involving observations, hypothesis, experiments, and conclusion. ID begins with the observation that intelligent agents produce complex and specified information (CSI). Design theorists hypothesize that if a natural object was designed, it will contain high levels of CSI. Scientists then perform experimental tests upon natural objects to determine if they contain complex and specified information. One easily testable form of CSI is irreducible complexity, which can be tested for by reverse-engineering biological structures through genetic knockout experiments to determine if they require all of their parts to function. When scientists experimentally uncover irreducible complexity in a biological structure, they conclude that it was designed.