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.

Answering two questions from Vincent Torley

Vincent Torley read a post by Jerry Coyne where Jerry wondered if Intelligent Design Creationism was in trouble because the Discovery Institute has lost Bill Dembski and Casey Luskin [Is the Discovery Institute falling apart?].

Torley disagrees, obviously, but he focuses on a couple of the scientific statements in Jerry Coyne's post and comes up with Two quick questions for Professor Coyne.

I hope Professor Coyne won't mind if I answer.

Before answering, let's take note of the fact that Vincent Torley has been convinced by the evidence that most of our genome is junk. I wonder how that will go over in the ID community?

Here's question #1 ...

Intelligent design explanations and speculations have all been refuted, discredited, or shown to be unnecessary

Intelligent Design Creationism is a movement based on bad science. Every single one of their positive, science-like, claims about ID have been refuted, or discredited, or shown to be completely unnecessary in the face of robust evolutionary explanations. Some of them have the distinction of being unnecessary AND refuted AND discredited (e.g irreducible complexity).

In addition to a small number of claims in support of ID, the proponents of Intelligent Design Creationism also advance dozens and dozens of arguments against evolution. In fact, this is by far the main activity of most adherents to the movement. Some of their arguments focus on legitimate scientific controversies. They are legitimate criticisms of some aspects of evolution but, even then, ID proponents often misrepresent and/or misunderstand the science behind the controversy (e.g. junk DNA).

However, the vast majority of their attacks on evolution are just as bad as their attempts to build a positive case for intelligent design. A disturbingly large number of such attacks exhibit a profound ignorance of science and how it works. In particular—surprisingly—they are ignorant of evolution. The movement is full of kooks. It will never become a credible source of information unless it purges itself by getting rid of the kooks.

Speaking of kooks,¹ Casey Luskin has been publishing a series of articles on the Kitzmiller v. Dover trial that was decided ten years ago. Some of the articles make valid points but the latest one is a joke: Ten Myths About Dover: #4, "The Dover Ruling Refuted Intelligent Design".

You should read the article. It's a remarkable example of apologetics and why lawyers shouldn't try and explain science. While it's true that Judge Jones said lots of things we could quibble about, the big-picture take-home lesson from the trial is correct. No ID explanation stood up to the scrutiny of science. They were all shown to be either irrelevant or wrong.

That's why none of them should be presented in science class except as examples of bad science and faulty scientific reasoning.²

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1. Luskin won't even admit that Young Earth Creationism is absurd.

2. In my opinion, they SHOULD be discussed in class since it's important to teach critical thinking and that requires that you directly confront common misconceptions.

Did Michael Behe say that astrology was scientific in Kitzmiller v. Dover?

Yes he did. But it doesn't mean what you think it means according to Casey Luskin [Ten Myths About Dover: #8, "Michael Behe Admitted that ID Is No More Scientific than Astrology"

I agree with Casey Luskin. During the trial, Behe was asked to define scientific theory and of course he adopted the broad view of science. He said, "Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences."

Here's the exchange that took place during the trial [Dover: Day 11].

Q In any event, in your expert report, and in your testimony over the last two days, you used a looser definition of "theory," correct?
A I think I used a broader definition, which is more reflective of how the word is actually used in the scientific community.
Q But the way you define scientific theory, you said it's just based on your own experience; it's not a dictionary definition, it's not one issued by a scientific organization.
A It is based on my experience of how the word is used in the scientific community.
Q And as you said, your definition is a lot broader than the NAS definition?
A That's right, intentionally broader to encompass the way that the word is used in the scientific community.
Q Sweeps in a lot more propositions.
A It recognizes that the word is used a lot more broadly than the National Academy of Sciences defined it.
Q In fact, your definition of scientific theory is synonymous with hypothesis, correct?
A Partly -- it can be synonymous with hypothesis, it can also include the National Academy's definition. But in fact, the scientific community uses the word "theory" in many times as synonymous with the word "hypothesis," other times it uses the word as a synonym for the definition reached by the National Academy, and at other times it uses it in other ways.
Q But the way you are using it is synonymous with the definition of hypothesis?
A No, I would disagree. It can be used to cover hypotheses, but it can also include ideas that are in fact well substantiated and so on. So while it does include ideas that are synonymous or in fact are hypotheses, it also includes stronger senses of that term.
Q And using your definition, intelligent design is a scientific theory, correct?
A Yes.
Q Under that same definition astrology is a scientific theory under your definition, correct?
A Under my definition, a scientific theory is a proposed explanation which focuses or points to physical, observable data and logical inferences. There are many things throughout the history of science which we now think to be incorrect which nonetheless would fit that -- which would fit that definition. Yes, astrology is in fact one, and so is the ether theory of the propagation of light, and many other -- many other theories as well.
Q The ether theory of light has been discarded, correct?
A That is correct.
Q But you are clear, under your definition, the definition that sweeps in intelligent design, astrology is also a scientific theory, correct?
A Yes, that's correct. And let me explain under my definition of the word "theory," it is -- a sense of the word "theory" does not include the theory being true, it means a proposition based on physical evidence to explain some facts by logical inferences. There have been many theories throughout the history of science which looked good at the time which further progress has shown to be incorrect. Nonetheless, we can't go back and say that because they were incorrect they were not theories. So many many things that we now realized to be incorrect, incorrect theories, are nonetheless theories.
Q Has there ever been a time when astrology has been accepted as a correct or valid scientific theory, Professor Behe?
A Well, I am not a historian of science. And certainly nobody -- well, not nobody, but certainly the educated community has not accepted astrology as a science for a long long time. But if you go back, you know, Middle Ages and before that, when people were struggling to describe the natural world, some people might indeed think that it is not a priori -- a priori ruled out that what we -- that motions in the earth could affect things on the earth, or motions in the sky could affect things on the earth.

I mostly agree with Behe.¹ Astrology was an attempt to explain human behaviors by relating them to the position of the Earth on the day you were born. There is no connection. So today we think of astrology as bad science. It's not true that the stars determine your behavior and whenever we make this claim to an astologist we make sure to point out that the evidence is against it.

What we don't do is tell astrologers that they are entitled to believe whatever they want because astrology is not science and therefore we can't make a scientific statement about whether it's correct or not.

Intelligent Design Creationism is bad science. So is most of evolutionary psychology and some of genomics. So is the attempt to find god in a football helmet [The God Helmet: Your Brain on Religion].

It's disingenuous to make fun of Behe's testimony without understanding that the real issue is epistemology and the demarcation problem. Behe's view of science is perfectly legitimate but it didn't jibe with what the plaintiffs were trying to establish during the trial. They wanted to prove that ID isn't science and the best way to do that was to show that something can't be science unless it's true. In other words, science isn't a "way of knowing," it's the end result.

What does this mean? It means that every discredited attempt to explain something using science as a way of knowing becomes "not science" with hindsight. All those people who tried to show that genes were proteins were wrong so it means that what they were doing is not science. It means that of the two sides arguing about junk DNA, one of them will be wrong so, at some time in the future, their current activities will be seen as "not science."

Isn't that bizarre?

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1. He should have been defining "science" not "scientific theory." That's the fault of his lawyers who failed to make this point during his direct testimony.

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.

Cornelius Hunter predicts that there's going to be function found for the vast majority of the genome according to the intelligent design paradigm

Listen to this Podcast where Casey Luskin interviews Dr. Cornelius Hunter.¹ It's only 9 minutes long.

Dr. Cornelius Hunter on ENCODE and "Junk" DNA, Part 2

Here's part of the transcript.

Casey Luskin: ... and, as we all know, or many ID the Future listeners probably know, for years Darwinian theorists and evolutionary scientists have said that our genomes ought to be full of junk if evolution is true

.....

Casey Luskin: So, Dr. Hunter, you think, just for the record, that in the long term there is going to be function found for probably the vast majority of the genome and so, maybe, you might call it a prediction you would make coming out of an intelligent design paradigm. Is that correct?

Cornelius Hunter: Yes, that's correct Casey, I'll definitely go on the record on that. Not to say I have a hundred percent confidence and also I wanna be clear that from a metaphysical perspective, from my personal belief, I don't have a problem wherever it lands. It doesn't matter to me whether it's 10% or 90% or any where in between or 100% ... just from the scientific perspective and just from the history of science and the history of what we've found in biology, it really does look like it's gonna be closer to 100 than zero.

Casey Luskin: Okay, great, I always like it when people put clear and concrete predictions out there and and I think that's very helpful.

I predict that about 90% of our genome will turn out to be junk DNA—DNA with no function. I base my prediction on the scientific perspective and the history of what we've found in biology. That's interesting because Cornelius Hunter and I are apparently reaching opposite conclusions based on the same data.

I also love it when people make predictions. Will the intelligent design paradigm be falsified if I turn out to be right?

Does it sound to you that Cornelius Hunter personally doesn't care if the prediction coming out of the intelligent design paradigm is correct or not?

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1. How come in the podcast they never refer to Dan Graur as Dr. Graur? Isn't that strange?

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 ...

Ten years after Dover - an excellent decade for Intelligent Design Creationism?

This month marks the tenth anniversary of the Kitzmiller v. Dover case in Pennsylvania [Tammy Kitzmiller, et al. v. Dover Area School District, et al.]. The legal victory will be celebrated by NCSE and Panda's Thumb and by many other supporters of science and evolution. If American law is your thing, then please join in the celebration of a legal victory.

It's much more interesting to evaluate whether the legal victory in Pennsylvania had any significant effect on the general public. Did it cause people to change their minds and abandon Intelligent Design Creationism to embrace science? Has America moved closer to the time when real science can be taught in the schools without interference from religion? Have politicians stopped trying to water down evolution in the public schools because of Judge Jones' decision in Kitzmiller v Dover? Have politicians stopped opposing evolution and has the public stopped voting for those who do?

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.

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].

The top ten problems with evolution according to Intelligent Design Creationists

Most of Intelligent Design Creationism consists of whining about evolution. Their main goal seems to be to discredit scientists and evolution in order to lay the ground work for a new approach to science, one that demonstrates the existence of an intelligent designer.

Most of their criticisms of evolution are ridiculous but a few of them require a response. So far, after more than 25 years of whining, the creationists have utterly failed to make a convincing case against evolution.

Are they still trying? You bet. Casey Luskin has done us the favor of listing "The Top Ten Scientific Problems with Biological and Chemical Evolution" in a series of blog posts on Evolution News & Views (sic).

Here they are for your amusement.

1. No Viable Mechanism to Generate a Primordial Soup. I think he's right about this one. But then, I don't think a primordial soup plays a role in the origin of life.
2. Unguided Chemical Processes Cannot Explain the Origin of the Genetic Code. This has nothing to do with the origin of the genetic code. It's an argument against "RNA world." Casey Luskin is correct. We don't know how the first information-containing molecules arose and how they came to be self-replicating.
3. Step-by-Step Random Mutations Cannot Generate the Genetic Information Needed for Irreducible Complexity. Luskin is dead wrong about this one.
4. Natural Selection Struggles to Fix Advantageous Traits in Populations. Casey Luskin doesn't understand modern evolutionary theory, and it shows.
5. Abrupt Appearance of Species in the Fossil Record Does Not Support Darwinian Evolution. Casey Luskin doesn't understand modern evolutionary theory, and he doesn't understand the scientific literature. What else is new?
6. Molecular Biology Has Failed to Yield a Grand "Tree of Life". Modern scientific discoveries have revealed that there may not be a universal tree of life common to all genes. Casey Luskin accepts the evidence but rejects the idea that scientific explanations can change when new data comes in.
7. Convergent Evolution Challenges Darwinism and Destroys the Logic Behind Common Ancestry. This is nonsense compounded by wishful thinking.
8. Differences Between Vertebrate Embryos Contradict the Predictions of Common Ancestry. Dead wrong.
9. Neo-Darwinism Struggles to Explain the Biogeographical Distribution of Many Specie. What?
10. Neo-Darwinism's Long History of Inaccurate Predictions about Junk Organs and Junk DNA. You'll have to read that post yourself to see how many different ways Casey Luskin can go wrong and the very few ways he can go right.

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What would happen if Intelligent Design Creationists understood evolution?

There's an interesting phenomenon taking place over on one of the main Intelligent Design Creationist websites. It started when a philosphopher, Vincent Torley, tried to understand how the sequences differences between chimpanzees and humans could be explained by evolution. In the beginning, he was skeptical of the explanation I offered and he was supported by a biochemist creationist named Branko Kozulic. Kozilic assured him that his skpeticism was justified and the population geneticists were wrong.

Then an amazing thing happened. Salvador Cordova, another well-known creationist, posted a comment on one of Torley's blog posts. You can see it as comment #39 on Branko Kozulic responds to Professor Moran. Cordova was responding to comments posted by Nick Matzke and "WD400" on that same post. Here's what Sal Cordova said,

A quiz for those of you who think you understand Intelligent Design Creationism

One of the great ironies of the Intelligent Design Creationist movement is that its proponents don't understand evolution and they don't understand what their movement stands for. They can't agree on the meaning of intelligent design.

You might think I'm exaggerating about not understanding their own goals but just think about it for a moment. The movement encompasses people like Michael Denton who promote a deist version of creation and it also welcomes huge numbers of Young Earth Creationists who believe in the literal truth of the biblical creation myth. Many proponents are somewhere in between these extremes but the vast majority think that there's something seriously wrong with evolution that demands the intervention of an intelligent designer. The designer may have just made bacterial flagella and a few other complex molecular machines or he/she may have stepped in to make all the animal phyla. Almost every proponent of Intelligent Design Creationism thinks that the designer intervened in the human lineage to make humans special.

Someone named "nullasalus" thinks that it's only critics of Intelligent Design Creationism who are confused. He tries to set us straight at: A Quiz for Intelligent Design Critics.

In the near decade that I’ve been watching the Intelligent Design movement, one thing has consistently amazed me: the pathological inability of many ID critics to accurately represent what ID actually is, what claims and assumptions are made on the part of the most noteworthy ID proponents, and so on. Even ID critics who have been repeatedly informed about what ID is seem to have a knack for forgetting this in later exchanges. It’s frustrating – and this from a guy who’s not even a defender of ID as science.

I try really hard not to misrepresent the Intelligent Design Creationist movement. That includes my preference for adding the word "Creationist" to their label. What they're talking about is creationism—a being who creates the universe and who creates some aspects of living organisms.

It's never easy to say exactly what "the most noteworthy ID proponents" mean by intelligent design. That's because they can't agree among themselves. The most common characteristic is that they are all anti-evolution in one way of another. Some of them accept microevolution and some accept common descent but almost all of their writings focus on some aspect of evolution that they don't accept. It could be the idea of junk DNA, or the evolution of animals in the Cambrian, or any one of a long list of "icons of evolution" that scientists get wrong.

A great many prominent ID proponents are opposed to "materialism"—that means they support non-materialism, otherwise known as supernaturalism (e.g. founder Phillip Johnson). A great many prominent ID proponents try to paint all supporters of evolution as social Darwinists. They try to link us to Nazis and they go out of their way to denigrate Charles Darwin. This seems to be an integral part of the Intelligent Design Creationist movement and it can't be ignored.

Just read the titles of the major ID books. They are all about attacking evolution.

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.

Darwin Doubters Want to Have their Cake and Eat it too

The phrase "to have your cake and eat it too" means that you can't have it both ways or "shouldn't try to have two incompatible things" [You can't have your cake and eat it].

The Intelligent Design Creationists are giving us a good example of just what this means. They have a new book coming out called "Darwin's Doubt." It's to be published by the religious arm of HarperCollins. The book will be available in a few months in the USA so the IDiots are ramping up the hype in preparation. We are told that this book, just like several previous books from the Discovery Institute, will definitively refute evolution and demonstrate the truth of Intelligent Design Creationism.

Here's how casey Luskin put it a few days ago [Three (or Four) Reasons Everyone Should Read Darwin's Doubt].

When published, Darwin's Doubt will be the single most up-to-date rebuttal to neo-Darwinian theory from the ID-paradigm. In this regard, one exciting element of Darwin's Doubt is that Meyer reviews much of the peer-reviewed research that's been published by the ID research community over the last few years, and highlights how ID proponents are doing relevant research answering key questions that show Darwinian evolution isn't up to the task of generating new functional information.

Here's how the strategy works. The IDiots are arguing the merits of Meyer's new book on the leading creationist blogs. They are generating lots of publicity and convincing their followers that the book is going to be a devastating rebuttal of "Darwinism." None of their followers have read the book but that doesn't matter. They won't have to.

How are scientist supposed to respond? None of us have read the book so we can't (yet) show that it is just more of the same old propaganda that we've seen before. What we can say is that we are very skeptical of the claims being made and we think it is disingenuous to promote those claims when we can't examine the "evidence." We can confidently speculate about what Stephen Meyer is going to say because he has a history and because he gives away some of his arguments in the publicity surrounding the book. The IDiots only sing one note and there's a very high probability that this isn't going to change.

That's exactly what Jerry Coyne said in his post: A (formerly) reputable publisher sells out to creationists. He puts it very nicely—and undoubtedly accurately— when he says, "But creationist Stephen Meyer, from the Discovery Institute, has apparently wrapped up the story. He’s hit upon the real reason for the Cambrian explosion: it’s intelligent design! Yes, baby Jesus made the phyla!"

Does anyone with an IQ over 50 think Coyne's prediction is wrong?

You know what's coming because we've seen it all before with the pre-publication hype for "The Myth of Junk DNA." "Science of Human Origins," and "Signature in the Cell." This time it's David Klinghoffer who is the designated whiner [Current Trends in Darwinian Book-Reviewing].

With a pub date of June 18, naturally no books are available. (Though you can preorder at a nice discount, for now, better than Amazon, over at DarwinsDoubt.com.) Nevertheless, at Why Evolution Is True, University of Chicago biologist Jerry Coyne assumes he knows what will be in the book. His absurd summary: "Yes, baby Jesus made the phyla!"

...

Darwinists have a curious way of responding to serious scientific and intellectual challenges to their beliefs. And it's getting more curious, isn't it? It's sort of evolving. If they had answers to ID's challenges, surely they would wait till they read the book, then accurately characterize what it says, and then tell us why Steve Meyer is wrong. But so far, and wasting no time, they have signaled in this strange prophylactic manner their unwillingness to do so.

The solution is obvious to everyone but the IDiots. Don't make outlandish claims about what's in a book until it's published and everyone can check for themselves. It you speculate about what the book is going to say then don't be surprised if others do as well.

You can't have your cake and eat it too.

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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.

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.

Intelligent Design Creationists Choose ENCODE Results as the #1 Evolution Story of 2012

The folks over at Evolution News & Views (sic) have selected the ENCODE papers as the Number 1 evolution-related story of 2012. Naturally, they fell for the hype of the ENCODE/Nature publicity campaign as you can see from the blog title: Our Top 10 Evolution-Related Stories: #1, ENCODE Project Buries "Junk DNA".

Most of the article is just the reposting of an article by Casey Luskin but some anonymous editor has added ...

Editor's note: For the No. 1 slot among evolution-related news stories of 2012, this one was an easy pick. The publication of the ENCODE project results detonated what had been considered among the sturdiest defenses that Darwinian evolutionary theory could still fall back upon: "Junk DNA." Casey Luskin's initial reporting is featured below. See also our response to the ensuing controversy over ENCODE ("Why the Case for Junk DNA 2.0 Still Fails").

Normally I would make fun of the creationists for misunderstanding the real scientific results in the papers that were published last September but, in this case, there are lots of real scientists who fell into the same trap.

Even Science magazine selected the ENCODE results as a top-ten breakthrough and noted that 80% of the human genome now has a function [Science Magazine Chooses ENCODE Results as One of the Top Ten Breakthroughs in 2012]. Oh well, I guess I'll just have to be content to point out that many scientists are as stupid as many Intelligent Design Creationists!

I can still mock the creationists for claiming that "Darwinian evolutionary theory" supports junk DNA.

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James Shapiro Responds to My Review of His Book

I reviewed Shapiro's book, Evolution: A View from the 21st Century for NCSE reports. (NCSE = National Center for Science Education.) You can read it here.

James Shapiro has responded to my review in the latest issue of NCSE reports: Reply to Laurence A Moran’s review of Evolution: A View
from the 21st Century.

Shapiro seems to be really upset that NCSE would choose someone like me to review his book. He opens his rebuttal with ...

Before I saw Laurence A Moran’s book review (Moran 2012), I wrote the following: “It is a shame that NCSE chose Larry Moran to review my book; not because of anything he said in the review but because he is hostile to new ideas and perspectives.”

A year ago, Moran posted a piece entitled “Physicists and biologists” on his Sandwalk blog [Physicists and Biologists¹]. In this post, he ridiculed the enthusiasm I expressed in the book for physicists coming into evolutionary studies and bringing new skills and new ideas.

Meanwhile, I welcome all those physicists who know nothing about evolution, protein structure, genetics, physiology, metabolism and ecology. That’s just what we need in the biological sciences to go along with all the contributions made by equally ignorant creationists.

What a great way to make new friends for evolution science—equating physicists with creationists and calling them “equally ignorant”!

An Honest Intelligent Design Proponent?

It's unusual to find a proponent of Intelligent Design Creationism who makes an honest attempt to evaluate scientific facts. Jonathan McLatchie (Jonathan M) seems to be one of those rare birds. I'm not going to refer to him as an IDiot.

Here's a bit from his latest post on Evolution News & Views (sic [Perspectives on ENCODE and Junk DNA].

The debate thus hinges on whether activity such as transcription, transcription factor association, and histone modification are signs of true function. My own view is that such activity is suggestive of functionality, but not proof. Therefore I would be cautious about claiming that these results show 80% of the genome to have function in the sense that we normally use that word.

On the other hand, the observation that the genome is buzzing with activity underscores what proponents of ID have been saying for years: not knowing what something does doesn't constitute evidence that it's doing nothing. Moreover, it wasn't long ago that Laurence Moran and PZ Myers were telling us that the genome is not even pervasively transcribed and that this amounted to evidence that the majority of our DNA is junk.

That's pretty good for someone who posts on a blog that also publishes stuff from Jonathan Wells and Casey Luskin. I wonder if they talk to each other?

On the other hand, it's not perfect. I've been arguing for years that there is good solid evidence that most of our genome is junk. I have never used the argument from ignorance that Jonathan attributes to me.

Also, I have never denied that the genome is pervasively transcribed. Instead, I have argued that pervasive transcription is something that one expects given what we know about DNA binding proteins and transcription. I've pointed out that the vast majority of our genome is transcribed very rarely—about one transcript per day in 100 cells—and this is consistent with accidental transcription. This is noise. The product is junk RNA and is has no function [Useful RNAs?] [Junk RNA] [Pervasive Transcription] [How to Frame a Null Hypothesis] [How to Evaluate Genome Level Transcription Papers ].

I discussed this thoroughly when I reviewed Jonathan Wells' book The Myth of Junk DNA [Junk & Jonathan: Part 6—Chapter 3]. Perhaps Jonathan McLatchie hasn't read my earlier posts?

Contrast McLatchie's post with that of Jonathan Wells [A Dishonest Intelligent Design Proponent?].

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