Pretty Money

Canada is about to release a new set of polymer banknotes. Watch the video to see all the security features and the cool windows in the notes. (BTW, is there any country other than the United States that has monocolor money? Is there a reason why the USA makes every denomination of bill the same color?)



What's on these banknotes? The $100 bill depicts Sir Robert L. Borden, Prime Minister of Canada from 1911 to 1920. Here's the description of the other images fron The Bank of Canada.

# Theme: Medical Innovation

Canadians have long been at the frontiers of medical research and as a result have helped to save millions of lives worldwide. Notable Canadian contributions include pioneering the use of insulin to treat diabetes, DNA and genetic research, the invention of the pacemaker, and the first hospital-to-hospital robot-assisted surgery.

Researcher at a microscope

The image of a researcher using a microscope depicts Canada’s long-standing commitment to medical research.

DNA strand

Deoxyribonucleic acid (DNA) is the genetic blueprint of life. Canadian researchers have been at the forefront of mapping our human genetic makeup in this field of medical science.

ECG

This electrocardiogram provides a visual cue to Canada’s contributions to heart health, including the invention of the pacemaker by John Hopps in 1950.

Insulin

The discovery of insulin to treat diabetes was made by Canadian researchers Frederick Banting and Charles Best in 1921.

It's nice that Canada is celebrating science.




The $50 dollar bill has a picture of William Lyon Mackenzie King who was Prime Minister from 1921–30 and from 1935–48. The other side has ...

# Theme: CCGS Amundsen, Research Icebreaker

The vastness and splendour of Canada’s northern frontier have helped to shape our cultural identity. The icebreaker plays an important role in the North, keeping Canada’s historic passages open, undertaking marine search and rescue, supporting isolated communities, and participating in international environmental research. The CCGS Amundsen helps Canada—the nation with the world’s longest stretch of Arctic coastline—to remain at the leading edge of Arctic research, providing the world’s oceanographers, geologists and ecologists with unparalleled access to the North.

CCGS Amundsen, Research Icebreaker

The Canadian Coast Guard Ship Amundsen became a research icebreaker in 2003. It is jointly operated by ArcticNet and the Canadian Coast Guard.

“Arctic” in Inuktitut

This syllabic text is taken from Inuktitut, a language of Canada’s Inuit population. It stands for “Arctic.”

Map of Canada’s northern regions

The map on the back of this note shows Canada’s northern regions in their entirety, including Inuit regions of the Arctic. This image was provided by Natural Resources Canada.

More mention of research and another language. The $50 dollar bill has words from three languages (French, English, and Inuktitut. (I think there's only two languages on American bills. )

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The Summer Solstice and Science Literacy

From time to time my colleagues and I discuss the basic requirements of science literacy. We envisage a group of intelligent people at a party discussing various topics. Let's restrict our discussion to Western European culture.

Everyone agrees that they should be familiar with the basic outlines of history (e.g. who did Paul Revere warn in 1775?) and politics (what's the difference between socialism and capitalism?). Everyone agrees that you would look like an idiot if you didn't know who Will Shakespeare was and what Hamlet said. Everyone agrees that you can't call yourself an intellectual if you don't know the difference between French Impressionists and Michelangelo. You're expected to know something about Socrates and Aristotle. You're expected to know at least a few foreign words and knowledge of a foreign language is almost a requirement.

You should know something about food even if it's only the difference between couche couche and curry. Any "intellectual" should be able to discourse for five minutes on a favorite wine. You get the picture—there are some things that you just have to know if you claim to be literate.

What about science? Are there any things in science that you just have to know if you want to be taken seriously as an informed literate person?

No, there aren't. We've all experienced the situation I describe where a group of non-scientists at a party or bar are showing off their knowledge. Knowledge of science and math is not a requirement. In fact, you get points if you brag about always being too stupid to understand mathematics and dropping it as soon as you could in high school, especially if you're a woman.

Are there scientific facts and concepts that you really should be expected to know if you claim to be literate? Yes there are, and it's up to us to make sure they are widely publicized.

Today's your chance to publicize one of those facts. The summer solstice happens two hours from now no matter where you are on the planet. Ask your non-science friends to explain the summer solstice (Northern Hemisphere). It's one of those simple science things that everyone should know about. Not being able to explain it is like not knowing that Libya is in Africa, Napoleon lost the battle of Waterloo, Charles Dickens wrote Oliver Twist, and Frank Lloyd Wright was an architect.

Can you explain the solstice? If so, you are on the way to scientific literacy. What are some other must-know scientific facts and concepts? Evolution is one. If you don't understand the basic concepts of evolution then you can't clam to be scientifically literate. My point is that I'd like to live in a world where you can't claim to be literate, period, if you aren't scientifically literate.

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[Image credit: Wikipedia]

Texas Prayed and God Answered

Back in April, Governor Rick Perry of Texas proclaimed a weekend of prayer (Friday, April 22, 2011, to Sunday, April 24, 2011). Texans were supposed to pray for God to relieve the terrible dought [Pray for Texas].

Bill Maher reminded me that it's been several months since Texans prayed so it's time to analyze the results.

On the site US Drought Monitor there are maps of the USA showing region of drought. The top map below shows the regions with severe drought (dark brown) for April 26, 2011, right after all the praying. The second map (below) shows regions of drought on June 14, 2011.

It looks like God hates Texas and/or Rick Perry. I'm told that Governor Perry is thinking of running for President of the United States. Is this a good idea?

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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."

Junk Poll Results

Here are the results of the most recent poll on junk DNA. Below it is the result from several years ago. I realize that the questions are different but the shift toward favoring junk DNA is still a surprise. I'd like to think it's because more and more Sandwalk readers are becoming aware of the science behind junk DNA but it could be just that more "junkers" are reading my blog.

Is there anyone out there who changed their minds over the past few years? Is The Myth of Junk DNA going to convert everyone to rejecting junk DNA? I'll have to do another poll in six months to see if the Intelligent Design Creationists are having an impact.

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Zoë and Window Shopping

Don't you just hate it when bloggers post cute pictures of their children, grandchildren, cats, or molluscs?

Tough. Here's my granddaughter, Zoë, window shopping in Barcelona (Spain) a few weeks ago. The window looked so inviting she decided to check out the shop.

She's only 16 months old and already enjoys shopping!

(Zoë took her parents to Barcelona to meet up with Ms. Sandwalk and our nephew for a week of zoo's, Cava, and Gaudí. You can read all about it on leslie jane moran.)

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Omnisaurus Games

My number one son¹, Gordon Moran, is a texture artist working for a video game company in Vancouver. He has hooked up with his programmer friend Kevin Forbes to found Omnisaurus Games. They are working on an iPhone/iPad game and the unique thing about this is that you can follow their progress on their blog. Did you ever wonder what goes into to making a fabulous app?

Omnisaurus Games is an independent game developer currently developing games for the iPhone, iPad, and iPod Touch. Founded May 2011 in Vancouver, Canada by Kevin Forbes and Gordon Moran, we stress open game development, meaning we share every aspect of our development cycle with you the players. Follow our game development journey through our blog, twitter, facebook, or rss feed. Watch our game grow from the conceptual phase, all the way through the entire development cycle. We regularly post our work in progress builds so that you can test them out online and most importantly give us your feedback and great ideas. After all, we’re making these games for you, so shouldn’t you have a say in how they’re made? Most importantly, keep in touch. We’d love to hear anything you have to say about our games, any games, or life in general. We’ll try really hard to implement the best and most popular ideas into our games and reward the most helpful suggestions and ideas with free copies of our game when it launches. We look forward to hearing from you!

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1. Note for the irony deficient - whenever someone says this it usually means they only have one son/daughter. Note that I did not say "number one child" 'cause that would have gotten me in trouble.

A Visit from Rick

It was late in the day when I heard a knock on my office door. I opened it to discover a strange man I hadn't seen in many years he introduced me to his wife and son. Rick Nicholson is a former graduate student in my lab. He got his Ph.D. 25 years ago ("The HSP70 Multi-Gene Family in Saccharomyces cerevisiae.") Rick was the first person to clone and sequence the yeast BiP gene.

Rick went from Toronto to Strasbourg (France) to work in Pierre Chambon's lab and from there he went to Australia. He is currently Professor at the Hunter Medical Research Institute in Newcastle, NSW where he works on peptide hormones expressed during pregnancy in humans.

I've reached the age where it's a real thrill to remember the "olden days" and how much better they were than today. Over dinner, Rick and I agreed that graduate students and young professors were much better 25 years ago than they are today.¹

We tried to remember everyone who was in the the lab during the early 1980's. Fortunately there was a list in Rick's thesis (undergraduates. graduate students, post-docs): Sean Blaine, Kim Bird, Eric Degan, Monica Fuchs, David Lowe, Marc Perry, Andrea Townsend, Sharon Shtang, Scott Young and Kee Wan. I know where most of them are but I haven't seen some of them for decades. That's sad.

Rick and his family are on their way to Strasbourg to celebrate Pierre Chambon's 80th birthday. When I reach 80 I'll have to throw a big party so I can invite all my former colleagues and students.

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1. I recently had dinner with my former Ph.D. supervisor and we reached the same conclusion only it was for 40 years ago. Isn't that strange?

Carnival of Evolution #36

This month's Carnival of Evolution (36th version) is hosted by Greg Laden at Greg Laden's Blog ["If You Love Evolution, Tweet About It!" COE # 36].

Here are the subtitles ...

• Hard Core Theory, Genetics, Mutations
• Kin Selection (or not)
• Ecology and evolution
• Microbes with ESP
• Applied Evolution
• Fish Physiology
• Crayfish Sex
• Human Evolution
• Darwinia
• Time and Deep Time
• Elephants
• Basic Concepts and Pedagogy
• Brains
• Extinction
• Blog The Controversy

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Gil Dodgen Explains the Salem Conjecture

The Salem Conjecture is the work of Bruce Salem. He suggested in the mid 1990s on talk.origins that of those creationists who claim professional expertise in evolution, a substantial percentage are engineers.

Bruce explained that most engineers are NOT creationists. It's only those who think they have special insight into biology who tend to be creationists.

This conjecture seems to hold but nobody knows why. It's one of the great mysteries of the world, right up there with why so many people hang toilet paper incorrectly and why it's only men who need to change after they get married.

Finally, after 15 years, Gil Dodgen offers an explanation for why engineers have such special insight into evolution [Who are the Real Freethinkers, Darwinists or ID Folks?].

The only thing I can think of is that the average Darwinist has no experience in designing any complex, functionally integrated system. The workings of the simplest cell make my AI program and the hardware on which it runs look like tinker toys.....

Self-replication does nothing to mitigate the probabilistic hurdles the Darwinian mechanism must overcome. How could this not be obvious to anyone with any experience in software or any other rigorous engineering discipline, and who has a basic understanding of combinatorial mathematics?

Oops, I forgot, most of these people have no experience in any rigorous engineering discipline. And those who do, and still believe in the Darwinian fantasy, have obviously undergone the atrophy and crippling of their basic reasoning powers — the product of many years of Darwinian indoctrination and suppression of free thought.

Who are the real freethinkers, Darwinists or ID folks? The Darwinian world is Orwellian.

Well, I'm glad that's settled. Now, I wish he'd turn his attention to some of the other serious mysteries that call out for an engineer's special insight. Maybe he can tell us the correct way to hang toilet paper?

(BTW, the posting just went up a few hours ago and there aren't any comments yet. I expect a flood of comments criticizing Gil for being rude to the scientists Darwinists. We all know that the IDiots are very sensitive about such behavior. They pride themselves on being polite and respectful toward their evolutionary biology Darwinist opponents.)

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Junk DNA Poll

If you haven't answered the junk DNA poll question in the margin then now's the time! There's only one week left.

The results so far are surprising—very different from my previous poll on this topic. It looks like one side is wining.

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The Central Dogma Strawman

Whenever you're trying to promote a new idea it's nice to have a scapegoat to beat up on. You're going to get a lot more attention if you can demonstrate that your latest results overthrow some key scientific concept that everyone took for granted. If you can't find a real "key concept" then the next best thing is to make one up.

For the past several decades that strawman target has been The Central Dogma of Molecular Biology. The Central Dogma is supposed to represent the key concept of molecular biology yet it gets "overthrown" on a regular basis every six months. Isn't that strange?

The latest example comes from a Nature review of a recent Science paper. The Science paper presents evidence that many mRNA sequences differ from the sequences in the exons that encode them (Li et al., 2011). RNA editing has been known for decades and every few years it is trotted out again as proof that the Central Dogma is wrong. The recent Li et al. (2011) paper doesn't present evidence for a new phenomenon but it does suggest that RNA editing may be much more common than previously suspected.

Here's what Nature staff writer Erika Check Hayden says about this paper ("Cells may stray from 'central dogma'" Hayden, 2011a).

All science students learn the 'central dogma' of molecular biology: that the sequence of bases encoded in DNA determines the sequence of amino acids that makes up the corresponding proteins. But now researchers suggest that human cells may complicate this tidy picture by making many proteins that do not match their underlying DNA sequences.

Now if that really was what the Central Dogma actually said then it would have disappeared thirty years ago.

The real Central Dogma of Molecular Biology is ...

... once (sequential) information has passed into protein it cannot get out again (F.H.C. Crick, 1958)

The central dogma of molecular biology deals with the detailed residue-by-residue transfer of sequential information. It states that such information cannot be transferred from protein to either protein or nucleic acid. (F.H.C. Crick, 1970)

I've explained why this is the correct version in an old blog posting from 2007: Basic Concepts: The Central Dogma of Molecular Biology. A very similar definition can be found on the Wikipedia site: Central Dogma of Molecular Biology. The key point is that once information flows into protein it can't flow back to nucleic acid. The standard misconception of the Central Dogma is actually the normal information flow pathway or what Crick called the "Sequence Hypothesis." It's a generality that was never meant to be an inviolate rule like the actual Central Dogma.

Hayden has another article in this week's print version of Nature (Hayden, 2011b). The second article emphasizes the controversy surrounding the Li et al. (2011) paper—lots of people are skeptical—but she doesn't back off the implications.

If verified, the findings would require a rewrite of the 'central dogma' of molecular biology, which posits that the RNA transcripts that carry genetic information to the ribosome, where they are used as templates for protein assembly, are generally faithful matches to the original DNA.

There are two remarkable things about such a statement. First, RNA editing has been an established fact for almost thirty years so if the Central Dogma needed rewriting it would have been done a long time ago. Second, Hayden was informed in the comments to her first article that there was a problem with her definition of the Central Dogma. Maybe she didn't have time to change the second version that was about to be published.

To be fair, this isn't just a problem with science writers who don't do their homework. Hayden is right when she says that most science students learn an incorrect version of the Central Dogma of Molecular Biology. It's true that most textbooks promote the information flow pathway as the Central Dogma and they fail to point out that the real version only precludes reverse translation. I don't understand why so many textbook writers and teachers continue to teach something they know to be false as the "Central Dogma" of molecular biology.

Is it because they don't know about the exceptions?

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Crick, F.H.C. (1958) On protein synthesis. Symp. Soc. Exp. Biol. XII:138-163.

Crick, F. (1970) Central Dogma of Molecular Biology. Nature 227, 561-563. [PDF file]

Hayden, E.C. (2011a) Cells may stray from 'central dogma.' Nature Published online 19 May 2011 [doi:10.1038/news.2011.304.

Hayden, E.C. (2011a) Evidence of altered RNA stirs debate. Nature 473:432. [doi:10.1038/473432a]

Li, M., Wang, I.X., Li, Y., Bruzel, A., Richards, A.L., Toung, J.M., and Cheung, V.G. (2011) Widespread RNA and DNA Sequence Differences in the Human Transcriptome. Science. 2011 May 19. [Epub ahead of print] [Science]

The Black Knight

It's been fun battling the IDiots over junk DNA but it's time for a break. For no particular reason I thought of this video.

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IDiots vs the Truth

I don't expect the IDiots to agree with me. I don't expect them to be happy about what I say. But I do expect them to tell the truth, or at least make the attempt.

Over at Evolution News & Views David Klinghoffer posted the following under: At Forbes, John Farrell Joins in "Ayala'ing" of Jonathan Wells.

Thus we have several posts from University of Toronto biochemist Larry Moran, criticizing Myth while being totally open about not having read it first. Moran wrote no fewer than four posts on the book in this fashion, claiming as an excuse that Myth would not be published in Canada until May 31. (In fact, the book was available for purchase from Amazon since early May.)

The four postings are:

1. Junk & Jonathan: Part 1—Getting the History Correct—a posting in which I addressed an interview of Jonathan Wells conducted by Denise O'Leary.
2. Junk & Jonathan: Part 2— What Did Biologists Really Say About Junk DNA?—a posting in which I addressed an interview of Jonathan Wells conducted by Denise O'Leary.
3. Junk & Jonathan: Part 3—The Preface—a discussion of the preface that was posted online.
4. See the IDiots Gloat over Jonathan Wells—a blog posting about what David Klinghoffer had to say about me and the book.

Only one of these postings was about the contents of the book and that one was about the preface, which I had read. In all these postings I was careful to say that I had not read the book but it was on order. I was waiting for it to arrive.

My order was placed weeks ago on amazon.ca. Their website said that the book would not be released until May 31. Fortunately amazon.ca was able to ship it to me last week and I was happy to get it.

Now that I've read the book it will be interesting to see if David Klinghoffer has any comments about my review.

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Junk & Jonathan: Part 8—Chapter 5

This is part 8 of my review of The Myth of Junk DNA. For a list of other postings on this topic see the link to Genomes & Junk DNA in the "theme box" below or in the sidebar under "Themes."

Pseudogenes are the classic example of junk DNA and, as pointed out by many evolutionary biologists, they represent a difficult challenge for Intelligent Design Creationists. It's especially difficult to explain pseudogenes that are located in the same place in different species.

Chapter 5: Pseudogenes—Not so Pseudo After All

Chapter 5 is Pseudogenes—Not so Pseudo After All. This is the chapter where Jonathan Wells takes the standard creationist approach to the problem of pseudogenes—he denies that they exist!

Wells begins the chapter by reminding us that several evolutionary biologists have challenged the IDiots to come up with an explanation for pseudogenes, especially those that are found in closely related species. The usual suspects are quoted: Ken Miller, Douglas Futuyma, Jerry Coyne, Richard Dawkins, and John Avise. All of these challenges are based on solid evidence that most pseudogenes are actually pseudogenes (non-functional, degenerate copies of functional genes). But Wells says, "Yet there is growing evidence that many pseudogenes are not functionless, after all."

Types of Pseudogenes

There are three kinds of pseudogenes [Pseudogenes]. The first category contains genes that used to be functional in our ancestors but currently are non-functional. The best example is the human GULOP pseudogene that used to encode a key enzyme in the pathway for synthesis of vitamin C [Human GULOP Pseudogene]. This gene is active in most animals but it has become a pseudogene in primates and, independently, in a few other animals.


UPDATE: see: Creationists questioning pseudogenes: the GULO pseudogene

The second category includes genes that arise from a gene duplication event followed by inactivation of one of the copies. These pseudogenes tend to be located near their active siblings and they retain most of the features of the original gene except they can't produce an active product. Many of them are transcribed, especially if they have only recently become pseudogenes.

The third category is called "processed" pseudogenes. They arise when a mature mRNA molecule is copied into DNA by reverse transcriptase and the resulting DNA is integrated into the genome. Processed pseudogenes will usually not have any introns and when they integrate they will not be near a promoter. Many of them are truncated because the copying process was not complete. Processed pseudogenes were never able to produce their original functional product (protein or RNA) and they accumulate mutations at the rate expected from fixation of neutral alleles by random genetic drift.

The first two categories of pseudogene will also accumulate mutations once they become inactive. It's a characteristic of pseudogenes that the older they are the more mutations they have. Thus a pseudogene that is only found in chimpanzees and humans will have fewer mutations than one found in monkeys and apes and even fewer that one found in both rodents and primates.

The human genome contains about 20,000 pseudogenes, about the same as the number of genes. Many of these pseudogenes belong to the same family so not every gene has a corresponding pseudogene. About 6,000 of these pseudogenes arose from duplication events and 14,000 are processed. (The first category is rare.)

The pseudogenes in the "duplicated" category tend to be associated with large families of related genes. For example, in the human genome there are 414 pseudogenes in the olfactory receptor gene family [Olfactory Receptor Genes, The Evolution of Gene Families]. It's difficult to imagine how any substantial number of these genes could have a function.

As expected, the processed pseudogenes are scattered thoughout the genome because they insert at random. Roughly 2,000 of them are found in introns and this is further evidence that introns are mostly junk. Of course, if a processed pseudogene plunks down in an intron sequence it will be transcribed. Processed pseudogenes tend to come from functional genes that are abundantly expressed in the germ line. That's because the processed pseudogene has to be integrated into germ line DNA in order to be passed on to the progeny. Most of these genes are standard housekeeping genes. For example, there are 1300 pseudogenes derived from ribosomal protein genes.

Jonathan Wells describes the three categories but doesn't explain any of the other things I just mentioned.

Transcribed Pseudogenes

The first important section of his chapter is "Transcribed Pseudogenes." He quotes a number of papers showing that some pseudogenes are transcribed in humans, cows, and plants. In humans he claims that about one-fifth of pseudogenes are transcirbed at some time or another. This is probably an upper limit since most workers suggest that only 10% are transcribed.

I'm sure that some pseudogenes are transcibed. Many of the pseudogenes derived from gene duplication events will still be transcribed from active promoters even though they may not produce a functional product. Many of the processed pseudogenes will be transcribed because they are found within a gene (introns) or have fortuitously integrated near a promoter.

'Pseudogenes' That Encode Proteins

The key question is whether any pseudogenes produce a functional product and that's addressed in the next section: "'Pseudogenes' That Encode Proteins." Wells describes five studies where presumed pseudogenes were found to be genes after all (three in humans and two in fruit flies). Interesting but irrelevant. These genes are not junk. What about the other 20,000 real pseudogenes? Here's what Wells says at this point in the chapter ...

To be sure, only a relatively small proportion of known pseudogenes have been shown to encode proteins. But there is growing evidence that RNAs transcribed from pseudogenes perform essential functions in the cell

Here's where we get to the most important part of the chapter. It's in a section called "RNA Interference."

RNA Interference

RNA interference arises when one RNA molecule interferes with the expression of another. The easiest example to understand is when part of a gene is transcribed in the opposite direction producing what's called "antisense" RNA. This antisense RNA will hybridize to the functional mRNA and either block translation or induce degradation. In either case, less protein is made.

If a pseudogene is transcribed in the opposite direction then its antisense RNA could interfere with the expression of the normal gene. Wells gives us three examples of this phenomenon: one famous one from snails (1999), one from mouse oocytes (2008), and one from rice (2009). I don't know whether all these results have been confirmed but even if they have it doesn't amount to much. All kinds of strange things happen in biology and the fact that a few pseudogenes might have acquired a regulatory function isn't shocking. What about the other 20,000 pseudogenes?

Pseudogene Enhancement of Gene Expression

Theme

Genomes
& Junk DNAWell, there's always the possibility that pseudogenes could enhance gene expression. The next section is "Pseudogene Enhancement of Gene Expression." Jonathan Wells begins this section with a description of the results on the mouse Mkrn-1-p1 pseudogene. The authors of this famous 2003 Nature paper claim that transcripts from the pseudogene protect the functional mRNA by shielding it from degradation. The title of their paper is "An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene" (Hirotsune et al., 2003).

Wells devotes three paragraphs to this important paper. There's only one slight problem. This work has been discredited in a 2006 PNAS paper with the title "The putatively functional Mkrn-1-p1 pseudogene is neither expressed nor imprinted nor does it regulate its source in trans." (Gray et., 2006) Oops!

Wells knows about this 2006 paper because he discusses it in Chapter 8 when he attacks the defenders of junk DNA. In chapter 5 he adds the following remark in parentheses, "Other biologists later challenged the Makorin-1 pseudogene results, which remain controversial." I think this is the only time when he mentions any legitimate scientific controversy.

There are three other examples of pseudogenes that might have an enhancement function: one from plants and two from humans. I don't know if these studies have been confirmed but even if they have they don't have much of an impact on the possible functions of the remaining 20,000 pseudogenes.

Sequence Conservation

The only significant evidence of widespread functionality of pseudogenes comes from two studies on sequence conservation. Wells covers this in a one-page section on "Sequence Conservation." The studies purport to show that pseudogene sequences are much more conserved than expected if they are really junk DNA. These studies have not been reproduced, as far as I know, and they fly in the face of much evidence to the contrary—evidence that Wells forgets to mention.

The first paper is a review by Balakirev and Ayala (2003). They review the possible functions of some pseudogenes in Drosophila and mammals. Some of them show evidence of sequence conservation. They conclude that most pseudogenes are probably functional. A study published that same year looked at all the known pseudogenes in the human genome and concluded that 95% of them evolved as though they had no function (i.e. they were not conserved) (Torrents et al., 2003)

The second paper that Wells mentions is Khachane and Harrison (2009). They identify 68 human pseudogenes whose sequences appear to be conserved in at least two other mammals. These are good candidates for functional genes.

The strange thing about this argument is that Wells doesn't believe in common descent so the evidence of sequence conservation really shouldn't have any meaning for him. Nevertheless, he says ...

How odd! As we saw in Chapter 2, Kenneth Miller, Richard Dawkins, Douglas Futuyma, Michael Shermer, Jerry Coyne and John Avise argue that pseudogenes confirm Darwinism because they are non-functional. But if we assume that Darwinism is true and then compare the DNA of unrelated organisms, sequence similarities imply that many of their pseudogenes are functional. So nonfunction supposedly implies Darwinism, but Darwinism plus sequence conservation implies function. When it comes to conserved pseudogenes, it seems, Darwinism saws off the very branch on which it sits.

For the record, if the majority of pseudogenes really are more conserved than expected from random mutations and fixation by random genetic drift then this would, indeed, be evidence that something is going on. Maybe they do have a function we don't know about. I don't think the evidence points in this direction at all—in fact much of the evidence contradicts it. Balakirov and Ayala (2003) are just speculating. I prefer the evidence of Torrents et al. (2003) suggesting that only a small number of potential pseudogenes have a function. This is consistent with the results of Khachane and Harrison (2009).

[If all 1,000 presumed pseudogenes turned out to be real genes then this moves about 0.06% of the genome from the junk category to the functional category. This isn't enough to save the IDiots.]

The Vitamin C Pseudogene

Finally, there's a section I haven't covered. It's titled "The Vitamin C Pseudogene." Wells has to address this particular pseudogene because it's the one that comes up most often when evolutionary biologists (e.g. Ken Miller and Jerry Coyne) criticize Intelligent Design Creationism. Here's what Wells says,

The evidence is not as straightforward as Miller and Coyne make it out to be, however, and their argument is ultimately circular. In any case, common ancestry and intelligent design are two different issues, and the vitamin C story would take us on a detour from the issue of junk DNA that's the focus of this book, so the details are omitted here and included in an appendix.

Which brings us to the Appendix: "The Vitamin C Pseudogene."

The main argument of scientists like Ken Miller and Jerry Coyne is not that the GULOP pseudogene exists. It's that the GULOP gene and its pseudogene are at the same location in the genomes of all mammals. In the primate lineage this gene is non-functional due to a number of mutations that make it impossible to produce a functional protein. Some of the same deactivating mutations are found in related species such as humans and chimpanzees. This suggests strongly that the non-functional pseudogene was inherited from a common ancestor. How do Intelligent Design Creationists deal with this evidence?

How does Wells respond?

... intelligent design and common ancestry are two different issues. Major ID proponents pointed this out before Miller wrote his book....Although some ID proponents (including me) question universal common ancestry on empirical grounds (as do some evolutionary biologists), intelligent design is not necessarily inconsistent with common ancestry.

I'm not sure what this means. Does it mean that people like Wells are completely bamboozled by this data since they can't refute either the evidence of common descent or the evidence of bad design? Other IDiots, like Michael Behe, only have to explain the bad design?

Jerry Coyne has published a similar argument but Wells attacks him on two fronts. First, he claims that human and chimpanzee Y chromosomes differ by 60 million nucleotide substitutions. If they really have a common ancestor then one would expect much greater sequence similarity. According to Wells, "If similarities in the vitamin C pseudogene are evidence for common ancestry, then differences in the Y chromosome are presumably evidence against it."

The Y chromosome paper is Hughes et al. (2010). Their results show that in orthologous regions of the Y chromosomes the human and chimp sequences are 98.3% identical. However, the chimp and human chromosomes differ in other regions because of large inserts and deletions. This is still evidence of common ancestry.

As usual, Wells is wanting to have his cake and eat it too.

The second attack is based on a number of quibbles. Coyne said that all primates need vitamin C in their diets but Wells points out that prosimians are primates and they can make vitamin C. Furthermore, according to Wells the requirement for vitamin C has only been established in nine species of monkeys. There are 251 other species and we don't know if they need vitamin C. Not only that, Coyne claimed that all primates have the same single nucleotide deletion in their GULOP pseudogene but Wells is quick to point out that only five primate sequences have been published.

Put that in your pipe and smoke it, Jerry Coyne! I assume that Wells is completely incapable of answering the challenge that's been issued and that's why he resorts to red herrings.

Continuing with this shotgun approach we quickly encounter several other arguments that are designed to distract from the main topic.

• "Miller and Coyne rely on speculations about the motives of the designer or creator that have no legitimate place in natural science." (I hope you turned off your irony meter before reading that.)
• Miller and Coyne have not provided any evidence to justify their claim that the GLO pseudogene is completely nonfunctional.
• (Turn off your irony meter!) Their argument is circular. The similarities in sequence between chimp and human pseudogenes could be due to natural selection. "To break the circle, Miller and Coyne would either have to establish the recent ancestry of humans and chimps on other grounds (but why then bother invoking the vitamin C pseudogene at all?), or they would first have to establish that the vitamin C pseudogene has no function whatsoever (but this is impossible). So their argument not only fails to refute ID, but it also fails to establish that humans and chimps are descended from a common ancestor."

I feel a bit sorry for Ken Miller and Jerry Coyne. If this is the best the IDiots can do then why bother trying to argue with them in the first place?

Thus endeth Chapter 5.

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Gray TA, Wilson A, Fortin PJ, Nicholls RD. (2006) The putatively functional Mkrn1-p1 pseudogene is neither expressed nor imprinted, nor does it regulate its source gene in trans. Proc. Natl. Acad. Sci. USA 103:12039-12044. [PDF]

Hirotsune, S., Yoshida, N., Chen, A., Garrett, L., Sugiyama, F., Takahashi, S., Yagami, K., Wynshaw-Boris, A., and Yoshiki, A. (2003) An expressed pseudogene regulates the messenger-RNA stability of its homologous coding gene. Nature 423:91-6. [PDF]

Hughes, J.F., Skaletsky, H., Pyntikova, T., Graves, T.A., van Daalen, S.K., Minx, P.J., Fulton, R.S., McGrath, S.D., Locke, D.P., Friedman, C., Trask, B.J., Mardis, E.R., Warren, W.C., Repping, S., Rozen, S., Wilson, R.K., and Page, D.C. (2010) Chimpanzee and human Y chromosomes are remarkably divergent in structure and gene content. Nature 463:536-539. [Nature]

Khachane, A.N., and Harrison, P.M. (2009) Assessing the genomic evidence for conserved transcribed pseudogenes under selection. BMC Genomics 15:435-449. [PDF]

Torrents, D., Suyama, M., Zdobnov, E., and Bork, P.. (2003) A genome-wide survey of human pseudogenes. Genome Res. 13:2559-2567. [PDF]