The Accommodationist Wars

Don't forget to join us tonight at the Fox & Fiddle, 27 Wellesley St., Toronto for an event sponsored by the Association for Science and Reason (ASR).

I'm going to be talking about The Accommodationist Wars.

Professor Moran will talk about the conflict between two types of atheists: those who think science and religion are not compatible, and those who think religion and science are not necessarily in conflict. The accommodationists believe it’s important to ally with moderate religious leaders to combat the intrusion of religious beliefs into our schools and political systems. An important part of this strategy is recognizing that science and religion can be compatible. The other side agrees that such alliances can be fruitful but that should not prevent atheists from speaking out against even moderate forms of religious belief. The National Center for Science Education (NCSE) in the USA is a prominent accommodationist organization and so are the science organizations such as the National Academies and the American Association for the Advancement of Science (AAAS). All of these organizations take a position on the compatibility of (some) religions. Many scientists think that these organizations should not be defending religion.

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Casey Luskin Is Confused (Again)

The IDiots have painted themselves into a corner and they don't know what to do. They have been ranting against "Darwinism" for so long that they've come to believe that their silly version of evolution is what is being taught in the schools. When scientists objected to the "Darwinist" version of evolution the IDiots assumed that this was an objection to evolution. Gradually it seems to be dawning on them that there are legitimate scientific debates over the mechanisms of evolution and the relative contributions of various processes. These controversies have nothing to do with the FACTS of evolution.

But now the IDiots are in a bind. They can't retreat by admitting that their characterization of evolution has been wrong for the past few decades. That would make them look foolish. On the other hand, they can't continue to ignore the fact that major critics of "Darwinism" (or the "Modern Synthesis" or "Neo-Darwinism") are strong supporters of evolution and opponents of creationism, including Intelligent Design Creationism. Oops!

What to do? Watch how Casey Luskin squirms as he tries to get out of the corner in Recant! Pushing Creeds as Damage Control for Darwin.

When writing in technical journals, evolutionary biologists like McPeek or Koonin admit stark problems with neo-Darwinian evolution--i.e.:

"elucidating the materialistic basis of the Cambrian explosion has become more elusive, not less, the more we know about the event itself, and cannot be explained away by coupling extinction of intermediates with long stretches of geologic time, despite the contrary claims of some modern neo-Darwinists" (McPeek)

"The edifice of the modern synthesis has crumbled, apparently, beyond repair" (Koonin)

But when their criticisms are cited by a proponent of intelligent design, they quickly toe the materialist party line, designed to reassure the masses that the paradigm has everything in order. Thus, when called upon by the NCSE to publicly defend the paradigm, Koonin eagerly endorses Dobzhansky's creed. As Newton eagerly boasted:

As the geneticist Theodosius Dobzhansky famously said - and as Eugene Koonin explicitly agreed - "Nothing in biology makes sense except in the light of evolution."

Since when do creeds take precedence over the evidence?

None of this, however, changes the fact that Koonin, McPeek, and many other scientists are writing technical papers stating that the neo-Darwinian model is flawed at its very core. Koonin undoubtedly believes Dobzhansky's statement is true, but I doubt he would say "Nothing in biology makes sense except in the light of neo-Darwinism." Why, then, must this model be taught to students as unadulterated fact?

Do you see the strategy? The IDiots are going to claim that their silly misunderstanding of evolution ("Darwinism" or "neo-Darwinism") is the "fact" of evolution that's being taught in the schools. Thus, it's not their fault that their understanding of evolution is wrong—blame it on the evolutionary biologists.

Yeah, that'll work! :-)

The alternative is to admit that the IDiots are, well .... idiots. Don't hold your breath waiting for that to happen.

I suppose we should be happy that they are finally beginning to see the very problem we've been telling them about for 25 years. They simply don't understand the real scientific version of evolution.

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[Image Credit: I got it from James Preller's Blog.]

Do Not Vote for the Anti-Science Green Party

There is no party platform that perfectly reflects my views on all issues. However, there is one thing I look for when deciding to support a political party and that's how they arrive at a particular policy. Is it scientific? Does the policy depend on evidence, healthy skepticism, and rational thinking?

The Green Party of Canada has outlined their platform in a document called Vision Green. Here's what they say in the introduction ...

Vision Green presents a well-researched analysis of critical environmental, economic and social challenges facing Canadians from coast to coast to coast, and presents practical solutions that can be achieved if there is the political will and leadership to take forward-looking action. It was developed by our Green Cabinet and was informed by experts, activists and citizens who participated in policy workshops held across Canada. Our vision is based on policies approved by the membership of the Green Party.

Sound promising. They don't actually say that their policies are based on sound scientific reasoning but it sounds like "well-researched" might be a synonym for "good science."

As you scan this document you encounter many positions that seem somewhat dogmatic and considerably beyond what the scientific evidence actually says. The Green Party is opposed to genetically engineered organisms, for example, and they propose to, "Phase out the use of genetically modified food products and ‘terminator’ seeds" (p. 74).

The Green Party is opposed to nuclear power and advocates a ban on new nuclear power plants and a shut-down of existing ones. The party proposes to ban uranium mining and refining. While some of their arguments are valid, the overall tone does not sound scientific.

But the real give-away comes when the document discusses health care. Here's one of the promises from page 70.

Provide funds to expand provincial health insurance to cover proven alternative therapies that are less expensive and invasive such as chiropractic, massage, acupuncture.

It is simply not true that these "alternative therapies" are proven in any scientific sense. What this tells me is that the Green Party platform is not based on scientific reasoning.

That's disappointing.

Everybody wants to promote good health. It's a motherhood issue. What's important is whether a political party has a realistic policy to achieve this goal. Most don't but the Green Party actually makes things worse ...

Health promotion is about more than health care or health education. It is about recognizing the profound health impacts of determinants of health outside the formal healthcare system and working with many stakeholders (policy-makers, NGOs, health agencies, multiple levels of government, the private sector, and most important, affected communities themselves) to reduce, eliminate, or overcome those factors that harm health or act as barriers to health enhancement, and to promote those factors that enhance the health, well-being and quality of life of all Canadians.

We will promote complimentary health care – through support of chiropractic, naturopathic, homeopathic, and other non-western practices. The Green Party of Canada recognizes the value of good health as a fundamental human right, and also the key to the most vibrant, inclusive and sustainable Canadian society possible.

I will never vote for a political party that promotes naturopathy and homeopathy in such a prominent manner. Naturopathy and homeopathy are examples of anti-science quack medicine. The fact that the leaders of the party would even include this in their platform tells me that scientific thinking is not part of their worldview and it calls into question their positions on everything else.

The Green Party wants to use my tax dollars to support these quacks.

Expand healthcare coverage to include qualified complementary/alternative health professionals such as naturopaths, acupuncturists, homeopaths, licensed massage therapists, chiropractors, and dietitians.

This is very wrong.

Do not vote for the Green Party. If you want to cast a protest vote then spoil your ballot or vote for some other party that cannot be elected in your riding. Every vote for the Green Party is a vote against science.

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[Hat Tips: Zak at Canadian Atheist: The Green Party Platform and Mitchell Gerskup at Skeptic North: Voting Green? Read This.]

Hunting and Gathering in Washington D.C.

Laurel Kartchner is a Biochem/MCB major at the University of Arizona. She is attending the Experimental Biology 2011 conference in Washington.

Laurel visited all the display booths and collected all the available free loot. Here's her collection. Congratulations, Laurel!



Her poster will be up tomorrow ...

Kartchner, L.B., Malinowski, P., and T-S.Tsao Role of glutathione S-transferase and endoplasmic reticulum chaperone DsbA-L in the assembly of adipocyte hormone adiponectin.

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Storm

This video is posted everywhere. In case you haven't watched it before you should do so right now. It's brilliant.

Imagine that you're at a dinner party and someone announces that all knowledge is relative, alternative medicine is better than real medicine, and science relies on faith—just like religion. That's the situation Tim Minchin found himself in. Here's how he struggled to keep quiet but eventually .....

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Guess Who I'm Voting For?

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Springtime in Washington

I'm off to Washington D.C. on Saturday to attend the American Society for Biochemistry and Molecular Biology (ASBMB) 2011 Annual Meeting [ASBMB]. It's part of a larger meeting called Experimental Biology 2011.

One of the reasons for going is to get together with the other members of the editorial board of the Biochemistry and Molecular Biology Education journal [BAMBED].Many of them are fellow textbook authors.

There's going to be a wild party on Sunday night when we all get together to talk about the citric acid cycle and free energy.

I should have recovered by Monday noon in case anyone in the Washington area wants to meet up for some more exciting discussions about biochemistry and molecular biology.

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Jonathan, Moonies, and Junk DNA

This video is supposed to support the evolution side versus the Intelligent Design Creationists. There are two major flaws in this presentation.

First, it spends too much time on the background of Jonathan Wells. While it's interesting to know where he's coming from, his motives are less important that the "scientific" case he's making. His religious motivation explains WHY he gets the science wrong but the important point is that the science IS wrong.

Second, it does a poor job of explaining the actual scientific controversy over the amount of junk DNA in our genome. It almost seems to imply that scientists don't believe in junk DNA.

This is a complicated issue. I don't expect the IDiots to get it right but I do expect scientists to explain it correctly.

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IDiots vs Francis Collins

Here's a video where several IDiots take on Francis Collins and his book The Language of God,. Jonathan Wells is prominently featured in this video and much of the attack is concerned with junk DNA. Wells makes his position very clear. He claims that modern scientific evidence has overthrown the "myth" of junk DNA and those of us who still believe in junk DNA are guilty of a "Darwin of the gaps" kind of argument. That's because, according to Welles, we don't have an explanation for junk DNA therefore we attribute it to Darwinian evolution (6.00 minute mark).

There is a lot of positive evidence that much of the DNA in our genome is non-functional. Wells is dead wrong about this. Furthermore, assuming that this junk DNA is non-functional and assuming that species share a common ancestor, we can explain many observations about genomes. IDiots can't do this. They have yet to provide an explanation for shared pseudogenes¹ in the chimp and human genomes, for example. And I haven't heard any IDiot explain why the primate genomes are chock full of Alu sequences derived from a particular rearranged 7SL RNA sequence while rodent genomes have SINES from a different rearranged 7SL sequence and lots of others from a tRNA pseudogene [Junk in Your Genome: SINES].


Did Francis Collins use the existence of junk DNA as support for Darwin's theory of evolution? Here's what Wells says in the video (50 second mark).

If fact he relies on so-called junk DNA—sequences of DNA that apparently have no function—as evidence that Darwin's theory explains everything we see in living things.

I searched in the The Language of God for proof that Wells is correct. The best example I could find is from pages 129-130 where Collins describes the results from comparing DNA sequences of different organisms. He points out that you can compare coding regions and detect similarities between humans and other mammals and even yeast and bacteria. On the other hand, if you look at non-coding regions the similarities fall off rapidly so that there's almost no similarity between human DNA and non-mammalian genomes (e.g. chicken). This is powerful support for "Darwin's theory of evolution" according to Francis Collins. First, because you can construct phylogenetic trees based on DNA sequences and ...

Second, within the genome, Darwin's theory predicts that mutations that do not affect function (namely, those located in "junk DNA") will accumulate steadily over time. Mutations in the coding regions of genes, however, are expected to be observed less frequently, since most of these will be deleterious, and only a rare such event will provide a selective advantage and be retained during the evolutionary process. That is exactly what is observed.

I leave it as an exercise for Sandwalk readers to figure out how to explain this observation if the regions that accumulate fixed mutations aren't really junk but functional DNA. Your explanation should consist of two parts: (1) why the DNA is functional even though the sequence isn't conserved (provide evidence)², and (2) why coding regions show fewer changes and why comparisons of different species lead to a tree-like organization.

I wasn't able to find where in Origin of Species Darwin discuss this prediction but I'm sure it must be there somewhere. Perhaps some kind reader can supply the page numbers?

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1. Every knowledgeable, intelligent biologist knows that pseudogenes exist and they are junk. That's not in dispute. I haven't heard any Intelligent Design Creationists admit that there are thousands of functionless pseudogenes in our genome.

2. I can think of two or three possibilities but no evidence to support them.

Toronto Skeptics in the Pub

Join us on Friday, April 15, 2011 at the Fox & Fiddle, 27 Wellesley St., Toronto for an event sponsored by the Association for Science and Reason (ASR).

The speaker will be me and the subject is The Accommodationist Wars.

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What Is Intelligent Design Creationism? - Is It Science?

One of the common claims of Intelligent Design Creationists is that their creationist worldview is actually real science. What they do, according to this claim, is investigate nature looking for solid evidence of design. This usually involves some form of specified complexity or irreducible complexity. The "scientific" evidence of design, according to the creationists, means that God must have played a role in the creation of intelligent god-fearing humans.

In fairness, they often try to avoid stating the obvious implication of their "findings" in order to avoid criticism. They pretend that just proving the existence of intelligent design is as far as they go and the rest ("God did it") isn't really part of their movement. Nobody is fooled by this silliness.

Any objective view of the IDiot literature reveals that attacks on evolution constitute >99% of their activity. It's rare to find an article or book that presents a positive case for a creator design. Whenever you poke an IDiot with this fact they will almost always deny it, saying that Intelligent Design Creationism really is scientific—it's the scientific demonstration of design.

Denyse O'Leary knows better. She wonders, Are ID researchers making progress?. She's troubled by the fact that much of the literature is just attacks on evolution and positive contributions to intelligent design are few and far between. She has an explanation for this focus on attacking evolution. I repeat it here because it's one of the few honest appraisals of the goals of the movement.

I have thought about that one for a while, and now usually reply:

Because, just as bad money drives out good, bad ideas drive out good. Let us say your country’s carefully regulated money supply is assaulted by counterfeiters. Does it make more sense to start by exposing them or to just virtuously ignore them and continue to print good money – while they continue to print bad money?

Remember, they have no obligation to balance the money supply with available goods, but you do.

To me, Darwinism is like bad money. It becomes an intellectual vice. People are always looking for natural selection to generate random mutation, the way they are always trying to pass on the likely-bogus G-bill (when they are not out looking for the lucky strike).

I too look forward to the day that ID researchers are free to do positive work, but right now we are swamped in a Darwinism whose fraudulence is often unrecognized because it is so often ridiculous. So, as with counterfeit money, the first goal is to demonstrate that much intellectual currency is bogus. Don’t accept it and don’t pass it on. And don’t imagine that everyone will want to know this. Quite the opposite.

So can good money ever drive out bad? Yes, but it is tough slogging.

I assume that the new book by Jonathan Wells will be mostly evolution-bashing. I'm not expecting to see any evidence of intelligent design.¹

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1. Yes, I know this can be taken two ways.

[Photo Credit: Canadian Writers Who Are Christian]

Cat Bowling

Jerry Coyne posted this [Caturday felids: Lasers!] but I just have to put it on Sandwalk for others to see. You need a cat and a laser pointer ...

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Carnival of Evolution #34

This month's Carnival of Evolution is hosted by Stephen Matheson at Quintessence of Dust [Carnival of Evolution: #34].

It's the April 1, 2011 version but don't be fooled. Some of the postings are serious!

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Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?

This is the second in a series of postings about a new book by Jonathan Wells: The Myth of Junk DNA. The book is published by Discovery Institute Press and it should go on sale on May 31 2011. I'm responding to an interview with Jonathan Wells on Uncommon Descent [Jonathan Wells on his book, The Myth of Junk DNA – yes, it is a Darwinist myth and he nails it as such].

Denyse O'Leary asks, "Interestingly, in the “nail dump is Ming vase” story, no one insists that nobody ever thought it was just another piece of junk. They almost always say, “Yes, we thought so but had no idea …” So what’s behind the failure to admit an error in this case?" It's hard to figure out what she means but I think she's wondering why biologists don't just admit they were wrong about junk DNA. Jonathan Wells interprets the question differently.

Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”

This claim is easily disproved: Francis Crick and Leslie Orgel published an article in Nature in 1980 (284: 604-607) arguing that such DNA “is little better than junk,” and “it would be folly in such cases to hunt obsessively” for functions in it. Since then, Brown University biologist Kenneth R. Miller, Oxford University biologist Richard Dawkins, University of Chicago biologist Jerry A. Coyne, and University of California–Irvine biologist John C. Avise have all argued that most of our DNA is junk, and that this provides evidence for Darwinian evolution and against intelligent design. National Institutes of Health director Francis Collins argued similarly in his widely read 2006 book The Language of God.

It is true that some biologists (such as Thomas Cavalier-Smith and Gabriel Dover) have long been skeptical of “junk DNA” claims, but probably a majority of biologists since 1980 have gone along with the myth. The revisionists are misinformed (or misinforming).

It's in the best interests of the IDiots to promote the idea that all "Darwinists" believed in the "myth" of junk DNA and that it wasn't until the predictions of the IDiots were confirmed (not) that the biologists changed their minds.

The truth is somewhat different. Wells says, "Some people revise history by claiming that no mainstream biologists ever regarded non-protein-coding DNA as “junk.”" The truth is that the mainstream biologist community never, ever claimed that all non-coding DNA was junk. Most of them didn't even believe that a majority of our genome was junk.

The issue has come up many times over the past few years on blogs and newsgroups. The last time I took a poll was a few years ago and here are the results.


As you can see, there's a wide range of opinion among people who read Sandwalk. I think this is a pretty good reflection of the opinions of most biologists.

In responding to the question, Wells makes one serious error when he claims that biologists promoted junk DNA because it "provides evidence for Darwinian evolution." It does nothing of the sort. In fact, it goes against any prediction of Darwinian evolution by natural selection. The reason why the concept of (huge amounts of) junk DNA was resisted by so many biologists was because of this conflict.

Wells also says that junk DNA was promoted by some biologists because it "provides evidence ... against intelligent design." This is partly true, especially when the arguments center on conserved pseudogenes. That part of junk DNA (pseudogenes) is accepted by almost all biologists but it's only a tiny part of our genome. There is no evidence to suggest that pseudogenes are anything but junk and all the evidence indicates that we have thousands of them in our genome. (If they have a function then they aren't pseudogenes.)

Many mainstream biologists have supported the idea that a majority of our genome is junk. There's no denying that. I agree with them. None of them are changing their minds in spite of what Jonathan Wells is telling you. What Wells is doing is picking sides in a genuine scientific dispute. He could have done this 30 years ago and the result would have been the same. The genuine scientific controversy is not about to be resolved and there's no new evidence that seals the case one way or the other.

In my opinion, our genome is almost 90% junk DNA and that's the view that's going to win in the end.

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Junk & Jonathan: Part 1—Getting the History Correct

This is the first in a series of postings about a new book by Jonathan Wells: The Myth of Junk DNA. The book is published by Discovery Institute Press and it should go on sale on May 31 2011. I'm responding to an interview with Jonathan Wells on Uncommon Descent [Jonathan Wells on his book, The Myth of Junk DNA – yes, it is a Darwinist myth and he nails it as such].

The first question is "what is junk/noncoding DNA?" And the answer is,

“Non-coding” in this context means “non-protein-coding.” An important function of our DNA is to specific the sequences of subunits (amino acids) in the proteins that (along with other types of molecules) make up our bodies. When molecular biologists discovered in the 1970s that about 98% of our DNA does not code for proteins, some biologists called non-protein- coding DNA “junk.”

This is misleading. You can consult the excellent article by Ryan Gregory on the origin of the term "junk DNA" to see what it meant in 1972: A word about "junk DNA". The bottom line is that the original meaning of the term "junk DNA" was much closer to what we now call pseudogenes. "Non-coding DNA" is that portion of the genome that does not encode amino acids. In the original paper by Susumu Ohno (1972) there was plenty of discussion about functional noncoding DNA (centromeres, regulatory sequences, spacer DNA). In addition, every scientist in 1972 knew that there were functional genes for tRNAs and ribosomal RNAs in the noncoding DNA.

There was never a time when knowledgeable molecular biologists equated "junk" DNA and "noncoding" DNA. That doesn't mean that there weren't slip-ups from time to time as less knowledgeable scientists published articles on genome organization. There are even modern scientists (and science writers) who make the mistake of confusing "noncoding" with "junk."

My point is that if you are going to answer the question accurately then you should represent the consensus view of most scientists who know that lots of noncoding DNA has a function. You should also attempt to present the modern view of junk DNA instead of implying that forty year old concepts still hold sway. The modern view is that junk DNA is that part of our genome that has no known function. It does not include noncoding regions like regulatory sequences, RNA genes, centromeres. telomeres, origins of replication, recombination hotspots, splice sites, minimal intron length, and scaffold attachment regions (SARs).

The interviewer is Denyse O'Leary and her sympathies are clear in the followup question, "Why was it called “junk” in the first place? And why does all this remind me of one of those auction program episodes where someone is storing leftover carpet nails in what turns out to be a Ming dynasty vase? My mom loves those."

Jonathan Wells answers,

According to Charles Darwin’s theory, all living things are descendants of common ancestors that have been modified solely by unguided natural processes that include variation and selection. In the modern version of his theory—neo-Darwinism— genes control embryo development, variations are due to differences in genes, and new variations originate in genetic mutations. In the 1950s, neo-Darwinists equated genes with DNA sequences (Francis Crick called DNA “the secret of life”) and assumed that their biological significance lay in the proteins they encoded. The 98% of our DNA that does not code for proteins was attributed to molecular accidents that have accumulated in the course of evolution.

“The amount of DNA in organisms,” neo-Darwinist Richard Dawkins wrote in 1976, “is more than is strictly necessary for building them: A large fraction of the DNA is never translated into protein. From the point of view of the individual organism this seems paradoxical. If the ‘purpose’ of DNA is to supervise the building of bodies, it is surprising to find a large quantity of DNA which does no such thing. Biologists are racking their brains trying to think what useful task this apparently surplus DNA is doing. But from the point of view of the selfish genes themselves, there is no paradox. The true ‘purpose’ of DNA is to survive, no more and no less. The simplest way to explain the surplus DNA is to suppose that it is a parasite, or at best a harmless but useless passenger, hitching a ride in the survival machines created by the other DNA.” (The Selfish Gene, p. 47)

Since the 1980s, however, and especially after completion of the Human Genome Project in 2003, biologists have discovered many functions for non-protein-coding DNA. If the Ming vase is a living cell and the leftover carpet nails are “junk DNA,” it turns out that the nails are not only made of gold, but they also make an essential contribution to the beauty of the vase.

There's so much wrong with this answer that it's difficult to know where to begin. Maybe I'll just summarize in point form and elaborate in the comments if anyone wants to discuss it further.

• Implying that junk DNA has anything to do with Darwin's theory of evolution by natural selection is totally wrong. No matter how you define "neo-Darwinism" the fact remains that most biologists who believed in adaptation were very skeptical of junk DNA precisely because it didn't fit with Darwin's view of evolution. The idea that as much as 90% of our genome could be junk was very much a minority view in the 1970s and it's probably still a minority view.
• Dawkins was writing about selfish DNA when he wrote that passage in The Selfish Gene. Selfish DNA is not junk DNA. It has an adaptive purpose and a function. It is completely wrong to claim that Richard Dawkins was a big fan of junk DNA in the 1970s. Dawkins makes that very clear in The Extended Phenotype when he proposes various explanations for the extra DNA in our genome.¹
• The statement, "The 98% of our DNA that does not code for proteins was attributed to molecular accidents that have accumulated in the course of evolution" is wrong. There was never a group of knowledgeable scientists who thought that all noncoding DNA was due to accidents. Beginning in the 1970s, there were some who thought that a majority of our genome is junk and some (I am one) still think that as much as 90% could be junk. It's worth emphasizing that this view (that most of our genome is junk) was promoted by a relatively small number of scientists and never adopted as the consensus view of the majority of biologists.
• It is misleading to imply that many functions of noncoding DNA have been recently discovered. The only discovery that could even remotely fall into that category would be additional categories of small RNAs that weren't known before. The well-characterized examples account for less than 2% of the genome. Everything else is speculative and controversial.

Denyse asks, "What caused the change of view about junk DNA? Can you suggest a couple of key findings?" And Wells replies,

In a word, evidence. The first to emerge was the fact that almost all of an organism’s DNA is transcribed into RNA. (So although most of it may be non-protein-coding, it codes for RNA.) From a Darwinian perspective, this is surprising: Why would an organism struggling to survive devote so many of its internal resources to producing supposedly useless RNA? Indeed, since 2003 it has become clear that non-protein-coding RNAs perform many essential functions in living cells.

Among those of us who advocate junk DNA there are very few who have changed their minds in the past decade. Why is that? It's because we simply don't believe that the "evidence" of widespread transcription is meaningful. Those scientists who oppose the concept of plentiful junk DNA may have taken comfort from the transcription data but their minds weren't changed either. The truth is that there was, and is, a genuine scientific controversy and it has not been settled in spite of what the Intelligent Design Creationists tell you.

Pseudogenes constitute one type of so-called “junk DNA.” These are segments of DNA that resemble segments that elsewhere (or in other organisms) code for protein. Yet RNAs transcribed from some pseudogenes have been found to function in regulating how much protein is produced by the DNA segments they resemble.

Even if you added up all of the known examples of this phenomenon from every investigated species and stuffed them into a single genome it wouldn't amount to more than 0.01% of the genome. And there's no reason to think that the phenomenon is anything more than an interesting exception.

Repetitive DNA, in which a non-protein-coding sequence is repeated many times, is another type of so-called “junk DNA.” Yet repetitive DNA is now known to regulate many essential functions, including embryo implantation in mammals.

Also misleading. A few examples from diverse species do not make a difference. Indeed these exceptions tend to "prove the rule" rather than overthrow it. Wells is deliberately misleading his audience but he's in good company since there are many scientists who do the same thing. In order to have a serious impact on the junk DNA debate it's not sufficient to show that a few bits of repetitive DNA have gained a function in some species. You have to show that this generalizes to the 50% of the genome that's made up of repeated DNA of various sorts.

There is also growing evidence that non-protein-coding DNA can perform functions that are independent of its sequence. One example is the region of a chromosome (called a “centromere”) that attaches it to other structures in the cell. Another example is the retina in the eyes of nocturnal mammals, in which non-protein-coding DNA acts like a liquid crystal to focus scarce rays of light.

There are many known functions of noncoding DNA. They've been known for decades. As a general rule, the proponents of junk DNA seem to be better informed about these regions of the genome than their opponents. It hasn't made a difference in the past and it doesn't now. (Centromeres account for about 2% of the genome. They fall into the 10% that's known not to be junk.)

Denyse's last question is about me. "Can you interpret this for me, from Larry Moran (University of Toronto evolutionary biologist): “I don’t demand civility, but I do demand accuracy. When Denyse and her friends say that Darwinists promoted junk DNA I have to draw the line.” But he must be referring to my observation that originated in Francis Collins’s (US government’s chief 2000 genome mapper’s [!]) statements in a well-received and widely read book. Are there two types of truths at work here? Evidence, and … what? "

When I use the term “Darwinist,” I mean someone who accepts and defends the theory I describe in my answer to Question 2. Crick and Orgel were Darwinists in this sense; so are Miller, Dawkins, Coyne, and Avise—all of whom have promoted the myth of junk DNA. When Collins published The Language of God in 2006, he not only promoted junk DNA but also wrote that “Darwin’s theory of evolution, that is, descent from a common ancestor with natural selection operating on randomly occurring variations” is “unquestionably correct” (pp. 127, 141). Sure sounds like a Darwinist to me.

Collins also wrote that intelligent design is a “God of the gaps” position that is doomed to collapse with further advances in science (p. 193). But Collins has it exactly backwards: He and other promoters of the myth of junk DNA have put their faith in a “Darwin of the gaps” argument that must now retreat in the face of new advances in genome research.

Several of these scientists have written about pseudogenes and the fact that their existence provides strong support for evolution and strong evidence against the existence of an intelligent designer. Most (all?) biologists understand that pseudogenes are an example of junk DNA. Wells has chosen the one example of junk DNA where there's an overwhelming consensus. They are junk.

But that's not what the scientific debate is about. Pseudogenes are not a myth. They are a fact, and they make up as much as 2% of the mammalian genome. The scientific debate is about whether most of our genome is really junk DNA. I think Francis Collins supports this idea, with some reservations, but I don't know about Jerry Coyne or Kenneth Miller or Richard Dawkins. John Avise is, of course, one the main proponents of junk DNA being a majority of our genome. His book Inside the Human Genome: A Case for Non-intelligent Design was published just last year (2010). It's for those needing an antidote after reading the upcoming train wreck by Jonathan Wells.

It is extremely misleading to claim that "Darwinists" promoted the idea that most of our genome is junk. Most biologists are skeptical of that claim and that's especially true of those who would be comfortable calling themselves "Darwinists."

Denyse closes with one of her characteristic comments.

Okay, everyone, back to work tomorrow in Darwinworld, where facts like these do not matter in the least.

That's why I call them "IDiots." Facts matter to real scientists. The tough part about being a scientist is deciding what's a fact and what's not. Well showed us that he was not up to the task of behaving like a real scientist when he wrote Icons of Evolution and I suspect he's about to provide us with another example of misinformation and selective reading of the scientific literature.

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1. Dawkins recognizes that there is some junk in our genome—pseudogenes are a good example—but that does not mean he buys into the idea that a huge percentage of our genome is just junk.